From 3f62f08d9ecbcc3b20d9c4126d17ff8d00eeb299 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:20:02 -0500 Subject: [PATCH 01/17] chore: init repo Signed-off-by: Cameron Smith --- .actrc | 3 + .beads/.gitignore | 44 + .beads/config.yaml | 62 + .beads/interactions.jsonl | 0 .beads/metadata.json | 4 + .dvc/.gitignore | 1 + .dvc/config | 11 + .github/CODE_OF_CONDUCT.md | 132 + .github/ISSUE_TEMPLATE/bug_report.md | 42 + .github/ISSUE_TEMPLATE/feature_request.md | 29 + .github/SECURITY.md | 3 + .sops.yaml | 15 + .taplo.toml | 15 + .vscode/extensions.json | 40 + .vscode/launch.json | 25 + .vscode/settings.json | 69 + .vscode/tasks.json | 13 + LICENSE | 201 + Makefile | 277 ++ bun.lock | 1170 ++++++ docs/.gitignore | 10 + docs/_extensions/machow/interlinks/.gitignore | 3 + .../machow/interlinks/_extension.yml | 7 + .../machow/interlinks/interlinks.lua | 411 ++ docs/_extensions/machow/interlinks/test.qmd | 22 + docs/_freeze.dvc | 6 + docs/_quarto.yml | 131 + docs/about/contributing.qmd | 0 docs/about/index.qmd | 18 + docs/bibstyle.csl | 152 + docs/cdark.scss | 10 + docs/clight.scss | 5 + docs/concepts/index.qmd | 18 + .../development/architecture/architecture.qmd | 20 + docs/development/architecture/index.qmd | 27 + docs/development/context/context.qmd | 20 + docs/development/context/index.qmd | 27 + docs/development/index.qmd | 23 + docs/development/requirements/index.qmd | 27 + .../development/requirements/requirements.qmd | 20 + docs/development/traceability/index.qmd | 20 + docs/development/traceability/testing.qmd | 16 + docs/development/work-items/index.qmd | 21 + docs/guides/development.qmd | 74 + docs/guides/installation.qmd | 48 + docs/include.html | 12 + docs/index.qmd | 28 + docs/mathjax.html | 7 + .../architecture/crane-uv2nix-integration.md | 450 ++ .../package-distribution-channels.md | 56 + docs/notes/archive/README.md | 391 ++ docs/references.bib | 49 + docs/styles.css | 28 + docs/tutorials/getting-started.qmd | 32 + flake.lock | 314 ++ flake.nix | 57 + justfile | 992 +++++ modules/containers.nix | 198 + modules/devshell.nix | 101 + modules/flake-parts.nix | 5 + modules/formatting.nix | 31 + modules/overrides.nix | 60 + modules/packages.nix | 41 + modules/python.nix | 156 + modules/systems.nix | 8 + modules/template-rename.nix | 97 + nix/.keep | 0 nix/disabled/containers-dev.nix.txt | 184 + nix/lib/mk-multi-arch-manifest.nix | 148 + package.json | 95 + packages/.keep | 0 packages/omicsio/.ci.json | 4 + packages/omicsio/README.md | 0 packages/omicsio/conda/README.md | 29 + .../conda/default_linux-64_conda_spec.txt | 25 + .../conda/default_osx-arm64_conda_spec.txt | 16 + .../omicsio/conda/dev_linux-64_conda_spec.txt | 25 + .../conda/dev_osx-arm64_conda_spec.txt | 16 + .../conda/docs_linux-64_conda_spec.txt | 25 + .../conda/docs_osx-arm64_conda_spec.txt | 16 + .../conda/interactive_linux-64_conda_spec.txt | 25 + .../interactive_osx-arm64_conda_spec.txt | 16 + .../conda/lint_linux-64_conda_spec.txt | 25 + .../conda/lint_osx-arm64_conda_spec.txt | 16 + .../conda/test_linux-64_conda_spec.txt | 25 + .../conda/test_osx-arm64_conda_spec.txt | 16 + .../conda/types_linux-64_conda_spec.txt | 25 + .../conda/types_osx-arm64_conda_spec.txt | 16 + packages/omicsio/package.json | 91 + packages/omicsio/pixi.lock | 3617 +++++++++++++++++ packages/omicsio/pyproject.toml | 119 + packages/omicsio/src/.keep | 0 packages/omicsio/src/omicsio/__init__.py | 12 + packages/omicsio/src/omicsio/tests/.keep | 0 .../omicsio/src/omicsio/tests/__init__.py | 1 + .../omicsio/src/omicsio/tests/test_main.py | 18 + packages/omicsio/uv.lock | 2037 ++++++++++ ruff.toml | 12 + scripts/bootstrap.sh | 78 + scripts/ci/ci-build-category.sh | 184 + scripts/preview-version.sh | 223 + scripts/sops-bootstrap.sh | 211 + scripts/sops-check-requirements.sh | 111 + scripts/sops-finalize-rotation.sh | 62 + scripts/sops-rotate.sh | 30 + scripts/sops-setup-github.sh | 101 + scripts/sops-upload-github-key.sh | 59 + vars/dvc-sa.json | 29 + vars/shared.yaml | 36 + wrangler.jsonc | 22 + 110 files changed, 14205 insertions(+) create mode 100644 .actrc create mode 100644 .beads/.gitignore create mode 100644 .beads/config.yaml create mode 100644 .beads/interactions.jsonl create mode 100644 .beads/metadata.json create mode 100644 .dvc/.gitignore create mode 100644 .dvc/config create mode 100644 .github/CODE_OF_CONDUCT.md create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/SECURITY.md create mode 100644 .sops.yaml create mode 100644 .taplo.toml create mode 100644 .vscode/extensions.json create mode 100644 .vscode/launch.json create mode 100644 .vscode/settings.json create mode 100644 .vscode/tasks.json create mode 100644 LICENSE create mode 100644 Makefile create mode 100644 bun.lock create mode 100644 docs/.gitignore create mode 100644 docs/_extensions/machow/interlinks/.gitignore create mode 100644 docs/_extensions/machow/interlinks/_extension.yml create mode 100644 docs/_extensions/machow/interlinks/interlinks.lua create mode 100644 docs/_extensions/machow/interlinks/test.qmd create mode 100644 docs/_freeze.dvc create mode 100644 docs/_quarto.yml create mode 100644 docs/about/contributing.qmd create mode 100644 docs/about/index.qmd create mode 100644 docs/bibstyle.csl create mode 100644 docs/cdark.scss create mode 100644 docs/clight.scss create mode 100644 docs/concepts/index.qmd create mode 100644 docs/development/architecture/architecture.qmd create mode 100644 docs/development/architecture/index.qmd create mode 100644 docs/development/context/context.qmd create mode 100644 docs/development/context/index.qmd create mode 100644 docs/development/index.qmd create mode 100644 docs/development/requirements/index.qmd create mode 100644 docs/development/requirements/requirements.qmd create mode 100644 docs/development/traceability/index.qmd create mode 100644 docs/development/traceability/testing.qmd create mode 100644 docs/development/work-items/index.qmd create mode 100644 docs/guides/development.qmd create mode 100644 docs/guides/installation.qmd create mode 100644 docs/include.html create mode 100644 docs/index.qmd create mode 100644 docs/mathjax.html create mode 100644 docs/notes/architecture/crane-uv2nix-integration.md create mode 100644 docs/notes/architecture/package-distribution-channels.md create mode 100644 docs/notes/archive/README.md create mode 100644 docs/references.bib create mode 100644 docs/styles.css create mode 100644 docs/tutorials/getting-started.qmd create mode 100644 flake.lock create mode 100644 flake.nix create mode 100644 justfile create mode 100644 modules/containers.nix create mode 100644 modules/devshell.nix create mode 100644 modules/flake-parts.nix create mode 100644 modules/formatting.nix create mode 100644 modules/overrides.nix create mode 100644 modules/packages.nix create mode 100644 modules/python.nix create mode 100644 modules/systems.nix create mode 100644 modules/template-rename.nix create mode 100644 nix/.keep create mode 100644 nix/disabled/containers-dev.nix.txt create mode 100644 nix/lib/mk-multi-arch-manifest.nix create mode 100644 package.json create mode 100644 packages/.keep create mode 100644 packages/omicsio/.ci.json create mode 100644 packages/omicsio/README.md create mode 100644 packages/omicsio/conda/README.md create mode 100644 packages/omicsio/conda/default_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/default_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/dev_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/dev_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/docs_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/docs_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/interactive_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/interactive_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/lint_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/lint_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/test_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/test_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/conda/types_linux-64_conda_spec.txt create mode 100644 packages/omicsio/conda/types_osx-arm64_conda_spec.txt create mode 100644 packages/omicsio/package.json create mode 100644 packages/omicsio/pixi.lock create mode 100644 packages/omicsio/pyproject.toml create mode 100644 packages/omicsio/src/.keep create mode 100644 packages/omicsio/src/omicsio/__init__.py create mode 100644 packages/omicsio/src/omicsio/tests/.keep create mode 100644 packages/omicsio/src/omicsio/tests/__init__.py create mode 100644 packages/omicsio/src/omicsio/tests/test_main.py create mode 100644 packages/omicsio/uv.lock create mode 100644 ruff.toml create mode 100755 scripts/bootstrap.sh create mode 100755 scripts/ci/ci-build-category.sh create mode 100755 scripts/preview-version.sh create mode 100755 scripts/sops-bootstrap.sh create mode 100755 scripts/sops-check-requirements.sh create mode 100755 scripts/sops-finalize-rotation.sh create mode 100755 scripts/sops-rotate.sh create mode 100755 scripts/sops-setup-github.sh create mode 100755 scripts/sops-upload-github-key.sh create mode 100644 vars/dvc-sa.json create mode 100644 vars/shared.yaml create mode 100644 wrangler.jsonc diff --git a/.actrc b/.actrc new file mode 100644 index 0000000..baf206d --- /dev/null +++ b/.actrc @@ -0,0 +1,3 @@ +--container-architecture linux/amd64 +--artifact-server-path $PWD/.artifacts +-P ubuntu-latest=catthehacker/ubuntu:full-latest diff --git a/.beads/.gitignore b/.beads/.gitignore new file mode 100644 index 0000000..d27a1db --- /dev/null +++ b/.beads/.gitignore @@ -0,0 +1,44 @@ +# SQLite databases +*.db +*.db?* +*.db-journal +*.db-wal +*.db-shm + +# Daemon runtime files +daemon.lock +daemon.log +daemon.pid +bd.sock +sync-state.json +last-touched + +# Local version tracking (prevents upgrade notification spam after git ops) +.local_version + +# Legacy database files +db.sqlite +bd.db + +# Worktree redirect file (contains relative path to main repo's .beads/) +# Must not be committed as paths would be wrong in other clones +redirect + +# Merge artifacts (temporary files from 3-way merge) +beads.base.jsonl +beads.base.meta.json +beads.left.jsonl +beads.left.meta.json +beads.right.jsonl +beads.right.meta.json + +# Sync state (local-only, per-machine) +# These files are machine-specific and should not be shared across clones +.sync.lock +sync_base.jsonl + +# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here. +# They would override fork protection in .git/info/exclude, allowing +# contributors to accidentally commit upstream issue databases. +# The JSONL files (issues.jsonl, interactions.jsonl) and config files +# are tracked by git by default since no pattern above ignores them. diff --git a/.beads/config.yaml b/.beads/config.yaml new file mode 100644 index 0000000..f242785 --- /dev/null +++ b/.beads/config.yaml @@ -0,0 +1,62 @@ +# Beads Configuration File +# This file configures default behavior for all bd commands in this repository +# All settings can also be set via environment variables (BD_* prefix) +# or overridden with command-line flags + +# Issue prefix for this repository (used by bd init) +# If not set, bd init will auto-detect from directory name +# Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc. +# issue-prefix: "" + +# Use no-db mode: load from JSONL, no SQLite, write back after each command +# When true, bd will use .beads/issues.jsonl as the source of truth +# instead of SQLite database +# no-db: false + +# Disable daemon for RPC communication (forces direct database access) +# no-daemon: false + +# Disable auto-flush of database to JSONL after mutations +# no-auto-flush: false + +# Disable auto-import from JSONL when it's newer than database +# no-auto-import: false + +# Enable JSON output by default +# json: false + +# Default actor for audit trails (overridden by BD_ACTOR or --actor) +# actor: "" + +# Path to database (overridden by BEADS_DB or --db) +# db: "" + +# Auto-start daemon if not running (can also use BEADS_AUTO_START_DAEMON) +# auto-start-daemon: true + +# Debounce interval for auto-flush (can also use BEADS_FLUSH_DEBOUNCE) +# flush-debounce: "5s" + +# Git branch for beads commits (bd sync will commit to this branch) +# IMPORTANT: Set this for team projects so all clones use the same sync branch. +# This setting persists across clones (unlike database config which is gitignored). +# Can also use BEADS_SYNC_BRANCH env var for local override. +# If not set, bd sync will require you to run 'bd config set sync.branch '. +# sync-branch: "beads-sync" + +# Multi-repo configuration (experimental - bd-307) +# Allows hydrating from multiple repositories and routing writes to the correct JSONL +# repos: +# primary: "." # Primary repo (where this database lives) +# additional: # Additional repos to hydrate from (read-only) +# - ~/beads-planning # Personal planning repo +# - ~/work-planning # Work planning repo + +# Integration settings (access with 'bd config get/set') +# These are stored in the database, not in this file: +# - jira.url +# - jira.project +# - linear.url +# - linear.api-key +# - github.org +# - github.repo diff --git a/.beads/interactions.jsonl b/.beads/interactions.jsonl new file mode 100644 index 0000000..e69de29 diff --git a/.beads/metadata.json b/.beads/metadata.json new file mode 100644 index 0000000..c787975 --- /dev/null +++ b/.beads/metadata.json @@ -0,0 +1,4 @@ +{ + "database": "beads.db", + "jsonl_export": "issues.jsonl" +} \ No newline at end of file diff --git a/.dvc/.gitignore b/.dvc/.gitignore new file mode 100644 index 0000000..20e0fb0 --- /dev/null +++ b/.dvc/.gitignore @@ -0,0 +1 @@ +/config.local diff --git a/.dvc/config b/.dvc/config new file mode 100644 index 0000000..5919cd3 --- /dev/null +++ b/.dvc/config @@ -0,0 +1,11 @@ +[core] + remote = gcs + analytics = false +['remote "gcs"'] + url = gs://sciexp/projects/omicsio/cas + credentialpath = ../.dvc-sa.json +['remote "drive"'] + url = gdrive://1yS1zpTqR4w2WFjXQuV8HypMrQqJvcM-x/dvcstore + gdrive_acknowledge_abuse = true + gdrive_use_service_account = true + gdrive_service_account_json_file_path = ../.dvc-sa.json diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..c821c6f --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,132 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or advances of + any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email address, + without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +cameronraysmtih@gmail.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][mozilla coc]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][faq]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[mozilla coc]: https://github.com/mozilla/diversity +[faq]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations \ No newline at end of file diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..19ac59c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,42 @@ +--- +name: report bug +about: report a development or usage problem +title: "" +labels: bug +assignees: "" +--- + +## description + +## example + +
+ code example + +```sh + +``` + +
+ +
+ error output + +```sh + +``` + +
+ +## environment + +
+ environment + +output of `nix doctor`, `nix flake metadata`, `nix flake show`, etc. + +```sh + +``` + +
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..c2f28fb --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,29 @@ +--- +name: request feature +about: suggest a new feature or update +title: "" +labels: enhancement +assignees: "" +--- + +## problem to address + +
+ code example + +```sh + +``` + +
+ +## description of proposed solution + +
+ code example + +```sh + +``` + +
diff --git a/.github/SECURITY.md b/.github/SECURITY.md new file mode 100644 index 0000000..9d7ebc2 --- /dev/null +++ b/.github/SECURITY.md @@ -0,0 +1,3 @@ +# security + +To report a potential security vulnerability, please follow the [instructions to create a draft security advisory](https://github.com/sciexp/omicsio/security/advisories/new). diff --git a/.sops.yaml b/.sops.yaml new file mode 100644 index 0000000..1501394 --- /dev/null +++ b/.sops.yaml @@ -0,0 +1,15 @@ +keys: + - &dev age1dn8w7y4t4h23fmeenr3dghfz5qh53jcjq9qfv26km3mnv8l44g0sghptu3 + - &ci age1m9m8h5vqr7dqlmvnzcwshmm4uk8umcllazum6eaulkdp3qc88ugs22j3p8 + +creation_rules: + - path_regex: vars/.*\.yaml$ + key_groups: + - age: + - *dev + - *ci + - path_regex: vars/.*\.json$ + key_groups: + - age: + - *dev + - *ci diff --git a/.taplo.toml b/.taplo.toml new file mode 100644 index 0000000..3ae4082 --- /dev/null +++ b/.taplo.toml @@ -0,0 +1,15 @@ +include = [ + ".taplo.toml", + "packages/*/pyproject.toml", + "pyproject.toml", +] + +[formatting] +align_entries = true +array_auto_collapse = false +column_width = 88 +indent_string = " " +indent_tables = false +reorder_arrays = true +reorder_keys = true +trailing_newline = true diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 0000000..1227de8 --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,40 @@ +{ + // https://go.microsoft.com/fwlink/?LinkId=827846 + "recommendations": [ + "alefragnani.project-manager", + "Catppuccin.catppuccin-vsc", + "charliermarsh.ruff", + "christian-kohler.path-intellisense", + "cweijan.vscode-database-client2", + // "donjayamanne.python-extension-pack", + // disable "donjayamanne.python-environment-manager" + // from "donjayamanne.python-extension-pack" + // due to https://github.com/microsoft/vscode/issues/210792/#issuecomment-2186965405 + // also leaves out + // "wholroyd.jinja" + // "batisteo.vscode-django" + "ms-python.python", + "njpwerner.autodocstring", + "KevinRose.vsc-python-indent", + "eamodio.gitlens", + "github.vscode-github-actions", + "GitHub.vscode-pull-request-github", + "ionutvmi.path-autocomplete", + "jnoortheen.nix-ide", + "ms-azuretools.vscode-docker", + "ms-kubernetes-tools.vscode-kubernetes-tools", + "ms-toolsai.jupyter", + "njzy.stats-bar", + "patbenatar.advanced-new-file", + "quarto.quarto", + "rangav.vscode-thunder-client", + "redhat.vscode-yaml", + "sleistner.vscode-fileutils", + "stkb.rewrap", + "streetsidesoftware.code-spell-checker", + "tamasfe.even-better-toml", + "vscode-icons-team.vscode-icons", + "vscodevim.vim", + "richie5um2.vscode-sort-json" + ] +} diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..a06a19d --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,25 @@ +{ + "version": "0.1.0", + "configurations": [ + { + "name": "omicsio: Debug CLI", + "type": "debugpy", + "request": "launch", + "module": "omicsio", + "args": [ + ], + "console": "integratedTerminal", + "cwd": "${workspaceFolder}", + "preLaunchTask": "direnv allow" + }, + { + "name": "Python: Debug Tests", + "type": "debugpy", + "request": "launch", + "program": "${file}", + "purpose": ["debug-test"], + "console": "integratedTerminal", + "justMyCode": false + } + ] +} diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..79cbb4d --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,69 @@ +{ + "[ipynb]": { + "editor.defaultFormatter": "charliermarsh.ruff" + }, + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff" + }, + "autoHide.autoHideAuxiliaryBar": false, + "autoHide.autoHidePanel": false, + "autoHide.autoHideSideBar": false, + "autoHide.hideOnOpen": false, + "cloudcode.autoDependencies": "on", + "editor.codeActionsOnSave": { + "source.fixAll": "always", + "source.organizeImports": "always" + }, + "editor.fontSize": 16, + "editor.formatOnSave": true, + "files.autoSave": "onWindowChange", + // "files.autoSave": "afterDelay", + // "files.autoSaveDelay": 1000, + "files.watcherExclude": { + "**/.devenv/**": true, + "**/.direnv/**": true, + "**/.hypothesis/**": true, + "**/.mypy_cache/**": true, + "**/.nox/**": true, + "**/.pytest_cache/**": true, + "**/.ruff_cache/**": true, + "**/.solid/**": true, + "**/.venv/**": true, + "**/bazel-*/**": true, + }, + "notebook.codeActionsOnSave": { + "notebook.source.fixAll": "explicit", + "notebook.source.organizeImports": "explicit" + }, + "notebook.formatOnCellExecution": true, + "notebook.formatOnSave.enabled": true, + "search.exclude": { + "**/.devenv/**": true, + "**/.direnv/**": true, + "**/.hypothesis/**": true, + "**/.mypy_cache/**": true, + "**/.pytest_cache/**": true, + "**/.ruff_cache/**": true, + "**/.solid/**": true, + "**/.venv/**": true, + "**/bazel-*/**": true, + }, + // this is a workaround for 1000% CPU usage by + // /Applications/Visual Studio Code.app/Contents/Resources/app/node_modules.asar.unpacked/@vscode/ripgrep/bin/rg + // https://github.com/microsoft/vscode/issues/186279#issuecomment-1633159669 + "search.followSymlinks": false, + "terminal.integrated.fontSize": 14, + "terminal.integrated.scrollback": 100000, + "workbench.colorTheme": "Catppuccin Mocha", + "workbench.iconTheme": "vscode-icons", + // Passing --no-cov to pytestArgs is required to respect breakpoints + // when debugging tests. + // https://github.com/microsoft/vscode-python/issues/693#issuecomment-367848085 + "python.testing.pytestArgs": [ + "-rA", + "--xdoc", + "--disable-warnings", + "-v", + "--no-cov" + ] +} diff --git a/.vscode/tasks.json b/.vscode/tasks.json new file mode 100644 index 0000000..31ea853 --- /dev/null +++ b/.vscode/tasks.json @@ -0,0 +1,13 @@ +{ + "version": "2.0.0", + "tasks": [ + { + "label": "direnv allow", + "type": "shell", + "command": "direnv allow && env", + "options": { + "cwd": "${workspaceFolder}" + } + } + ] +} diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..0d381b2 --- /dev/null +++ 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + +Copyright [yyyy] [name of copyright owner] + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..053beb2 --- /dev/null +++ b/Makefile @@ -0,0 +1,277 @@ +# infra bootstrap makefile +# +# tl;dr: +# +# 1. Run 'make bootstrap' to install nix and direnv +# 2. Run 'make verify' to check your installation +# 3. Run 'make setup-user' to generate age keys for secrets (first time only) +# 4. Run 'nix develop' to enter the development environment +# 5. Use 'just ...' to run configuration tasks +# +# This Makefile helps bootstrap a development environment with nix and direnv. +# After bootstrap is complete, see the justfile for managing configurations. + +.DEFAULT_GOAL := help + +#------- +##@ help +#------- + +# based on "https://gist.github.com/prwhite/8168133?permalink_comment_id=4260260#gistcomment-4260260" +.PHONY: help +help: ## Display this help. (Default) + @grep -hE '^(##@|[A-Za-z0-9_ \-]*?:.*##).*$$' $(MAKEFILE_LIST) | \ + awk 'BEGIN {FS = ":.*?## "}; /^##@/ {print "\n" substr($$0, 5)} /^[A-Za-z0-9_ \-]*?:.*##/ {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' + +help-sort: ## Display alphabetized version of help (no section headings). + @grep -hE '^[A-Za-z0-9_ \-]*?:.*##.*$$' $(MAKEFILE_LIST) | sort | \ + awk 'BEGIN {FS = ":.*?## "}; /^[A-Za-z0-9_ \-]*?:.*##/ {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' + +HELP_TARGETS_PATTERN ?= test +help-targets: ## Print commands for all targets matching a given pattern. Copy this example into your shell: +help-targets: ## Copy this example into your shell: +help-targets: ## eval "$(make help-targets HELP_TARGETS_PATTERN=bootstrap | sed 's/\x1b\[[0-9;]*m//g')" + @make help-sort | awk '{print $$1}' | grep '$(HELP_TARGETS_PATTERN)' | xargs -I {} printf "printf '___\n\n{}:\n\n'\nmake -n {}\nprintf '\n'\n" + +# catch-all pattern rule +# +# This rule matches any targets that are not explicitly defined in this +# Makefile. It prevents 'make' from failing due to unrecognized targets, which +# is particularly useful when passing arguments or targets to sub-Makefiles. The +# '@:' command is a no-op, indicating that nothing should be done for these +# targets within this Makefile. +# +%: + @: + +#------- +##@ bootstrap +#------- + +.PHONY: bootstrap-prep-darwin +bootstrap-prep-darwin: ## Install darwin prerequisites (Xcode CLI tools + Homebrew) before 'make bootstrap' + @printf "Installing darwin prerequisites...\n\n" + @printf "Step 1: Xcode Command Line Tools\n" + @if xcode-select -p &>/dev/null; then \ + printf " ● Xcode CLI tools already installed\n"; \ + else \ + printf " Installing Xcode CLI tools (this will open a dialog)...\n"; \ + xcode-select --install; \ + printf " ⏳ Wait for installation to complete, then re-run this target\n"; \ + exit 1; \ + fi + @printf "\nStep 2: Homebrew\n" + @if command -v brew &>/dev/null; then \ + printf " ● Homebrew already installed\n"; \ + else \ + printf " Installing Homebrew...\n"; \ + /bin/bash -c "$$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"; \ + fi + @printf "\n● Darwin prerequisites complete!\n" + @printf "Next: Run 'make bootstrap' to install Nix\n" + +.PHONY: bootstrap +bootstrap: ## Main bootstrap target that runs all necessary setup steps +bootstrap: install-nix install-direnv + @printf "\n● Bootstrap of nix and direnv complete!\n\n" + @printf "Next steps:\n" + @echo "1. Start a new shell session (to load nix in PATH)" + @echo "2. Run 'make verify' to check your installation" + @echo "3. Run 'make setup-user' to generate age keys (first time setup)" + @echo "4. Run 'nix develop' to enter the development environment" + @echo "" + @printf "Optional: Auto-activate development environment with direnv\n" + @echo " - See https://direnv.net/docs/hook.html to add direnv to your shell" + @echo " - Start a new shell session" + @echo " - cd out and back into the project directory" + @echo " - Run 'direnv allow' to activate" + @echo "" + @printf "For detailed documentation, see docs/new-user-host.md\n" + +.PHONY: install-nix +# Download platform-specific binary directly from GitHub Releases. +# This bypasses both the Fastly CDN (HTTP 618 errors) and the shell wrapper +# (which has template placeholders that aren't filled in for raw source files). +# To update version, change NIX_INSTALLER_VERSION below. +# Note: versioning jumped from 0.27.0 to 3.11.3, then back to 2.33.0 when +# NixOS/nix-installer removed the 3.x tags (repo renamed from experimental-nix-installer). +# https://github.com/NixOS/nix-installer/releases +# +# The nix-installer 2.33.0 defaults include settings equivalent to: +# --extra-conf "experimental-features = nix-command flakes" +# --extra-conf "auto-optimise-store = true" +# --extra-conf "always-allow-substitutes = true" +# --extra-conf "max-jobs = auto" +# --extra-conf "extra-nix-path = nixpkgs=flake:nixpkgs" +# --extra-conf "bash-prompt-prefix = (nix:\$name)\\040" +# +# We add trusted-users to allow flake-specified substituters and public keys: +# --extra-conf "trusted-users = root @admin @wheel" +# This enables accepting flake nixConfig without prompts or warnings. +# +# If using the upstream nix installer (https://nixos.org/download/) which lacks +# these defaults, add the --extra-conf flags above to the install command. +NIX_INSTALLER_VERSION := 2.33.0 +install-nix: ## Install Nix using the NixOS community installer + @echo "Installing Nix..." + @if command -v nix >/dev/null 2>&1; then \ + echo "Nix is already installed."; \ + else \ + case "$$(uname -s)-$$(uname -m)" in \ + Linux-x86_64) PLATFORM="x86_64-linux" ;; \ + Linux-aarch64) PLATFORM="aarch64-linux" ;; \ + Darwin-x86_64) PLATFORM="x86_64-darwin" ;; \ + Darwin-arm64) PLATFORM="aarch64-darwin" ;; \ + *) echo "Unsupported platform: $$(uname -s)-$$(uname -m)"; exit 1 ;; \ + esac; \ + INSTALLER_URL="https://github.com/NixOS/nix-installer/releases/download/$(NIX_INSTALLER_VERSION)/nix-installer-$$PLATFORM"; \ + echo "Platform: $$PLATFORM"; \ + echo "Downloading from: $$INSTALLER_URL"; \ + max_attempts=3; \ + attempt=1; \ + while [ $$attempt -le $$max_attempts ]; do \ + echo "Attempt $$attempt of $$max_attempts..."; \ + if curl --proto '=https' --tlsv1.2 -sSf -L --retry 3 --retry-delay 5 \ + "$$INSTALLER_URL" -o /tmp/nix-installer && chmod +x /tmp/nix-installer; then \ + /tmp/nix-installer install --no-confirm \ + --extra-conf "trusted-users = root @admin @wheel" && break; \ + fi; \ + attempt=$$((attempt + 1)); \ + if [ $$attempt -le $$max_attempts ]; then \ + echo "Download or install failed, waiting 10 seconds before retry..."; \ + sleep 10; \ + fi; \ + done; \ + if [ $$attempt -gt $$max_attempts ]; then \ + echo "Failed to install nix after $$max_attempts attempts"; \ + exit 1; \ + fi; \ + fi + +.PHONY: install-direnv +install-direnv: ## Install direnv (requires nix to be installed first) + @echo "Installing direnv..." + @if command -v direnv >/dev/null 2>&1; then \ + echo "direnv is already installed."; \ + else \ + . /nix/var/nix/profiles/default/etc/profile.d/nix-daemon.sh && nix profile install nixpkgs#direnv; \ + fi + @echo "" + @echo "See https://direnv.net/docs/hook.html if you would like to add direnv to your shell" + +#------- +##@ verify +#------- + +.PHONY: verify +verify: ## Verify nix installation and environment setup + @printf "\nVerifying installation...\n\n" + @printf "Checking nix installation: " + @if command -v nix >/dev/null 2>&1; then \ + printf "● nix found at %s\n" "$$(command -v nix)"; \ + nix --version; \ + else \ + printf "⊘ nix not found\n"; \ + printf "Run 'make install-nix' to install nix\n"; \ + exit 1; \ + fi + @printf "\nChecking nix flakes support: " + @if nix flake --help >/dev/null 2>&1; then \ + printf "● flakes enabled\n"; \ + else \ + printf "⊘ flakes not enabled\n"; \ + exit 1; \ + fi + @printf "\nChecking direnv installation: " + @if command -v direnv >/dev/null 2>&1; then \ + printf "● direnv found\n"; \ + else \ + printf "⚠️ direnv not found (optional but recommended)\n"; \ + printf "Run 'make install-direnv' to install\n"; \ + fi + @printf "\nChecking flake validity: " + @if nix flake metadata . >/dev/null 2>&1; then \ + printf "● flake is valid\n"; \ + else \ + printf "⊘ flake has errors\n"; \ + exit 1; \ + fi + @printf "\nChecking required tools in devShell: " + @if nix develop --command bash -c 'command -v just && command -v python && command -v uv && command -v pixi && command -v ruff' >/dev/null 2>&1; then \ + printf "● just, python, uv, pixi, ruff available\n"; \ + else \ + printf "⊘ some tools missing from devShell\n"; \ + exit 1; \ + fi + @printf "\n/etc/nix/nix.conf:\n" + @printf "==================\n" + @cat /etc/nix/nix.conf 2>/dev/null || printf "(file not found)\n" + @printf "==================\n" + @if [ -f /etc/nix/nix.custom.conf ]; then \ + printf "\n/etc/nix/nix.custom.conf:\n"; \ + printf "==================\n"; \ + cat /etc/nix/nix.custom.conf; \ + printf "==================\n"; \ + fi + @printf "\n● All verification checks passed!\n\n" + +#------- +##@ setup +#------- + +.PHONY: setup-user +setup-user: ## Generate age key for sops-nix secrets (first time user setup) + @printf "\nGenerating age key for secrets management...\n\n" + @. /nix/var/nix/profiles/default/etc/profile.d/nix-daemon.sh && \ + if [ -f ~/.config/sops/age/keys.txt ]; then \ + printf "⚠️ Age key already exists at ~/.config/sops/age/keys.txt\n"; \ + printf "To regenerate, manually delete the file first\n"; \ + printf "\nYour public key is:\n"; \ + nix shell nixpkgs#age -c age-keygen -y ~/.config/sops/age/keys.txt 2>/dev/null || printf "Error reading existing key\n"; \ + else \ + mkdir -p ~/.config/sops/age; \ + nix shell nixpkgs#age -c age-keygen -o ~/.config/sops/age/keys.txt; \ + chmod 600 ~/.config/sops/age/keys.txt; \ + printf "\n● Age key generated successfully!\n\n"; \ + printf "Your public key is:\n"; \ + nix shell nixpkgs#age -c age-keygen -y ~/.config/sops/age/keys.txt; \ + printf "\n⚠️ IMPORTANT: Back up your private key to Bitwarden!\n"; \ + printf "1. Copy the content of ~/.config/sops/age/keys.txt\n"; \ + printf "2. Store in Bitwarden as secure note: 'age-key-'\n"; \ + printf "3. Send your PUBLIC key (shown above) to the admin\n"; \ + printf "\nSee docs/new-user-host.md for complete setup instructions\n"; \ + fi + +.PHONY: check-secrets +check-secrets: ## Check if you can decrypt shared secrets (requires age key and admin setup) + @printf "\nChecking secrets access...\n\n" + @if [ ! -f ~/.config/sops/age/keys.txt ]; then \ + printf "⊘ No age key found. Run 'make setup-user' first\n"; \ + exit 1; \ + fi + @if [ -f secrets/shared.yaml ]; then \ + if nix develop --command sops -d secrets/shared.yaml >/dev/null 2>&1; then \ + printf "● Successfully decrypted shared secrets!\n"; \ + printf "You have proper access to the secrets system\n"; \ + else \ + printf "⊘ Cannot decrypt shared secrets\n"; \ + printf "Possible reasons:\n"; \ + printf "1. Admin hasn't added your key to .sops.yaml yet\n"; \ + printf "2. Admin hasn't run 'sops updatekeys' after adding you\n"; \ + printf "3. Your age key is incorrect\n"; \ + printf "\nSend your public key to admin:\n"; \ + age-keygen -y ~/.config/sops/age/keys.txt; \ + exit 1; \ + fi; \ + else \ + printf "No secrets/shared.yaml found. Secrets not yet configured for this project.\n"; \ + fi + +#------- +##@ clean +#------- + +.PHONY: clean +clean: ## Clean any temporary files or build artifacts + @echo "Cleaning up..." + @rm -rf result result-* diff --git a/bun.lock b/bun.lock new file mode 100644 index 0000000..6958c8a --- /dev/null +++ b/bun.lock @@ -0,0 +1,1170 @@ +{ + "lockfileVersion": 1, + "configVersion": 1, + "workspaces": { + "": { + "name": "omicsio-template", + "devDependencies": { + "@semantic-release/changelog": "^6.0.3", + "@semantic-release/github": "^12.0.0", + "conventional-changelog-conventionalcommits": "^9.0.0", + "cross-env": "^10.0.0", + "semantic-release": "^25.0.0", + "semantic-release-major-tag": "^0.3.2", + "semantic-release-monorepo": "^8.0.2", + }, + }, + "packages/pnt-cli": { + "name": "pnt-cli", + "version": "0.0.0-development", + "devDependencies": { + "@semantic-release/changelog": "^6.0.3", + "@semantic-release/github": "^12.0.0", + "conventional-changelog-conventionalcommits": 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b/docs/_extensions/machow/interlinks/.gitignore @@ -0,0 +1,3 @@ +*.html +*.pdf +*_files/ diff --git a/docs/_extensions/machow/interlinks/_extension.yml b/docs/_extensions/machow/interlinks/_extension.yml new file mode 100644 index 0000000..c8a8121 --- /dev/null +++ b/docs/_extensions/machow/interlinks/_extension.yml @@ -0,0 +1,7 @@ +title: Interlinks +author: Michael Chow +version: 1.1.0 +quarto-required: ">=1.2.0" +contributes: + filters: + - interlinks.lua diff --git a/docs/_extensions/machow/interlinks/interlinks.lua b/docs/_extensions/machow/interlinks/interlinks.lua new file mode 100644 index 0000000..cc538a2 --- /dev/null +++ b/docs/_extensions/machow/interlinks/interlinks.lua @@ -0,0 +1,411 @@ +local inventory = {} -- sphinx inventories +local autolink -- set in Meta +local autolink_ignore_token = "qd-no-link" + +local function _debug_log(text, debug) + if debug then + quarto.log.warning(text) + end +end + +local function read_inv_text(filename) + -- read file + local file = io.open(filename, "r") + if file == nil then + return nil + end + local str = file:read("a") + file:close() + + + local project = str:match("# Project: (%S+)") + local version = str:match("# Version: (%S+)") + + local data = { project = project, version = version, items = {} } + + local ptn_data = + "^" .. + "(.-)%s+" .. -- name + "([%S:]-):" .. -- domain + "([%S]+)%s+" .. -- role + "(%-?%d+)%s+" .. -- priority + "(%S*)%s+" .. -- uri + "(.-)\r?$" -- dispname + + + -- Iterate through each line in the file content + for line in str:gmatch("[^\r\n]+") do + if not line:match("^#") then + -- Match each line against the pattern + local name, domain, role, priority, uri, dispName = line:match(ptn_data) + + -- if name is nil, raise an error + if name == nil then + error("Error parsing line: " .. line) + end + + data.items[#data.items + 1] = { + name = name, + domain = domain, + role = role, + priority = priority, + uri = uri, + dispName = dispName + } + end + end + return data +end + +local function read_json(filename) + local file = io.open(filename, "r") + if file == nil then + return nil + end + local str = file:read("a") + file:close() + + local decoded = quarto.json.decode(str) + return decoded +end + +local function read_inv_text_or_json(base_name) + local file = io.open(base_name .. ".txt", "r") + if file then + -- TODO: refactors so we don't just close the file immediately + io.close(file) + json = read_inv_text(base_name .. ".txt") + else + json = read_json(base_name .. ".json") + end + + return json +end + +-- each inventory has entries: project, version, items +local function lookup(search_object, debug) + local results = {} + for _, inv in ipairs(inventory) do + for _, item in ipairs(inv.items) do + -- e.g. :external+:::`` + if item.inv_name and item.inv_name ~= search_object.inv_name then + goto continue + end + + if item.name ~= search_object.name then + goto continue + end + + if search_object.role and item.role ~= search_object.role then + goto continue + end + + if search_object.domain and item.domain ~= search_object.domain then + goto continue + else + if search_object.domain or item.domain == "py" then + table.insert(results, item) + end + + goto continue + end + + ::continue:: + end + end + + if #results == 1 then + return results[1] + end + if #results > 1 then + _debug_log("Found multiple matches for " .. search_object.name .. ", using the first match.", debug) + return results[1] + end + if #results == 0 then + _debug_log("Found no matches for object:\n", debug) + _debug_log(search_object, debug) + end + + return nil +end + +local function mysplit(inputstr, sep) + if sep == nil then + sep = "%s" + end + local t = {} + for str in string.gmatch(inputstr, "([^" .. sep .. "]+)") do + table.insert(t, str) + end + return t +end + +local function normalize_role(role) + if role == "func" then + return "function" + end + return role +end + +local function copy_replace(original, key, new_value) + -- First create a copy of the table + local copy = {} + for k, v in pairs(original) do + copy[k] = v + end + + -- Then replace the specific value + copy[key] = new_value + + return copy +end + +local function contains(list, value) + -- check if list contains a value + for i, v in ipairs(list) do + if v == value then + return true + end + end + return false +end + +local function flatten_alias_list(list) + -- flatten a list of lists into a single list, + -- where each entry has the form {key, subvalue}} + -- e.g. + -- input: {key1 = {subval1, subval2}, key2 = subval3} + -- output: {{key1, subval1}, {key1, subval2}, {key2, subval3}} + local flat = {} + for key, sublist in pairs(list) do + if type(sublist) == "table" then + for _, subvalue in ipairs(sublist) do + table.insert(flat, { key, subvalue }) + end + else + table.insert(flat, { key, sublist }) + end + end + return flat +end + +local function prepend_aliases(flat_aliases) + -- if str up to first period starts with an alias, then + -- replace it with the full name. + -- For example, suppose we have the alias quartodoc -> qd + -- e.g. qd.Auto -> quartodoc.Auto + -- e.g. qda.Auto -> qda.Auto + + local new_inv = {} + new_inv["project"] = "aliases" + new_inv["version"] = "0.0.9999" -- I have not begun to think about version... + new_inv["items"] = {} + + for _, name_pair in pairs(flat_aliases) do + local full = name_pair[1] + local alias = name_pair[2] + for _, inv in ipairs(inventory) do + for _, item in ipairs(inv.items) do + if string.sub(item.name, 1, string.len(full) + 1) == (full .. ".") then + -- replace full .. "." with alias .. "." + local prefix + if not alias or pandoc.utils.stringify(alias) == "" then + prefix = "" + else + -- TODO: ensure alias doesn't end with period + prefix = pandoc.utils.stringify(alias) .. "." + end + local new_name = prefix .. string.sub(item.name, string.len(full) + 2) + table.insert(new_inv.items, copy_replace(item, "name", new_name)) + end + end + end + end + table.insert(inventory, new_inv) +end + +local function build_search_object(str, debug) + local starts_with_colon = str:sub(1, 1) == ":" + local search = {} + if starts_with_colon then + local t = mysplit(str, ":") + if #t == 2 then + -- e.g. :py:func:`my_func` + search.role = normalize_role(t[1]) + search.name = t[2]:match("%%60(.*)%%60") + elseif #t == 3 then + -- e.g. :py:func:`my_func` + search.domain = t[1] + search.role = normalize_role(t[2]) + search.name = t[3]:match("%%60(.*)%%60") + elseif #t == 4 then + -- e.g. :ext+inv:py:func:`my_func` + search.external = true + + search.inv_name = t[1]:match("external%+(.*)") + search.domain = t[2] + search.role = normalize_role(t[3]) + search.name = t[4]:match("%%60(.*)%%60") + else + _debug_log("couldn't parse this link: " .. str, debug) + return {} + end + else + search.name = str:match("%%60(.*)%%60") + end + + if search.name == nil then + _debug_log("couldn't parse this link: " .. str, debug) + return {} + end + + if search.name:sub(1, 1) == "~" then + search.shortened = true + search.name = search.name:sub(2, -1) + end + return search +end + +local function report_broken_link(link, search_object, replacement) + -- TODO: how to unescape html elements like [? + return pandoc.Code(pandoc.utils.stringify(link.content)) +end + +function Link(link) + -- do not process regular links ---- + if not link.target:match("%%60") then + return link + end + + -- lookup item ---- + local search = build_search_object(link.target) + local item = lookup(search) + + -- determine replacement, used if no link text specified ---- + local original_text = pandoc.utils.stringify(link.content) + local replacement = search.name + if search.shortened then + local t = mysplit(search.name, ".") + replacement = t[#t] + end + + -- set link text ---- + if original_text == "" and replacement ~= nil then + link.content = pandoc.Code(replacement) + end + + -- report broken links ---- + if item == nil then + return report_broken_link(link, search) + end + link.target = item.uri:gsub("%$$", search.name) + + + return link +end + +function Code(code) + if (not autolink) or contains(code.classes, autolink_ignore_token) then + return code + end + + -- allow text for lookup to be simple function call + -- and also support shortened syntax (~~ prefix) + -- e.g. my_func() -> my_func + -- e.g. a.b.call() -> a.b.call + -- e.g. ~~my_func() -> my_func + local text + + -- detect and remove shortening syntax (~~ prefix) + local is_shortened = code.text:sub(1, 2) == "~~" + local is_short_dot = code.text:sub(1, 3) == "~~." + local unprefixed = code.text:gsub("^~~%.?", "") + if unprefixed:match("%(%s*%)") then + text = unprefixed:gsub("%(%s*%)", "") + else + text = unprefixed + end + + + -- return code.attr + local search = build_search_object("%60" .. text .. "%60") + local item = lookup(search) + + -- determine replacement, used if no link text specified ---- + if item == nil then + code.text = unprefixed + return code + end + + -- shorten text if shortening syntax used + if is_shortened then + -- keep text after last period (.) + local split = mysplit(unprefixed, ".") + if #split > 0 then + local new_name = split[#split] + if is_short_dot then + -- if shortened with dot, keep the dot + new_name = "." .. new_name + end + code.text = new_name + else + code.text = unprefixed + end + end + + + return pandoc.Link(code, item.uri:gsub("%$$", search.name)) +end + +local function fixup_json(json, prefix, attach) + for _, item in ipairs(json.items) do + item.uri = prefix .. item.uri + end + table.insert(inventory, json) +end + +return { + { + Meta = function(meta) + local json + local prefix + local aliases + + -- set globals from config + if meta.interlinks and meta.interlinks.autolink then + autolink = true + else + autolink = false + end + + local aliases + if meta.interlinks and meta.interlinks.aliases then + aliases = meta.interlinks.aliases + else + aliases = {} + end + + -- process sources + if meta.interlinks and meta.interlinks.sources then + for k, v in pairs(meta.interlinks.sources) do + local base_name = quarto.project.offset .. "/_inv/" .. k .. "_objects" + json = read_inv_text_or_json(base_name) + prefix = pandoc.utils.stringify(v.url) + if json ~= nil then + fixup_json(json, prefix) + end + end + end + json = read_inv_text_or_json(quarto.project.offset .. "/objects") + if json ~= nil then + fixup_json(json, "/") + end + + prepend_aliases(flatten_alias_list(aliases)) + end + }, + { + Link = Link, + Code = Code + } +} diff --git a/docs/_extensions/machow/interlinks/test.qmd b/docs/_extensions/machow/interlinks/test.qmd new file mode 100644 index 0000000..d096eb4 --- /dev/null +++ b/docs/_extensions/machow/interlinks/test.qmd @@ -0,0 +1,22 @@ +--- +filters: + - interlinks.lua +interlinks: + autolink: true + aliases: + quartodoc: null + #sources: + # test: + # url: https://example.com +--- + +* `some_func` +* `some_func()` +* `some_func(a=1)` +* `some_func()`{.qd-no-link} +* `some_func + some_func` +* `a.b.c` +* `~a.b.c` +* `a.b.c()` +* `quartodoc.Auto()` +* `Auto()` \ No newline at end of file diff --git a/docs/_freeze.dvc b/docs/_freeze.dvc new file mode 100644 index 0000000..59f5966 --- /dev/null +++ b/docs/_freeze.dvc @@ -0,0 +1,6 @@ +outs: +- md5: 481f00b14626c9c558a990f58cc704f7.dir + size: 9160 + nfiles: 2 + hash: md5 + path: _freeze diff --git a/docs/_quarto.yml b/docs/_quarto.yml new file mode 100644 index 0000000..f1bb697 --- /dev/null +++ b/docs/_quarto.yml @@ -0,0 +1,131 @@ +project: + type: website + output-dir: _site + preview: + port: 7779 + +format: + html: + highlight-style: gruvbox + theme: + dark: [darkly, cdark.scss] + light: [cosmo, clight.scss] + include-in-header: include.html + css: styles.css + grid: + sidebar-width: 300px + body-width: 900px + margin-width: 300px + gutter-width: 1.5rem + toc: true + +execute: + warning: false + error: false + +filters: + - interlinks + +interlinks: + fast: true + sources: + python: + url: https://docs.python.org/3/ + beartype: + url: https://beartype.readthedocs.io/en/latest/ + matplotlib: + url: https://matplotlib.org/stable/ + numpy: + url: https://numpy.org/doc/stable/ + +website: + title: "omicsio" + description: "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns" + site-url: "https://sciexp.github.io/omicsio" + back-to-top-navigation: false + page-navigation: true + + page-footer: + border: false + left: "" + right: + - icon: github + href: https://github.com/sciexp/omicsio + + search: + type: overlay + + navbar: + background: primary + tools: + - icon: github + href: https://github.com/sciexp/omicsio + left: + - sidebar:tutorials + - sidebar:guides + - sidebar:concepts + - href: reference + text: Reference + - sidebar:development + - sidebar:about + + sidebar: + - id: "" + - id: tutorials + title: "Tutorials" + style: "floating" + contents: + - tutorials/getting-started.qmd + - id: guides + title: "Guides" + style: "floating" + contents: + - guides/installation.qmd + - guides/development.qmd + - id: concepts + title: "Concepts" + style: "floating" + contents: + - concepts/index.qmd + - id: development + title: "Development" + style: "floating" + contents: + - text: "Overview" + href: development/index.qmd + - text: "Context" + href: development/context/index.qmd + - text: "Requirements" + href: development/requirements/index.qmd + - text: "Architecture" + href: development/architecture/index.qmd + - text: "Traceability" + href: development/traceability/index.qmd + - text: "Work Items" + href: development/work-items/index.qmd + - id: about + title: "About" + style: "floating" + contents: + - text: "Overview" + href: about/index.qmd + - text: "Contributing" + href: about/contributing.qmd + +quartodoc: + dir: reference + parser: google + package: omicsio + title: Reference + sidebar: reference/_sidbar.yml + render_interlinks: true + options: + signature_name: full + sections: + - title: API Reference + desc: | + API reference for omicsio. + contents: + - name: main + children: embedded + dynamic: true diff --git a/docs/about/contributing.qmd b/docs/about/contributing.qmd new file mode 100644 index 0000000..e69de29 diff --git a/docs/about/index.qmd b/docs/about/index.qmd new file mode 100644 index 0000000..8fc61e1 --- /dev/null +++ b/docs/about/index.qmd @@ -0,0 +1,18 @@ +--- +title: "Overview" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../references.bib +csl: ../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +This section provides background information for the omicsio project. diff --git a/docs/bibstyle.csl b/docs/bibstyle.csl new file mode 100644 index 0000000..e6efba5 --- /dev/null +++ b/docs/bibstyle.csl @@ -0,0 +1,152 @@ + + diff --git a/docs/cdark.scss b/docs/cdark.scss new file mode 100644 index 0000000..8a85a33 --- /dev/null +++ b/docs/cdark.scss @@ -0,0 +1,10 @@ +/*-- scss:defaults --*/ +$spacer: 1rem; +$navbar-padding-y: $spacer * 0.5; +$body-color: #dfdfd6; +$primary: #1b1b1f; +$body-bg: #1b1b1f; +$link-color: #2ea356; +// $sidebar-bg: #161618; +$code-bg: #161618; +$code-color: #4188f6; diff --git a/docs/clight.scss b/docs/clight.scss new file mode 100644 index 0000000..8167c42 --- /dev/null +++ b/docs/clight.scss @@ -0,0 +1,5 @@ +/*-- scss:defaults --*/ +$spacer: 1rem; +$navbar-padding-y: $spacer * 0.5; +$primary: #111111; +$link-color: #2ea356; diff --git a/docs/concepts/index.qmd b/docs/concepts/index.qmd new file mode 100644 index 0000000..0bd7c6a --- /dev/null +++ b/docs/concepts/index.qmd @@ -0,0 +1,18 @@ +--- +title: "Overview" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../references.bib +csl: ../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +This section provides an overview of the concepts and terminology used in the omicsio project. diff --git a/docs/development/architecture/architecture.qmd b/docs/development/architecture/architecture.qmd new file mode 100644 index 0000000..4e292c2 --- /dev/null +++ b/docs/development/architecture/architecture.qmd @@ -0,0 +1,20 @@ +--- +title: "System Architecture and Design Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This system specification provides a glass-box view of the architecture of the omicsio package, detailing its internal structure, computational methods, and implementation approach. diff --git a/docs/development/architecture/index.qmd b/docs/development/architecture/index.qmd new file mode 100644 index 0000000..592f49d --- /dev/null +++ b/docs/development/architecture/index.qmd @@ -0,0 +1,27 @@ +--- +title: "System Architecture and Design Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This system specification outlines the system architecture and design for the omicsio project. + +| Topic | Reference | +|-------|-----------| +| System Architecture and Design Specification | [System Architecture and Design Specification](architecture.qmd) | + +When the architecture document is sharded into distinct files per subsection, the above table +may serve as a reference to the different architecture specification documents. diff --git a/docs/development/context/context.qmd b/docs/development/context/context.qmd new file mode 100644 index 0000000..7a2e661 --- /dev/null +++ b/docs/development/context/context.qmd @@ -0,0 +1,20 @@ +--- +title: "Context Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document specifies the context to establish the motivation and conceptual foundation for the omicsio project. diff --git a/docs/development/context/index.qmd b/docs/development/context/index.qmd new file mode 100644 index 0000000..bc4c33e --- /dev/null +++ b/docs/development/context/index.qmd @@ -0,0 +1,27 @@ +--- +title: "Context Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document outlines the context for the omicsio project. + +| Topic | Reference | +|-------|-----------| +| Context Specification | [Context Specification](context.qmd) | + +When the context document is sharded into distinct files per subsection, the above table +may serve as a reference to the different context specification documents. diff --git a/docs/development/index.qmd b/docs/development/index.qmd new file mode 100644 index 0000000..8f4c962 --- /dev/null +++ b/docs/development/index.qmd @@ -0,0 +1,23 @@ +--- +title: Development Overview +format: + html: + toc: true + toc-depth: 3 + number-sections: true + mermaid-format: js + mermaid: + theme: dark +bibliography: ../references.bib +csl: ../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +This section provides comprehensive technical documentation for developers working on omicsio. It follows the AMDiRE (Artefact-based Model for Domain-independent Requirements Engineering) framework to ensure a structured, traceable approach to development documentation [@Mendez-Fernandez2015-xj;@Chuprina2021-xx]. + +## Artifact-based requirements framework {#sec-amdire} + +::: {.callout-note collapse="true" title="Relationships to international standards"} +Note that the Requirements Specification is related to the [software requirements specification](https://en.wikipedia.org/wiki/Software_requirements_specification) associated to the [IEEE/ISO/IEC 29148-2018](https://standards.ieee.org/ieee/29148/6937/) [@Unknown2018-jr] and the System Specification is related to the [software design description](https://en.wikipedia.org/wiki/Software_design_description) associated to the [IEEE 1016-2009](https://standards.ieee.org/ieee/1016/4502/) [@Unknown2009-wv]. +::: diff --git a/docs/development/requirements/index.qmd b/docs/development/requirements/index.qmd new file mode 100644 index 0000000..f52e2ae --- /dev/null +++ b/docs/development/requirements/index.qmd @@ -0,0 +1,27 @@ +--- +title: "Requirements Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document will outline the requirements for the omicsio project. + +| Topic | Reference | +|-------|-----------| +| Requirements Specification | [Requirements Specification](requirements.qmd) | + +When the requirements document is sharded into distinct files per subsection, the above table +may serve as a reference to the different requirements specification documents. diff --git a/docs/development/requirements/requirements.qmd b/docs/development/requirements/requirements.qmd new file mode 100644 index 0000000..00a59d6 --- /dev/null +++ b/docs/development/requirements/requirements.qmd @@ -0,0 +1,20 @@ +--- +title: "Requirements Specification" +format: + html: + mermaid-format: js + mermaid: + theme: dark + toc: true + toc-depth: 3 + number-sections: true + code-fold: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This requirements specification document defines what omicsio should do from an external (black-box) perspective without specifying how it will be implemented internally. diff --git a/docs/development/traceability/index.qmd b/docs/development/traceability/index.qmd new file mode 100644 index 0000000..505bdaa --- /dev/null +++ b/docs/development/traceability/index.qmd @@ -0,0 +1,20 @@ +--- +title: Traceability and Validation +format: + html: + toc: true + toc-depth: 3 + number-sections: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document outlines the traceability and validation approach for the omicsio project. + +| Topic | Reference | +|-------|-----------| +| Testing Framework and Reference | [Testing Framework and Reference](testing.qmd) | diff --git a/docs/development/traceability/testing.qmd b/docs/development/traceability/testing.qmd new file mode 100644 index 0000000..ac8557e --- /dev/null +++ b/docs/development/traceability/testing.qmd @@ -0,0 +1,16 @@ +--- +title: Testing Framework and Reference +format: + html: + toc: true + toc-depth: 3 + number-sections: true +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document describes the testing approach and infrastructure for the omicsio library. diff --git a/docs/development/work-items/index.qmd b/docs/development/work-items/index.qmd new file mode 100644 index 0000000..08f93c8 --- /dev/null +++ b/docs/development/work-items/index.qmd @@ -0,0 +1,21 @@ +--- +title: Work items +format: + html: + toc: true + toc-depth: 3 + number-sections: true + mermaid-format: js + mermaid: + theme: dark +bibliography: ../../references.bib +csl: ../../bibstyle.csl +--- + +# Introduction {#sec-introduction} + +## Purpose of this Document {#sec-purpose} + +This document provides an overview of the work items for the omicsio project. +In the Agile methodology, these might correspond to stories from epics, but they will generally +be associated with GitHub issues and pull requests. \ No newline at end of file diff --git a/docs/guides/development.qmd b/docs/guides/development.qmd new file mode 100644 index 0000000..b23539e --- /dev/null +++ b/docs/guides/development.qmd @@ -0,0 +1,74 @@ +--- +title: "Development" +description: "Development guide for omicsio" +--- + +# Development Guide + +This guide covers development workflows for omicsio. + +## Development Environment + +### Nix Development Shell + +For the most reproducible development experience: + +```bash +nix develop +``` + +### UV Virtual Environment + +For Python-only development: + +```bash +uv sync +source .venv/bin/activate +``` + +### Conda Environment + +Using pixi for conda compatibility: + +```bash +pixi shell +``` + +## Common Tasks + +### Running Tests + +```bash +just test +``` + +### Linting and Type Checking + +```bash +just lint +just type +``` + +### Running All Checks + +```bash +just check +``` + +## Documentation + +### Building Documentation + +```bash +just docs-build +``` + +### Live Preview + +```bash +just docs-dev +``` + +## Contributing + +Please see our [contribution guidelines](../about/contributing.qmd) for more information. diff --git a/docs/guides/installation.qmd b/docs/guides/installation.qmd new file mode 100644 index 0000000..5be1791 --- /dev/null +++ b/docs/guides/installation.qmd @@ -0,0 +1,48 @@ +--- +title: "Installation" +description: "How to install omicsio" +--- + +# Installation + +This guide covers different ways to install omicsio. + +## Using UV (Recommended) + +The fastest way to get started is with UV: + +```bash +uv pip install omicsio +``` + +## Using Pip + +You can also install with standard pip: + +```bash +pip install omicsio +``` + +## Development Installation + +For development, clone the repository and set up the environment: + +```bash +git clone https://github.com/sciexp/omicsio.git +cd omicsio + +# With Nix (recommended) +nix develop + +# Or with UV +uv sync +``` + +## Verification + +Verify your installation by running: + +```python +import omicsio +print(omicsio.__version__) +``` \ No newline at end of file diff --git a/docs/include.html b/docs/include.html new file mode 100644 index 0000000..d90f630 --- /dev/null +++ b/docs/include.html @@ -0,0 +1,12 @@ + + diff --git a/docs/index.qmd b/docs/index.qmd new file mode 100644 index 0000000..2271730 --- /dev/null +++ b/docs/index.qmd @@ -0,0 +1,28 @@ +--- +title: "omicsio" +description: "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns" +format: + html: + toc: false +--- + +# omicsio + +Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns + +## Quick Start + +[Get started with installation](guides/installation.qmd) or jump into the [tutorials](tutorials/getting-started.qmd). + +## Features + +- Modern Python development with UV and Nix +- Type-safe development with beartype +- Comprehensive testing with pytest +- Professional documentation with Quarto + +## Links + +- [GitHub Repository](https://github.com/sciexp/omicsio) +- [Installation Guide](guides/installation.qmd) +- [API Reference](reference/index.qmd) \ No newline at end of file diff --git a/docs/mathjax.html b/docs/mathjax.html new file mode 100644 index 0000000..3699f2b --- /dev/null +++ b/docs/mathjax.html @@ -0,0 +1,7 @@ + diff --git a/docs/notes/architecture/crane-uv2nix-integration.md b/docs/notes/architecture/crane-uv2nix-integration.md new file mode 100644 index 0000000..68ce3e4 --- /dev/null +++ b/docs/notes/architecture/crane-uv2nix-integration.md @@ -0,0 +1,450 @@ +# Crane + uv2nix + maturin integration architecture + +This document describes the target architecture for integrating Rust extension modules into omicsio's federated Python monorepo pattern. + +## Context + +The template is migrating from a single-lock uv workspace (Cargo-style) to a federated independent-lock pattern (LangChain-style). +Some Python packages may contain Rust extension modules built via pyo3/maturin. +These Rust extensions may themselves be federated cargo workspaces with multiple crates. + +The goal is optimal build caching at both the Rust (crane's cargoArtifacts) and Python (uv2nix virtualenvs) levels while maintaining full federation—no root-level coordination required. + +## Reference implementations + +Local repositories demonstrating component patterns: + +- `~/projects/rust-workspace/ironstar` — crane + rust-flake patterns, cargoArtifacts sharing, CI matrix builds +- `~/projects/planning-workspace/langchain` — federated Python monorepo, per-package independence, path dependencies via `[tool.uv.sources]` +- `~/projects/planning-workspace/langgraph` — federated Python with PEP 420 namespace packages, PEP 735 dependency groups +- `~/projects/nix-workspace/uv` — uv workspace mechanics, Cargo-inspired design +- `~/projects/nix-workspace/uv2nix` — Python packaging via pyproject-nix overlays +- `~/projects/nix-workspace/pyproject.nix` — maturin build system support, importCargoLock +- `~/projects/maturin` — pyo3 build backend, cargo workspace integration via manifest-path + +## Target directory structure + +``` +omicsio/ +├── flake.nix # Top-level orchestration +├── nix/ +│ ├── modules/ +│ │ ├── python.nix # uv2nix integration, per-package overlays +│ │ └── rust/ # Shared crane utilities +│ │ ├── lib.nix # mkCraneLib, buildRustPackage helpers +│ │ └── overlays.nix # Cross-package Rust overlay composition +│ └── packages/ # Per-package Nix modules +│ ├── pnt-cli/ +│ │ ├── default.nix # Python + Rust composition +│ │ └── rust.nix # crane configuration for this package's crates +│ └── pnt-functional/ +│ └── default.nix # Pure Python package +│ +├── packages/ # Python packages (federated, independent locks) +│ ├── pnt-cli/ # Example: CLI with Rust backend +│ │ ├── pyproject.toml # maturin build-system, manifest-path binding +│ │ ├── uv.lock # Independent lock (optional) +│ │ ├── src/pnt_cli/ # Python wrapper code +│ │ └── crates/ # Federated Rust workspace for THIS package +│ │ ├── Cargo.toml # [workspace] members = ["pnt-cli-core", "pnt-cli-py"] +│ │ ├── Cargo.lock +│ │ ├── pnt-cli-core/ # Pure Rust library +│ │ │ └── Cargo.toml +│ │ └── pnt-cli-py/ # pyo3 extension module +│ │ └── Cargo.toml # depends on pnt-cli-core via workspace +│ │ +│ └── pnt-functional/ # Pure Python package +│ ├── pyproject.toml +│ └── src/pnt_functional/ +``` + +## Integration patterns + +### Pattern 1: Per-package Rust module (rust.nix) + +Each Python package with Rust extensions gets a `nix/packages/{name}/rust.nix` that encapsulates crane configuration. + +```nix +# nix/packages/pnt-cli/rust.nix +{ pkgs, crane, lib, ... }: +let + src = ../../../packages/pnt-cli/crates; + + # Standard crane pattern from ironstar + crane-lib = crane.mkLib pkgs; + + commonArgs = { + inherit src; + pname = "pnt-cli-rust"; + strictDeps = true; + CARGO_PROFILE = "release"; + nativeBuildInputs = [ pkgs.pkg-config ]; + buildInputs = lib.optionals pkgs.stdenv.isDarwin [ + pkgs.darwin.apple_sdk.frameworks.Security + ]; + }; + + # Shared dependency artifacts (expensive compilation cached) + cargoArtifacts = crane-lib.buildDepsOnly commonArgs; + +in { + # Export for Python package to consume + inherit cargoArtifacts; + + # Individual crate derivations (for testing, inspection) + pnt-cli-core = crane-lib.buildPackage (commonArgs // { + inherit cargoArtifacts; + cargoExtraArgs = "-p pnt-cli-core"; + }); + + # Vendored deps for maturin's cargo invocation + cargoVendorDir = crane-lib.vendorCargoDeps { inherit src; }; + + # Checks (clippy, tests) reusing cached artifacts + clippy = crane-lib.cargoClippy (commonArgs // { + inherit cargoArtifacts; + cargoClippyExtraArgs = "--all-targets -- --deny warnings"; + }); + + nextest = crane-lib.cargoNextest (commonArgs // { + inherit cargoArtifacts; + partitions = 1; + partitionType = "count"; + }); +} +``` + +Key principles from `~/projects/rust-workspace/ironstar/modules/rust.nix`: + +- Single `buildDepsOnly` call creates `cargoArtifacts` shared by all build targets +- `commonArgs` pattern ensures derivation hash consistency (see ironstar FAQ on constant rebuilds) +- `vendorCargoDeps` provides offline cargo builds without IFD + +### Pattern 2: Python package overlay (default.nix) + +The Python package Nix module composes the Rust derivation with uv2nix's overlay system. + +```nix +# nix/packages/pnt-cli/default.nix +{ pkgs, lib, crane, ... }: +let + rustPkgs = import ./rust.nix { inherit pkgs crane lib; }; + +in { + # Override for this package in the Python package set + overlay = final: prev: { + pnt-cli = prev.pnt-cli.overrideAttrs (old: { + # Configure cargo to use crane's vendored dependencies for offline builds. + # Crane's vendorCargoDeps output includes a config.toml with source + # replacement directives pointing to the vendored crate store paths. + preBuild = '' + mkdir -p .cargo + cp ${rustPkgs.cargoVendorDir}/config.toml .cargo/config.toml + ''; + + nativeBuildInputs = old.nativeBuildInputs ++ [ + pkgs.cargo + pkgs.rustc + ] ++ final.resolveBuildSystem { + maturin = [ ]; + }; + + buildInputs = (old.buildInputs or [ ]) ++ + lib.optionals pkgs.stdenv.isDarwin [ + pkgs.darwin.apple_sdk.frameworks.Security + ]; + }); + }; + + # Export Rust checks for flake checks + checks = { + pnt-cli-clippy = rustPkgs.clippy; + pnt-cli-nextest = rustPkgs.nextest; + }; +} +``` + +### Pattern 3: Top-level Python module composition + +The `nix/modules/python.nix` composes all package overlays into the final Python set. + +Version-conflict invariant: all federated packages must resolve compatible versions for shared dependencies. +Per-package uv2nix overlays are composed sequentially into a single package set via `lib.composeManyExtensions`. +If two packages resolve different versions of the same dependency, the later overlay silently wins with no error. +Enforce version alignment by running `uv lock --check` in each package directory after updating any shared dependency. + +```nix +# nix/modules/python.nix +{ inputs, ... }: +{ + perSystem = { pkgs, lib, system, ... }: + let + # Load each Python package independently (no root workspace) + loadPackage = name: path: + let + workspace = inputs.uv2nix.lib.workspace.loadWorkspace { + workspaceRoot = path; + }; + in { + inherit workspace; + overlay = workspace.mkPyprojectOverlay { sourcePreference = "sdist"; }; + }; + + packages = { + pnt-cli = loadPackage "pnt-cli" ../../packages/pnt-cli; + pnt-functional = loadPackage "pnt-functional" ../../packages/pnt-functional; + }; + + # Package-specific Nix modules with optional Rust overlays + packageModules = { + pnt-cli = import ../packages/pnt-cli { inherit pkgs lib; crane = inputs.crane; }; + pnt-functional = { overlay = _: _: { }; checks = { }; }; + }; + + # Compose all overlays + pythonBase = pkgs.callPackage inputs.pyproject-nix.build.packages { + python = pkgs.python313; + }; + + pythonSet = pythonBase.overrideScope (lib.composeManyExtensions [ + # uv2nix overlays for each package + packages.pnt-cli.overlay + packages.pnt-functional.overlay + # Custom Rust integration overlays + packageModules.pnt-cli.overlay + ]); + + in { + packages = { + pnt-cli = pythonSet.pnt-cli; + pnt-functional = pythonSet.pnt-functional; + }; + + checks = packageModules.pnt-cli.checks // packageModules.pnt-functional.checks; + }; +} +``` + +### Pattern 4: pyproject.toml maturin binding + +The Python package's pyproject.toml binds maturin to the specific pyo3 crate. + +```toml +# packages/pnt-cli/pyproject.toml +[build-system] +requires = ["maturin>=1.5"] +build-backend = "maturin" + +[project] +name = "pnt-cli" +version = "0.1.0" +requires-python = ">=3.12" +dependencies = [] + +[tool.maturin] +manifest-path = "crates/pnt-cli-py/Cargo.toml" +module-name = "pnt_cli._native" +features = ["pyo3/extension-module"] +python-source = "src" + +[tool.uv.sources] +# Path dependencies for local development (federated pattern) +pnt-functional = { path = "../pnt-functional", editable = true } + +[dependency-groups] +dev = ["pytest>=8.0", "mypy>=1.10"] +``` + +Key maturin configuration: + +- `manifest-path` points to the pyo3 crate within the Rust workspace +- `module-name` controls where the compiled extension appears in the Python package +- `python-source` tells maturin where Python code lives (alongside the native module) + +### Pattern 5: CI matrix strategy + +Extend ironstar's category-based CI to handle mixed packages. + +```yaml +# .github/workflows/ci.yaml +jobs: + nix-build: + strategy: + matrix: + include: + # Rust dependency caching (expensive, cached aggressively) + - package: pnt-cli + category: rust-deps + cache-key: rust-deps-${{ hashFiles('packages/pnt-cli/crates/Cargo.lock') }} + + # Rust checks (clippy, tests) + - package: pnt-cli + category: rust-checks + + # Python wheel build (depends on rust-deps) + - package: pnt-cli + category: python-wheel + + # Pure Python packages + - package: pnt-functional + category: python-wheel + + steps: + - uses: DeterminateSystems/nix-installer-action@main + - uses: DeterminateSystems/flake-checker-action@main + + - name: Build category + run: | + case "${{ matrix.category }}" in + rust-deps) + nix build ".#packages.x86_64-linux.${{ matrix.package }}-cargoArtifacts" + ;; + rust-checks) + nix build ".#checks.x86_64-linux.${{ matrix.package }}-clippy" + nix build ".#checks.x86_64-linux.${{ matrix.package }}-nextest" + ;; + python-wheel) + nix build ".#packages.x86_64-linux.${{ matrix.package }}" + ;; + esac +``` + +## Caching strategy + +The architecture achieves optimal caching through layered artifact reuse. + +### Layer 1: Rust dependency artifacts (cargoArtifacts) + +Crane's `buildDepsOnly` compiles all Cargo dependencies without project code. +This derivation changes only when `Cargo.lock` changes. +CI caches this derivation via Cachix or GitHub Actions cache. +Rebuild time: minutes → seconds when cached. + +### Layer 2: Rust project artifacts + +Crane's `buildPackage` with `inherit cargoArtifacts` compiles only project code. +Changes when Rust source files change. +Incremental: only changed crates recompile. + +### Layer 3: Python wheel + +Maturin produces a wheel containing the compiled `.so` and Python source. +uv2nix converts this to a Nix derivation. +Changes when Python source or Rust output changes. + +### Layer 4: Python virtualenv + +uv2nix's `mkVirtualEnv` composes all package wheels. +Changes when any dependency wheel changes. +For development, use editable installs to avoid full rebuilds. + +## Testing strategy + +Rust-level tests run via crane (cargoNextest) for fast iteration and artifact reuse. +Python-level tests run via pytest within the uv2nix virtualenv. +Integration tests exercise the full Python → Rust boundary. + +```nix +# In nix/packages/pnt-cli/default.nix +checks = { + # Rust unit tests (fast, cached) + pnt-cli-rust-unit = rustPkgs.nextest; + + # Rust lint (fast, cached) + pnt-cli-clippy = rustPkgs.clippy; + + # Python integration tests + pnt-cli-pytest = pythonSet.mkVirtualEnv "pnt-cli-test-env" { + pnt-cli = [ "dev" ]; + } // { + checkPhase = '' + pytest packages/pnt-cli/tests/ + ''; + }; +}; +``` + +## Migration path + +The implementation follows the beads epic dependency chain: + +1. **pnt-dre**: Infrastructure alignment (concurrent with pnt-4jg) + - Establishes nix/modules/ and nix/packages/ structure + - Aligns CI patterns with this architecture + +2. **pnt-4jg**: Dependency model migration (concurrent with pnt-dre) + - Removes root uv workspace + - Establishes per-package path dependencies + - Documents federated pattern + +3. **pnt-btz**: pyo3/Rust extension integration (after pnt-dre and pnt-4jg) + - Creates pnt-cli package scaffold with crates/ directory + - Implements rust.nix and default.nix patterns + - Validates full crane + uv2nix + maturin integration + +## Resolved decisions + +These decisions emerged during pnt-btz implementation and diverge from or refine the original design above. + +### Crane's config.toml reuse for vendored dependencies + +Maturin needs cargo configured for offline builds using crane's vendored crate store. +Rather than hand-crafting a `.cargo/config.toml` with source replacement directives, the overlay copies crane's `vendorCargoDeps` output config.toml directly. +This works because crane generates deterministic `nix-sources-` source names in its config.toml that correspond to the vendored store paths. +The Pattern 2 overlay above reflects this approach. + +### No CARGO_TARGET_DIR sharing between crane checks and maturin wheel builds + +The original design proposed sharing crane's `cargoArtifacts` with the maturin wheel build via `CARGO_TARGET_DIR`. +In practice the nix store is read-only, so `cargoArtifacts` cannot serve as a writable target directory for maturin's cargo invocation. + +The resolved architecture separates the two build paths: + +- Crane check derivations (`cargoClippy`, `cargoNextest`) inherit `cargoArtifacts` for fast cached feedback on Rust code quality. +- The maturin wheel build within pyproject.nix compiles Rust from source using only `cargoVendorDir` for offline dependency resolution. + +This is a deliberate tradeoff: check caching provides fast CI feedback on the Rust side, while full wheel builds remain hermetic without depending on mutable build artifacts. + +### Editable overlay exclusion for maturin packages + +Maturin packages are incompatible with uv2nix's `pyprojectFixupEditableHook`, which expects `EDITABLE_ROOT` to be set during the build process. +Maturin's build backend does not set this variable. + +The `mkEditablePythonSet` in `nix/modules/python.nix` composes editable overlays only for pure Python packages (`pnt-functional`, `omicsio`), excluding `pnt-cli`. +The pnt-cli package is built as a regular wheel in the devshell. + +For iterative Rust development, the workflow is: enter the devshell via `nix develop`, then run `maturin develop --uv` in the package directory. +This rebuilds the native extension in-place without a full Nix rebuild. + +## Open questions + +### Cross-package Rust dependencies + +If multiple Python packages share Rust crates, options include: + +1. **Workspace-level Rust crates**: A shared `crates/` at repository root, imported by multiple Python packages +2. **Published crates**: Publish shared crates to crates.io or a private registry +3. **Path dependencies**: Use Cargo's workspace-level path dependencies across package boundaries + +The federated model prefers option 2 (published crates) for maximum independence, but option 1 may be pragmatic during development. + +### cargoArtifacts sharing across Python packages + +If multiple Python packages have Rust extensions with overlapping dependencies, we could share cargoArtifacts. +This requires a shared `Cargo.lock` or careful alignment of dependency versions. +Initial recommendation: keep cargoArtifacts per-package for simplicity, optimize later if build times warrant. + +### Editable development workflow + +Resolved: maturin packages use `maturin develop --uv` within `nix develop` for iterative Rust compilation (see "Editable overlay exclusion" in resolved decisions above). +Pure Python packages use uv2nix editable overlays as designed. +Nix derivations remain the source of truth; local development uses native tooling for speed. + +## References + +- ironstar crane patterns: `~/projects/rust-workspace/ironstar/modules/rust.nix` +- ironstar CI matrix: `~/projects/rust-workspace/ironstar/.github/workflows/ci.yaml` +- LangChain federation: `~/projects/planning-workspace/langchain/libs/` +- uv2nix overlay pattern: `~/projects/nix-workspace/uv2nix/doc/patterns/` +- pyproject.nix maturin: `~/projects/nix-workspace/pyproject.nix/doc/src/builders.md` +- maturin workspace support: `~/projects/maturin/guide/src/project_layout.md` diff --git a/docs/notes/architecture/package-distribution-channels.md b/docs/notes/architecture/package-distribution-channels.md new file mode 100644 index 0000000..3d8f635 --- /dev/null +++ b/docs/notes/architecture/package-distribution-channels.md @@ -0,0 +1,56 @@ +# Package distribution channels + +This document describes the distribution channel support for each package in the repository, covering the uv/PyPI and pixi/conda-forge dependency resolution paths. + +## Channel overview + +Both packages support dual-channel distribution through uv (PyPI) and pixi (conda-forge). +Each package maintains independent lock files for both channels: `uv.lock` for PyPI resolution and `pixi.lock` for conda-forge resolution. + +The nix devshell is the primary execution environment. +Justfile recipes wrap both uv and pixi commands, invoked via `nix develop -c just `. +uv and pixi serve as dependency resolution tools consumed by the nix layer, not standalone execution contexts. + +## Per-package channel support + +### pnt-functional + +| Channel | Supported | Lock file | Runtime dependencies | +|---------|-----------|-----------|---------------------| +| uv/PyPI | Yes | `packages/pnt-functional/uv.lock` | beartype, expression | +| pixi/conda-forge | Yes | `packages/pnt-functional/pixi.lock` | beartype, expression, python | + +Runtime dependencies (`beartype`, `expression`) are available on both PyPI and conda-forge. +No channel-specific dependency graph differences for this package. + +### omicsio + +| Channel | Supported | Lock file | Runtime dependencies | +|---------|-----------|-----------|---------------------| +| uv/PyPI | Yes | `packages/omicsio/uv.lock` | (none) | +| pixi/conda-forge | Yes | `packages/omicsio/pixi.lock` | python | + +This package has no runtime dependencies beyond the Python interpreter. +Dev dependencies (pytest, ruff, hypothesis, pyright, jupyter, quartodoc) are available on both channels. + +## Dependency graph differences + +The conda-forge channel resolves the full native dependency tree including system libraries (libffi, openssl, ncurses, etc.) that PyPI assumes are provided by the system. +This means pixi.lock files are substantially larger than uv.lock files for the same package, reflecting the completeness of the conda dependency graph. + +The pixi configuration includes `pixi-build` preview feature for conda package building via `pixi-build-python` backend. +This allows packages to be built as conda packages in addition to PyPI wheels. + +## Justfile recipe mapping + +| Operation | uv/PyPI recipe | pixi/conda recipe | +|-----------|---------------|-------------------| +| Test | `just test ` | `just conda-test ` | +| Lint | `just lint ` | `just conda-lint ` | +| Lint + fix | `just lint-fix ` | `just conda-lint-fix ` | +| Type check | `just type ` | `just conda-type ` | +| All checks | `just check ` | `just conda-check ` | +| Build | `just uv-build ` | `just conda-build ` | +| Lock | `just uv-lock ` | `just pixi-lock ` | + +All recipes accept a package parameter defaulting to `omicsio`. diff --git a/docs/notes/archive/README.md b/docs/notes/archive/README.md new file mode 100644 index 0000000..293526a --- /dev/null +++ b/docs/notes/archive/README.md @@ -0,0 +1,391 @@ +# omicsio + +A nix template for python packages managed with +[uv2nix](https://github.com/pyproject-nix/uv2nix) and +[flake-parts](https://github.com/hercules-ci/flake-parts). +The structure mirrors those in the [omnix registry](#credits) to the extent possible with python and its ecosystem. + +## Template usage + +You can use [omnix](https://omnix.page/om/init.html)[^omnix] to initialize this template: + +```sh +nix --accept-flake-config run github:juspay/omnix -- \ +init github:sciexp/omicsio -o new-python-project +``` + +[^omnix]: If you have omnix installed you just need `om init ...` and not `nix run ... -- init` + +tl;dr + +
instantiate a monorepo variant of the template + +```sh +PROJECT_DIRECTORY=pnt-mono && \ +PROJECT_SNAKE_CASE=$(echo "$PROJECT_DIRECTORY" | tr '-' '_') && \ +PARAMS=$(cat </dev/null 2>&1 && direnv revoke "./$PROJECT_DIRECTORY/" || true) && \ +cd "$PROJECT_DIRECTORY" && \ +git init && \ +git commit --allow-empty -m "initial commit (empty)" && \ +git add . && \ +for pkg in packages/*/; do [ -f "$pkg/pyproject.toml" ] && (cd "$pkg" && nix run github:NixOS/nixpkgs/nixos-unstable#uv -- lock); done && \ +git add . && \ +nix develop --accept-flake-config -c just test-all +``` + +
+ +You can run `direnv allow` to enter the shell environment that contains +development dependencies or `nix develop --accept-flake-config` to enter (or add +`-c command` to execute individual commands within) the development shell. + +
instantiate a single-package variant of the template + +```sh +PROJECT_DIRECTORY=pnt-new && \ +PROJECT_SNAKE_CASE=$(echo "$PROJECT_DIRECTORY" | tr '-' '_') && \ +PARAMS=$(cat </dev/null 2>&1 && direnv revoke "./$PROJECT_DIRECTORY/" || true) && \ +cd "$PROJECT_DIRECTORY" && \ +git init && \ +git commit --allow-empty -m "initial commit (empty)" && \ +git add . && \ +for pkg in packages/*/; do [ -f "$pkg/pyproject.toml" ] && (cd "$pkg" && nix run github:NixOS/nixpkgs/nixos-unstable#uv -- lock); done && \ +git add . && \ +nix develop --accept-flake-config -c just test-all +``` + +
+ +except you may want to update the git ref/rev of the template if you need to pin to a +particular version: + +- `github:sciexp/omicsio/main` +- `github:sciexp/omicsio/v0.1.0` +- `github:sciexp/omicsio/3289dla` +- `github:sciexp/omicsio/devbranch`. + +### Quick start + +#### Nix-managed environment + +The template supports three types of development environments: + +1. nix devshell +2. python virtualenv via uv +3. conda environments via pixi + +The intended workflow is to run + +```sh +make bootstrap +``` + +only the very first time you are setting up one of these templates. +This will verify you have the [nix package manager](https://nix.dev) and [direnv](https://direnv.net/) installed. +Registration of the repository contents requires creating a git repository, for example with + +```sh +git init && git commit --allow-empty -m "initial commit (empty)" && git add . +``` + +but does not require committing. +After this running + +```sh +direnv allow +``` + +will ensure you have all development tools on a project directory-specific version of your PATH variable. +These include the `just` task runner, which provides an alternative to using [GNU Make](https://www.gnu.org/software/make/) as a task runner. +See the [task runner](#task-runner) section for a listing of development commands. + +You should now be able to run `just test-all` to confirm all package tests pass in the devshell environment, or `just test ` to test a specific package. + +> [!NOTE] +> This template uses an independent-lock pattern where each package under +> `packages/` maintains its own `pyproject.toml` and `uv.lock`. There is no root +> `pyproject.toml` or uv workspace. After instantiation, lock each package +> individually: +> +> ```sh +> for pkg in packages/*/; do [ -f "$pkg/pyproject.toml" ] && (cd "$pkg" && uv lock); done +> ``` + +If you choose to modify packages or add dependencies, run `just uv-lock ` to update the lock file for that specific package. + +#### Python virtualenv + +1. Create and sync virtual environment: + + ```sh + just venv + source .venv/bin/activate + ``` + +2. Run tests: + + ```sh + just test + ``` + +3. Run linting: + + ```sh + just lint + ``` + +4. Build package: + + ```sh + just build + ``` + +## Features + +- Modern python packaging with `pyproject.toml` +- Fast dependency management with `uv` +- Reproducible developer environments and builds with `nix` and `uv2nix` +- conda ecosystem compatibility via `pixi` + +
Optional packages + +The template includes optional packages controlled by omnix template parameters. +Both default to false for the single-package variant and can be set to true individually or together. + +*pnt-functional* (`monorepo-package` parameter) provides a brief illustration of functional programming patterns in Python. +It demonstrates railway-oriented programming with `expression` for type-safe error handling, effect tracking via monad transformers for composable side effects, runtime type checking with `beartype`, pure functions and immutable data types, and composition of effectful functions using monadic bind operations. +See [packages/pnt-functional](./packages/pnt-functional) for details. + +*pnt-cli* (`pyo3-package` parameter) is a Rust extension module demonstrating Python-Rust interop via [pyo3](https://pyo3.rs) and [maturin](https://www.maturin.rs). +It exposes Rust functions callable from Python through a compiled native module (`pnt_cli._native`). +The Rust side is organized as a Cargo workspace with a core library crate and a pyo3 binding crate under `packages/pnt-cli/crates/`. +On the Nix side, the build uses [crane](https://github.com/ipetkov/crane) for incremental Rust compilation caching and [crane-maturin](https://github.com/vlaci/crane-maturin) for producing maturin-compatible wheels. +The resulting artifact is installed into the uv2nix package set via `pyproject-nix`'s `nixpkgsPrebuilt`, avoiding duplicate Rust compilation during Nix evaluation. +See [packages/pnt-cli](./packages/pnt-cli) and [nix/packages/pnt-cli](./nix/packages/pnt-cli) for the implementation. + +
+ +## Development + +### Prerequisites + +If you'd like to develop `omicsio` you'll need the [nix package manager](https://nix.dev). +You can optionally make use of [direnv](https://direnv.net/) to automatically activate the environment. +The project includes a Makefile to help bootstrap your development environment. + +It provides: + +1. Installation of the nix package manager using the Determinate Systems installer +2. Installation of direnv for automatic environment activation +3. Link to instructions for shell configuration + +To get started, run: + +```shell +make bootstrap +``` + +Run `make` alone for a listing of available targets. + +After nix and direnv are installed, you can either run `direnv allow` or `nix develop` to enter a [development shell](./nix/modules/devshell.nix) that will contain necessary system-level dependencies. + +### Task runner + +This project uses [`just`](https://just.systems/man/en/) as a task runner, which is provided in the [development shell](#prerequisites). +List available commands by running `just` alone. + +
+just recipes + +```sh +Available recipes: + default # List all recipes + + [CI/CD] + ci-build-category system category # Build a category of nix flake outputs for CI matrix + ci-check package # Run all checks for a package (lint, typecheck, test) + ci-lint package # Run linting for a package + ci-sync package # Sync dependencies for a package via uv + ci-test package # Run tests for a package + ci-typecheck package # Run type checking for a package + gcloud-context # Set gcloud context + gh-docs-build branch=`git branch --show-current` debug="false" # Trigger docs build job remotely on GitHub (requires workflow on main) + gh-docs-cancel run_id="" # Cancel a running docs workflow + gh-docs-logs run_id="" job="" # View logs for a specific docs workflow run + gh-docs-rerun run_id="" failed_only="true" # Re-run a failed docs workflow + gh-docs-watch run_id="" # Watch a specific docs workflow run + gh-workflow-status workflow="deploy-docs.yaml" branch=`git branch --show-current` limit="5" # View recent workflow runs status + ghsecrets repo="sciexp/omicsio" # Update github secrets for repo from environment variables + ghvars repo="sciexp/omicsio" # Update github vars for repo from environment variables + list-packages-json # Discover packages as JSON array for CI matrix + list-workflows # List available workflows and associated jobs using act + pre-commit # Run pre-commit hooks (see pre-commit.nix and note the yaml is git-ignored) + scan-secrets # Scan repository for hardcoded secrets + scan-staged # Scan staged files for hardcoded secrets (pre-commit) + test-docs-build branch=`git branch --show-current` # Test build-docs job locally with act + test-docs-deploy branch=`git branch --show-current` # Test full deploy-docs workflow locally with act + + [conda] + conda-build package="omicsio" # Package commands (conda) + conda-check package="omicsio" # Run all checks in conda environment (lint, type, test) + conda-env package="omicsio" # Create and sync conda environment with pixi + conda-lint package="omicsio" # Run linting in conda environment with pixi + conda-lint-fix package="omicsio" # Run linting and fix errors in conda environment with pixi + conda-lock package="omicsio" # Update conda environment + conda-test package="omicsio" # Run tests in conda environment with pixi + conda-type package="omicsio" # Run type checking in conda environment with pixi + pixi-lock package="omicsio" # Update pixi lockfile + + [containers] + container-build-production CONTAINER="pnt-cli" # Build production container image + container-load-production CONTAINER="pnt-cli" # Load production container to local Docker daemon + container-matrix # Display container CI matrix + container-push-production CONTAINER="pnt-cli" VERSION="0.0.0" +TAGS="" # Push production container manifest (requires registry auth) + + [docs] + data-sync # Sync data from drive (using encrypted service account) + docs-build # Build docs + docs-check # Check docs + docs-deploy-preview branch=`git branch --show-current` # Deploy documentation to Cloudflare Workers (preview) + docs-deploy-production # Deploy documentation to Cloudflare Workers (production) + docs-deployments # List recent Cloudflare Workers deployments + docs-dev # Run local docs deployment + docs-extensions # Add quartodoc extension + docs-local # Preview docs locally + docs-reference # Build quartodoc API reference + docs-sync # Sync docs freeze data to DVC remote + docs-tail # Tail live logs from Cloudflare Workers + docs-versions # List recent Cloudflare Workers versions + + [nix] + ci # Run CI checks locally with `om ci` + dev # Enter the Nix development shell + flake-check # Validate the Nix flake configuration for the current system + flake-update # Update all flake inputs to their latest versions + + [python] + check package="omicsio" # Run all checks for a package (lint, type, test) + lint package="omicsio" # Run linting for a package + lint-all # Run linting for all packages + lint-fix package="omicsio" # Run linting and fix errors for a package + test package="omicsio" # Run tests for a package + test-all # Run tests for all packages + type package="omicsio" # Run type checking for a package + uv-build package="omicsio" # Build a package with uv + uv-lock package="omicsio" # Update lockfile for a package + uv-sync package="omicsio" # Sync a package environment with uv + + [release] + preview-version base-branch package-path # Preview release version for a package (dry-run semantic-release with merge simulation) + release-package package-name dry-run="false" # Run semantic-release for a package + test-package-release package-name="omicsio" branch="main" # Test package release + test-release # Release testing with bun + test-release-as-main # Test release as if on main branch + test-release-direct # Test release directly on release branch + test-release-on-current-branch # Test release with explicit branch override + update-version package-name version # Update version for a specific package across all relevant files + + [rust] + cargo-build package="pnt-cli" # Build Rust crates for a package + cargo-check package="pnt-cli" # Run all Rust checks (clippy, test) + cargo-clippy package="pnt-cli" # Run Rust clippy lints + cargo-nextest package="pnt-cli" # Run Rust tests via cargo-nextest + cargo-test package="pnt-cli" # Run Rust tests via cargo test + + [secrets] + check-secrets # Check secrets are available in sops environment + dvc-run +command # Helper: Run any DVC command with decrypted service account + edit-secrets # Edit shared secrets file + export-secrets # Export unique secrets to dotenv format using sops + gcp-enable-drive-api # Enable Google Drive API in GCP project + gcp-sa-create # Create GCP service account for DVC access (run once) + gcp-sa-key-delete key_id # Delete a specific service account key + gcp-sa-key-download # Download service account key (for key rotation) + gcp-sa-key-encrypt # Encrypt service account key with sops + gcp-sa-key-rotate # Rotate service account key + gcp-sa-keys-list # List existing service account keys (for auditing) + gcp-sa-storage-user # Grant Storage Object User role for GCS access + get-secret key # Show specific secret value from shared secrets + new-secret file # Create a new sops encrypted file + rotate-secret secret_name # Rotate a specific secret interactively + run-with-secrets +command # Run command with all shared secrets as environment variables + set-secret secret_name secret_value # Add or update a secret non-interactively + show-secrets # Show existing secrets using sops + sops-add-key # Add existing age key to local configuration + sops-init # Initialize sops age key for new developers + updatekeys # Update keys for existing secrets files after adding new recipients + validate-secrets # Validate all sops encrypted files can be decrypted + + [template] + template-init # Initialize new project from template + template-verify # Verify template functionality by creating and checking a test project +``` + +
+ +## Credits + +### Python + +- [beartype](https://github.com/beartype/beartype) -- gradual runtime type checking +- [Expression](https://github.com/dbrattli/Expression) -- functional programming abstractions for Python + +### Python in Nix + +- [uv2nix](https://github.com/pyproject-nix/uv2nix) -- Nix integration for uv-managed Python workspaces +- [pyproject.nix](https://github.com/pyproject-nix/pyproject.nix) -- Nix library for Python project management, used by uv2nix for build-system resolution +- [pyproject-build-systems](https://github.com/pyproject-nix/build-system-pkgs) -- pre-built Python build-system packages for Nix + +### Rust in Nix + +- [crane](https://github.com/ipetkov/crane) -- Nix library for building Rust projects with incremental compilation caching +- [crane-maturin](https://github.com/vlaci/crane-maturin) -- crane extension for building maturin/pyo3 Python-Rust packages +- [rust-overlay](https://github.com/oxalica/rust-overlay) -- Nix overlay providing nightly and stable Rust toolchains + +### Nix + +
omnix registry and flake-parts ecosystem + +See the [omnix registry flake](https://github.com/juspay/omnix/blob/1.0.0/crates/omnix-init/registry/flake.nix) + +- [srid/haskell-template](https://github.com/srid/haskell-template) +- [srid/rust-nix-template](https://github.com/srid/rust-nix-template) +- [hercules-ci/flake-parts](https://github.com/hercules-ci/flake-parts) + +
diff --git a/docs/references.bib b/docs/references.bib new file mode 100644 index 0000000..04ac76c --- /dev/null +++ b/docs/references.bib @@ -0,0 +1,49 @@ +@ARTICLE{Mendez-Fernandez2015-xj, + title = "Artefact-based requirements engineering: the {AMDiRE} approach", + author = "Méndez Fernández, Daniel and Penzenstadler, Birgit", + journal = "Requir. Eng.", + publisher = "Springer Science and Business Media LLC", + volume = 20, + number = 4, + pages = "405--434", + month = nov, + year = 2015, + doi = "10.1007/s00766-014-0206-y", + issn = "0947-3602,1432-010X", + language = "en" +} + +@ARTICLE{Chuprina2021-xx, + title = "Towards artefact-based Requirements Engineering for + data-centric systems", + author = "Chuprina, Tatiana and Mendez, Daniel and Wnuk, Krzysztof", + journal = "arXiv [cs.SE]", + month = mar, + year = 2021, + archivePrefix = "arXiv", + primaryClass = "cs.SE", + eprint = "2103.05233" +} + +@MISC{Unknown2018-jr, + title = "{ISO}/{IEC}/{IEEE} International Standard - Systems and + software engineering -- Life cycle processes -- Requirements + engineering", + institution = "IEEE", + address = "Piscataway, NJ, USA", + pages = "1--104", + year = 2018, + doi = "10.1109/ieeestd.2018.8559686", + language = "en" +} + +@MISC{Unknown2009-wv, + title = "{IEEE} Standard for Information Technology--Systems + Design--Software Design Descriptions", + institution = "IEEE", + address = "Piscataway, NJ, USA", + pages = "1--35", + year = 2009, + doi = "10.1109/ieeestd.2009.5167255", + language = "en" +} diff --git a/docs/styles.css b/docs/styles.css new file mode 100644 index 0000000..45c834a --- /dev/null +++ b/docs/styles.css @@ -0,0 +1,28 @@ +body { + font-family: "Latin Modern Sans", sans-serif; +} +.navbar { + border-bottom: 1px solid #000000; +} +.quarto-color-scheme-toggle .bi::before { + height: 1.6rem; + width: 1.5rem; + background-size: 1.5rem 1.5rem; +} +.quarto-navigation-tool { + font-size: 1.7rem; + margin: 0.4rem; +} +@media (max-width: 435px) { + /* #quarto-search { + display: none; + } */ + .quarto-navigation-tool { + display: none; + } +} +@media (min-width: 435px) { + /* #quarto-search { + display: block; + } */ +} diff --git a/docs/tutorials/getting-started.qmd b/docs/tutorials/getting-started.qmd new file mode 100644 index 0000000..8b9b034 --- /dev/null +++ b/docs/tutorials/getting-started.qmd @@ -0,0 +1,32 @@ +--- +title: "Getting Started" +description: "Quick tutorial to get up and running with omicsio" +--- + +# Getting Started with omicsio + +This tutorial will walk you through the basic usage of omicsio. + +## Prerequisites + +Before you begin, make sure you have: + +- Python 3.12 or higher +- UV package manager +- Nix (optional, but recommended) + +## Installation + +See the [Installation Guide](../guides/installation.qmd) for detailed installation instructions. + +## Basic Usage + +```python +# Example usage will be added here +print("Hello from omicsio!") +``` + +## Next Steps + +- Explore the [Development Guide](../guides/development.qmd) +- Check out the [API Reference](../reference/index.qmd) \ No newline at end of file diff --git a/flake.lock b/flake.lock new file mode 100644 index 0000000..ecd7c9e --- /dev/null +++ b/flake.lock @@ -0,0 +1,314 @@ +{ + "nodes": { + "crane": { + "locked": { + "lastModified": 1771121070, + "narHash": "sha256-aIlv7FRXF9q70DNJPI237dEDAznSKaXmL5lfK/Id/bI=", + "owner": "ipetkov", + "repo": "crane", + "rev": "a2812c19f1ed2e5ed5ce2ef7109798b575c180e1", + "type": "github" + }, + "original": { + "owner": "ipetkov", + "repo": "crane", + "type": "github" + } + }, + "crane-maturin": { + "inputs": { + "flake-parts": [ + "flake-parts" + ] + }, + "locked": { + "lastModified": 1762971636, + "narHash": "sha256-Xq99+5Q6amg6Uxf5D/80s8Wfb5/ohEpC1b6jkift04w=", + "owner": "vlaci", + "repo": "crane-maturin", + "rev": "46b5ebcd3bda30c8dcf917bd2a4828c64c48177d", + "type": "github" + }, + "original": { + "owner": "vlaci", + "repo": "crane-maturin", + "type": "github" + } + }, + "flake-parts": { + "inputs": { + "nixpkgs-lib": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1769996383, + "narHash": "sha256-AnYjnFWgS49RlqX7LrC4uA+sCCDBj0Ry/WOJ5XWAsa0=", + "owner": "hercules-ci", + "repo": "flake-parts", + "rev": "57928607ea566b5db3ad13af0e57e921e6b12381", + "type": "github" + }, + "original": { + "owner": "hercules-ci", + "repo": "flake-parts", + "type": "github" + } + }, + "git-hooks": { + "inputs": { + "flake-compat": [], + "gitignore": "gitignore", + "nixpkgs": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1770726378, + "narHash": "sha256-kck+vIbGOaM/dHea7aTBxdFYpeUl/jHOy5W3eyRvVx8=", + "owner": "cachix", + "repo": "git-hooks.nix", + "rev": "5eaaedde414f6eb1aea8b8525c466dc37bba95ae", + "type": "github" + }, + "original": { + "owner": "cachix", + "repo": "git-hooks.nix", + "type": "github" + } + }, + "gitignore": { + "inputs": { + "nixpkgs": [ + "git-hooks", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1709087332, + "narHash": "sha256-HG2cCnktfHsKV0s4XW83gU3F57gaTljL9KNSuG6bnQs=", + "owner": "hercules-ci", + "repo": "gitignore.nix", + "rev": "637db329424fd7e46cf4185293b9cc8c88c95394", + "type": "github" + }, + "original": { + "owner": "hercules-ci", + "repo": "gitignore.nix", + "type": "github" + } + }, + "import-tree": { + "locked": { + "lastModified": 1771045967, + "narHash": "sha256-oYO4poyw0Sb/db2PigqugMlDwsvwLg6CSpFrMUWxA3Q=", + "owner": "vic", + "repo": "import-tree", + "rev": "c968d3b54d12cf5d9c13f16f7c545a06c9d1fde6", + "type": "github" + }, + "original": { + "owner": "vic", + "repo": "import-tree", + "type": "github" + } + }, + "nix2container": { + "inputs": { + "nixpkgs": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1767430085, + "narHash": "sha256-SiXJ6xv4pS2MDUqfj0/mmG746cGeJrMQGmoFgHLS25Y=", + "owner": "nlewo", + "repo": "nix2container", + "rev": "66f4b8a47e92aa744ec43acbb5e9185078983909", + "type": "github" + }, + "original": { + "owner": "nlewo", + "repo": "nix2container", + "type": "github" + } + }, + "nixpkgs": { + "locked": { + "lastModified": 1771147098, + "narHash": "sha256-VlfaC6fMRQml69frXVZ9ysuVEumYY3oWBE+16pIHTno=", + "rev": "e3cb16bccd9facebae3ba29c6a76a4cc1b73462a", + "type": "tarball", + "url": "https://releases.nixos.org/nixpkgs/nixpkgs-26.05pre946663.e3cb16bccd9f/nixexprs.tar.xz" + }, + "original": { + "type": "tarball", + "url": "https://channels.nixos.org/nixpkgs-unstable/nixexprs.tar.xz" + } + }, + "nixpkgs_2": { + "locked": { + "lastModified": 1770841267, + "narHash": "sha256-9xejG0KoqsoKEGp2kVbXRlEYtFFcDTHjidiuX8hGO44=", + "owner": "nixos", + "repo": "nixpkgs", + "rev": "ec7c70d12ce2fc37cb92aff673dcdca89d187bae", + "type": "github" + }, + "original": { + "owner": "nixos", + "ref": "nixos-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_3": { + "locked": { + "lastModified": 1758690382, + "narHash": "sha256-NY3kSorgqE5LMm1LqNwGne3ZLMF2/ILgLpFr1fS4X3o=", + "owner": "nixos", + "repo": "nixpkgs", + "rev": "e643668fd71b949c53f8626614b21ff71a07379d", + "type": "github" + }, + "original": { + "owner": "nixos", + "ref": "nixos-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_4": { + "locked": { + "lastModified": 1771008912, + "narHash": "sha256-gf2AmWVTs8lEq7z/3ZAsgnZDhWIckkb+ZnAo5RzSxJg=", + "owner": "nixos", + "repo": 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"github" + }, + "original": { + "owner": "pyproject-nix", + "repo": "pyproject.nix", + "type": "github" + } + }, + "root": { + "inputs": { + "crane": "crane", + "crane-maturin": "crane-maturin", + "flake-parts": "flake-parts", + "git-hooks": "git-hooks", + "import-tree": "import-tree", + "nix2container": "nix2container", + "nixpkgs": "nixpkgs", + "pyproject-build-systems": "pyproject-build-systems", + "pyproject-nix": "pyproject-nix", + "systems": "systems", + "treefmt-nix": "treefmt-nix", + "uv2nix": "uv2nix" + } + }, + "systems": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } + }, + "treefmt-nix": { + "inputs": { + "nixpkgs": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1770228511, + "narHash": "sha256-wQ6NJSuFqAEmIg2VMnLdCnUc0b7vslUohqqGGD+Fyxk=", + "owner": "numtide", + "repo": "treefmt-nix", + "rev": "337a4fe074be1042a35086f15481d763b8ddc0e7", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "treefmt-nix", + "type": "github" + } + }, + "uv2nix": { + "inputs": { + "nixpkgs": "nixpkgs_4", + "pyproject-nix": [ + "pyproject-nix" + ] + }, + "locked": { + "lastModified": 1771207897, + "narHash": "sha256-TGjeQ7t5BDKS+YjPCcssFKIqbAKrjfKvGkCEG5Ioio0=", + "owner": "pyproject-nix", + "repo": "uv2nix", + "rev": "53205134c56241315b05a5c05946c2d1a10f6d3c", + "type": "github" + }, + "original": { + "owner": "pyproject-nix", + "repo": "uv2nix", + "type": "github" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 0000000..f9ae2f3 --- /dev/null +++ b/flake.nix @@ -0,0 +1,57 @@ +{ + description = "omicsio: federated monorepo with uv2nix and pyo3/Rust extension modules"; + + outputs = + inputs@{ flake-parts, ... }: + flake-parts.lib.mkFlake { inherit inputs; } (inputs.import-tree ./modules); + + inputs = { + nixpkgs.url = "https://channels.nixos.org/nixpkgs-unstable/nixexprs.tar.xz"; + systems.url = "github:nix-systems/default"; + + flake-parts.url = "github:hercules-ci/flake-parts"; + flake-parts.inputs.nixpkgs-lib.follows = "nixpkgs"; + + import-tree.url = "github:vic/import-tree"; + + pyproject-nix.url = "github:pyproject-nix/pyproject.nix"; + uv2nix.url = "github:pyproject-nix/uv2nix"; + uv2nix.inputs.pyproject-nix.follows = "pyproject-nix"; + pyproject-build-systems.url = "github:pyproject-nix/build-system-pkgs"; + pyproject-build-systems.inputs.pyproject-nix.follows = "pyproject-nix"; + pyproject-build-systems.inputs.uv2nix.follows = "uv2nix"; + + crane.url = "github:ipetkov/crane"; + crane-maturin.url = "github:vlaci/crane-maturin"; + crane-maturin.inputs.flake-parts.follows = "flake-parts"; + + nix2container.url = "github:nlewo/nix2container"; + nix2container.inputs.nixpkgs.follows = "nixpkgs"; + + treefmt-nix.url = "github:numtide/treefmt-nix"; + treefmt-nix.inputs.nixpkgs.follows = "nixpkgs"; + + git-hooks.url = "github:cachix/git-hooks.nix"; + git-hooks.inputs.nixpkgs.follows = "nixpkgs"; + git-hooks.inputs.flake-compat.follows = ""; + }; + + nixConfig = { + extra-substituters = [ + "https://cache.nixos.org" + "https://nix-community.cachix.org" + "https://crane.cachix.org" + "https://numtide.cachix.org" + "https://pyproject-nix.cachix.org" + "https://sciexp.cachix.org" + ]; + extra-trusted-public-keys = [ + "cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=" + "nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=" + "crane.cachix.org-1:8Scfpmn9w+hGdXH/Q9tTLiYAE/2dnJYRJP7kl80GuRk=" + "numtide.cachix.org-1:2ps1kLBUWjxIneOy1Ik6cQjb41X0iXVXeHigGmycPPE=" + "pyproject-nix.cachix.org-1:UNzugsOlQIu2iOz0VyZNBQm2JSrL/kwxeCcFGw+jMe0=" + "sciexp.cachix.org-1:HaliIGqJrFN7CDrzYVHqWS4uSISorWAY1bWNmNl8T08=" + ]; + }; +} diff --git a/justfile b/justfile new file mode 100644 index 0000000..9c6facd --- /dev/null +++ b/justfile @@ -0,0 +1,992 @@ +# List all recipes +default: + @just --list + +# Contents +## CI/CD +## Conda +## Containers +## Docs +## Nix +## Python +## Release +## Rust +## Secrets +## Template + +## CI/CD + +# Build a category of nix flake outputs for CI matrix +[group('CI/CD')] +ci-build-category system category: + bash scripts/ci/ci-build-category.sh {{system}} {{category}} + +# Scan repository for hardcoded secrets +[group('CI/CD')] +scan-secrets: + gitleaks detect --verbose --redact + +# Scan staged files for hardcoded secrets (pre-commit) +[group('CI/CD')] +scan-staged: + gitleaks protect --staged --verbose --redact + +# Set gcloud context +[group('CI/CD')] +gcloud-context: + gcloud config configurations activate "$GCP_PROJECT_NAME" + +# Update github vars for repo from environment variables +[group('CI/CD')] +ghvars repo="sciexp/omicsio": + @echo "vars before updates:" + @echo + PAGER=cat gh variable list --repo={{ repo }} + @echo + gh variable set CACHIX_CACHE_NAME --repo={{ repo }} --body="$CACHIX_CACHE_NAME" + gh variable set FAST_FORWARD_ACTOR --repo={{ repo }} --body="$FAST_FORWARD_ACTOR" + @echo + @echo "vars after updates (wait 3 seconds for github to update):" + sleep 3 + @echo + PAGER=cat gh variable list --repo={{ repo }} + +# Update github secrets for repo from environment variables +[group('CI/CD')] +ghsecrets repo="sciexp/omicsio": + @echo "secrets before updates:" + @echo + PAGER=cat gh secret list --repo={{ repo }} + @echo + sops exec-env vars/shared.yaml '\ + gh secret set CACHIX_AUTH_TOKEN --repo={{ repo }} --body="$CACHIX_AUTH_TOKEN" && \ + gh secret set CODECOV_TOKEN --repo={{ repo }} --body="$CODECOV_TOKEN" && \ + gh secret set FAST_FORWARD_PAT --repo={{ repo }} --body="$FAST_FORWARD_PAT" && \ + gh secret set GITGUARDIAN_API_KEY --repo={{ repo }} --body="$GITGUARDIAN_API_KEY" && \ + gh secret set UV_PUBLISH_TOKEN --repo={{ repo }} --body="$UV_PUBLISH_TOKEN" && \ + gh secret set CLOUDFLARE_ACCOUNT_ID --repo={{ repo }} --body="$CLOUDFLARE_ACCOUNT_ID" && \ + gh secret set CLOUDFLARE_API_TOKEN --repo={{ repo }} --body="$CLOUDFLARE_API_TOKEN" && \ + gh secret set FLAKE_UPDATER_APP_ID --repo={{ repo }} --body="$FLAKE_UPDATER_APP_ID" && \ + gh secret set FLAKE_UPDATER_PRIVATE_KEY --repo={{ repo }} --body="$FLAKE_UPDATER_PRIVATE_KEY"' + @echo + @echo "secrets after updates (wait 3 seconds for github to update):" + sleep 3 + @echo + PAGER=cat gh secret list --repo={{ repo }} + +# Run pre-commit hooks (see pre-commit.nix and note the yaml is git-ignored) +[group('CI/CD')] +pre-commit: + pre-commit run --all-files + +# List available workflows and associated jobs using act +[group('CI/CD')] +list-workflows: + @act -l + +# Test build-docs job locally with act +[group('CI/CD')] +test-docs-build branch=`git branch --show-current`: + @echo "Testing docs build job locally (branch: {{branch}})..." + @sops exec-env vars/shared.yaml 'act workflow_dispatch \ + -W .github/workflows/deploy-docs.yaml \ + -j build-docs \ + -s CI_AGE_KEY -s CACHIX_AUTH_TOKEN \ + -s GITHUB_TOKEN="$(gh auth token)" \ + --var CACHIX_CACHE_NAME \ + --input debug_enabled=false \ + --input branch={{branch}}' + +# Test full deploy-docs workflow locally with act +[group('CI/CD')] +test-docs-deploy branch=`git branch --show-current`: + @echo "Testing full docs deployment workflow locally (branch: {{branch}})..." + @echo "Note: Cloudflare deployment may not work in local environment" + @sops exec-env vars/shared.yaml 'act workflow_dispatch \ + -W .github/workflows/deploy-docs.yaml \ + -s CI_AGE_KEY -s CACHIX_AUTH_TOKEN \ + -s CLOUDFLARE_API_TOKEN -s CLOUDFLARE_ACCOUNT_ID \ + -s GITHUB_TOKEN="$(gh auth token)" \ + --var CACHIX_CACHE_NAME \ + --input debug_enabled=false \ + --input branch={{branch}}' + +# Trigger docs build job remotely on GitHub (requires workflow on main) +[group('CI/CD')] +gh-docs-build branch=`git branch --show-current` debug="false": + #!/usr/bin/env bash + echo "Triggering docs build workflow on GitHub (branch: {{branch}}, debug: {{debug}})..." + echo "Note: This requires deploy-docs.yaml to exist on the default branch" + gh workflow run deploy-docs.yaml \ + --repo ${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)} \ + --ref "{{branch}}" \ + --field debug_enabled="{{debug}}" \ + --field branch="{{branch}}" + echo "Check workflow status with: just gh-docs-status" + +# View recent workflow runs status +[group('CI/CD')] +gh-workflow-status workflow="deploy-docs.yaml" branch=`git branch --show-current` limit="5": + #!/usr/bin/env bash + echo "Recent docs workflow runs:" + gh run list \ + --workflow={{workflow}} \ + --branch={{branch}} \ + --limit={{limit}} \ + --repo ${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)} + +# Watch a specific docs workflow run +[group('CI/CD')] +gh-docs-watch run_id="": + #!/usr/bin/env bash + if [ -z "{{run_id}}" ]; then + echo "Getting latest workflow run..." + RUN_ID=$(gh run list --workflow=deploy-docs.yaml --limit=1 --json databaseId -q '.[0].databaseId' \ + --repo ${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}) + echo "Watching run: $RUN_ID" + gh run watch $RUN_ID --repo ${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)} + else + gh run watch {{run_id}} --repo ${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)} + fi + +# View logs for a specific docs workflow run +[group('CI/CD')] +gh-docs-logs run_id="" job="": + #!/usr/bin/env bash + REPO="${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}" + if [ -z "{{run_id}}" ]; then + echo "Getting latest workflow run..." + RUN_ID=$(gh run list --workflow=deploy-docs.yaml --limit=1 --json databaseId -q '.[0].databaseId' --repo $REPO) + else + RUN_ID="{{run_id}}" + fi + + if [ -z "{{job}}" ]; then + echo "Available jobs in run $RUN_ID:" + gh run view $RUN_ID --repo $REPO --json jobs -q '.jobs[].name' + echo "" + echo "Viewing full run logs..." + gh run view $RUN_ID --log --repo $REPO + else + echo "Viewing logs for job '{{job}}' in run $RUN_ID..." + gh run view $RUN_ID --log --repo $REPO | grep -A 100 "{{job}}" + fi + +# Re-run a failed docs workflow +[group('CI/CD')] +gh-docs-rerun run_id="" failed_only="true": + #!/usr/bin/env bash + REPO="${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}" + if [ -z "{{run_id}}" ]; then + echo "Getting latest workflow run..." + RUN_ID=$(gh run list --workflow=deploy-docs.yaml --limit=1 --json databaseId -q '.[0].databaseId' --repo $REPO) + else + RUN_ID="{{run_id}}" + fi + + if [ "{{failed_only}}" = "true" ]; then + echo "Re-running failed jobs in run $RUN_ID..." + gh run rerun --failed $RUN_ID --repo $REPO + else + echo "Re-running all jobs in run $RUN_ID..." + gh run rerun $RUN_ID --repo $REPO + fi + +# Cancel a running docs workflow +[group('CI/CD')] +gh-docs-cancel run_id="": + #!/usr/bin/env bash + REPO="${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}" + if [ -z "{{run_id}}" ]; then + echo "Getting latest workflow run..." + RUN_ID=$(gh run list --workflow=deploy-docs.yaml --limit=1 --json databaseId -q '.[0].databaseId' --repo $REPO) + echo "Canceling run: $RUN_ID" + gh run cancel $RUN_ID --repo $REPO + else + gh run cancel {{run_id}} --repo $REPO + fi + +# Discover packages as JSON array for CI matrix +[group('CI/CD')] +list-packages-json: + @ls -d packages/*/pyproject.toml | while read f; do \ + d=$(dirname "$f"); \ + n=$(basename "$d"); \ + if [ -f "$d/Cargo.toml" ]; then m=true; else m=false; fi; \ + printf '{"name":"%s","path":"%s","maturin":%s}\n' "$n" "$d" "$m"; \ + done | jq -sc '.' + +# Discover maturin (Rust/pyo3) packages as JSON array +[group('CI/CD')] +list-maturin-packages: + @just list-packages-json | jq '[.[] | select(.maturin)]' + +# Sync dependencies for a package via uv +[group('CI/CD')] +ci-sync package: + cd packages/{{package}} && uv sync --all-extras --dev + +# Run linting for a package +[group('CI/CD')] +ci-lint package: + cd packages/{{package}} && uv run ruff check src/ + +# Run tests for a package +[group('CI/CD')] +ci-test package: + cd packages/{{package}} && uv run pytest + +# Run type checking for a package +[group('CI/CD')] +ci-typecheck package: + cd packages/{{package}} && uv run pyright src/ + +# Run all checks for a package (lint, typecheck, test) +[group('CI/CD')] +ci-check package: (ci-lint package) (ci-typecheck package) (ci-test package) + @printf "\nAll CI checks passed for {{package}}.\n" + +## Conda + +# Package commands (conda) +[group('conda')] +conda-build package="omicsio": + pixi build --manifest-path=packages/{{package}}/pyproject.toml + +# Create and sync conda environment with pixi +[group('conda')] +conda-env package="omicsio": + pixi install --manifest-path=packages/{{package}}/pyproject.toml + @echo "Conda environment is ready. Activate it with 'pixi shell'" + +# Update pixi lockfile +[group('conda')] +pixi-lock package="omicsio": + pixi list --manifest-path=packages/{{package}}/pyproject.toml + pixi tree --manifest-path=packages/{{package}}/pyproject.toml + +# Update conda environment +[group('conda')] +conda-lock package="omicsio": + pixi project export conda-explicit-spec packages/{{package}}/conda/ --manifest-path=packages/{{package}}/pyproject.toml --ignore-pypi-errors + +# Run tests in conda environment with pixi +[group('conda')] +conda-test package="omicsio": + pixi run -e test --manifest-path=packages/{{package}}/pyproject.toml test + +# Run linting in conda environment with pixi +[group('conda')] +conda-lint package="omicsio": + pixi run -e lint --manifest-path=packages/{{package}}/pyproject.toml lint-check + +# Run linting and fix errors in conda environment with pixi +[group('conda')] +conda-lint-fix package="omicsio": + pixi run -e lint --manifest-path=packages/{{package}}/pyproject.toml lint + +# Run type checking in conda environment with pixi +[group('conda')] +conda-type package="omicsio": + pixi run -e types --manifest-path=packages/{{package}}/pyproject.toml types + +# Run all checks in conda environment (lint, type, test) +[group('conda')] +conda-check package="omicsio": (conda-lint package) (conda-type package) (conda-test package) + @printf "\n\033[92mAll conda checks passed!\033[0m\n" + +## Containers + +# Build production container image +[group('containers')] +container-build-production CONTAINER: + nix build ".#{{CONTAINER}}ProductionImage" -L + +# Load production container to local Docker daemon +[group('containers')] +container-load-production CONTAINER: + nix run ".#{{CONTAINER}}ProductionImage.copyToDockerDaemon" + +# Push production container manifest (requires registry auth) +[group('containers')] +container-push-production CONTAINER VERSION="0.0.0" +TAGS="": + VERSION={{VERSION}} TAGS={{TAGS}} nix run --impure ".#{{CONTAINER}}Manifest" -L + +# Display container CI matrix +[group('containers')] +container-matrix: + nix eval .#containerMatrix --json | jq . + +## Nix + +# Enter the Nix development shell +[group('nix')] +dev: + nix develop + +# Validate the Nix flake configuration for the current system +[group('nix')] +flake-check: + #!/usr/bin/env bash + set -euo pipefail + SYSTEM=$(nix eval --impure --raw --expr builtins.currentSystem) + echo "Validating flake for $SYSTEM..." + nix flake metadata + echo "Evaluating checks for $SYSTEM..." + nix eval ".#checks.$SYSTEM" --apply builtins.attrNames --json + echo "Building checks for $SYSTEM..." + for check in $(nix eval ".#checks.$SYSTEM" --apply builtins.attrNames --json | jq -r '.[]'); do + echo "Building check: $check" + nix build ".#checks.$SYSTEM.$check" --no-link -L + done + +# Update all flake inputs to their latest versions +[group('nix')] +flake-update: + nix flake update + +# Run CI checks locally with `om ci` +[group('nix')] +ci: + om ci + +## Python + +# Run tests for a package +[group('python')] +test package="omicsio": + cd packages/{{package}} && pytest + +# Run tests for all packages +[group('python')] +test-all: + #!/usr/bin/env bash + set -euo pipefail + for dir in packages/*/; do + pkg=$(basename "$dir") + echo "Testing $pkg..." + (cd "$dir" && pytest) + done + +# Build a package with uv +[group('python')] +uv-build package="omicsio": + cd packages/{{package}} && uv build + +# Sync a package environment with uv +[group('python')] +uv-sync package="omicsio": + cd packages/{{package}} && uv sync + +# Update lockfile for a package +[group('python')] +uv-lock package="omicsio": + cd packages/{{package}} && uv lock + +# Run linting for a package +[group('python')] +lint package="omicsio": + cd packages/{{package}} && ruff check src/ + +# Run linting for all packages +[group('python')] +lint-all: + ruff check packages/ + +# Run linting and fix errors for a package +[group('python')] +lint-fix package="omicsio": + cd packages/{{package}} && ruff check --fix src/ + +# Run type checking for a package +[group('python')] +type package="omicsio": + cd packages/{{package}} && pyright src/ + +# Run all checks for a package (lint, type, test) +[group('python')] +check package="omicsio": (lint package) (type package) (test package) + @printf "\nAll Python checks passed for {{package}}.\n" + +## Rust + +# Build Rust crates for a package +[group('rust')] +cargo-build package: + cd packages/{{package}}/crates && cargo build + +# Run Rust tests via cargo test +[group('rust')] +cargo-test package: + cd packages/{{package}}/crates && cargo test + +# Run Rust clippy lints +[group('rust')] +cargo-clippy package: + cd packages/{{package}}/crates && cargo clippy --all-targets -- --deny warnings + +# Run Rust tests via cargo-nextest +[group('rust')] +cargo-nextest package: + cd packages/{{package}}/crates && cargo nextest run --no-tests=pass + +# Run all Rust checks (clippy, test) +[group('rust')] +cargo-check package: (cargo-clippy package) (cargo-test package) + @printf "\nAll Rust checks passed for {{package}}.\n" + +## Secrets + +# Show existing secrets using sops +[group('secrets')] +show-secrets: + @echo "=== Shared secrets (vars/shared.yaml) ===" + @sops -d vars/shared.yaml + @echo + +# Edit shared secrets file +[group('secrets')] +edit-secrets: + @sops vars/shared.yaml + +# Create a new sops encrypted file +[group('secrets')] +new-secret file: + @sops {{ file }} + +# Export unique secrets to dotenv format using sops +[group('secrets')] +export-secrets: + @echo "# Exported from sops secrets" > .secrets.env + @sops -d vars/shared.yaml | grep -E '^[A-Z_]+:' | sed 's/: /=/' >> .secrets.env + @sort -u .secrets.env -o .secrets.env + +# Run command with all shared secrets as environment variables +[group('secrets')] +run-with-secrets +command: + @sops exec-env vars/shared.yaml '{{ command }}' + +# Check secrets are available in sops environment +[group('secrets')] +check-secrets: + @printf "Check sops environment for secrets\n\n" + @sops exec-env vars/shared.yaml 'env | grep -E "GITHUB|CACHIX|CLOUDFLARE" | sed "s/=.*$/=***REDACTED***/"' + +# Show specific secret value from shared secrets +[group('secrets')] +get-secret key: + @sops -d vars/shared.yaml | grep "^{{ key }}:" | cut -d' ' -f2- + +# Validate all sops encrypted files can be decrypted +[group('secrets')] +validate-secrets: + @echo "Validating sops encrypted files..." + @for file in $(find vars \( -name "*.yaml" -o -name "*.json" \)); do \ + echo "Testing: $file"; \ + sops -d "$file" > /dev/null && echo " ✅ Valid" || echo " ❌ Failed"; \ + done + +# Initialize sops age key for new developers +[group('secrets')] +sops-init: + @echo "Checking sops configuration..." + @if [ ! -f ~/.config/sops/age/keys.txt ]; then \ + echo "Generating age key..."; \ + mkdir -p ~/.config/sops/age; \ + age-keygen -o ~/.config/sops/age/keys.txt; \ + echo ""; \ + echo "✅ Age key generated. Add this public key to .sops.yaml:"; \ + grep "public key:" ~/.config/sops/age/keys.txt; \ + else \ + echo "✅ Age key already exists"; \ + grep "public key:" ~/.config/sops/age/keys.txt; \ + fi + +# Add existing age key to local configuration +[group('secrets')] +sops-add-key: + #!/usr/bin/env bash + set -euo pipefail + + # Ensure keys.txt exists and has proper permissions + mkdir -p ~/.config/sops/age + touch ~/.config/sops/age/keys.txt + chmod 600 ~/.config/sops/age/keys.txt + + # Prompt for key description + printf "Enter age key description (e.g., 'omicsio [dev|ci]'): " + read -r key_description + [[ -z "${key_description}" ]] && { echo "❌ Description cannot be empty"; exit 1; } + + # Prompt for public key + printf "Enter age public key (age1...): " + read -r public_key + if [[ ! "${public_key}" =~ ^age1[a-z0-9]{58}$ ]]; then + echo "❌ Invalid age public key format (must start with 'age1' and be 62 chars)" + exit 1 + fi + + # Prompt for private key (hidden input) + printf "Enter age private key (AGE-SECRET-KEY-...): " + read -rs private_key + echo # New line after hidden input + if [[ ! "${private_key}" =~ ^AGE-SECRET-KEY-[A-Z0-9]{59}$ ]]; then + echo "❌ Invalid age private key format" + exit 1 + fi + + # Check if key already exists + if grep -q "${private_key}" ~/.config/sops/age/keys.txt 2>/dev/null; then + echo "⚠️ This private key already exists in keys.txt" + exit 1 + fi + + # Append to keys.txt with proper formatting + { + echo "" + echo "# ${key_description}" + echo "# public key: ${public_key}" + echo "${private_key}" + } >> ~/.config/sops/age/keys.txt + + echo "✅ Age key added successfully for: ${key_description}" + echo " Public key: ${public_key}" + +# Add or update a secret non-interactively +[group('secrets')] +set-secret secret_name secret_value: + @sops set vars/shared.yaml '["{{ secret_name }}"]' '"{{ secret_value }}"' + @echo "✅ {{ secret_name }} has been set/updated" + +# Rotate a specific secret interactively +[group('secrets')] +rotate-secret secret_name: + @echo "Rotating {{ secret_name }}..." + @echo "Enter new value for {{ secret_name }}:" + @read -s NEW_VALUE && \ + sops set vars/shared.yaml '["{{ secret_name }}"]' "\"$NEW_VALUE\"" && \ + echo "✅ {{ secret_name }} rotated successfully" + +# Update keys for existing secrets files after adding new recipients +[group('secrets')] +updatekeys: + @for file in $(find vars \( -name "*.yaml" -o -name "*.json" \)); do \ + echo "Updating keys for: $file"; \ + sops updatekeys -y "$file"; \ + done + @echo "✅ Keys updated for all secrets files" + +# Bootstrap or rotate SOPS age keys (unified recipe for first-time and rotation) +[group('secrets')] +sops-bootstrap role='dev' method='ssh': + @scripts/sops-bootstrap.sh "{{ role }}" "{{ method }}" + +# Upload SOPS_AGE_KEY to GitHub (separate from other secrets to avoid chicken-and-egg) +[group('secrets')] +sops-upload-github-key repo="": + @scripts/sops-upload-github-key.sh "{{ repo }}" + +# Enumerate required secrets by parsing GitHub workflows +[group('secrets')] +sops-check-requirements: + @scripts/sops-check-requirements.sh + +# Comprehensive GitHub setup (uploads everything except SOPS_AGE_KEY) +[group('secrets')] +sops-setup-github repo="": + @scripts/sops-setup-github.sh "{{ repo }}" + +# Finalize key rotation by removing old keys +[group('secrets')] +sops-finalize-rotation role='dev': + @scripts/sops-finalize-rotation.sh "{{ role }}" + +# Quick rotation workflow (combines bootstrap + finalize after verification) +[group('secrets')] +sops-rotate role='dev' method='ssh': + @scripts/sops-rotate.sh "{{ role }}" "{{ method }}" + +## Template + +# Initialize new project from template +[group('template')] +template-init: + echo "Use: nix --accept-flake-config run github:juspay/omnix/v1.3.2 -- init github:sciexp/omicsio -o new-python-project" + +# Verify template functionality by creating and checking a test project +[group('template')] +template-verify: + om init -t .#default ./tmp-verify-template + cd ./tmp-verify-template && nix flake check + rm -rf ./tmp-verify-template + +# GCP service account for DVC + +# Enable Google Drive API in GCP project +[group('secrets')] +gcp-enable-drive-api: + @echo "Enabling Google Drive API..." + @sops exec-env vars/shared.yaml 'gcloud services enable drive.googleapis.com --project="$GCP_PROJECT_ID"' + @echo "✅ Google Drive API enabled" + @echo "Verifying..." + @sops exec-env vars/shared.yaml 'gcloud services list --enabled --project="$GCP_PROJECT_ID" | grep drive || echo "⚠️ Drive API not found in enabled services"' + +# Create GCP service account for DVC access (run once) +[group('secrets')] +gcp-sa-create: + @echo "Creating GCP service account for DVC..." + @sops exec-env vars/shared.yaml 'gcloud iam service-accounts create dvc-sa \ + --display-name="DVC Service Account" \ + --project="$GCP_PROJECT_ID"' + @echo "✅ Service account created: dvc-sa@$GCP_PROJECT_ID.iam.gserviceaccount.com" + +# Grant Storage Object User role for GCS access +[group('secrets')] +gcp-sa-storage-user: + @echo "Granting Storage Object User role for GCS access..." + @sops exec-env vars/shared.yaml 'gcloud projects add-iam-policy-binding "$GCP_PROJECT_ID" \ + --member="serviceAccount:dvc-sa@$GCP_PROJECT_ID.iam.gserviceaccount.com" \ + --role="roles/storage.objectUser"' + @echo "✅ Storage Object User role granted" + @echo "" + @echo "⚠️ IMPORTANT: Add dvc-sa@$GCP_PROJECT_ID.iam.gserviceaccount.com as an editor to your relevant folder or bucket." + +# Download service account key (for key rotation) +[group('secrets')] +gcp-sa-key-download: + @echo "Downloading service account key..." + @sops exec-env vars/shared.yaml 'gcloud iam service-accounts keys create vars/dvc-sa.tmp.json \ + --iam-account=dvc-sa@"$GCP_PROJECT_ID".iam.gserviceaccount.com \ + --project="$GCP_PROJECT_ID"' + +# Encrypt service account key with sops +[group('secrets')] +gcp-sa-key-encrypt: + @echo "Encrypting service account key with sops..." + @sops -e vars/dvc-sa.tmp.json > vars/dvc-sa.json + @rm -f vars/dvc-sa.tmp.json + @echo "✅ Service account key encrypted and saved to vars/dvc-sa.json" + +# Helper: Run any DVC command with decrypted service account +[group('secrets')] +dvc-run +command: + #!/usr/bin/env bash + set -euo pipefail + sops -d vars/dvc-sa.json > .dvc-sa.json + trap 'rm -f .dvc-sa.json' EXIT + uvx --with dvc-gdrive,dvc-gs dvc {{command}} + +# List existing service account keys (for auditing) +[group('secrets')] +gcp-sa-keys-list: + @sops exec-env vars/shared.yaml 'gcloud iam service-accounts keys list \ + --iam-account=dvc-sa@"$GCP_PROJECT_ID".iam.gserviceaccount.com \ + --project="$GCP_PROJECT_ID"' + +# Rotate service account key +[group('secrets')] +gcp-sa-key-rotate: + @echo "Rotating service account key..." + @echo "Step 1: Creating new key..." + @just gcp-sa-key-download + @echo "" + @echo "Step 2: List existing keys (note the KEY_ID to delete):" + @just gcp-sa-keys-list + @echo "" + @echo "Step 3: After verifying new key works, delete old key with:" + @echo " just gcp-sa-key-delete KEY_ID" + +# Delete a specific service account key +[group('secrets')] +gcp-sa-key-delete key_id: + @sops exec-env vars/shared.yaml 'gcloud iam service-accounts keys delete {{key_id}} \ + --iam-account=dvc-sa@"$GCP_PROJECT_ID".iam.gserviceaccount.com \ + --project="$GCP_PROJECT_ID" --quiet' + @echo "✅ Key {{key_id}} deleted" + +## Release + +# Release testing with bun +[group('release')] +test-release: + bun run test-release + +# Test release as if on main branch +[group('release')] +test-release-as-main: + bun run test-release:main + +# Test release with explicit branch override +[group('release')] +test-release-on-current-branch: + bun run test-release:current + +# Test release directly on release branch +[group('release')] +test-release-direct: + bun run test-release:direct + +# Test package release +[group('release')] +test-package-release package-name="omicsio" branch="main": + cd packages/{{package-name}} && bun run test-release -- -b {{branch}} + +# Preview release version for a package (dry-run semantic-release with merge simulation) +[group('release')] +preview-version base-branch package-path: + ./scripts/preview-version.sh "{{base-branch}}" "{{package-path}}" + +# Run semantic-release for a package +[group('release')] +release-package package-name dry-run="false": + #!/usr/bin/env bash + set -euo pipefail + cd packages/{{package-name}} + if [ "{{dry-run}}" = "true" ]; then + npx semantic-release --dry-run --no-ci + else + echo "This will create a real release. Use dry_run=true for testing." + npx semantic-release + fi + +# Update version for a specific package across all relevant files +[group('release')] +update-version package-name version: + #!/usr/bin/env bash + set -euo pipefail + PACKAGE_PATH="packages/{{package-name}}" + + if [ ! -d "$PACKAGE_PATH" ]; then + echo "Error: package directory $PACKAGE_PATH does not exist" + exit 1 + fi + + PYPROJECT="$PACKAGE_PATH/pyproject.toml" + if [ ! -f "$PYPROJECT" ]; then + echo "Error: $PYPROJECT not found" + exit 1 + fi + + # Extract current version from pyproject.toml [project] section + CURRENT=$(sed -n '/^\[project\]/,/^\[/{ + /^version = /p + }' "$PYPROJECT" | head -1 | sed 's/version = "\(.*\)"/\1/') + if [ -z "$CURRENT" ]; then + echo "Error: could not extract current version from $PYPROJECT" + exit 1 + fi + + echo "Updating {{package-name}} from $CURRENT to {{version}}" + + # Update pyproject.toml [project] version + sed -i'' -e '/^\[project\]/,/^\[/ s/^version = "'"$CURRENT"'"$/version = "{{version}}"/' "$PYPROJECT" + echo " Updated $PYPROJECT [project] version" + + # Update [tool.pixi.package] version if present + if grep -q '^\[tool\.pixi\.package\]' "$PYPROJECT"; then + sed -i'' -e '/^\[tool\.pixi\.package\]/,/^\[/ s/^version = "'"$CURRENT"'"$/version = "{{version}}"/' "$PYPROJECT" + echo " Updated $PYPROJECT [tool.pixi.package] version" + fi + + # For maturin packages: update Cargo.toml workspace version + CARGO_TOML="$PACKAGE_PATH/Cargo.toml" + if [ -f "$CARGO_TOML" ]; then + CARGO_CURRENT=$(sed -n '/^\[workspace\.package\]/,/^\[/{ + /^version = /p + }' "$CARGO_TOML" | head -1 | sed 's/version = "\(.*\)"/\1/') + if [ -n "$CARGO_CURRENT" ]; then + sed -i'' -e '/^\[workspace\.package\]/,/^\[/ s/^version = "'"$CARGO_CURRENT"'"$/version = "{{version}}"/' "$CARGO_TOML" + echo " Updated $CARGO_TOML [workspace.package] version" + fi + echo "Regenerating Cargo.lock in $PACKAGE_PATH..." + cargo generate-lockfile --manifest-path "$CARGO_TOML" + fi + + echo "Running uv lock in $PACKAGE_PATH..." + uv lock --directory "$PACKAGE_PATH" + echo "Version update complete for {{package-name}}" + +## Docs + +# Add quartodoc extension +[group('docs')] +docs-extensions: + (cd docs && quarto add machow/quartodoc) + +# Build quartodoc API reference +[group('docs')] +docs-reference: + quartodoc build --verbose --config docs/_quarto.yml + (cd docs && quartodoc interlinks) + +# Build docs +[group('docs')] +docs-build: data-sync docs-reference + quarto render docs + +# Preview docs locally +[group('docs')] +docs-local: + quarto preview docs --no-browser --port 7780 + +# Check docs +[group('docs')] +docs-check: + quarto check docs + +# Run local docs deployment +[group('docs')] +docs-dev: docs-build + bunx wrangler dev + +# Deploy documentation to Cloudflare Workers (production) +[group('docs')] +docs-deploy-production: docs-build + #!/usr/bin/env bash + set -euo pipefail + CURRENT_SHA=$(git rev-parse HEAD) + CURRENT_TAG=$(git rev-parse --short=12 HEAD) + CURRENT_SHORT=$(git rev-parse --short HEAD) + CURRENT_BRANCH=$(git branch --show-current) + if [ -n "${GITHUB_ACTIONS:-}" ]; then + DEPLOYER="${GITHUB_ACTOR:-github-actions}" + DEPLOY_CONTEXT="${GITHUB_WORKFLOW:-CI}" + DEPLOY_MSG="Deployed by ${DEPLOYER} from ${CURRENT_BRANCH} via ${DEPLOY_CONTEXT}" + else + DEPLOYER=$(whoami) + DEPLOY_HOST=$(hostname -s) + DEPLOY_MSG="Deployed by ${DEPLOYER} from ${CURRENT_BRANCH} on ${DEPLOY_HOST}" + fi + echo "Deploying to production from branch: ${CURRENT_BRANCH}" + echo "Current commit: ${CURRENT_SHORT}" + echo "Full SHA: ${CURRENT_SHA}" + echo "Looking for existing version with tag: ${CURRENT_TAG}" + echo "Deployment message: ${DEPLOY_MSG}" + echo "" + EXISTING_VERSION=$(sops exec-env vars/shared.yaml \ + "bunx wrangler versions list --json" | \ + jq -r --arg tag "$CURRENT_TAG" \ + '.[] | select(.annotations["workers/tag"] == $tag) | .id' | head -1) + if [ -n "$EXISTING_VERSION" ]; then + echo "Found existing version: ${EXISTING_VERSION}" + echo " This version was already built and tested in preview" + echo " Promoting to 100% production traffic..." + echo "" + export DEPLOYMENT_MESSAGE="${DEPLOY_MSG}" + if sops exec-env vars/shared.yaml " + bunx wrangler versions deploy ${EXISTING_VERSION}@100% --yes --message \"\$DEPLOYMENT_MESSAGE\" + "; then + echo "" + echo "Successfully promoted version ${EXISTING_VERSION} to production" + echo " Tag: ${CURRENT_TAG}" + echo " Full SHA: ${CURRENT_SHA}" + echo " Deployed by: ${DEPLOY_MSG}" + echo " Production URL: https://omicsio.scientistexperience.net" + else + echo "" + echo "Failed to promote version ${EXISTING_VERSION}" + echo " Deployment was cancelled or failed" + exit 1 + fi + else + echo "No existing version found with tag: ${CURRENT_TAG}" + echo " This should only happen if:" + echo " - This is the first deployment" + echo " - Commit was made directly on main (not recommended)" + echo " - Version was cleaned up (retention policy)" + echo "" + echo " Falling back to direct build and deploy..." + echo "" + if sops exec-env vars/shared.yaml ' + bunx wrangler deploy + '; then + echo "" + echo "Built and deployed to production" + echo " Full SHA: ${CURRENT_SHA}" + echo " Deployed by: ${DEPLOY_MSG}" + echo " Production URL: https://omicsio.scientistexperience.net" + else + echo "" + echo "Failed to build and deploy" + exit 1 + fi + fi + +# Deploy documentation to Cloudflare Workers (preview) +[group('docs')] +docs-deploy-preview branch=`git branch --show-current`: docs-build + #!/usr/bin/env bash + set -euo pipefail + SAFE_BRANCH=$(echo "{{branch}}" | tr '/' '-' | tr -c 'a-zA-Z0-9-' '-' | sed 's/--*/-/g; s/^-//; s/-$//' | cut -c1-40) + COMMIT_SHA=$(git rev-parse HEAD) + COMMIT_TAG=$(git rev-parse --short=12 HEAD) + COMMIT_SHORT=$(git rev-parse --short HEAD) + COMMIT_MSG=$(git log -1 --pretty=format:'%s') + GIT_STATUS=$(git diff-index --quiet HEAD -- && echo "clean" || echo "dirty") + TAG="${COMMIT_TAG}" + MESSAGE="[{{branch}}] ${COMMIT_MSG} (${COMMIT_TAG}, ${GIT_STATUS})" + echo "Deploying preview for branch: {{branch}}" + echo "Sanitized alias: b-${SAFE_BRANCH}" + echo "Commit: ${COMMIT_SHORT} (${GIT_STATUS})" + echo "Full SHA: ${COMMIT_SHA}" + echo "Tag: ${COMMIT_TAG}" + echo "Message: ${COMMIT_MSG}" + echo "" + export VERSION_TAG="${TAG}" VERSION_MESSAGE="${MESSAGE}" SAFE_BRANCH="${SAFE_BRANCH}" + sops exec-env vars/shared.yaml ' + bunx wrangler versions upload \ + --tag "$VERSION_TAG" \ + --message "$VERSION_MESSAGE" \ + --preview-alias "b-${SAFE_BRANCH}" + ' + echo "" + echo "Version uploaded successfully" + echo " Tag: ${COMMIT_TAG}" + echo " Full SHA: ${COMMIT_SHA}" + echo " Message: ${MESSAGE}" + echo " Preview URL: https://b-${SAFE_BRANCH}-omicsio.sciexp.workers.dev" + +# List recent Cloudflare Workers versions +[group('docs')] +docs-versions: + sops exec-env vars/shared.yaml "bunx wrangler versions list" + +# List recent Cloudflare Workers deployments +[group('docs')] +docs-deployments: + sops exec-env vars/shared.yaml "bunx wrangler deployments list" + +# Tail live logs from Cloudflare Workers +[group('docs')] +docs-tail: + sops exec-env vars/shared.yaml "bunx wrangler tail" + +# Sync data from drive (using encrypted service account) +[group('docs')] +data-sync: + #!/usr/bin/env bash + set -euo pipefail + echo "Decrypting service account for DVC..." + sops -d vars/dvc-sa.json > .dvc-sa.json + trap 'rm -f .dvc-sa.json' EXIT + uvx --with dvc-gdrive,dvc-gs dvc pull --force --allow-missing + echo "✅ DVC data synced" + +# docs-sync: docs-build +# Sync docs freeze data to DVC remote +[group('docs')] +docs-sync: + #!/usr/bin/env bash + set -euo pipefail + echo "Syncing docs freeze data to DVC remote..." + sops -d vars/dvc-sa.json > .dvc-sa.json + chmod 600 .dvc-sa.json + trap 'rm -f .dvc-sa.json' EXIT + uvx --with dvc-gdrive,dvc-gs dvc status + uvx --with dvc-gdrive,dvc-gs dvc add docs/_freeze -v + uvx --with dvc-gdrive,dvc-gs dvc push + uvx --with dvc-gdrive,dvc-gs dvc status + git status + printf "\n\033[92mCommit relevant updates to the docs/_freeze.dvc lock file to the git repo\033[0m\n" + + diff --git a/modules/containers.nix b/modules/containers.nix new file mode 100644 index 0000000..055b2a2 --- /dev/null +++ b/modules/containers.nix @@ -0,0 +1,198 @@ +{ + inputs, + lib, + ... +}: +let + gitHubOrg = "sciexp"; + repoName = "omicsio"; + + # Discover maturin packages from packages/ directory. Each subdirectory + # containing a Cargo.toml is a maturin/pyo3 package that gets a production + # container. This mirrors the discovery logic in python.nix. + packageDirs = builtins.readDir ../packages; + packageNames = builtins.filter (name: packageDirs.${name} == "directory") ( + builtins.attrNames packageDirs + ); + isMaturin = name: builtins.pathExists (../packages + "/${name}/Cargo.toml"); + maturinPackageNames = builtins.filter isMaturin packageNames; + + # Production container definitions derived from discovered maturin packages. + # Each maturin package exposes a CLI binary via pyo3 and gets a container. + productionContainerDefs = lib.genAttrs maturinPackageNames (name: { + inherit name; + entrypoint = name; + description = "${name} with pyo3 native bindings"; + }); +in +{ + perSystem = + { + config, + self', + inputs', + pkgs, + lib, + system, + packageWorkspaces, + pythonSets, + pythonVersions, + ... + }: + let + isLinux = pkgs.stdenv.isLinux; + + # --- Python environments --- + + defaultPythonVersion = "py313"; + defaultPythonSet = pythonSets.${defaultPythonVersion}; + + # Merge deps from all independent package workspaces, unioning extras lists + # for shared dependency names rather than silently dropping via // + defaultDeps = lib.foldlAttrs ( + acc: _: pkg: + lib.zipAttrsWith (_: values: lib.unique (lib.flatten values)) [ + acc + pkg.workspace.deps.default + ] + ) { } packageWorkspaces; + + defaultPythonEnv = defaultPythonSet.mkVirtualEnv "${repoName}-env" defaultDeps; + + # --- Production container infrastructure (nix2container) --- + # Built natively per-system. Cross-compilation via pkgsCross for the + # Python + maturin + Cargo stack is orthogonal and tracked separately. + + nix2container = inputs'.nix2container.packages.nix2container; + skopeo-nix2container = inputs'.nix2container.packages.skopeo-nix2container; + + mkMultiArchManifest = pkgs.callPackage ../nix/lib/mk-multi-arch-manifest.nix { }; + + productionBaseLayer = nix2container.buildLayer { + deps = [ + pkgs.bashInteractive + pkgs.coreutils + pkgs.cacert + ]; + }; + + mkProductionContainer = + { + name, + entrypoint, + pythonEnv ? defaultPythonEnv, + tag ? "latest", + description ? "", + }: + nix2container.buildImage { + inherit name tag; + layers = [ productionBaseLayer ]; + copyToRoot = pkgs.buildEnv { + name = "${name}-root"; + paths = [ + pythonEnv + pkgs.cacert + ]; + pathsToLink = [ + "/bin" + "/lib" + "/etc" + ]; + }; + config = { + entrypoint = [ "${pythonEnv}/bin/${entrypoint}" ]; + Env = [ + "PATH=${pythonEnv}/bin:${pkgs.coreutils}/bin:${pkgs.bashInteractive}/bin" + "SSL_CERT_FILE=${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt" + ]; + Labels = { + "org.opencontainers.image.description" = description; + "org.opencontainers.image.source" = "https://github.com/${gitHubOrg}/${repoName}"; + }; + }; + maxLayers = 2; + }; + + productionContainerPackages = lib.mapAttrs' ( + containerName: def: + lib.nameValuePair "${containerName}ProductionImage" (mkProductionContainer { + inherit (def) name entrypoint description; + }) + ) productionContainerDefs; + + # --- Manifest generation (crane-based, replaces flocken) --- + # Env vars (require --impure): VERSION, TAGS, GITHUB_REF_NAME, GITHUB_ACTOR, GITHUB_TOKEN + + getEnvOr = + var: default: + let + val = builtins.getEnv var; + in + if val == "" then default else val; + + getEnvList = + var: + let + val = builtins.getEnv var; + in + if val == "" then [ ] else lib.splitString "," val; + + # Systems to include in multi-arch manifests + includedSystems = + let + envVar = builtins.getEnv "NIX_IMAGE_SYSTEMS"; + in + if envVar == "" then + [ + "x86_64-linux" + "aarch64-linux" + ] + else + builtins.filter (sys: sys != "") (builtins.split " " envVar); + + manifestVersion = getEnvOr "VERSION" "0.0.0"; + manifestTags = getEnvList "TAGS"; + manifestBranch = getEnvOr "GITHUB_REF_NAME" "main"; + manifestUsername = getEnvOr "GITHUB_ACTOR" "cameronraysmith"; + + # Production manifests use nix: transport (skopeo-nix2container) + productionManifestPackages = lib.mapAttrs' ( + containerName: _def: + lib.nameValuePair "${containerName}Manifest" (mkMultiArchManifest { + name = containerName; + images = lib.listToAttrs ( + map (sys: { + name = sys; + value = inputs.self.packages.${sys}."${containerName}ProductionImage"; + }) includedSystems + ); + registry = { + name = "ghcr.io"; + repo = "${gitHubOrg}/${repoName}/${containerName}"; + username = manifestUsername; + password = "$GITHUB_TOKEN"; + }; + version = manifestVersion; + tags = manifestTags; + branch = manifestBranch; + skopeo = skopeo-nix2container; + }) + ) productionContainerDefs; + + in + { + packages = lib.optionalAttrs isLinux (productionContainerPackages // productionManifestPackages); + }; + + # CI matrix data (pure evaluation): nix eval .#containerMatrix --json + flake.containerMatrix = { + build = lib.mapAttrsToList (containerName: _: { + package = "${containerName}ProductionImage"; + type = "production"; + }) productionContainerDefs; + manifest = lib.mapAttrsToList (containerName: _: { + name = containerName; + type = "production"; + }) productionContainerDefs; + }; +} diff --git a/modules/devshell.nix b/modules/devshell.nix new file mode 100644 index 0000000..9be55aa --- /dev/null +++ b/modules/devshell.nix @@ -0,0 +1,101 @@ +{ + inputs, + ... +}: +{ + perSystem = + { + config, + self', + pkgs, + lib, + packageWorkspaces, + editablePythonSets, + pythonVersions, + hasMaturinPackages ? false, + ... + }: + let + # Merge deps from all independent package workspaces, unioning extras lists + # for shared dependency names rather than silently dropping via // + allDeps = lib.foldlAttrs ( + acc: _: pkg: + lib.zipAttrsWith (_: values: lib.unique (lib.flatten values)) [ + acc + pkg.workspace.deps.all + ] + ) { } packageWorkspaces; + + mkDevShell = + { + name, + pythonVersion, + }: + let + python = pythonVersions.${pythonVersion}; + pythonEnv = editablePythonSets.${pythonVersion}; + virtualenv = pythonEnv.mkVirtualEnv "${name}-dev-env" allDeps; + in + pkgs.mkShell { + inherit name; + inputsFrom = [ config.pre-commit.devShell ]; + packages = + with pkgs; + [ + just + pixi + quarto + uv + bun + nodejs + virtualenv + age + gitleaks + sops + ssh-to-age + ] + ++ lib.optionals hasMaturinPackages ( + with pkgs; + [ + # Rust tooling for maturin/pyo3 packages + cargo + rustc + clippy + cargo-nextest + maturin + ] + ); + + env = { + UV_NO_SYNC = "1"; + UV_PYTHON = "${virtualenv}/bin/python"; + UV_PYTHON_DOWNLOADS = "never"; + }; + + shellHook = '' + unset PYTHONPATH + export REPO_ROOT=$(git rev-parse --show-toplevel) + export GIT_REPO_NAME=$(basename -s .git "$(git config --get remote.origin.url 2>/dev/null || echo "unknown-repo")") + export GIT_REF=$(git symbolic-ref -q --short HEAD 2>/dev/null || git rev-parse HEAD 2>/dev/null || echo "unknown-ref") + export GIT_SHA=$(git rev-parse HEAD 2>/dev/null || echo "unknown-sha") + export GIT_SHA_SHORT=$(git rev-parse --short HEAD 2>/dev/null || echo "unknown") + printf "\n%s %s %s %s\n\n" "$GIT_REPO_NAME" "$GIT_REF" "$GIT_SHA_SHORT" "$GIT_SHA" + ''; + }; + in + { + devShells = rec { + omicsio312 = mkDevShell { + name = "omicsio-3.12"; + pythonVersion = "py312"; + }; + + omicsio313 = mkDevShell { + name = "omicsio-3.13"; + pythonVersion = "py313"; + }; + + default = omicsio313; + }; + }; +} diff --git a/modules/flake-parts.nix b/modules/flake-parts.nix new file mode 100644 index 0000000..b12635a --- /dev/null +++ b/modules/flake-parts.nix @@ -0,0 +1,5 @@ +{ ... }: +{ + # External flake-parts module imports. + # git-hooks and treefmt-nix are imported in formatting.nix. +} diff --git a/modules/formatting.nix b/modules/formatting.nix new file mode 100644 index 0000000..d216726 --- /dev/null +++ b/modules/formatting.nix @@ -0,0 +1,31 @@ +{ inputs, ... }: +{ + imports = [ + inputs.treefmt-nix.flakeModule + inputs.git-hooks.flakeModule + ]; + + perSystem = + { pkgs, ... }: + { + treefmt = { + projectRootFile = "flake.nix"; + programs.nixfmt.enable = true; + programs.ruff-format.enable = true; + programs.ruff-check.enable = true; + programs.taplo.enable = true; + }; + + pre-commit.settings = { + package = pkgs.prek; + hooks.treefmt.enable = true; + hooks.gitleaks = { + enable = true; + name = "gitleaks"; + entry = "${pkgs.gitleaks}/bin/gitleaks protect --staged --verbose --redact"; + language = "system"; + pass_filenames = false; + }; + }; + }; +} diff --git a/modules/overrides.nix b/modules/overrides.nix new file mode 100644 index 0000000..e3dd66e --- /dev/null +++ b/modules/overrides.nix @@ -0,0 +1,60 @@ +{ + inputs, + ... +}: +{ + perSystem = + { + config, + self', + pkgs, + lib, + ... + }: + let + # Function to create package-specific overrides + mkPackageOverrides = + { pkgs }: + final: prev: { + # Example overrides for specific packages + # numpy = prev.numpy.overrideAttrs (old: { + # buildInputs = (old.buildInputs or []) ++ [ pkgs.openblas ]; + # }); + + # Example of fixing a package that needs specific build system dependencies + # tensorflow = prev.tensorflow.overrideAttrs (old: { + # nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ + # (final.resolveBuildSystem { + # setuptools = []; + # wheel = []; + # numpy = []; + # }) + # ]; + # }); + }; + + # Function to create sdist-specific overrides + mkSdistOverrides = + { pkgs }: + final: prev: { + # Example overrides for source distributions + # pyzmq = prev.pyzmq.overrideAttrs (old: { + # buildInputs = (old.buildInputs or []) ++ [ pkgs.zeromq ]; + # nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ + # (final.resolveBuildSystem { + # cmake = []; + # ninja = []; + # packaging = []; + # }) + # ]; + # }); + }; + in + { + # Expose the override functions for use in other modules + _module.args = { + packageOverrides = mkPackageOverrides { inherit pkgs; }; + sdistOverrides = mkSdistOverrides { inherit pkgs; }; + }; + }; +} diff --git a/modules/packages.nix b/modules/packages.nix new file mode 100644 index 0000000..43c2d44 --- /dev/null +++ b/modules/packages.nix @@ -0,0 +1,41 @@ +{ + inputs, + ... +}: +{ + perSystem = + { + config, + self', + pkgs, + lib, + packageWorkspaces, + pythonSets, + editablePythonSets, + pythonVersions, + ... + }: + let + # Merge deps from all independent package workspaces, unioning extras lists + # for shared dependency names rather than silently dropping via // + mergeWorkspaceDeps = + selector: + lib.foldlAttrs ( + acc: _: pkg: + lib.zipAttrsWith (_: values: lib.unique (lib.flatten values)) [ + acc + (selector pkg.workspace.deps) + ] + ) { } packageWorkspaces; + + defaultDeps = mergeWorkspaceDeps (deps: deps.default); + in + { + packages = rec { + omicsio312 = pythonSets.py312.mkVirtualEnv "omicsio-3.12" defaultDeps; + omicsio313 = pythonSets.py313.mkVirtualEnv "omicsio-3.13" defaultDeps; + + default = omicsio313; + }; + }; +} diff --git a/modules/python.nix b/modules/python.nix new file mode 100644 index 0000000..b9e60bf --- /dev/null +++ b/modules/python.nix @@ -0,0 +1,156 @@ +{ + inputs, + ... +}: +{ + perSystem = + { + config, + self', + pkgs, + lib, + packageOverrides ? (_: _: { }), + sdistOverrides ? (_: _: { }), + ... + }: + let + pythonVersions = { + py312 = pkgs.python312; + py313 = pkgs.python313; + }; + + # Discover packages from packages/ directory. Each subdirectory is a + # Python package. Packages containing Cargo.toml are maturin/pyo3 + # packages requiring a corresponding nix/packages/{name}/default.nix + # module that exports { overlay, checks }. + packageDirs = builtins.readDir ../packages; + packageNames = builtins.filter (name: packageDirs.${name} == "directory") ( + builtins.attrNames packageDirs + ); + + isMaturin = name: builtins.pathExists (../packages + "/${name}/Cargo.toml"); + maturinPackageNames = builtins.filter isMaturin packageNames; + purePackageNames = builtins.filter (name: !(isMaturin name)) packageNames; + hasMaturinPackages = maturinPackageNames != [ ]; + + # Load each Python package independently (no root workspace). + # Each package directory contains its own pyproject.toml and uv.lock, + # resolved independently following the LangChain federation model. + loadPackage = + name: path: + let + workspace = inputs.uv2nix.lib.workspace.loadWorkspace { + workspaceRoot = path; + }; + in + { + inherit workspace; + overlay = workspace.mkPyprojectOverlay { + sourcePreference = "wheel"; + }; + editableOverlay = workspace.mkEditablePyprojectOverlay { + root = "$REPO_ROOT/packages/${name}"; + }; + }; + + packageWorkspaces = lib.genAttrs packageNames (name: loadPackage name (../packages + "/${name}")); + + # Per-package Nix modules with Rust overlays. Each maturin package + # requires nix/packages/{name}/default.nix exporting { overlay, checks }. + # Eval-time error when Cargo.toml exists but the module is missing. + mkPackageModule = + name: python: + let + modulePath = ../nix/packages + "/${name}/default.nix"; + in + if builtins.pathExists modulePath then + import modulePath { + inherit pkgs lib python; + crane = inputs.crane; + inherit (inputs) crane-maturin pyproject-nix; + } + else + throw "Maturin package ${name} requires nix/packages/${name}/default.nix"; + + # Compose per-package uv2nix overlays with shared overrides. + # + # Invariant: all federated packages must resolve compatible versions for + # shared dependencies. Per-package uv2nix overlays are composed sequentially + # into a single package set — if two packages resolve different versions of + # the same dependency, the later overlay silently wins. Enforce version + # alignment across packages by running: + # uv lock --check + # in each package directory after updating any shared dependency. + mkPythonSet = + python: + (pkgs.callPackage inputs.pyproject-nix.build.packages { + inherit python; + }).overrideScope + ( + lib.composeManyExtensions ( + [ + inputs.pyproject-build-systems.overlays.default + ] + ++ map (name: packageWorkspaces.${name}.overlay) packageNames + ++ map (name: (mkPackageModule name python).overlay) maturinPackageNames + ++ [ + packageOverrides + sdistOverrides + ] + ) + ); + + # Editable set excludes maturin packages: maturin packages are + # incompatible with uv2nix's editable overlay (pyprojectFixupEditableHook + # expects EDITABLE_ROOT which maturin's build process does not set). + # Maturin packages are built as regular wheels in the devshell; use + # `maturin develop` for iterative Rust development. + mkEditablePythonSet = + python: + (mkPythonSet python).overrideScope ( + lib.composeManyExtensions ( + map (name: packageWorkspaces.${name}.editableOverlay) purePackageNames + ++ [ + ( + final: prev: + lib.genAttrs purePackageNames ( + name: + prev.${name}.overrideAttrs (old: { + nativeBuildInputs = + old.nativeBuildInputs + ++ final.resolveBuildSystem { + editables = [ ]; + }; + }) + ) + ) + ] + ) + ); + + pythonSets = lib.mapAttrs (_: mkPythonSet) pythonVersions; + editablePythonSets = lib.mapAttrs (_: mkEditablePythonSet) pythonVersions; + + # Rust checks from per-package modules (using default Python version) + rustChecks = lib.foldl' ( + acc: name: acc // (mkPackageModule name pythonVersions.py313).checks + ) { } maturinPackageNames; + in + { + checks = lib.optionalAttrs hasMaturinPackages rustChecks; + + _module.args = { + inherit + packageWorkspaces + pythonSets + editablePythonSets + pythonVersions + packageNames + maturinPackageNames + purePackageNames + hasMaturinPackages + ; + defaultPython = pythonVersions.py313; + }; + }; +} diff --git a/modules/systems.nix b/modules/systems.nix new file mode 100644 index 0000000..8669711 --- /dev/null +++ b/modules/systems.nix @@ -0,0 +1,8 @@ +{ + systems = [ + "x86_64-linux" + "aarch64-linux" + "aarch64-darwin" + "x86_64-darwin" + ]; +} diff --git a/modules/template-rename.nix b/modules/template-rename.nix new file mode 100644 index 0000000..6af3217 --- /dev/null +++ b/modules/template-rename.nix @@ -0,0 +1,97 @@ +{ + inputs, + lib, + config, + pkgs, + ... +}: + +{ + perSystem = + { system, pkgs, ... }: + { + packages.fix-template-names = pkgs.writeShellApplication { + name = "fix-template-names"; + runtimeInputs = with pkgs; [ + coreutils + gnused + gnugrep + findutils + file + ]; + text = '' + #!/usr/bin/env bash + + set -euo pipefail + + # Colors for output + GREEN='\033[0;32m' + YELLOW='\033[1;33m' + RED='\033[0;31m' + NC='\033[0m' # No Color + + # Get the current directory name as default new name + DEFAULT_NEW_NAME=$(basename "$(pwd)") + # Convert to underscore version + DEFAULT_NEW_UNDERSCORE=$(echo "$DEFAULT_NEW_NAME" | tr '-' '_') + + # Check for required arguments + if [ $# -lt 1 ]; then + echo -e "''${RED}Error: Missing required argument.''${NC}" + echo "Usage: fix-template-names OLD_NAME [NEW_NAME]" + echo "OLD_NAME: The original template name to be replaced" + echo "NEW_NAME: The new name to use (optional, defaults to current directory name: $DEFAULT_NEW_NAME)" + exit 1 + fi + + # Set old name from first argument + OLD_NAME="$1" + # Convert to underscore version + OLD_UNDERSCORE=$(echo "$OLD_NAME" | tr '-' '_') + + # Use second command line argument if provided, otherwise use defaults + if [ $# -eq 2 ]; then + NEW_NAME="$2" + # Convert to underscore version + NEW_UNDERSCORE=$(echo "$NEW_NAME" | tr '-' '_') + else + NEW_NAME="$DEFAULT_NEW_NAME" + NEW_UNDERSCORE="$DEFAULT_NEW_UNDERSCORE" + fi + + echo -e "''${YELLOW}Starting replacement of template names...''${NC}" + echo -e "''${YELLOW}Replacing $OLD_NAME with $NEW_NAME''${NC}" + echo -e "''${YELLOW}Replacing $OLD_UNDERSCORE with $NEW_UNDERSCORE''${NC}" + + # Find all text files in the project (excluding .git, node_modules, and other common directories to ignore) + # and replace the strings in-place + find . -type f \ + -not -path "*/\.*" \ + -not -path "*/node_modules/*" \ + -not -path "*/venv/*" \ + -not -path "*/build/*" \ + -not -path "*/dist/*" \ + -not -path "*/\__pycache__/*" \ + -exec grep -l "$OLD_NAME\|$OLD_UNDERSCORE" {} \; | while read -r file; do + echo "Processing: $file" + + # Check if file is binary + if file "$file" | grep -q "binary"; then + echo " Skipping binary file" + continue + fi + + # Make replacements + sed -i.bak "s/$OLD_NAME/$NEW_NAME/g" "$file" + sed -i.bak "s/$OLD_UNDERSCORE/$NEW_UNDERSCORE/g" "$file" + + # Remove backup files + rm -f "''${file}.bak" + done + + echo -e "''${GREEN}Replacement complete!''${NC}" + echo -e "''${YELLOW}Note: You may need to rebuild or reinstall your package after these changes.''${NC}" + ''; + }; + }; +} diff --git a/nix/.keep b/nix/.keep new file mode 100644 index 0000000..e69de29 diff --git a/nix/disabled/containers-dev.nix.txt b/nix/disabled/containers-dev.nix.txt new file mode 100644 index 0000000..c3b824d --- /dev/null +++ b/nix/disabled/containers-dev.nix.txt @@ -0,0 +1,184 @@ +# Dev containers disabled pending nixpod nix2container migration (pnt-mgq). +# Re-enable after sciexp-h0g completes. +# +# This file preserves the dev container code that was removed from +# modules/containers.nix. It lives outside modules/ so import-tree +# does not attempt to import it. + +# Required flake input (add back to flake.nix): +# nixpod = { +# url = "github:cameronraysmith/nixpod/00-lock"; +# inputs.nixpkgs.follows = "nixpkgs"; +# inputs.flake-parts.follows = "flake-parts"; +# }; + +# --- Dev container definitions (top-level let binding) --- +# +# devContainerDefs = { +# ${repoName} = { +# imageAttr = "containerImage"; +# }; +# "${repoName}-dev" = { +# imageAttr = "devcontainerImage"; +# }; +# }; + +# --- Dev container infrastructure (perSystem let binding) --- +# +# buildMultiUserNixImage = import "${inputs.nixpod.outPath}/containers/nix.nix"; +# +# containerUsername = "jovyan"; +# containerUserInfo = { +# uid = 1000; +# gid = 0; +# uname = containerUsername; +# gname = "wheel"; +# }; +# +# containerSysPackages = with pkgs; [ +# bashInteractive +# cacert +# coreutils +# direnv +# gnutar +# gzip +# less +# nix +# procps +# sudo +# zsh +# ]; +# +# containerDevPackages = with pkgs; [ +# git +# helix +# lazygit +# neovim +# starship +# ]; +# +# mkBaseContainer = +# { +# name, +# tag ? "latest", +# pythonPackageEnv, +# extraContents ? [ ], +# extraPkgs ? [ ], +# extraEnv ? [ ], +# extraConfig ? { }, +# }: +# buildMultiUserNixImage { +# inherit pkgs name tag; +# storeOwner = containerUserInfo; +# maxLayers = 121; +# fromImage = inputs'.nixpod.packages.sudoImage; +# compressor = "zstd"; +# +# extraPkgs = containerSysPackages ++ extraPkgs ++ [ pythonPackageEnv ]; +# extraContents = [ +# inputs'.nixpod.legacyPackages.homeConfigurations.${containerUsername}.activationPackage +# ] +# ++ extraContents; +# +# extraFakeRootCommands = '' +# chown -R ${containerUsername}:wheel /nix +# ''; +# +# nixConf = { +# allowed-users = [ "*" ]; +# experimental-features = [ +# "nix-command" +# "flakes" +# ]; +# max-jobs = [ "auto" ]; +# sandbox = "false"; +# trusted-users = [ +# "root" +# "${containerUsername}" +# "runner" +# ]; +# }; +# +# extraEnv = [ +# "NB_USER=${containerUsername}" +# "NB_UID=1000" +# "NB_PREFIX=/" +# "LD_LIBRARY_PATH=${pythonPackageEnv}/lib:/usr/local/nvidia/lib64" +# "NVIDIA_DRIVER_CAPABILITIES='compute,utility'" +# "NVIDIA_VISIBLE_DEVICES=all" +# "QUARTO_PYTHON=${pythonPackageEnv}/bin/python" +# ] +# ++ extraEnv; +# +# extraConfig = { +# ExposedPorts."8888/tcp" = { }; +# } +# // extraConfig; +# }; + +# --- Dev container Python environments (perSystem let binding) --- +# +# defaultEditablePythonSet = editablePythonSets.${defaultPythonVersion}; +# +# allDeps = lib.foldlAttrs ( +# acc: _: pkg: +# lib.zipAttrsWith (_: values: lib.unique (lib.flatten values)) [ +# acc +# pkg.workspace.deps.all +# ] +# ) { } packageWorkspaces; +# +# defaultEditablePythonEnv = defaultEditablePythonSet.mkVirtualEnv "${repoName}-editable-env" allDeps; + +# --- Dev container package outputs (perSystem packages) --- +# +# containerImage = mkBaseContainer { +# name = repoName; +# pythonPackageEnv = defaultPythonEnv; +# }; +# +# devcontainerImage = mkBaseContainer { +# name = "${repoName}-dev"; +# pythonPackageEnv = defaultEditablePythonEnv; +# extraPkgs = containerDevPackages; +# }; + +# --- Dev manifest packages (perSystem let binding) --- +# +# devManifestPackages = lib.mapAttrs' ( +# manifestName: def: +# lib.nameValuePair "${manifestName}Manifest" (mkMultiArchManifest { +# name = manifestName; +# images = lib.listToAttrs ( +# map (sys: { +# name = sys; +# value = inputs.self.packages.${sys}.${def.imageAttr}; +# }) includedSystems +# ); +# registry = { +# name = "ghcr.io"; +# repo = "${gitHubOrg}/${manifestName}"; +# username = manifestUsername; +# password = "$GITHUB_TOKEN"; +# }; +# version = manifestVersion; +# tags = manifestTags; +# branch = manifestBranch; +# skopeo = pkgs.skopeo; +# mkSourceUri = image: "docker-archive:${image}"; +# }) +# ) devContainerDefs; + +# --- Dev containerMatrix entries (flake-level) --- +# +# Append to containerMatrix.build: +# ++ (lib.mapAttrsToList (_: def: { +# package = def.imageAttr; +# type = "dev"; +# }) devContainerDefs); +# +# Append to containerMatrix.manifest: +# ++ (lib.mapAttrsToList (manifestName: _: { +# name = manifestName; +# type = "dev"; +# }) devContainerDefs); diff --git a/nix/lib/mk-multi-arch-manifest.nix b/nix/lib/mk-multi-arch-manifest.nix new file mode 100644 index 0000000..52843fc --- /dev/null +++ b/nix/lib/mk-multi-arch-manifest.nix @@ -0,0 +1,148 @@ +# Multi-arch manifest builder using skopeo and crane (manifest lists) +# Single-arch builds auto-detected and skip manifest list creation +# Supports both nix2container (nix: transport) and dockerTools (docker-archive: transport) +{ + lib, + writeShellApplication, + coreutils, + crane, + jq, +}: +{ + images, + name, + registry, + version, + tags ? [ ], + branch ? "main", + skopeo, + mkSourceUri ? (image: "nix:${image}"), +}: +let + # Tags: version first, then explicit tags or "latest" on main branch + parsedTags = [ + version + ] + ++ (if tags != [ ] then tags else (if branch == "main" then [ "latest" ] else [ ])); + isSingleArch = lib.length (lib.attrNames images) == 1; + systemToArch = { + "x86_64-linux" = "amd64"; + "aarch64-linux" = "arm64"; + }; + + # Single-arch: push to primary tag; multi-arch: push with arch suffix, then create manifest list + archImages = lib.mapAttrs' ( + system: image: + let + arch = systemToArch.${system}; + primaryTag = lib.head parsedTags; + in + lib.nameValuePair arch { + inherit system image arch; + tag = if isSingleArch then primaryTag else "${version}-${arch}"; + uri = "${registry.name}/${registry.repo}:${ + if isSingleArch then primaryTag else "${version}-${arch}" + }"; + } + ) images; + + manifestName = "${registry.name}/${registry.repo}:${lib.head parsedTags}"; + repoBase = "${registry.name}/${registry.repo}"; + + skopeoExe = lib.getExe skopeo; + craneExe = lib.getExe crane; + jqExe = lib.getExe jq; + +in +assert lib.assertMsg (images != { }) "At least one image must be provided"; +assert lib.assertMsg (parsedTags != [ ]) "At least one tag must be set"; + +writeShellApplication { + name = "multi-arch-manifest-${name}"; + runtimeInputs = [ + skopeo + crane + jq + coreutils + ]; + + text = '' + function cleanup { + set -x + ${skopeoExe} logout "${registry.name}" || true + ${craneExe} auth logout "${registry.name}" || true + } + trap cleanup EXIT + + set -x + + if [[ ! -f "/etc/containers/policy.json" && ! -f "$HOME/.config/containers/policy.json" ]]; then + mkdir -p "$HOME/.config/containers" + install -Dm444 "${skopeo.policy}/default-policy.json" "$HOME/.config/containers/policy.json" + fi + + set +x + echo "Logging in to ${registry.name}" + ${skopeoExe} login \ + --username "${registry.username}" \ + --password "${registry.password}" \ + "${registry.name}" + ${craneExe} auth login "${registry.name}" \ + --username "${registry.username}" \ + --password "${registry.password}" + set -x + + declare -A PUSHED_DIGESTS + ${lib.concatMapStringsSep "\n" (archImage: '' + echo "Pushing ${archImage.arch} image to ${archImage.uri}" + DIGESTFILE=$(mktemp) + ${skopeoExe} copy \ + --digestfile "$DIGESTFILE" \ + --dest-creds "${registry.username}:${registry.password}" \ + "${mkSourceUri archImage.image}" \ + "docker://${archImage.uri}" + PUSHED_DIGESTS["${archImage.arch}"]=$(cat "$DIGESTFILE") + rm "$DIGESTFILE" + echo "Pushed ${archImage.arch} with digest: ''${PUSHED_DIGESTS["${archImage.arch}"]}" + '') (lib.attrValues archImages)} + + ${lib.optionalString (!isSingleArch) '' + echo "Creating multi-arch manifest list: ${manifestName}" + ${craneExe} index append \ + ${ + lib.concatMapStringsSep " \\\n " ( + archImage: ''-m "${repoBase}@''${PUSHED_DIGESTS["${archImage.arch}"]}"'' + ) (lib.attrValues archImages) + } \ + -t "${manifestName}" + + set +x + echo "Manifest: ${manifestName}" + ${craneExe} manifest "${manifestName}" | ${jqExe} . + echo "Tags: ${toString parsedTags}" + set -x + ''} + + ${lib.concatMapStringsSep "\n" (tag: '' + ${craneExe} tag \ + "${registry.name}/${registry.repo}:${lib.head parsedTags}" \ + "${tag}" + '') (lib.tail parsedTags)} + + set +x + ${ + if isSingleArch then + '' + echo "Successfully pushed single-arch image for ${name}" + '' + else + '' + echo "Successfully pushed multi-arch manifest for ${name}" + '' + } + echo "Available at: ${registry.name}/${registry.repo}:${lib.head parsedTags}" + ${lib.concatMapStringsSep "\n" (tag: '' + echo " Also tagged: ${registry.name}/${registry.repo}:${tag}" + '') (lib.tail parsedTags)} + ''; +} diff --git a/package.json b/package.json new file mode 100644 index 0000000..3de1252 --- /dev/null +++ b/package.json @@ -0,0 +1,95 @@ +{ + "name": "omicsio", + "version": "0.0.0-development", + "private": true, + "description": "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns", + "repository": { + "type": "git", + "url": "https://github.com/sciexp/omicsio.git" + }, + "license": "MIT", + "engines": { + "node": ">=18" + }, + "workspaces": [ + "packages/*" + ], + "packageManager": "bun@1.3.4", + "devDependencies": { + "@semantic-release/changelog": "^6.0.3", + "@semantic-release/github": "^12.0.0", + "conventional-changelog-conventionalcommits": "^9.0.0", + "cross-env": "^10.0.0", + "semantic-release": "^25.0.0", + "semantic-release-major-tag": "^0.3.2", + "semantic-release-monorepo": "^8.0.2" + }, + "scripts": { + "reinstall": "rm -rf node_modules packages/*/node_modules && bun install", + "test-release": "semantic-release --dry-run --no-ci" + }, + "release": { + "extends": "semantic-release-monorepo", + "branches": [ + { + "name": "main" + }, + { + "name": "beta", + "prerelease": true + } + ], + "plugins": [ + [ + "@semantic-release/commit-analyzer", + { + "preset": "conventionalcommits", + "parserOpts": { + "noteKeywords": [ + "BREAKING CHANGE", + "BREAKING-CHANGE" + ] + } + } + ], + [ + "@semantic-release/release-notes-generator", + { + "preset": "conventionalcommits", + "parserOpts": { + "noteKeywords": [ + "BREAKING CHANGE", + "BREAKING-CHANGE", + "NOTABLE CHANGE", + "NOTABLE-CHANGE" + ] + } + } + ], + [ + "@semantic-release/changelog", + { + "changelogTitle": "# Changelog" + } + ], + [ + "@semantic-release/github", + { + "failComment": false, + "successComment": false, + "addReleases": "bottom" + } + ], + [ + "semantic-release-major-tag", + { + "customTags": [ + "v${major}", + "v${major}.${minor}" + ] + } + ] + ], + "npmPublish": false + } +} diff --git a/packages/.keep b/packages/.keep new file mode 100644 index 0000000..e69de29 diff --git a/packages/omicsio/.ci.json b/packages/omicsio/.ci.json new file mode 100644 index 0000000..a7359b7 --- /dev/null +++ b/packages/omicsio/.ci.json @@ -0,0 +1,4 @@ +{ + "build-images": false, + "images": ["omicsio", "omicsio-dev"] +} diff --git a/packages/omicsio/README.md b/packages/omicsio/README.md new file mode 100644 index 0000000..e69de29 diff --git a/packages/omicsio/conda/README.md b/packages/omicsio/conda/README.md new file mode 100644 index 0000000..9ed528c --- /dev/null +++ b/packages/omicsio/conda/README.md @@ -0,0 +1,29 @@ +# conda + +The files in this directory are automatically generated from the +[pyproject.toml](../pyproject.toml) by running + +```sh +just -n conda-lock +``` + +in the repository root directory. + +To create a corresponding conda environment, use the environment and platform +specific lockfile to construct a command of the form + +```sh +mamba create --name --file +``` + +For example, for a conda environment named `omicsio` and the `dev` environment +from the [pyproject.toml](../pyproject.toml) on x86_64-linux architecture run + +```sh +mamba create --name omicsio --file dev_linux-64_conda_spec.txt +``` + +These environments will be missing packages that are sourced from pypi in the +[pixi.lock](../pixi.lock). See [pixi export explicit +spec](https://pixi.sh/dev/reference/cli/#project-export-conda-explicit-spec) for +details. diff --git a/packages/omicsio/conda/default_linux-64_conda_spec.txt b/packages/omicsio/conda/default_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/default_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/default_osx-arm64_conda_spec.txt b/packages/omicsio/conda/default_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/default_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/dev_linux-64_conda_spec.txt b/packages/omicsio/conda/dev_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/dev_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/dev_osx-arm64_conda_spec.txt b/packages/omicsio/conda/dev_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/dev_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/docs_linux-64_conda_spec.txt b/packages/omicsio/conda/docs_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/docs_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/docs_osx-arm64_conda_spec.txt b/packages/omicsio/conda/docs_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/docs_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/interactive_linux-64_conda_spec.txt b/packages/omicsio/conda/interactive_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/interactive_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/interactive_osx-arm64_conda_spec.txt b/packages/omicsio/conda/interactive_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/interactive_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/lint_linux-64_conda_spec.txt b/packages/omicsio/conda/lint_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/lint_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/lint_osx-arm64_conda_spec.txt b/packages/omicsio/conda/lint_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/lint_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/test_linux-64_conda_spec.txt b/packages/omicsio/conda/test_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/test_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/test_osx-arm64_conda_spec.txt b/packages/omicsio/conda/test_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/test_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 +https://conda.anaconda.org/conda-forge/osx-arm64/liblzma-5.6.4-h39f12f2_0.conda#e3fd1f8320a100f2b210e690a57cd615 +https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2#086914b672be056eb70fd4285b6783b6 +https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda#38d2656dd914feb0cab8c629370768bf +https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda#fc6948412dbbbe9a4c9ddbbcfe0a79ab +https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.9-hc22306f_1_cpython.conda#d9fac7b334ff6e5f93abd27509a53060 diff --git a/packages/omicsio/conda/types_linux-64_conda_spec.txt b/packages/omicsio/conda/types_linux-64_conda_spec.txt new file mode 100644 index 0000000..3821b27 --- /dev/null +++ b/packages/omicsio/conda/types_linux-64_conda_spec.txt @@ -0,0 +1,25 @@ +# Generated by `pixi workspace export` +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h767d61c_2.conda#06d02030237f4d5b3d9a7e7d348fe3c6 +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h767d61c_2.conda#ef504d1acbd74b7cc6849ef8af47dd03 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_2.conda#a2222a6ada71fb478682efe483ce0f92 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda#19f3a56f68d2fd06c516076bff482c52 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.1-h7b32b05_0.conda#41adf927e746dc75ecf0ef841c454e48 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.1-hee588c1_1.conda#73cea06049cc4174578b432320a003b8 +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.4-hb9d3cd8_0.conda#42d5b6a0f30d3c10cd88cb8584fda1cb +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_0.conda#e3eb7806380bc8bcecba6d749ad5f026 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/python-3.12.9-h9e4cc4f_1_cpython.conda#d82342192dfc9145185190e651065aa9 diff --git a/packages/omicsio/conda/types_osx-arm64_conda_spec.txt b/packages/omicsio/conda/types_osx-arm64_conda_spec.txt new file mode 100644 index 0000000..0c5a416 --- /dev/null +++ b/packages/omicsio/conda/types_osx-arm64_conda_spec.txt @@ -0,0 +1,16 @@ +# Generated by `pixi workspace export` +# platform: osx-arm64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-h8359307_2.conda#369964e85dc26bfe78f41399b366c435 +https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h5083fa2_1.conda#b50a57ba89c32b62428b71a875291c9b +https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae +https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda#63ef3f6e6d6d5c589e64f11263dc5676 +https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda#3569d6a9141adc64d2fe4797f3289e06 +https://conda.anaconda.org/conda-forge/osx-arm64/openssl-3.4.1-h81ee809_0.conda#75f9f0c7b1740017e2db83a53ab9a28e +https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.49.1-h3f77e49_1.conda#c83357a21092bd952933c36c5cb4f4d6 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diff --git a/packages/omicsio/src/.keep b/packages/omicsio/src/.keep new file mode 100644 index 0000000..e69de29 diff --git a/packages/omicsio/src/omicsio/__init__.py b/packages/omicsio/src/omicsio/__init__.py new file mode 100644 index 0000000..f36a1e0 --- /dev/null +++ b/packages/omicsio/src/omicsio/__init__.py @@ -0,0 +1,12 @@ +from importlib import metadata + +try: + __version__ = metadata.version(__package__) +except metadata.PackageNotFoundError: + __version__ = "unknown" + +del metadata + + +def main() -> None: + print("Hello from omicsio!") diff --git a/packages/omicsio/src/omicsio/tests/.keep b/packages/omicsio/src/omicsio/tests/.keep new file mode 100644 index 0000000..e69de29 diff --git a/packages/omicsio/src/omicsio/tests/__init__.py b/packages/omicsio/src/omicsio/tests/__init__.py new file mode 100644 index 0000000..2572118 --- /dev/null +++ b/packages/omicsio/src/omicsio/tests/__init__.py @@ -0,0 +1 @@ +# This file is intentionally left empty to mark the directory as a 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for curl one-liner pre-clone onboarding: +# curl -sSf https://raw.githubusercontent.com/sciexp/omicsio/main/scripts/bootstrap.sh | bash +# +# This script must be kept in sync with the Makefile bootstrap targets +# manually (discipline-based, not DRY import) since it must remain +# self-contained for the curl use case. +set -euo pipefail + +echo "omicsio bootstrap" +echo "==============================" +echo + +# Install Nix +echo "Checking Nix installation..." +if command -v nix >/dev/null 2>&1; then + echo "Nix is already installed." + nix --version +else + echo "Installing Nix via NixOS community installer..." + NIX_INSTALLER_VERSION="2.33.0" + case "$(uname -s)-$(uname -m)" in + Linux-x86_64) PLATFORM="x86_64-linux" ;; + Linux-aarch64) PLATFORM="aarch64-linux" ;; + Darwin-x86_64) PLATFORM="x86_64-darwin" ;; + Darwin-arm64) PLATFORM="aarch64-darwin" ;; + *) echo "Unsupported platform: $(uname -s)-$(uname -m)"; exit 1 ;; + esac + INSTALLER_URL="https://github.com/NixOS/nix-installer/releases/download/${NIX_INSTALLER_VERSION}/nix-installer-${PLATFORM}" + echo "Platform: ${PLATFORM}" + echo "Downloading from: ${INSTALLER_URL}" + curl --proto '=https' --tlsv1.2 -sSf -L --retry 3 --retry-delay 5 \ + "${INSTALLER_URL}" -o /tmp/nix-installer && chmod +x /tmp/nix-installer + /tmp/nix-installer install --no-confirm \ + --extra-conf "trusted-users = root @admin @wheel" +fi +echo + +# Install direnv +echo "Checking direnv installation..." +if command -v direnv >/dev/null 2>&1; then + echo "direnv is already installed." +else + echo "Installing direnv..." + curl -sfL https://direnv.net/install.sh | bash +fi +echo + +# Verify +echo "Verifying installation..." +echo + +if ! command -v nix >/dev/null 2>&1; then + echo "Nix not found after installation. Start a new shell session and re-run." + exit 1 +fi + +if ! nix flake --help >/dev/null 2>&1; then + echo "Nix flakes not enabled." + exit 1 +fi + +echo "Nix and flakes verified." +echo + +echo "Bootstrap complete." +echo +echo "Next steps:" +echo " 1. Start a new shell session" +echo " 2. Clone the repository" +echo " 3. cd into the project directory" +echo " 4. Run 'nix develop' to enter the development environment" +echo " 5. Run 'make verify' for full environment verification" +echo " 6. Run 'make setup-user' to generate your age key for secrets" +echo " 7. Use 'just ...' to run tasks" +echo +echo "See https://direnv.net/docs/hook.html to set up automatic environment activation." diff --git a/scripts/ci/ci-build-category.sh b/scripts/ci/ci-build-category.sh new file mode 100755 index 0000000..b7d6bbc --- /dev/null +++ b/scripts/ci/ci-build-category.sh @@ -0,0 +1,184 @@ +#!/usr/bin/env bash +set -euo pipefail + +# ============================================================================ +# CI Category Builder +# ============================================================================ +# Build specific categories of flake outputs for GitHub Actions matrix jobs. +# Designed to minimize disk space usage per job by building subsets of outputs. +# +# Usage: +# ci-build-category.sh +# +# Arguments: +# system - Target system (x86_64-linux, aarch64-linux, aarch64-darwin) +# category - Output category to build (lowercase): +# - packages: all packages for system +# - checks: checks only +# - devshells: devshells only (maps to devShells flake attr) +# +# Examples: +# ci-build-category.sh x86_64-linux packages +# ci-build-category.sh x86_64-linux checks +# ci-build-category.sh x86_64-linux devshells +# ============================================================================ + +# ============================================================================ +# Argument parsing +# ============================================================================ + +if [ $# -lt 2 ]; then + echo "usage: $0 " + echo "" + echo "system: x86_64-linux, aarch64-linux, aarch64-darwin" + echo "category: packages, checks, devshells" + exit 1 +fi + +SYSTEM="$1" +CATEGORY="$2" + +# ============================================================================ +# Validation +# ============================================================================ + +case "$SYSTEM" in + x86_64-linux|aarch64-linux|aarch64-darwin) + ;; + *) + echo "error: unsupported system '$SYSTEM'" + echo "supported: x86_64-linux, aarch64-linux, aarch64-darwin" + exit 1 + ;; +esac + +case "$CATEGORY" in + packages|checks|devshells) + ;; + *) + echo "error: unknown category '$CATEGORY'" + echo "valid: packages, checks, devshells" + exit 1 + ;; +esac + +# Map lowercase category arg to the flake attribute name +map_flake_attr() { + case "$1" in + packages) echo "packages" ;; + checks) echo "checks" ;; + devshells) echo "devShells" ;; + esac +} + +FLAKE_ATTR=$(map_flake_attr "$CATEGORY") + +# ============================================================================ +# Helper functions +# ============================================================================ + +print_header() { + local title="$1" + echo "" + echo "---" + echo "$title" + echo "---" +} + +print_step() { + local step="$1" + echo "" + echo "step: $step" +} + +report_disk_usage() { + echo "" + echo "disk usage:" + df -h / | tail -1 +} + +# ============================================================================ +# Generic build function +# ============================================================================ + +build_category() { + local system="$1" + local flake_attr="$2" + local label="$3" + + print_header "building $label for $system" + + print_step "discovering $label" + local attrs + attrs=$(nix eval ".#${flake_attr}.${system}" --apply 'builtins.attrNames' --json 2>/dev/null | jq -r '.[]' || echo "") + + # Exclude multi-arch manifest packages from single-system CI builds. + # Manifests reference packages from other systems and are built by + # the dedicated build-nix-images workflow instead. + if [ "$flake_attr" = "packages" ]; then + attrs=$(echo "$attrs" | grep -v 'Manifest$' || echo "") + fi + + if [ -z "$attrs" ]; then + echo "no $label found for $system" + return 0 + fi + + local count + count=$(echo "$attrs" | wc -l | tr -d ' ') + echo "found $count $label" + + print_step "building $label" + local failed=0 + while read -r attr; do + if [ -n "$attr" ]; then + echo "" + echo "building ${flake_attr}.${system}.${attr}" + if ! nix build ".#${flake_attr}.${system}.${attr}" -L --no-link --accept-flake-config; then + echo "failed to build ${flake_attr}.${system}.${attr}" + failed=$((failed + 1)) + fi + fi + done <<< "$attrs" + + if [ $failed -gt 0 ]; then + echo "" + echo "failed to build $failed $label" + return 1 + fi + + echo "" + echo "successfully built $count $label" +} + +# ============================================================================ +# Main execution +# ============================================================================ + +echo "system: $SYSTEM" +echo "category: $CATEGORY (flake attr: $FLAKE_ATTR)" + +START_TIME=$(date +%s) +echo "start time: $(date)" +report_disk_usage + +build_category "$SYSTEM" "$FLAKE_ATTR" "$CATEGORY" +BUILD_STATUS=$? + +END_TIME=$(date +%s) +DURATION=$((END_TIME - START_TIME)) + +print_header "build summary" +echo "" +echo "category: $CATEGORY" +echo "duration: ${DURATION}s" +report_disk_usage +echo "" + +if [ $BUILD_STATUS -eq 0 ]; then + echo "status: success" + exit 0 +else + echo "status: failed" + exit 1 +fi diff --git a/scripts/preview-version.sh b/scripts/preview-version.sh new file mode 100755 index 0000000..df413bc --- /dev/null +++ b/scripts/preview-version.sh @@ -0,0 +1,223 @@ +#!/usr/bin/env bash +# preview-version.sh - Preview semantic-release version after merging to target branch +# +# Usage: +# ./scripts/preview-version.sh [target-branch] [package-path] +# +# Examples: +# ./scripts/preview-version.sh # Preview root version on main +# ./scripts/preview-version.sh main packages/docs # Preview docs package version on main +# ./scripts/preview-version.sh beta packages/docs # Preview docs version on beta +# +# This script simulates merging the current branch into the target branch and +# runs semantic-release in dry-run mode to preview what version would be released. +# It expects to be invoked inside a nix develop shell (e.g. via `nix develop -c just preview-version`). + +set -euo pipefail + +# Configuration +TARGET_BRANCH="${1:-main}" +PACKAGE_PATH="${2:-}" +CURRENT_BRANCH=$(git branch --show-current) +REPO_ROOT=$(git rev-parse --show-toplevel) +WORKTREE_DIR=$(mktemp -d "${TMPDIR:-/tmp}/semantic-release-preview.XXXXXX") + +# Save original target branch HEAD for restoration +ORIGINAL_TARGET_HEAD="" +ORIGINAL_REMOTE_HEAD="" + +# Colors for output +RED='\033[0;31m' +GREEN='\033[0;32m' +YELLOW='\033[1;33m' +BLUE='\033[0;34m' +NC='\033[0m' # No Color + +# Cleanup function +cleanup() { + local exit_code=$? + + # Always restore target branch to original state if we modified it + if [ -n "$ORIGINAL_TARGET_HEAD" ]; then + echo -e "\n${BLUE}restoring ${TARGET_BRANCH} to original state...${NC}" + git update-ref "refs/heads/$TARGET_BRANCH" "$ORIGINAL_TARGET_HEAD" 2>/dev/null || true + fi + + # Always restore remote-tracking branch to original state if we modified it + if [ -n "$ORIGINAL_REMOTE_HEAD" ]; then + git update-ref "refs/remotes/origin/$TARGET_BRANCH" "$ORIGINAL_REMOTE_HEAD" 2>/dev/null || true + fi + + # Clean up worktree + if [ -d "$WORKTREE_DIR" ]; then + echo -e "${BLUE}cleaning up worktree...${NC}" + git worktree remove --force "$WORKTREE_DIR" 2>/dev/null || true + # Prune any stale worktree references + git worktree prune 2>/dev/null || true + fi + + exit $exit_code +} + +trap cleanup EXIT INT TERM + +# Validation +if [ "$CURRENT_BRANCH" == "$TARGET_BRANCH" ]; then + echo -e "${YELLOW}already on target branch ${TARGET_BRANCH}${NC}" + echo -e "${YELLOW}running test-release instead of preview${NC}\n" + if [ -n "$PACKAGE_PATH" ]; then + cd "$REPO_ROOT/$PACKAGE_PATH" + fi + exec bun run test-release +fi + +# Display what we're doing +echo -e "${BLUE}═══════════════════════════════════════════════════════════════${NC}" +echo -e "${BLUE}semantic-release version preview${NC}" +echo -e "${BLUE}═══════════════════════════════════════════════════════════════${NC}" +echo -e "current branch: ${GREEN}${CURRENT_BRANCH}${NC}" +echo -e "target branch: ${GREEN}${TARGET_BRANCH}${NC}" +if [ -n "$PACKAGE_PATH" ]; then + echo -e "package: ${GREEN}${PACKAGE_PATH}${NC}" +else + echo -e "package: ${GREEN}(root)${NC}" +fi +echo -e "${BLUE}───────────────────────────────────────────────────────────────${NC}\n" + +# Verify target branch exists +if ! git show-ref --verify --quiet "refs/heads/$TARGET_BRANCH"; then + echo -e "${RED}error: target branch '${TARGET_BRANCH}' does not exist${NC}" >&2 + exit 1 +fi + +# Save original target branch HEAD before any modifications +ORIGINAL_TARGET_HEAD=$(git rev-parse "$TARGET_BRANCH") + +# Save original remote-tracking branch HEAD before any modifications +ORIGINAL_REMOTE_HEAD=$(git rev-parse "origin/$TARGET_BRANCH" 2>/dev/null || echo "") + +# Create merge tree to test if merge is possible +echo -e "${BLUE}simulating merge of ${CURRENT_BRANCH} → ${TARGET_BRANCH}...${NC}" + +# Perform merge-tree operation to test if merge is possible +MERGE_OUTPUT=$(git merge-tree --write-tree "$TARGET_BRANCH" "$CURRENT_BRANCH" 2>&1) +MERGE_EXIT=$? + +if [ $MERGE_EXIT -ne 0 ]; then + echo -e "${RED}error: merge conflicts detected${NC}" >&2 + echo -e "${YELLOW}please resolve conflicts in your branch before previewing${NC}" >&2 + echo -e "\n${YELLOW}conflict details:${NC}" >&2 + echo "$MERGE_OUTPUT" >&2 + exit 1 +fi + +# Extract tree hash from merge-tree output (first line) +MERGE_TREE=$(echo "$MERGE_OUTPUT" | head -1) + +if [ -z "$MERGE_TREE" ]; then + echo -e "${RED}error: failed to create merge tree${NC}" >&2 + exit 1 +fi + +# Create temporary merge commit +echo -e "${BLUE}creating temporary merge commit...${NC}" +TEMP_COMMIT=$(git commit-tree -p "$TARGET_BRANCH" -p "$CURRENT_BRANCH" \ + -m "Temporary merge for semantic-release preview" "$MERGE_TREE") + +if [ -z "$TEMP_COMMIT" ]; then + echo -e "${RED}error: failed to create temporary merge commit${NC}" >&2 + exit 1 +fi + +# Temporarily update target branch to point to merge commit +# This allows semantic-release to analyze the correct commit history +# The cleanup function will ALWAYS restore the original branch HEAD +echo -e "${BLUE}temporarily updating ${TARGET_BRANCH} ref for analysis...${NC}" +git update-ref "refs/heads/$TARGET_BRANCH" "$TEMP_COMMIT" + +# Also update remote-tracking branch to match (so semantic-release sees them as synchronized) +git update-ref "refs/remotes/origin/$TARGET_BRANCH" "$TEMP_COMMIT" + +# Create worktree at target branch (now pointing to merge commit) +echo -e "${BLUE}creating temporary worktree at ${TARGET_BRANCH}...${NC}" +git worktree add --quiet "$WORKTREE_DIR" "$TARGET_BRANCH" + +# Navigate to worktree +cd "$WORKTREE_DIR" + +# Install dependencies in worktree +echo -e "${BLUE}installing dependencies in worktree...${NC}" +bun install --silent + +# Navigate to package if specified +if [ -n "$PACKAGE_PATH" ]; then + if [ ! -d "$PACKAGE_PATH" ]; then + echo -e "${RED}error: package path '${PACKAGE_PATH}' does not exist${NC}" >&2 + exit 1 + fi + cd "$PACKAGE_PATH" +fi + +# Run semantic-release in dry-run mode +echo -e "\n${BLUE}running semantic-release analysis...${NC}\n" + +# Capture output and parse version +# Exclude @semantic-release/github to avoid GitHub token requirement for preview +# This is safe because dry-run skips publish/success/fail steps anyway +PLUGINS="@semantic-release/commit-analyzer,@semantic-release/release-notes-generator" + +if [ -n "$PACKAGE_PATH" ]; then + # For monorepo packages, check if package.json has specific plugins configured + OUTPUT=$(GITHUB_REF="refs/heads/$TARGET_BRANCH" bun run semantic-release --dry-run --no-ci --branches "$TARGET_BRANCH" --plugins "$PLUGINS" 2>&1 || true) +else + # For root package + OUTPUT=$(GITHUB_REF="refs/heads/$TARGET_BRANCH" bun run semantic-release --dry-run --no-ci --branches "$TARGET_BRANCH" --plugins "$PLUGINS" 2>&1 || true) +fi + +# Display semantic-release summary (filter out verbose plugin repetition) +echo "$OUTPUT" | grep -v "^$" | grep -vE "(No more plugins|does not provide step)" | \ + grep -E "(semantic-release|Running|analyzing|Found.*commits|release version|Release note|Features|Bug Fixes|Breaking Changes|Published|\*\s)" || true + +echo -e "\n${BLUE}═══════════════════════════════════════════════════════════════${NC}" + +# Extract and display the next version +if echo "$OUTPUT" | grep -q "There are no relevant changes"; then + echo -e "${YELLOW}no version bump required${NC}" + echo -e "no semantic commits found since last release" + if [ -n "${GITHUB_OUTPUT:-}" ]; then + echo "next-version=" >> "$GITHUB_OUTPUT" + echo "release-pending=false" >> "$GITHUB_OUTPUT" + fi +elif echo "$OUTPUT" | grep -q "is not configured to publish from"; then + echo -e "${YELLOW}cannot determine version${NC}" + echo -e "branch ${TARGET_BRANCH} is not in release configuration" + if [ -n "${GITHUB_OUTPUT:-}" ]; then + echo "next-version=" >> "$GITHUB_OUTPUT" + echo "release-pending=false" >> "$GITHUB_OUTPUT" + fi +elif VERSION=$(echo "$OUTPUT" | grep -oP 'next release version is \K[0-9]+\.[0-9]+\.[0-9]+(-[a-z]+\.[0-9]+)?' | head -1); then + echo -e "${GREEN}next version: ${VERSION}${NC}" + + # Extract release type if available + if TYPE=$(echo "$OUTPUT" | grep -oP 'Release type: \K[a-z]+' | head -1); then + echo -e "release type: ${TYPE}" + fi + + if [ -n "${GITHUB_OUTPUT:-}" ]; then + echo "next-version=$VERSION" >> "$GITHUB_OUTPUT" + echo "release-pending=true" >> "$GITHUB_OUTPUT" + fi +else + echo -e "${YELLOW}could not parse version from output${NC}" + echo -e "check the semantic-release output above for details" + if [ -n "${GITHUB_OUTPUT:-}" ]; then + echo "next-version=" >> "$GITHUB_OUTPUT" + echo "release-pending=false" >> "$GITHUB_OUTPUT" + fi +fi + +echo -e "${BLUE}═══════════════════════════════════════════════════════════════${NC}\n" + +# Preview completed successfully - exit 0 regardless of whether a version bump is pending. +# "No version bump required" is a valid outcome, not an error. +exit 0 diff --git a/scripts/sops-bootstrap.sh b/scripts/sops-bootstrap.sh new file mode 100755 index 0000000..fd05494 --- /dev/null +++ b/scripts/sops-bootstrap.sh @@ -0,0 +1,211 @@ +#!/usr/bin/env bash +set -euo pipefail + +ROLE="${1:-dev}" # 'dev' or 'ci' +METHOD="${2:-ssh}" # 'ssh' or 'age' + +echo "🔐 SOPS Key Bootstrap/Rotation" +echo " Role: $ROLE" +echo " Method: $METHOD" +echo + +# Verify .sops.yaml exists +if [ ! -f .sops.yaml ]; then + echo "❌ .sops.yaml not found. Cannot proceed." + exit 1 +fi + +# Check if this is rotation (key already exists) or bootstrap (placeholder) +CURRENT_KEY=$(grep "^ - &${ROLE} " .sops.yaml | awk '{print $3}') + +# Placeholder keys indicate this is a fresh bootstrap +# gitleaks:allow - age public keys used as placeholders +if [ "$CURRENT_KEY" = "age1dn8w7y4t4h23fmeenr3dghfz5qh53jcjq9qfv26km3mnv8l44g0sghptu3" ] || \ + [ "$CURRENT_KEY" = "age1m9m8h5vqr7dqlmvnzcwshmm4uk8umcllazum6eaulkdp3qc88ugs22j3p8" ]; then + IS_ROTATION=false + echo "🆕 Placeholder key detected - this is BOOTSTRAP" +else + IS_ROTATION=true + echo "🔄 Real key detected - this is a ROTATION" +fi + +# Generate new key +if [ "$METHOD" = "ssh" ]; then + echo "🔑 Generating SSH key pair..." + KEY_FILE=$(mktemp) + trap "rm -f $KEY_FILE ${KEY_FILE}.pub" EXIT + + ssh-keygen -t ed25519 -f "$KEY_FILE" -N "" -C "${ROLE}@omicsio" + PUBLIC_KEY=$(ssh-to-age < "${KEY_FILE}.pub") + PRIVATE_KEY=$(cat "$KEY_FILE") + PRIVATE_AGE_KEY=$(ssh-to-age -private-key -i "$KEY_FILE") + + echo " SSH public key: $(cat ${KEY_FILE}.pub)" + echo " Age public key: $PUBLIC_KEY" +else + echo "🔑 Generating age key pair..." + KEY_FILE=$(mktemp) + rm -f "$KEY_FILE" # age-keygen expects to create the file itself + trap "rm -f $KEY_FILE" EXIT + + age-keygen -o "$KEY_FILE" 2>&1 | tee /tmp/keygen-output.txt + PUBLIC_KEY=$(grep -i "public key:" /tmp/keygen-output.txt | cut -d: -f2 | xargs) + PRIVATE_KEY=$(cat "$KEY_FILE") + rm -f /tmp/keygen-output.txt +fi + +echo +echo "📋 Generated key:" +echo " Public: $PUBLIC_KEY" +echo + +# Check if key already exists in .sops.yaml +if grep -q "$PUBLIC_KEY" .sops.yaml; then + echo "⚠️ This public key already exists in .sops.yaml" + exit 1 +fi + +# Update .sops.yaml based on rotation or bootstrap +cp .sops.yaml .sops.yaml.backup + +if [ "$IS_ROTATION" = true ]; then + echo "📝 Adding new key as ${ROLE}-next for rotation..." + + # Add new key anchor after current key + sed -i.tmp "/^ - &${ROLE} /a\\ + - \&${ROLE}-next ${PUBLIC_KEY}" .sops.yaml + + # Add to creation_rules (both yaml and json) + sed -i.tmp "/- \*${ROLE}$/a\\ + - \*${ROLE}-next" .sops.yaml + + rm .sops.yaml.tmp + echo "✅ Added ${ROLE}-next to .sops.yaml" +else + echo "📝 Replacing ${ROLE} key in .sops.yaml..." + sed -i.tmp "s|^ - \&${ROLE} .*| - \&${ROLE} ${PUBLIC_KEY}|" .sops.yaml + rm .sops.yaml.tmp + echo "✅ Updated ${ROLE} key in .sops.yaml" +fi + +# Create or update encrypted files +if [ ! -f vars/shared.yaml ]; then + echo + echo "📝 Creating vars/shared.yaml template..." + mkdir -p vars + cat > /tmp/shared-template.yaml << 'EOF' +CACHIX_AUTH_TOKEN: REPLACE_ME +CACHIX_CACHE_NAME: REPLACE_ME +GITGUARDIAN_API_KEY: REPLACE_ME +CLOUDFLARE_API_TOKEN: REPLACE_ME +CLOUDFLARE_ACCOUNT_ID: REPLACE_ME +CI_AGE_KEY: REPLACE_ME +EOF + + # For bootstrap, we can encrypt immediately + if [ "$ROLE" = "dev" ]; then + # Move template to vars/ first so path regex matches + mv /tmp/shared-template.yaml vars/shared-template.yaml + + # Create temporary .sops.yaml with only dev key to avoid encrypting for placeholder CI key + cat > /tmp/sops-bootstrap.yaml << SOPSEOF +keys: + - &dev ${PUBLIC_KEY} + +creation_rules: + - path_regex: vars/.*\.yaml$ + key_groups: + - age: + - *dev +SOPSEOF + + echo "$PRIVATE_KEY" > /tmp/bootstrap-key.txt + SOPS_AGE_KEY_FILE=/tmp/bootstrap-key.txt sops --config /tmp/sops-bootstrap.yaml -e vars/shared-template.yaml > vars/shared.yaml + rm /tmp/bootstrap-key.txt /tmp/sops-bootstrap.yaml vars/shared-template.yaml + echo "✅ Created vars/shared.yaml (edit with: just edit-secrets)" + echo " Note: After generating CI key, run 'just updatekeys' to add it" + else + echo "⚠️ Cannot encrypt without dev key. Create dev key first." + echo " Unencrypted template at: /tmp/shared-template.yaml" + echo " Run: just sops-bootstrap dev" + rm -f /tmp/shared-template.yaml + fi +else + echo + echo "🔄 Updating keys for existing encrypted files..." + just updatekeys + echo "✅ Keys updated" +fi + +# Display private key and next steps +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "🔐 SAVE THIS PRIVATE KEY SECURELY!" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +if [ "$METHOD" = "ssh" ]; then + echo + echo "SSH Private Key:" + echo "$PRIVATE_KEY" + echo + echo "Age Private Key (for SOPS):" + echo "$PRIVATE_AGE_KEY" +else + echo + echo "Age Private Key:" + echo "$PRIVATE_KEY" +fi + +echo +echo "Public Key (safe to share):" +echo "$PUBLIC_KEY" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo + +# Role-specific instructions +if [ "$ROLE" = "dev" ]; then + echo "📥 To install this dev key locally:" + echo + echo " Option 1: Use sops-add-key recipe (interactive)" + echo " just sops-add-key" + echo + echo " Option 2: Manual installation" + echo " mkdir -p ~/.config/sops/age" + echo " cat >> ~/.config/sops/age/keys.txt << KEYEOF" + echo " # omicsio dev key" + echo " # public key: ${PUBLIC_KEY}" + echo " ${PRIVATE_KEY}" + echo " KEYEOF" + echo + echo " Then test: just show-secrets" +elif [ "$ROLE" = "ci" ]; then + echo "📤 To use this CI key:" + echo + echo " 1. Save private key to Bitwarden (for backup/recovery)" + echo + echo " 2. Add to vars/shared.yaml as CI_AGE_KEY:" + echo " just edit-secrets" + echo " # Add line: CI_AGE_KEY: ${PRIVATE_KEY}" + echo + echo " 3. Upload to GitHub secrets:" + echo " just sops-upload-github-key" + echo " # Paste the private key when prompted" +fi + +echo +echo "📋 Next steps:" +if [ "$IS_ROTATION" = true ]; then + echo " 1. Install/upload the new key (see instructions above)" + echo " 2. Test decryption works: just show-secrets" + echo " 3. Test CI workflow: just gh-ci-run" + echo " 4. After verification, remove old key: just sops-finalize-rotation ${ROLE}" +else + echo " 1. Install/upload the key (see instructions above)" + echo " 2. If bootstrapping dev key, generate CI key: just sops-bootstrap ci" + echo " 3. Edit secrets: just edit-secrets" + echo " 4. Check requirements: just sops-check-requirements" + echo " 5. Upload to GitHub: just sops-setup-github" +fi + +echo +echo "💾 Backup saved: .sops.yaml.backup" diff --git a/scripts/sops-check-requirements.sh b/scripts/sops-check-requirements.sh new file mode 100755 index 0000000..fdf10da --- /dev/null +++ b/scripts/sops-check-requirements.sh @@ -0,0 +1,111 @@ +#!/usr/bin/env bash +set -euo pipefail + +echo "🔍 Analyzing required secrets for GitHub workflows" +echo + +# Find all secrets and vars referenced in workflows +if [ ! -d .github/workflows ]; then + echo "❌ .github/workflows not found" + exit 1 +fi + +WORKFLOW_SECRETS=$(grep -rh '\${{ secrets\.' .github/workflows/*.yaml 2>/dev/null | \ + grep -oP 'secrets\.\K[A-Z_]+' | sort -u || true) + +WORKFLOW_VARS=$(grep -rh '\${{ vars\.' .github/workflows/*.yaml 2>/dev/null | \ + grep -oP 'vars\.\K[A-Z_]+' | sort -u || true) + +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "📋 REQUIRED GITHUB SECRETS (set via gh secret set)" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +for secret in $WORKFLOW_SECRETS; do + if [ "$secret" = "GITHUB_TOKEN" ]; then + echo " ✓ $secret (automatic, provided by GitHub)" + elif [ "$secret" = "SOPS_AGE_KEY" ]; then + echo " ! $secret (CI age key - upload with: just sops-upload-github-key)" + else + echo " → $secret (can be in vars/shared.yaml and uploaded via just ghsecrets)" + fi +done + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "📋 REQUIRED GITHUB VARIABLES (set via gh variable set)" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +if [ -z "$WORKFLOW_VARS" ]; then + echo " (none found)" +else + for var in $WORKFLOW_VARS; do + echo " → $var (upload with: just ghvars)" + done +fi + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "🔐 SOPS-MANAGED SECRETS (in vars/shared.yaml)" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +if [ ! -f vars/shared.yaml ]; then + echo " ❌ vars/shared.yaml not found" + echo " Run: just sops-bootstrap dev" +else + # Try to decrypt and check contents + if ! SOPS_SECRETS=$(sops -d vars/shared.yaml 2>/dev/null); then + echo " ❌ Cannot decrypt vars/shared.yaml" + echo " Ensure you have the dev key installed: just sops-add-key" + else + # Check each secret + SECRET_KEYS=$(echo "$SOPS_SECRETS" | grep -E '^[A-Z_]+:' | cut -d: -f1 || true) + + for key in $SECRET_KEYS; do + VALUE=$(echo "$SOPS_SECRETS" | grep "^$key:" | cut -d: -f2- | xargs) + if [ "$VALUE" = "REPLACE_ME" ] || [ -z "$VALUE" ]; then + echo " ❌ $key (NOT SET - edit with: just edit-secrets)" + else + # Show first/last few chars for verification + DISPLAY="${VALUE:0:4}...${VALUE: -4}" + echo " ✓ $key ($DISPLAY)" + fi + done + + # Check for missing secrets that workflows need + echo + echo " Missing from vars/shared.yaml but found in workflows:" + FOUND_MISSING=false + for secret in $WORKFLOW_SECRETS; do + if [ "$secret" != "GITHUB_TOKEN" ] && [ "$secret" != "SOPS_AGE_KEY" ]; then + if ! echo "$SECRET_KEYS" | grep -q "^$secret$"; then + echo " ❌ $secret" + FOUND_MISSING=true + fi + fi + done + if [ "$FOUND_MISSING" = false ]; then + echo " ✓ All workflow secrets present in vars/shared.yaml" + fi + fi +fi + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "💡 NEXT STEPS" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo +echo "1. Ensure dev key is installed:" +echo " just sops-add-key" +echo +echo "2. Edit secrets to add missing values:" +echo " just edit-secrets" +echo +echo "3. Upload SOPS_AGE_KEY to GitHub:" +echo " just sops-upload-github-key" +echo +echo "4. Upload other secrets and variables to GitHub:" +echo " just sops-setup-github" +echo +echo "5. Verify GitHub secrets are set:" +echo " gh secret list" +echo " gh variable list" diff --git a/scripts/sops-finalize-rotation.sh b/scripts/sops-finalize-rotation.sh new file mode 100755 index 0000000..0e59e4b --- /dev/null +++ b/scripts/sops-finalize-rotation.sh @@ -0,0 +1,62 @@ +#!/usr/bin/env bash +set -euo pipefail + +ROLE="${1:-dev}" + +echo "🧹 Finalize SOPS key rotation for role: $ROLE" +echo +echo "This will:" +echo " 1. Remove old ${ROLE} key from .sops.yaml" +echo " 2. Rename ${ROLE}-next to ${ROLE}" +echo " 3. Update all encrypted files" +echo +echo "⚠️ Only proceed if you have verified the new key works!" +echo +read -p "Continue? (y/N) " -n 1 -r +echo +if [[ ! $REPLY =~ ^[Yy]$ ]]; then + exit 0 +fi + +# Check if -next key exists +if ! grep -q "\&${ROLE}-next" .sops.yaml; then + echo "❌ No ${ROLE}-next key found in .sops.yaml" + echo " Nothing to finalize. Run rotation first: just sops-bootstrap $ROLE" + exit 1 +fi + +# Backup +cp .sops.yaml .sops.yaml.pre-finalize + +# Get old and new keys +OLD_KEY=$(grep "^ - &${ROLE} " .sops.yaml | awk '{print $3}') +NEW_KEY=$(grep "^ - &${ROLE}-next " .sops.yaml | awk '{print $3}') + +echo "Old ${ROLE} key: $OLD_KEY" +echo "New ${ROLE} key: $NEW_KEY" +echo + +# Remove old key line +sed -i.tmp "/^ - &${ROLE} ${OLD_KEY}/d" .sops.yaml + +# Rename anchor definition, delete reference lines (original *dev now points to new key) +sed -i.tmp "s/&${ROLE}-next/\&${ROLE}/g" .sops.yaml +sed -i.tmp "/- \*${ROLE}-next/d" .sops.yaml + +rm .sops.yaml.tmp + +echo "📝 Updated .sops.yaml" +echo +echo "🔄 Updating encrypted files to remove old key..." +just updatekeys + +echo +echo "✅ Rotation finalized!" +echo " Old key: $OLD_KEY (REMOVED)" +echo " New key: $NEW_KEY (now $ROLE)" +echo +echo "💾 Backup saved: .sops.yaml.pre-finalize" +echo +echo "⚠️ Update Bitwarden/key storage:" +echo " - Mark old $ROLE key as 'revoked' or delete" +echo " - Ensure new key is saved" diff --git a/scripts/sops-rotate.sh b/scripts/sops-rotate.sh new file mode 100755 index 0000000..351ebfb --- /dev/null +++ b/scripts/sops-rotate.sh @@ -0,0 +1,30 @@ +#!/usr/bin/env bash +set -euo pipefail + +ROLE="${1:-dev}" +METHOD="${2:-ssh}" # 'ssh' or 'age' + +echo "🔄 Quick rotation workflow for $ROLE key (method: $METHOD)" +echo +echo "Step 1/3: Bootstrap new key..." +scripts/sops-bootstrap.sh "$ROLE" "$METHOD" +echo +read -p "Install/upload the new key, then press Enter to continue..." _ +echo +echo "Step 2/3: Verify new key works..." +echo "Testing decryption..." +if just show-secrets > /dev/null 2>&1; then + echo "✅ Decryption works!" +else + echo "❌ Decryption failed. Fix the issue before finalizing." + exit 1 +fi +echo +read -p "Step 3/3: Finalize rotation? This removes the old key. (y/N) " -n 1 -r +echo +if [[ $REPLY =~ ^[Yy]$ ]]; then + scripts/sops-finalize-rotation.sh "$ROLE" +else + echo "Rotation not finalized. Run manually when ready:" + echo " just sops-finalize-rotation $ROLE" +fi diff --git a/scripts/sops-setup-github.sh b/scripts/sops-setup-github.sh new file mode 100755 index 0000000..15176ee --- /dev/null +++ b/scripts/sops-setup-github.sh @@ -0,0 +1,101 @@ +#!/usr/bin/env bash +set -euo pipefail + +REPO="${1:-}" +if [ -z "$REPO" ]; then + REPO="${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}" +fi + +echo "🚀 Comprehensive GitHub Secrets & Variables Setup" +echo " Repository: $REPO" +echo +echo "This will:" +echo " 1. Upload GitHub variables (from environment or vars/shared.yaml)" +echo " 2. Upload GitHub secrets (from vars/shared.yaml)" +echo " 3. Skip SOPS_AGE_KEY (use sops-upload-github-key separately)" +echo +read -p "Continue? (y/N) " -n 1 -r +echo +if [[ ! $REPLY =~ ^[Yy]$ ]]; then + exit 0 +fi + +# Check if SOPS_AGE_KEY is set +echo "Checking SOPS_AGE_KEY status..." +if gh secret list --repo="$REPO" 2>/dev/null | grep -q "SOPS_AGE_KEY"; then + echo "✅ SOPS_AGE_KEY already set in GitHub" +else + echo "⚠️ SOPS_AGE_KEY not set in GitHub" + echo " This is required for CI to decrypt secrets." + echo + read -p "Upload SOPS_AGE_KEY now? (y/N) " -n 1 -r + echo + if [[ $REPLY =~ ^[Yy]$ ]]; then + scripts/sops-upload-github-key.sh "$REPO" + else + echo " Skipping SOPS_AGE_KEY upload." + echo " Run later: just sops-upload-github-key" + fi +fi + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "📤 Uploading GitHub variables..." +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +just ghvars "$REPO" + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "📤 Uploading GitHub secrets (except SOPS_AGE_KEY)..." +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" + +# Upload secrets from vars/shared.yaml +sops exec-env vars/shared.yaml " + set -euo pipefail + + if [ -n \"\${CACHIX_AUTH_TOKEN:-}\" ] && [ \"\$CACHIX_AUTH_TOKEN\" != \"REPLACE_ME\" ]; then + gh secret set CACHIX_AUTH_TOKEN --repo='$REPO' --body=\"\$CACHIX_AUTH_TOKEN\" + echo ' ✅ CACHIX_AUTH_TOKEN' + fi + + if [ -n \"\${GITGUARDIAN_API_KEY:-}\" ] && [ \"\$GITGUARDIAN_API_KEY\" != \"REPLACE_ME\" ]; then + gh secret set GITGUARDIAN_API_KEY --repo='$REPO' --body=\"\$GITGUARDIAN_API_KEY\" + echo ' ✅ GITGUARDIAN_API_KEY' + fi + + if [ -n \"\${CLOUDFLARE_API_TOKEN:-}\" ] && [ \"\$CLOUDFLARE_API_TOKEN\" != \"REPLACE_ME\" ]; then + gh secret set CLOUDFLARE_API_TOKEN --repo='$REPO' --body=\"\$CLOUDFLARE_API_TOKEN\" + echo ' ✅ CLOUDFLARE_API_TOKEN' + fi + + if [ -n \"\${CLOUDFLARE_ACCOUNT_ID:-}\" ] && [ \"\$CLOUDFLARE_ACCOUNT_ID\" != \"REPLACE_ME\" ]; then + gh secret set CLOUDFLARE_ACCOUNT_ID --repo='$REPO' --body=\"\$CLOUDFLARE_ACCOUNT_ID\" + echo ' ✅ CLOUDFLARE_ACCOUNT_ID' + fi + + if [ -n \"\${FLAKE_UPDATER_APP_ID:-}\" ] && [ \"\$FLAKE_UPDATER_APP_ID\" != \"REPLACE_ME\" ]; then + gh secret set FLAKE_UPDATER_APP_ID --repo='$REPO' --body=\"\$FLAKE_UPDATER_APP_ID\" + echo ' ✅ FLAKE_UPDATER_APP_ID' + fi + + if [ -n \"\${FLAKE_UPDATER_PRIVATE_KEY:-}\" ] && [ \"\$FLAKE_UPDATER_PRIVATE_KEY\" != \"REPLACE_ME\" ]; then + gh secret set FLAKE_UPDATER_PRIVATE_KEY --repo='$REPO' --body=\"\$FLAKE_UPDATER_PRIVATE_KEY\" + echo ' ✅ FLAKE_UPDATER_PRIVATE_KEY' + fi + + echo + echo ' ℹ️ SOPS_AGE_KEY skipped (upload separately with: just sops-upload-github-key)' +" + +echo +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo "✅ GitHub setup complete!" +echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" +echo +echo "Verification:" +echo " gh secret list --repo=$REPO" +echo " gh variable list --repo=$REPO" +echo +echo "Test CI:" +echo " just gh-ci-run" diff --git a/scripts/sops-upload-github-key.sh b/scripts/sops-upload-github-key.sh new file mode 100755 index 0000000..0f3a00c --- /dev/null +++ b/scripts/sops-upload-github-key.sh @@ -0,0 +1,59 @@ +#!/usr/bin/env bash +set -euo pipefail + +REPO="${1:-}" +if [ -z "$REPO" ]; then + REPO="${GITHUB_REPOSITORY:-$(gh repo view --json nameWithOwner -q .nameWithOwner)}" +fi + +echo "🔐 Upload SOPS_AGE_KEY to GitHub Secrets" +echo " Repository: $REPO" +echo +echo "This uploads the CI age private key so GitHub Actions can decrypt secrets." +echo +echo "You have two options:" +echo " 1. Paste the CI_AGE_KEY from Bitwarden (recommended for rotation)" +echo " 2. Extract from vars/shared.yaml (requires dev key to decrypt)" +echo +printf "Choose option (1/2): " +read -r OPTION + +if [ "$OPTION" = "1" ]; then + echo + echo "Paste the AGE-SECRET-KEY (input will be hidden):" + read -rs PRIVATE_KEY + echo + + if [[ ! "$PRIVATE_KEY" =~ ^AGE-SECRET-KEY- ]]; then + echo "❌ Invalid age private key format (must start with AGE-SECRET-KEY-)" + exit 1 + fi +elif [ "$OPTION" = "2" ]; then + if [ ! -f vars/shared.yaml ]; then + echo "❌ vars/shared.yaml not found" + exit 1 + fi + + echo "Extracting CI_AGE_KEY from vars/shared.yaml..." + PRIVATE_KEY=$(sops -d vars/shared.yaml | grep "^CI_AGE_KEY:" | cut -d: -f2- | xargs) + + if [ -z "$PRIVATE_KEY" ] || [ "$PRIVATE_KEY" = "REPLACE_ME" ]; then + echo "❌ CI_AGE_KEY not set in vars/shared.yaml" + echo " Run: just edit-secrets" + exit 1 + fi +else + echo "❌ Invalid option" + exit 1 +fi + +echo "Uploading to GitHub..." +echo "$PRIVATE_KEY" | gh secret set SOPS_AGE_KEY --repo="$REPO" + +echo "✅ SOPS_AGE_KEY uploaded successfully" +echo +echo "Verify with:" +echo " gh secret list --repo=$REPO | grep SOPS_AGE_KEY" +echo +echo "Test with:" +echo " just gh-ci-run --debug=true" diff --git a/vars/dvc-sa.json b/vars/dvc-sa.json new file mode 100644 index 0000000..47b15cc --- /dev/null +++ b/vars/dvc-sa.json @@ -0,0 +1,29 @@ +{ + "type": "ENC[AES256_GCM,data:uZJjwwm9GV4v4W7mv7ES,iv:J7by8JERK5RNVS7p37YHMx/991N9Wrd90PJEquFiSnM=,tag:HFc7skNPgadgf78HaLBsdQ==,type:str]", + "project_id": "ENC[AES256_GCM,data:f3T5vy19RlV3ACpyzw==,iv:6ctCRIsCmL46gWFFzC+zACd1HG+VIPWMJ7AP6Voc0/Q=,tag:VvGjKwfHOZzMtxga+boc6A==,type:str]", + "private_key_id": "ENC[AES256_GCM,data:44Ktjg22AsbCmRDIXmZIw4YE/7fnhDnWTYX05LTXSy7aOBFkQAvRAw==,iv:1jviobyXHEBO/xN8wAqoig2LTIaMsXZtF7R6nlGBGqo=,tag:dubCKsiWb5OwMTAs66obRw==,type:str]", + "private_key": "ENC[AES256_GCM,data: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,iv:fkW+O3bx0NhJ+Mghy+W8Hz8ymJAmnUoiAeyLilDZDfQ=,tag:h5S3W34EVehuPcoxQcPYyA==,type:str]", + "client_email": "ENC[AES256_GCM,data:M9GQbfZRjHAWh3ib+W7fTAdqIvtTyPLjHtCdh608H4nhUjywIelprvVgtzM=,iv:s+qaj2RNcfD0s9CLa7Z0r6J1sqQL0W21yBIrJF6dLPk=,tag:DxcvosS0TeZQ3Kx79mAWgA==,type:str]", + "client_id": "ENC[AES256_GCM,data:IBDt7lxXTNGYioG760VlDuaNv7mj,iv:qg1ooIslKx9Ah0e1amY2dfxSkqZ8Kd65Nvl0f7YEQX4=,tag:XnVl3ZfrMbzbyNVLVmVvug==,type:str]", + "auth_uri": "ENC[AES256_GCM,data:vKl6nsRNFyZyujlmfG3QbSK4MPG9iZiyJi2MvAtaG2Qb5QWqyupgJmg=,iv:P+6eeS4EPMeWwg14nl/0cm+nHjPzY7++l/QN8oWtnJc=,tag:lH3lV9Nh37GOf5UsMEiP9A==,type:str]", + "token_uri": "ENC[AES256_GCM,data:d/J5gtqwBnyup8Eec8Gkv7vX/deVTvauuhhv+mrC7u64uOo=,iv:O+1kgGHIhtvPrpQVxy/OYInUdr7RctreJY3I430vS9U=,tag:k15q0odLmvq1VOvWjPhyOA==,type:str]", + "auth_provider_x509_cert_url": "ENC[AES256_GCM,data:q4bWtmloWNfwh5WmLAdx62Sm70/wGHgXI9sPqR59OuoQkX01vY+hiewD,iv:a6voMAFePo6l7J++P3/GdE1hPiHgOOKey6OxvPCbD94=,tag:r8ioLqKu/HVFlYyQ9P+Tew==,type:str]", + "client_x509_cert_url": "ENC[AES256_GCM,data:42Xc2tqPkDT3RsLb/NG/JtcD9s+qTF/v3un9RGZH+TmrEyVkp4lkNupri8HVODaVv4n8ztfzfrNFPwv5TyjMlf48WL1Nupgy69BTt6zQfBoR/++9gIVbw+eaq+wfRC7r,iv:WHI1a5vOAI4cj4M6ikB4JWJWDBR+75ZAeKeEWugxZLw=,tag:n3GkfY9o0m8TdXcZXBVtDA==,type:str]", + "universe_domain": "ENC[AES256_GCM,data:GVTf1uIGHWbr29/TEYc=,iv:ehZg0XjQ7wLj+sL0vlOwjzcvre9Y+T1zCRIOBK56rdg=,tag:sKT1FXe310x6zEKMGxqWwQ==,type:str]", + "sops": { + "age": [ + { + "recipient": "age1dn8w7y4t4h23fmeenr3dghfz5qh53jcjq9qfv26km3mnv8l44g0sghptu3", + "enc": "-----BEGIN AGE ENCRYPTED FILE-----\nYWdlLWVuY3J5cHRpb24ub3JnL3YxCi0+IFgyNTUxOSBuZ3VhaXBsNHNmd2hvaG0r\nSXJwb3NENVAwNzJCc280c3dZVnJOOFB2MEJJCkxOcjh1czE2VWRsNGNPU3VvUWp3\nYXJWK0gvU3kyV01VbExlRmx1dlRVMWcKLS0tIGxvUm00UjJoODd2UDRzc2pFS1Fu\nNGRPRGo3M1d2MVR4RW1BMGJRZWxFNkUK2uz/EyhK9aFCb53oEJckT/cZDL8WfvIo\n//2DbBQSWxk4bz5f37U3j8UkhmYc6g5as3tjUwtj2dYTU8X3F/NyZg==\n-----END AGE ENCRYPTED FILE-----\n" + }, + { + "recipient": "age1m9m8h5vqr7dqlmvnzcwshmm4uk8umcllazum6eaulkdp3qc88ugs22j3p8", + "enc": "-----BEGIN AGE ENCRYPTED FILE-----\nYWdlLWVuY3J5cHRpb24ub3JnL3YxCi0+IFgyNTUxOSBUSG15OWs4eHphS1lkem1i\nSGxwZE9QRWVXVXVCbWhmY0pGY21OMEhwWjEwCjlldVlBUWMvNDhoai9RQlV0Smtl\nelFKZUF6c1IrMEV6OHNiMTZNZVNKRUkKLS0tIGlseVFWcjRPYnk5MThneTVXYU5n\nZm1XTTFGOUpHKzRUN1o1b2R4M0lyOGcKOZ0d/M8Rg0S1GPzUFhQe5XbLV8RDQ043\nf+wOUHT1LU5xXrsraCv/XEM8civNpOv9QCMxswlThllrwmtX2XN0Iw==\n-----END AGE ENCRYPTED FILE-----\n" + } + ], + "lastmodified": "2025-09-15T21:19:42Z", + "mac": "ENC[AES256_GCM,data:3BSMlii/PGXKgVblPif+2gUPZYkvHAzGWidJO+5lHbPKBra2yuOybA5FWyGupaHna5SpdIB1NwZsqRhg6R7kM2+G2Xu6E/TW9exeRIIGFVqHPhlDYnn2qdHBPqpCxkJOH1/J8HsGexpDjantHes5XWOlN8BZ+o94p44o+pvcjaM=,iv:9Mrg5MF2e4MEWN/9pkf8FEv/1FO7O5g9nzoRybXs0cY=,tag:AXwyVZgIa3DzMd/fh7D4KA==,type:str]", + "unencrypted_suffix": "_unencrypted", + "version": "3.10.2" + } +} diff --git a/vars/shared.yaml b/vars/shared.yaml new file mode 100644 index 0000000..b51cbc1 --- /dev/null +++ b/vars/shared.yaml @@ -0,0 +1,36 @@ +CACHIX_AUTH_TOKEN: ENC[AES256_GCM,data:s6AfM6VDke4dgAOr0vkP7/3l3vGQu8px+EckmxrQ0Tl8EAMtLSJ+PHKZH74YxpL+6GoJnwFCGg8cOWLosVGW1t7pY/TgM5LjXMmt7GYTLP3bo21QxqvzeTdV1tjZbYkWEzFUVmB3Lt0wt0DFDCxLLwQyGXnc1u5w3OAVlekbXp4Ox8khjP2Oj57NBg/5AStn3Q==,iv:UeVazb+evLGDvEAISReJc4N7tckFD44+cNmhvwcxtYI=,tag:VouZ1nosY9v/PvcX8JEryg==,type:str] +CACHIX_CACHE_NAME: ENC[AES256_GCM,data:BZOqquT+,iv:zpyN2K5Xw3zgGgDwUaFXScrWzExPdxGCE+6wAVbP1Y8=,tag:Oa9XkFXr20rMcJA4X0aHuw==,type:str] +CODECOV_TOKEN: ENC[AES256_GCM,data:vkQYxG3jkUymvSOrR8sYw2JlHZ592y8/Corux+226Ic15khy,iv:a3CP27baGaIIeGWlmPrclLseHXCXNxhTQZhrJk2M/us=,tag:2MQLJXJGnKBzq83wk8TvWA==,type:str] +FAST_FORWARD_PAT: ENC[AES256_GCM,data:YhOrdG5H/tez+iYoH9tOp6Tb1sVxqoxhfC+06MeoM7aZrQeIhDd6Mw==,iv:xMAhNJMvOzGCvUcSmKL5+4bC9CwWeccsKETbFNxRFkM=,tag:oEUY8zlsRbH4rqF0AGBVUA==,type:str] +GITGUARDIAN_API_KEY: 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lastmodified: "2026-02-12T20:13:42Z" + mac: ENC[AES256_GCM,data:g46k2sIzsvsBeMJmy67KOuGc21xDGnn7OjIG7PhR3raIz9oENAscn7XoWUCyHOgcbSZFVL+Ak9kHI8MCeOtz/iqx7A97KlHb74lw+1Gc5CelRKPC9j9itWaWGHHDGHDOzzZQguJn7vD6TaZCX2pX/y01WqKEzwy5HHu9HDB2iLI=,iv:pUdAaNnS2okhV4/USxU2k+3mJkrA9gSk2fnphlcH2z4=,tag:ceSLzV5YbguH4yD0tV7muQ==,type:str] + unencrypted_suffix: _unencrypted + version: 3.11.0 diff --git a/wrangler.jsonc b/wrangler.jsonc new file mode 100644 index 0000000..3616d67 --- /dev/null +++ b/wrangler.jsonc @@ -0,0 +1,22 @@ +{ + "$schema": "node_modules/wrangler/config-schema.json", + "name": "omicsio", + "compatibility_date": "2025-09-09", + "assets": { + "directory": "docs/_site" + }, + "observability": { + "enabled": true + }, + "dev": { + "port": 8787 + }, + "workers_dev": false, + "preview_urls": true, + "routes": [ + { + "pattern": "omicsio.scientistexperience.net", + "custom_domain": true + } + ] +} From 63dc98d82a87ed8a10061ca75a19f8811fce8afc Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:39:15 -0500 Subject: [PATCH 02/17] fix(github): correct repo name in issue template URLs --- .github/ISSUE_TEMPLATE/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index e29c1c2..2ad6a0f 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,4 +1,4 @@ contact_links: - name: questions - url: https://github.com/sciexp/omicsio/discussions - about: please post and host discussion in https://github.com/sciexp/omicsio/discussions + url: https://github.com/sciexp/data/discussions + about: please post and host discussion in https://github.com/sciexp/data/discussions From 44fe5fcff9ef0b2cfaf2a6b3d2bffcfe97d7c6e0 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:39:28 -0500 Subject: [PATCH 03/17] fix(justfile): correct repo name in ghvars and ghsecrets recipes --- justfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/justfile b/justfile index 9c6facd..b6c3aa3 100644 --- a/justfile +++ b/justfile @@ -38,7 +38,7 @@ gcloud-context: # Update github vars for repo from environment variables [group('CI/CD')] -ghvars repo="sciexp/omicsio": +ghvars repo="sciexp/data": @echo "vars before updates:" @echo PAGER=cat gh variable list --repo={{ repo }} @@ -53,7 +53,7 @@ ghvars repo="sciexp/omicsio": # Update github secrets for repo from environment variables [group('CI/CD')] -ghsecrets repo="sciexp/omicsio": +ghsecrets repo="sciexp/data": @echo "secrets before updates:" @echo PAGER=cat gh secret list --repo={{ repo }} From a918672b3799898698c51534176740f8a560869b Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:39:44 -0500 Subject: [PATCH 04/17] fix: correct repo name and package scope in root package.json --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 3de1252..9279459 100644 --- a/package.json +++ b/package.json @@ -1,11 +1,11 @@ { - "name": "omicsio", + "name": "@sciexp/data", "version": "0.0.0-development", "private": true, "description": "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns", "repository": { "type": "git", - "url": "https://github.com/sciexp/omicsio.git" + "url": "https://github.com/sciexp/data.git" }, "license": "MIT", "engines": { From 61a57fcd7333523b8ddd6191908141a250220161 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:39:56 -0500 Subject: [PATCH 05/17] fix: correct repo URL in omicsio package.json --- packages/omicsio/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/omicsio/package.json b/packages/omicsio/package.json index 8689b4e..855b74c 100644 --- a/packages/omicsio/package.json +++ b/packages/omicsio/package.json @@ -82,7 +82,7 @@ }, "repository": { "type": "git", - "url": "https://github.com/sciexp/omicsio.git" + "url": "https://github.com/sciexp/data.git" }, "scripts": { "test-release": "semantic-release --dry-run --no-ci" From 0975f6a3d7ca948baa8bdda1f5b2dfc4b00f7d15 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:40:08 -0500 Subject: [PATCH 06/17] fix(scripts): correct repo name in bootstrap URL and banner --- scripts/bootstrap.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/bootstrap.sh b/scripts/bootstrap.sh index 6b503be..1838995 100755 --- a/scripts/bootstrap.sh +++ b/scripts/bootstrap.sh @@ -1,14 +1,14 @@ #!/usr/bin/env bash # Self-contained bootstrap script for omicsio. # Intended for curl one-liner pre-clone onboarding: -# curl -sSf https://raw.githubusercontent.com/sciexp/omicsio/main/scripts/bootstrap.sh | bash +# curl -sSf https://raw.githubusercontent.com/sciexp/data/main/scripts/bootstrap.sh | bash # # This script must be kept in sync with the Makefile bootstrap targets # manually (discipline-based, not DRY import) since it must remain # self-contained for the curl use case. set -euo pipefail -echo "omicsio bootstrap" +echo "data bootstrap" echo "==============================" echo From 6a159f503e4ba0b04a067fe065255f85414923af Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:40:17 -0500 Subject: [PATCH 07/17] fix(docs): correct clone URL in installation guide --- docs/guides/installation.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/guides/installation.qmd b/docs/guides/installation.qmd index 5be1791..6ad92ba 100644 --- a/docs/guides/installation.qmd +++ b/docs/guides/installation.qmd @@ -28,7 +28,7 @@ pip install omicsio For development, clone the repository and set up the environment: ```bash -git clone https://github.com/sciexp/omicsio.git +git clone https://github.com/sciexp/data.git cd omicsio # With Nix (recommended) From d341a98de620bcbb9d98166b9b84554ff37079e5 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:40:32 -0500 Subject: [PATCH 08/17] fix(docs): correct repo references and title in quarto config --- docs/_quarto.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/_quarto.yml b/docs/_quarto.yml index f1bb697..534063b 100644 --- a/docs/_quarto.yml +++ b/docs/_quarto.yml @@ -39,9 +39,9 @@ interlinks: url: https://numpy.org/doc/stable/ website: - title: "omicsio" + title: "sciexp data platform" description: "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns" - site-url: "https://sciexp.github.io/omicsio" + site-url: "https://sciexp.github.io/data" back-to-top-navigation: false page-navigation: true @@ -50,7 +50,7 @@ website: left: "" right: - icon: github - href: https://github.com/sciexp/omicsio + href: https://github.com/sciexp/data search: type: overlay @@ -59,7 +59,7 @@ website: background: primary tools: - icon: github - href: https://github.com/sciexp/omicsio + href: https://github.com/sciexp/data left: - sidebar:tutorials - sidebar:guides From be9b1f38e906455db708aee00cdc5103d92dd681 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:40:47 -0500 Subject: [PATCH 09/17] fix(docs): correct title and repo link in docs index --- docs/index.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/index.qmd b/docs/index.qmd index 2271730..4196202 100644 --- a/docs/index.qmd +++ b/docs/index.qmd @@ -1,12 +1,12 @@ --- -title: "omicsio" +title: "sciexp data platform" description: "Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns" format: html: toc: false --- -# omicsio +# sciexp data platform Scientific data platform for omics I/O, lakehouse orchestration, and data mesh patterns @@ -23,6 +23,6 @@ Scientific data platform for omics I/O, lakehouse orchestration, and data mesh p ## Links -- [GitHub Repository](https://github.com/sciexp/omicsio) +- [GitHub Repository](https://github.com/sciexp/data) - [Installation Guide](guides/installation.qmd) - [API Reference](reference/index.qmd) \ No newline at end of file From 92bb7683c91a8b1676807027032b362a7febe2c7 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:40:56 -0500 Subject: [PATCH 10/17] fix(nix): correct repoName in containers module --- modules/containers.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/containers.nix b/modules/containers.nix index 055b2a2..961c18d 100644 --- a/modules/containers.nix +++ b/modules/containers.nix @@ -5,7 +5,7 @@ }: let gitHubOrg = "sciexp"; - repoName = "omicsio"; + repoName = "data"; # Discover maturin packages from packages/ directory. Each subdirectory # containing a Cargo.toml is a maturin/pyo3 package that gets a production From da97d61cb861582570edba662a7f38e9d1c84c57 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:41:08 -0500 Subject: [PATCH 11/17] fix(cloudflare): use data platform domain in wrangler config --- wrangler.jsonc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrangler.jsonc b/wrangler.jsonc index 3616d67..bf70898 100644 --- a/wrangler.jsonc +++ b/wrangler.jsonc @@ -1,6 +1,6 @@ { "$schema": "node_modules/wrangler/config-schema.json", - "name": "omicsio", + "name": "data", "compatibility_date": "2025-09-09", "assets": { "directory": "docs/_site" @@ -15,7 +15,7 @@ "preview_urls": true, "routes": [ { - "pattern": "omicsio.scientistexperience.net", + "pattern": "data.scientistexperience.net", "custom_domain": true } ] From 7b7ecdd351cc68db7c5af3982bdb04fb94ea794e Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:41:19 -0500 Subject: [PATCH 12/17] fix(ci): correct worker and domain URLs in docs deployment --- .github/workflows/deploy-docs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml index b84399b..9aa89d0 100644 --- a/.github/workflows/deploy-docs.yaml +++ b/.github/workflows/deploy-docs.yaml @@ -67,7 +67,7 @@ jobs: runs-on: ubuntu-latest environment: name: ${{ inputs.environment }} - url: ${{ inputs.environment == 'preview' && format('https://b-{0}-omicsio.sciexp.workers.dev', inputs.sanitized_branch || inputs.branch) || 'https://omicsio.scientistexperience.net' }} + url: ${{ inputs.environment == 'preview' && format('https://b-{0}-data.sciexp.workers.dev', inputs.sanitized_branch || inputs.branch) || 'https://data.scientistexperience.net' }} permissions: contents: read deployments: write From 75a56433aaae443099e993a63181c08879847704 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:41:32 -0500 Subject: [PATCH 13/17] fix(justfile): correct cloudflare domain and worker URLs --- justfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/justfile b/justfile index b6c3aa3..06ce785 100644 --- a/justfile +++ b/justfile @@ -881,7 +881,7 @@ docs-deploy-production: docs-build echo " Tag: ${CURRENT_TAG}" echo " Full SHA: ${CURRENT_SHA}" echo " Deployed by: ${DEPLOY_MSG}" - echo " Production URL: https://omicsio.scientistexperience.net" + echo " Production URL: https://data.scientistexperience.net" else echo "" echo "Failed to promote version ${EXISTING_VERSION}" @@ -904,7 +904,7 @@ docs-deploy-production: docs-build echo "Built and deployed to production" echo " Full SHA: ${CURRENT_SHA}" echo " Deployed by: ${DEPLOY_MSG}" - echo " Production URL: https://omicsio.scientistexperience.net" + echo " Production URL: https://data.scientistexperience.net" else echo "" echo "Failed to build and deploy" @@ -944,7 +944,7 @@ docs-deploy-preview branch=`git branch --show-current`: docs-build echo " Tag: ${COMMIT_TAG}" echo " Full SHA: ${COMMIT_SHA}" echo " Message: ${MESSAGE}" - echo " Preview URL: https://b-${SAFE_BRANCH}-omicsio.sciexp.workers.dev" + echo " Preview URL: https://b-${SAFE_BRANCH}-data.sciexp.workers.dev" # List recent Cloudflare Workers versions [group('docs')] From 33fbb264f1165d4087fa76a72e0e09d64c1f9bfe Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:41:42 -0500 Subject: [PATCH 14/17] fix(justfile): correct flake template reference to upstream --- justfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/justfile b/justfile index 06ce785..081d898 100644 --- a/justfile +++ b/justfile @@ -611,7 +611,7 @@ sops-rotate role='dev' method='ssh': # Initialize new project from template [group('template')] template-init: - echo "Use: nix --accept-flake-config run github:juspay/omnix/v1.3.2 -- init github:sciexp/omicsio -o new-python-project" + echo "Use: nix --accept-flake-config run github:juspay/omnix/v1.3.2 -- init github:sciexp/python-nix-template -o new-python-project" # Verify template functionality by creating and checking a test project [group('template')] From 52c8dbee04e687480ab31c6f7d908179a8bd2856 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:41:53 -0500 Subject: [PATCH 15/17] fix(nix): update flake description for data platform identity --- flake.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/flake.nix b/flake.nix index f9ae2f3..ae49edd 100644 --- a/flake.nix +++ b/flake.nix @@ -1,5 +1,5 @@ { - description = "omicsio: federated monorepo with uv2nix and pyo3/Rust extension modules"; + description = "sciexp data platform: omics I/O, lakehouse orchestration, and data mesh patterns"; outputs = inputs@{ flake-parts, ... }: From 05c451988626e9d80c49a2a6d31f56528ef2dccb Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:42:45 -0500 Subject: [PATCH 16/17] fix(docs): correct repo references in archived README --- docs/notes/archive/README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/notes/archive/README.md b/docs/notes/archive/README.md index 293526a..721f1b6 100644 --- a/docs/notes/archive/README.md +++ b/docs/notes/archive/README.md @@ -11,7 +11,7 @@ You can use [omnix](https://omnix.page/om/init.html)[^omnix] to initialize this ```sh nix --accept-flake-config run github:juspay/omnix -- \ -init github:sciexp/omicsio -o new-python-project +init github:sciexp/python-nix-template -o new-python-project ``` [^omnix]: If you have omnix installed you just need `om init ...` and not `nix run ... -- init` @@ -40,7 +40,7 @@ PARAMS=$(cat </dev/null 2>&1 && direnv revoke "./$PROJECT_DIRECTORY/" || true) && \ cd "$PROJECT_DIRECTORY" && \ git init && \ @@ -79,7 +79,7 @@ PARAMS=$(cat </dev/null 2>&1 && direnv revoke "./$PROJECT_DIRECTORY/" || true) && \ cd "$PROJECT_DIRECTORY" && \ git init && \ @@ -95,10 +95,10 @@ nix develop --accept-flake-config -c just test-all except you may want to update the git ref/rev of the template if you need to pin to a particular version: -- `github:sciexp/omicsio/main` -- `github:sciexp/omicsio/v0.1.0` -- `github:sciexp/omicsio/3289dla` -- `github:sciexp/omicsio/devbranch`. +- `github:sciexp/python-nix-template/main` +- `github:sciexp/python-nix-template/v0.1.0` +- `github:sciexp/python-nix-template/3289dla` +- `github:sciexp/python-nix-template/devbranch`. ### Quick start @@ -251,8 +251,8 @@ Available recipes: gh-docs-rerun run_id="" failed_only="true" # Re-run a failed docs workflow gh-docs-watch run_id="" # Watch a specific docs workflow run gh-workflow-status workflow="deploy-docs.yaml" branch=`git branch --show-current` limit="5" # View recent workflow runs status - ghsecrets repo="sciexp/omicsio" # Update github secrets for repo from environment variables - ghvars repo="sciexp/omicsio" # Update github vars for repo from environment variables + ghsecrets repo="sciexp/data" # Update github secrets for repo from environment variables + ghvars repo="sciexp/data" # Update github vars for repo from environment variables list-packages-json # Discover packages as JSON array for CI matrix list-workflows # List available workflows and associated jobs using act pre-commit # Run pre-commit hooks (see pre-commit.nix and note the yaml is git-ignored) From 149c29c00f3d6ca21e40bfc6a0792f42ea994257 Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 18 Feb 2026 13:55:27 -0500 Subject: [PATCH 17/17] chore(omicsio): v0.0.0 -> v0.0.1 update version Signed-off-by: Cameron Smith --- packages/omicsio/pyproject.toml | 4 +- packages/omicsio/uv.lock | 138 ++++++++++++++++---------------- 2 files changed, 71 insertions(+), 71 deletions(-) diff --git a/packages/omicsio/pyproject.toml b/packages/omicsio/pyproject.toml index 9885a9d..4bdc086 100644 --- a/packages/omicsio/pyproject.toml +++ b/packages/omicsio/pyproject.toml @@ -7,7 +7,7 @@ description = "Add your description here" name = "omicsio" readme = "README.md" requires-python = ">=3.12,<3.14" -version = "0.2.1" +version = "0.0.1" [project.scripts] omicsio = "omicsio:main" @@ -83,7 +83,7 @@ types = "pyright src/" [tool.pixi.package] name = "omicsio" -version = "0.2.1" +version = "0.0.1" [tool.pixi.package.run-dependencies] diff --git a/packages/omicsio/uv.lock b/packages/omicsio/uv.lock index d359b5f..604264e 100644 --- a/packages/omicsio/uv.lock +++ b/packages/omicsio/uv.lock @@ -1116,6 +1116,75 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/f9/33/bd5b9137445ea4b680023eb0469b2bb969d61303dedb2aac6560ff3d14a1/notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef", size = 13307, upload-time = "2024-02-14T23:35:16.286Z" }, ] +[[package]] +name = "omicsio" +version = "0.0.1" +source = { editable = "." } + +[package.dev-dependencies] +dev = [ + { name = "hypothesis" }, + { name = "ipython" }, + { name = "jupyter" }, + { name = "jupyter-cache" }, + { name = "pyright" }, + { name = "pytest" }, + { name = "pytest-cov" }, + { name = "quartodoc" }, + { name = "ruff" }, + { name = "xdoctest" }, +] +docs = [ + { name = "jupyter" }, + { name = "jupyter-cache" }, + { name = "quartodoc" }, +] +interactive = [ + { name = "ipython" }, +] +lint = [ + { name = "ruff" }, +] +test = [ + { name = "hypothesis" }, + { name = "pytest" }, + { name = "pytest-cov" }, + { name = "xdoctest" }, +] +types = [ + { name = "pyright" }, +] + +[package.metadata] + +[package.metadata.requires-dev] +dev = [ + { name = "hypothesis", specifier = ">=6.125.1" }, + { name = "ipython", specifier = ">=8.32.0" }, + { name = "jupyter", specifier = ">=1.1.1" }, + { name = "jupyter-cache", specifier = ">=1.0.1" }, + { name = "pyright", specifier = ">=1.1.395" }, + { name = "pytest", specifier = ">=8.3.4" }, + { name = "pytest-cov", specifier = ">=6.0.0" }, + { name = "quartodoc", specifier = ">=0.9.1" }, + { name = "ruff", specifier = ">=0.9.4" }, + { name = "xdoctest", specifier = ">=1.2.0" }, +] +docs = [ + { name = "jupyter", specifier = ">=1.1.1" }, + { name = "jupyter-cache", specifier = ">=1.0.1" }, + { name = "quartodoc", specifier = ">=0.9.1" }, +] +interactive = [{ name = "ipython", specifier = ">=8.32.0" }] +lint = [{ name = "ruff", specifier = ">=0.9.4" }] +test = [ + { name = "hypothesis", specifier = ">=6.125.1" }, + { name = "pytest", specifier = ">=8.3.4" }, + { name = "pytest-cov", specifier = ">=6.0.0" }, + { name = "xdoctest", specifier = ">=1.2.0" }, +] +types = [{ name = "pyright", specifier = ">=1.1.395" }] + [[package]] name = "packaging" version = "26.0" @@ -1397,75 +1466,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/51/e5/fecf13f06e5e5f67e8837d777d1bc43fac0ed2b77a676804df5c34744727/python_json_logger-4.0.0-py3-none-any.whl", hash = "sha256:af09c9daf6a813aa4cc7180395f50f2a9e5fa056034c9953aec92e381c5ba1e2", size = 15548, upload-time = "2025-10-06T04:15:17.553Z" }, ] -[[package]] -name = "omicsio" -version = "0.2.1" -source = { editable = "." } - -[package.dev-dependencies] -dev = [ - { name = "hypothesis" }, - { name = "ipython" }, - { name = "jupyter" }, - { name = "jupyter-cache" }, - { name = "pyright" }, - { name = "pytest" }, - { name = "pytest-cov" }, - { name = "quartodoc" }, - { name = "ruff" }, - { name = "xdoctest" }, -] -docs = [ - { name = "jupyter" }, - { name = "jupyter-cache" }, - { name = "quartodoc" }, -] -interactive = [ - { name = "ipython" }, -] -lint = [ - { name = "ruff" }, -] -test = [ - { name = "hypothesis" }, - { name = "pytest" }, - { name = "pytest-cov" }, - { name = "xdoctest" }, -] -types = [ - { name = "pyright" }, -] - -[package.metadata] - -[package.metadata.requires-dev] -dev = [ - { name = "hypothesis", specifier = ">=6.125.1" }, - { name = "ipython", specifier = ">=8.32.0" }, - { name = "jupyter", specifier = ">=1.1.1" }, - { name = "jupyter-cache", specifier = ">=1.0.1" }, - { name = "pyright", specifier = ">=1.1.395" }, - { name = "pytest", specifier = ">=8.3.4" }, - { name = "pytest-cov", specifier = ">=6.0.0" }, - { name = "quartodoc", specifier = ">=0.9.1" }, - { name = "ruff", specifier = ">=0.9.4" }, - { name = "xdoctest", specifier = ">=1.2.0" }, -] -docs = [ - { name = "jupyter", specifier = ">=1.1.1" }, - { name = "jupyter-cache", specifier = ">=1.0.1" }, - { name = "quartodoc", specifier = ">=0.9.1" }, -] -interactive = [{ name = "ipython", specifier = ">=8.32.0" }] -lint = [{ name = "ruff", specifier = ">=0.9.4" }] -test = [ - { name = "hypothesis", specifier = ">=6.125.1" }, - { name = "pytest", specifier = ">=8.3.4" }, - { name = "pytest-cov", specifier = ">=6.0.0" }, - { name = "xdoctest", specifier = ">=1.2.0" }, -] -types = [{ name = "pyright", specifier = ">=1.1.395" }] - [[package]] name = "pytokens" version = "0.4.1"