DEVOPS-693: migrate from conda-lock to pixi

.gitattributes

@@ -1,3 +1,6 @@
 # Shell scripts
 *.sh eol=lf
 *.gif 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

@@ -26,14 +26,14 @@ jobs:
     name: Static analysis
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main
     with:
-      package-manager: 'poetry'
+      package-manager: 'pixi'
       app-name: 'geoh5py'
       python-version: '3.10'
   call-workflow-pytest:
     name: Pytest
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@main
     with:
-      package-manager: 'poetry'
+      package-manager: 'pixi'
       python-versions: '["3.10", "3.11", "3.12"]'
       os: '["ubuntu-latest", "windows-latest"]'
       cache-number: 1

.gitignore

@@ -145,5 +145,13 @@ dmypy.json
 # geoh5 locks
 *.geoh5.lock
 
-#version ignore
+# auto-generated version file
 geoh5py/_version.py
+
+# not using poetry to lock, but pixi
+poetry.lock
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+/docs/conf.py

.pre-commit-config.yaml

@@ -15,7 +15,6 @@ repos:
     rev: 2.1.3
     hooks:
     -   id: poetry-check
-        args: [--lock, --no-plugins]
 -   repo: https://github.com/hadialqattan/pycln
     rev: v2.5.0
     hooks:
@@ -74,7 +73,7 @@ repos:
     hooks:
     -   id: pylint
         name: pylint
-        entry: poetry run pylint
+        entry: pixi run --locked pylint
         language: system
         require_serial: true  # pylint does its own parallelism
         types: [text]

.readthedocs.yml

@@ -1,42 +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:
-      - echo "[RTD] Configure Git LFS"
+      # Download and uncompress binary for the desired version of Git LFS
       - |
         set -e
-        # Update version of Git LFS as needed here:
         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${LFS_VERSION}.tar.gz"
-      - |
-        set -e
-        git_lfs_path="$(pwd)"
-        git config filter.lfs.process "$git_lfs_path/git-lfs filter-process"
-        git config filter.lfs.smudge  "$git_lfs_path/git-lfs smudge -- %f"
-        git config filter.lfs.clean "$git_lfs_path/git-lfs clean -- %f"
-      - |
-        set -e
-        ./git-lfs install
-        ./git-lfs fetch
-        ./git-lfs checkout
+      # Modify LFS config paths to point where git-lfs binary was downloaded
+      - git config filter.lfs.process "$(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"
+      # 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"
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  builder: html
-  configuration: docs/conf.py
-  fail_on_warning: false
+    install:
+      - pixi install -e docs
 
-conda:
-    environment: docs/environment.yml
+    build:
+      html:
+        - pixi run --frozen -e docs build-docs html $READTHEDOCS_OUTPUT

docs/_config.yml

@@ -2,7 +2,8 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: Geoh5py
-author: Mira Geoscience
+author: Mira Geoscience Ltd.
+copyright: "2025"
 logo: images/geoh5py_logo.png
 
 # Force re-execution of notebooks on each build.
@@ -13,10 +14,38 @@ execute:
 
 sphinx:
   extra_extensions:
-  - 'sphinx.ext.autodoc'
+    - sphinx.ext.autodoc
+    - sphinx.ext.intersphinx
+    - sphinx.ext.todo
+    - sphinx_issues
+    - sphinxcontrib.googleanalytics
+    #- sphinx.ext.autosummary  # TODO: restore? for now, tons of error
+    #- sphinx.ext.viewcode  # TODO: restore? for now, tons of error
+  local_extensions:
+    dynamic_config: _ext/
+  recursive_update: true
   config:
-    suppress_warnings : ["etoc.toctree"]
-
+    project: geoh5py
+    html_static_path:
+      - _static/custom.css
+    html_theme: alabaster
+    autodoc_typehints: signature
+    autodoc_typehints_format: short
+    suppress_warnings:
+      - etoc.toctree
+    intersphinx_mapping:
+      # use None to auto‑fetch objects.inv
+      numpy:
+        - https://numpy.org/doc/1.26/
+        - null
+      python:
+        - https://docs.python.org/3/
+        - null
+    todo_include_todos: true
+    issues_github_path: mirageoscience/geoh5py
+    autodoc_type_aliases:
+      np.ndarray: numpy.ndarray
+      UUID: uuid.UUID
 
 # Define the name of the latex output file for PDF builds
 latex:

docs/_ext/dynamic_config.py

@@ -0,0 +1,37 @@
+import logging
+import os
+
+from datetime import datetime
+from importlib.metadata import version as get_version
+from packaging.version import Version
+
+
+dated_copyright = f"{datetime.now().strftime('%Y, Mira Geoscience Ltd')}"
+
+def get_copyright_notice():
+    return f"Copyright {dated_copyright}."
+
+
+def setup(app):
+    # The full version, including alpha/beta/rc tags.
+    release = get_version("geoh5py")
+    # The shorter X.Y.Z version.
+    version = Version(release).base_version
+
+    app.config.project_copyright = f"{dated_copyright}"
+    app.config.release = release
+    app.config.version = version
+    app.config.html_theme_options = {
+        "description": f"version {release}",
+        "fixed_sidebar": True,
+        "logo_name": "Geoh5py",
+        "show_relbars": True,
+    }
+    app.config.rst_epilog = f"\n.. |copyright_notice| replace:: {get_copyright_notice()}\n"
+
+    app.config.googleanalytics_id = os.environ.get("GOOGLE_ANALYTICS_ID", "")
+    if not app.config.googleanalytics_id:
+        logging.warning("Environment variable GOOGLE_ANALYTICS_ID is not set")
+        app.config.googleanalytics_enabled = False
+
+    return {"version": "0.1", "parallel_read_safe": True}