DEVOPS-693: migration to pixi [WIP]

.gitattributes

@@ -4,3 +4,6 @@
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.min.js filter=lfs diff=lfs merge=lfs -text
 *.npy filter=lfs diff=lfs merge=lfs -text
+
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/python_analysis.yml

@@ -31,7 +31,7 @@ jobs:
       contents: read
       pull-requests: read
     with:
-      package-manager: 'conda'
+      package-manager: 'pixi'
       app-name: 'simpeg_drivers'
       python-version: '3.10'
   call-workflow-pytest:
@@ -41,7 +41,7 @@ jobs:
       contents: read
       pull-requests: read
     with:
-      package-manager: 'conda'
+      package-manager: 'pixi'
       python-versions: '["3.10", "3.11", "3.12"]'
       os: '["ubuntu-latest", "windows-latest"]'
       cache-number: 1

.github/workflows/security_scan.yml

@@ -25,19 +25,19 @@ concurrency:
 
 jobs:
   call-workflow-zizmor-annotate:
-    name: Zizmor analysis (advanced security)
-    if: ${{ github.event_name != 'pull_request' }}
+    name: Zizmor analysis (annotate)
+    if: ${{ github.event_name == 'pull_request' }}
     permissions:
-      security-events: write
+      checks: write
       contents: read
       actions: read
-    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-advanced-security.yml@v2
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-annotate.yml@v2
 
   call-workflow-zizmor-advanced-security:
-    name: Zizmor analysis (annotate)
-    if: ${{ github.event_name == 'pull_request' }}
+    name: Zizmor analysis (advanced security)
+    if: ${{ github.event_name != 'pull_request' }}
     permissions:
-      checks: write
+      security-events: write
       contents: read
       actions: read
-    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-annotate.yml@v2
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-advanced-security.yml@v2

.gitignore

@@ -73,6 +73,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+# conf.py is generated  by jupyter-book
+docs/conf.py
 
 # PyBuilder
 target/
@@ -142,8 +144,15 @@ dmypy.json
 # geoh5 locks
 *.geoh5.lock
 
-# tempory generated files
-pyproject-sha.toml
+# not using poetry to lock, but pixi
+poetry.lock
 
-#version ignore
+# auto-generated version file
 simpeg_drivers/_version.py
+/_version.json
+
+# not using poetry to lock, but pixi
+poetry.lock
+
+# generated conda env files by pixi
+*.pixi.conda.yml

.pre-commit-config.yaml

@@ -1,115 +1,116 @@
-
 default_language_version:
-    python: python3
+  python: python3
 exclude: ^docs/(conf.py|_ext/)
 default_stages: [pre-commit,pre-push]
 fail_fast: false
 
 ci:
-    skip: [pylint]
-    autoupdate_branch: develop
-    autoupdate_schedule: monthly
+  skip: [pylint]
+  autoupdate_branch: develop
+  autoupdate_schedule: monthly
 
 repos:
-# -   repo: https://github.com/python-poetry/poetry  # TODO: re-enable with pixi (does not support source=pypi)
-#     rev: 2.2.1
-#     hooks:
-#     -   id: poetry-check
-#         args: [--no-plugins]
--   repo: https://github.com/hadialqattan/pycln
-    rev: v2.6.0
-    hooks:
-    -   id: pycln
-        args: [--config=pyproject.toml]
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.4
-    hooks:
-    -   id: ruff-check
-        args:
-        -   --fix
-        -   --exit-non-zero-on-fix
-#        -   --unsafe-fixes
-    -   id: ruff-format
-# -  repo: https://github.com/pre-commit/mirrors-mypy  # TODO: fix mypy errors
-#    rev: v1.18.2
-#    hooks:
-#    -   id: mypy
-#        additional_dependencies: [
-#            numpy==1.26.*,
-#            types-toml,
-#            types-PyYAML,
-#            tomli  # to read config from pyproject.toml
-#        ]
-#        exclude: ^(docs|simpeg_drivers-assets)/
--   repo: https://github.com/codingjoe/relint
-    rev: 3.3.1
-    hooks:
-    -   id: relint
-        args: [-W]  # to fail on warnings
--   repo: https://github.com/MiraGeoscience/pre-commit-hooks
-    rev: v1.1.0
-    hooks:
-    -   id: check-copyright
-        files: (^package\.rst|LICENSE|^README(|-dev).rst|^docs/intro\.md|\.py|\.pyi)$
-        exclude: (^\.|^docs/(?!intro\.md))
-        args:
-        -   --full-scan-files
-        -   intro.md
-    -   id: prepare-commit-msg
-    -   id: check-commit-msg
--   repo: local
-    hooks:
-    -   id: pylint
-        name: pylint
-        entry: .\\devtools\\conda_env_pylint.bat
-        language: system
-        require_serial: true  # pylint does its own parallelism
-        types: [python]
-        exclude: ^(devtools|docs)/
--   repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
-    hooks:
-    -   id: codespell
-        exclude: (-lock\.ya?ml|\benvironments/.*\.ya?ml|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$
-        entry: codespell -I .codespellignore
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
-    hooks:
-    -   id: trailing-whitespace
-        exclude: \.mdj$
-    -   id: check-json
-        exclude_types: [jupyter]
-    -   id: check-toml
-    -   id: check-yaml
-    -   id: check-added-large-files
-        exclude: (\.ipynb)$
-    -   id: check-case-conflict
-    -   id: check-merge-conflict
-    -   id: debug-statements
-    -   id: detect-private-key
-    -   id: end-of-file-fixer
-        exclude: (^\.idea/.*\.xml|\.mdj)$
-    -   id: mixed-line-ending
-        exclude: ^\.idea/.*\.xml$
-    -   id: name-tests-test
-        exclude: ^tests/utils/
-    -   id: pretty-format-json
-        args:
-            - --autofix
-            - --indent=4
-            - --no-sort-keys
-            - --top-keys
-            - version,title,icon,documentation,conda_environment,run_command,geoh5,monitoring_directory,workspace_geoh5
-        exclude_types: [jupyter]
-        exclude: ^docs/(.*/)?images/
--   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.5
-    hooks:
-    -   id: rstcheck
-        exclude: ^THIRD_PARTY_SOFTWARE.rst$
-        additional_dependencies: [sphinx]
--   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-    -   id: rst-backticks
-        exclude: ^THIRD_PARTY_SOFTWARE.rst$
+- repo: https://github.com/python-poetry/poetry
+  rev: 2.2.1
+  hooks:
+  - id: poetry-check
+    args: [--no-plugins]
+- repo: https://github.com/hadialqattan/pycln
+  rev: v2.6.0
+  hooks:
+  - id: pycln
+    args: [ --config=pyproject.toml ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.14.10
+  hooks:
+  - id: ruff-check
+    args:
+    - --fix
+    - --exit-non-zero-on-fix
+    # - --unsafe-fixes
+  - id: ruff-format
+# - repo: https://github.com/pre-commit/mirrors-mypy  # TODO: fix mypy errors
+#   rev: v1.19.1
+#   hooks:
+#   - id: mypy
+#     additional_dependencies: [
+#       numpy==1.26.*,
+#       types-toml,
+#       types-PyYAML,
+#       tomli, # to read config from pyproject.toml
+#     ]
+#     exclude: ^(docs|simpeg_drivers-assets)/
+- repo: https://github.com/codingjoe/relint
+  rev: 3.3.1
+  hooks:
+  - id: relint
+    args: [-W]  # to fail on warnings
+- repo: https://github.com/MiraGeoscience/pre-commit-hooks
+  rev: v1.1.0
+  hooks:
+  - id: check-copyright
+    files: (^package\.rst|^LICENSE|^README(|-dev).rst|^docs/intro\.md|\.py|\.pyi)$
+    exclude: (^\.|^docs/(?!intro\.md))
+    args:
+      - --full-scan-files
+      - intro.md
+  - id: prepare-commit-msg
+  - id: check-commit-msg
+- repo: local
+  hooks:
+  - id: pylint
+    name: pylint
+    entry: pixi run -e linter --as-is lint
+    language: system
+    require_serial: true  # pylint does its own parallelism
+    types: [text]
+    types_or: [python, pyi]
+    exclude: ^(devtools|docs|simpeg_drivers-assets)/
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+  - id: codespell
+    exclude: (\.ipynb|THIRD_PARTY_SOFTWARE\.rst|^pixi\.lock)$
+    entry: codespell -I .codespellignore
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: trailing-whitespace
+    exclude: \.mdj$
+  - id: check-json
+    exclude_types: [jupyter]
+  - id: check-toml
+  - id: check-yaml
+  - id: check-added-large-files
+    exclude: (\.ipynb)$
+    # args: [--enforce-all]
+  - id: check-case-conflict
+  - id: check-merge-conflict
+  - id: debug-statements
+  - id: detect-private-key
+  - id: end-of-file-fixer
+    exclude: (^\.idea/.*\.xml|\.mdj)$
+  - id: mixed-line-ending
+    exclude: ^\.idea/.*\.xml$
+  - id: name-tests-test
+    exclude: ^tests/utils/
+  - id: pretty-format-json
+    args:
+      - --autofix
+      - --indent=4
+      - --no-sort-keys
+      - --top-keys
+      - version,title,icon,documentation,conda_environment,run_command,geoh5,monitoring_directory,workspace_geoh5
+    exclude_types: [jupyter]
+    exclude: ^docs/(.*/)?images/
+- repo: https://github.com/rstcheck/rstcheck
+  rev: v6.2.5
+  hooks:
+  - id: rstcheck
+    exclude: ^THIRD_PARTY_SOFTWARE.rst$
+    additional_dependencies: [sphinx]
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: rst-backticks
+    exclude: ^THIRD_PARTY_SOFTWARE.rst$

.readthedocs.yml

@@ -1,35 +1,37 @@
 version: 2
 
-# Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-22.9"
+    python: "3.10"  # pre-install for the py310 environment of pixi
   jobs:
     post_checkout:
-      # Download and uncompress the binary
-      # https://git-lfs.github.com/
-      - wget https://github.com/git-lfs/git-lfs/releases/download/v3.1.4/git-lfs-linux-amd64-v3.1.4.tar.gz
-      - tar xvfz git-lfs-linux-amd64-v3.1.4.tar.gz
+      # Download and uncompress binary for the desired version of Git LFS
+      - |
+        set -e
+        LFS_VERSION="3.4.0"
+        wget "https://github.com/git-lfs/git-lfs/releases/download/v${LFS_VERSION}/git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz"
+        tar xzf "git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz" --strip-components=1 "git-lfs-${LFS_VERSION}/git-lfs"
+        rm "git-lfs-linux-amd64-v${LFS_VERSION}.tar.gz"
       # Modify LFS config paths to point where git-lfs binary was downloaded
-      - git config filter.lfs.process "`pwd`/git-lfs filter-process"
-      - git config filter.lfs.smudge  "`pwd`/git-lfs smudge -- %f"
-      - git config filter.lfs.clean "`pwd`/git-lfs clean -- %f"
+      - git config filter.lfs.process "$(pwd)/git-lfs filter-process"
+      - git config filter.lfs.smudge  "$(pwd)/git-lfs smudge -- %f"
+      - git config filter.lfs.clean "$(pwd)/git-lfs clean -- %f"
       # Make LFS available in current repository
       - ./git-lfs install
       # Download content from remote
       - ./git-lfs fetch
       # Make local files to have the real content on them
       - ./git-lfs checkout
-    pre_build:
-      # Generate on-the-fly Sphinx configuration from Jupyter Book's _config.yml
-      - "jupyter-book config sphinx docs/"
-      - "pip install . --no-deps"
 
-sphinx:
-  builder: html
-  configuration: docs/conf.py
-  fail_on_warning: false
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
 
-conda:
-  environment: docs/environment.yml
+    install:
+      - pixi install -e docs
+
+    build:
+      html:
+        - pixi run --frozen -e docs build-docs html $READTHEDOCS_OUTPUT