chore: init

.actrc

@@ -0,0 +1,3 @@
+--container-architecture linux/amd64
+--artifact-server-path $PWD/.artifacts
+-P ubuntu-latest=catthehacker/ubuntu:full-latest

.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.

.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 <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

.beads/metadata.json

@@ -0,0 +1,4 @@
+{
+  "database": "beads.db",
+  "jsonl_export": "issues.jsonl"
+}

.dvc/.gitignore

@@ -0,0 +1 @@
+/config.local

.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

.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

.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
+
+<details>
+  <summary>code example</summary>
+
+```sh
+
+```
+
+</details>
+
+<details>
+  <summary>error output</summary>
+
+```sh
+
+```
+
+</details>
+
+## environment
+
+<details>
+  <summary>environment</summary>
+
+output of `nix doctor`, `nix flake metadata`, `nix flake show`, etc.
+
+```sh
+
+```
+
+</details>

.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

.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
+
+<details>
+  <summary>code example</summary>
+
+```sh
+
+```
+
+</details>
+
+## description of proposed solution
+
+<details>
+  <summary>code example</summary>
+
+```sh
+
+```
+
+</details>

.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).

.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

.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

.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