DEVOPS-693: migrate from conda-lock to pixi

.gitattributes

@@ -3,3 +3,6 @@
 *.h5 filter=lfs diff=lfs merge=lfs -text
 *.ipynb filter=lfs diff=lfs merge=lfs -text
 *.min.js 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: 'las_geoh5'
       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

@@ -142,5 +142,12 @@ dmypy.json
 # geoh5 locks
 *.geoh5.lock
 
-#version ignore
+# auto-generated version file
 las_geoh5/_version.py
+
+# not using poetry to lock, but pixi
+poetry.lock
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.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:
@@ -59,7 +58,7 @@ 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: [python]
@@ -68,7 +67,7 @@ repos:
     rev: v2.4.1
     hooks:
     -   id: codespell
-        exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$
+        exclude: (^pixi.lock|-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

.readthedocs.yml

@@ -2,16 +2,37 @@ 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:
-    pre_build:
-      - "pip install . --no-deps"
+    post_checkout:
+      # 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"
+      # 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
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/source/conf.py
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
 
-conda:
-  environment: docs/environment.yml
+    build:
+      html:
+        - pixi run --frozen build-docs html $READTHEDOCS_OUTPUT

docs/source/conf.py

@@ -5,27 +5,72 @@
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+
 from datetime import datetime
-from importlib.metadata import version
+from importlib.metadata import version as get_version
+
 from packaging.version import Version
 
 project = "las-geoh5"
 project_copyright = "%Y, Mira Geoscience Ltd"
 author = "Mira Geoscience Ltd."
 
 # The full version.
-release = version("las-geoh5")
+package_name = "las-geoh5"
+
+full_version = Version(get_version(package_name))
+# The full public version, including alpha/beta/rc tags
+release = full_version.public
+# remove the post release segment, if any
+if full_version.is_postrelease:
+    release = release.rsplit(".post", 1)[0]
 # The base X.Y.Z version.
-version = Version(release).base_version
+version = full_version.base_version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = []
+nitpicky = True
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx_issues",
+    "sphinxcontrib.googleanalytics",
+]
+intersphinx_mapping = {
+    # use None to auto-fetch objects.inv
+    "numpy": ("https://numpy.org/doc/1.26/", None),
+    "python": ("http://docs.python.org/3", None),
+}
 
 templates_path = ["_templates"]
 exclude_patterns: list[str] = []
 
+googleanalytics_id = os.environ.get("GOOGLE_ANALYTICS_ID", "")
+if not googleanalytics_id:
+    googleanalytics_enabled = False
+
+issues_github_path = f"mirageoscience/{package_name}"
+
+# -- Options for auto-doc ----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#module-sphinx.ext.autodoc
+
+autodoc_typehints = "signature"
+
+autodoc_mock_imports = [
+    "geoapps_utils",
+    "geoh5py",
+    "numpy",
+    "pydantic",
+    "scipy",
+    "skimage",
+    "tqdm",
+]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output