[DEVOPS-693] pixi all the way, including for doc

- fix test for remove the jinja dependency
- pixi task for build the doc, used in RTD
- tweak RTD configuration
- replace install_in_analyst bat by pixi task
- use pixi to run pylint from pre-commit

Author: sebhmg

.github/workflows/python_analysis.yml

@@ -31,7 +31,7 @@ jobs:
       contents: read
       pull-requests: read
     with:
-      package-manager: 'conda'
+      package-manager: 'pixi'
       app-name: 'grid_apps'
       python-version: '3.10'
   call-workflow-pre-commmit:
@@ -49,7 +49,7 @@ jobs:
       contents: read
       pull-requests: read
     with:
-      package-manager: 'conda'
+      package-manager: 'pixi'
       python-versions: '["3.10", "3.11", "3.12"]'
       cache-number: 1
       os: '["ubuntu-latest", "windows-latest"]'

.gitignore

@@ -145,5 +145,15 @@ dmypy.json
 # tempory generated files
 pyproject-sha.toml
 
-#version ignore
+# auto-generated version file
 grid_apps/_version.py
+
+# not using poetry to lock, but pixi
+poetry.lock
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+# generated conda env files by pixi
+*.pixi.conda.yml

.pre-commit-config.yaml

@@ -63,7 +63,7 @@ repos:
     hooks:
     -   id: pylint
         name: pylint
-        entry: .\\devtools\\conda_env_pylint.bat
+        entry: pixi run --locked pylint
         language: system
         require_serial: true  # pylint does its own parallelism
         types: [python]
@@ -72,7 +72,7 @@ repos:
     rev: v2.3.0
     hooks:
     -   id: codespell
-        exclude: (-lock\.ya?ml|\benvironments/.*\.ya?ml|\.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: v5.0.0

.readthedocs.yml

@@ -1,19 +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 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
-
-python:
-  install:
-    - method: pip
-      path: .
+    build:
+      html:
+        - pixi run --frozen build-docs html $READTHEDOCS_OUTPUT

deps-lock-config.yaml

@@ -8,8 +8,9 @@
 #                                                                                        '
 # ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 
+import os
 from datetime import datetime
-from importlib.metadata import version
+from importlib.metadata import version as get_version
 
 from packaging.version import Version
 
@@ -26,38 +27,63 @@
 author = "Mira Geoscience Ltd."
 project_copyright = "%Y, Mira Geoscience Ltd"
 
+package_name = "grid-apps"
+
+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 short X.Y.Z version.
+version = full_version.base_version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# The full version, including alpha/beta/rc tags.
-release = version("grid-apps")
-# The shorter X.Y.Z version.
-version = Version(release).base_version
-
-autodoc_mock_imports = [
-    "numpy",
-    "geoh5py",
-    "geoapps_utils",
-    "pydantic",
-    "discretize",
-]
+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 = []
 todo_include_todos = True
 
+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 = [
+    "discretize",
+    "geoapps_utils",
+    "geoh5py",
+    "numpy",
+    "pydantic",
+    "scipy",
+    "tqdm",
+]
+
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output