Update packaging following uv advancements (#106)

* update packaging

* fix stubgen

* update pre-commit

Author: mscheltienne

.github/workflows/doc.yaml

@@ -13,15 +13,14 @@ jobs:
     timeout-minutes: 10
     runs-on: ubuntu-latest
     steps:
+      - run: sudo apt update && sudo apt install -y optipng
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-      - run: sudo apt update && sudo apt install -y optipng
       - uses: astral-sh/setup-uv@v6
-      - run: uv pip install --quiet --system .[doc]
+        with:
+          activate-environment: true
+      - run: uv sync -q --locked --no-default-groups --group doc
       - run: template sys-info --developer
       - run: make -C doc html
       - name: Prune sphinx environment

.github/workflows/publish.yaml

@@ -1,27 +1,32 @@
 name: publish
 on:  # yamllint disable-line rule:truthy
-  workflow_dispatch:
+  workflow_dispatch:  # remove in favor of release
+  # release:
+  #   types: [published]
 
 jobs:
   pypi:
     timeout-minutes: 10
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/template-python
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
       - uses: astral-sh/setup-uv@v6
-      - run: uv pip install --quiet --system -e .[build,stubs]
+        with:
+          activate-environment: true
+      - run: uv sync -q --locked --no-default-groups --group stubs
       - run: template sys-info --developer
       - run: python tools/stubgen.py
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN  }}
-        run: |
-          python -m build
-          twine check --strict dist/*
-          twine upload dist/*
+      - run: uv build
+      - uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          tag_name: ${{ github.event.release.tag_name }}
+      - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pytest.yaml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -27,47 +27,39 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
+          activate-environment: true
           python-version: ${{ matrix.python-version }}
-      - uses: astral-sh/setup-uv@v6
-      - run: uv pip install --quiet --system .[test]
+      - run: uv sync -q --locked --no-default-groups --group test
       - run: template sys-info --developer
       - run: pytest template --cov=template --cov-report=xml --cov-config=pyproject.toml
       - uses: codecov/codecov-action@v5
         with:
-          files: ./coverage.xml
-          flags: unittests  # optional
-          name: codecov-umbrella  # optional
           token: ${{ secrets.CODECOV_TOKEN }}
-          verbose: true  # optional (default = false)
 
   pytest-pip-pre:
     timeout-minutes: 30
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.13"]
     name: pip pre-release - py${{ matrix.python-version }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
+          activate-environment: true
           python-version: ${{ matrix.python-version }}
-      - uses: astral-sh/setup-uv@v6
       - name: Install package
         run: |
-          uv pip install --quiet --system .[test]
-          uv pip install --quiet --system --upgrade --prerelease allow --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
+          uv sync -q --locked --no-default-groups --group test
+          uv pip install -q --upgrade --prerelease allow --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
       - run: template sys-info --developer
       - run: pytest template --cov=template --cov-report=xml --cov-config=pyproject.toml
       - uses: codecov/codecov-action@v5
         with:
-          files: ./coverage.xml
-          flags: unittests  # optional
-          name: codecov-umbrella  # optional
           token: ${{ secrets.CODECOV_TOKEN }}
-          verbose: true  # optional (default = false)

.github/workflows/stubs.yaml

@@ -16,11 +16,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
       - uses: astral-sh/setup-uv@v6
-      - run: uv pip install --quiet --system -e .[stubs]
+        with:
+          activate-environment: true
+      - run: uv sync -q --locked --no-default-groups --group stubs
       - run: template sys-info --developer
       - run: python tools/stubgen.py
       - name: Push stub files

.pre-commit-config.yaml

@@ -1,6 +1,11 @@
 repos:
+    - repo: https://github.com/astral-sh/uv-pre-commit
+      rev: 0.7.3
+      hooks:
+          - id: uv-lock
+
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.10
+      rev: v0.11.11
       hooks:
           - id: ruff
             name: ruff linter

doc/conf.py

@@ -98,10 +98,10 @@
     ],
 }
 
-# -- autosummary -----------------------------------------------------------------------
+# -- autosummary / autodoc--------------------------------------------------------------
 autosummary_generate = True
-
-# -- autodoc ---------------------------------------------------------------------------
+autodoc_pydantic_model_show_config_summary = False
+autodoc_pydantic_model_show_json = False
 autodoc_typehints = "none"
 autodoc_member_order = "groupwise"
 autodoc_warningiserror = True

pyproject.toml

@@ -2,6 +2,44 @@
 build-backend = 'setuptools.build_meta'
 requires = ['setuptools >= 64.0.0', 'setuptools_scm>=8']
 
+[dependency-groups]
+doc = [
+  'autodoc_pydantic',
+  'furo',
+  'intersphinx_registry',
+  'matplotlib',
+  'memory-profiler',
+  'numpydoc',
+  'sphinx',
+  'sphinx-copybutton',
+  'sphinx-design',
+  'sphinx-gallery',
+  'sphinx-issues',
+  'sphinxcontrib-bibtex',
+]
+ide = [
+  'ipykernel',
+  'ipython',
+]
+stubs = [
+  'mypy',
+  'ruff>=0.6.0',
+]
+style = [
+  'bibclean',
+  'codespell[toml]>=2.2.4',
+  'pre-commit',
+  'ruff>=0.6.0',
+  'toml-sort',
+  'yamllint',
+]
+test = [
+  'pytest-cov',
+  'pytest-randomly',
+  'pytest-timeout',
+  'pytest>=8.0',
+]
+
 [project]
 authors = [
   {email = 'mathieu.scheltienne@gmail.com', name = 'Mathieu Scheltienne'},
@@ -12,7 +50,6 @@ classifiers = [
   'Operating System :: Microsoft :: Windows',
   'Operating System :: Unix',
   'Programming Language :: Python :: 3 :: Only',
-  'Programming Language :: Python :: 3.10',
   'Programming Language :: Python :: 3.11',
   'Programming Language :: Python :: 3.12',
   'Programming Language :: Python :: 3.13',
@@ -36,56 +73,10 @@ maintainers = [
 ]
 name = 'template'
 readme = 'README.md'
-requires-python = '>=3.10'
-
-[project.optional-dependencies]
-all = [
-  'template[build]',
-  'template[doc]',
-  'template[stubs]',
-  'template[style]',
-  'template[test]',
-]
-build = [
-  'build',
-  'twine',
-]
-doc = [
-  'furo',
-  'intersphinx_registry',
-  'matplotlib',
-  'memory-profiler',
-  'numpydoc',
-  'sphinx',
-  'sphinx-copybutton',
-  'sphinx-design',
-  'sphinx-gallery',
-  'sphinx-issues',
-  'sphinxcontrib-bibtex',
-]
-full = [
-  'template[all]',
-]
-stubs = [
-  'mypy',
-  'ruff>=0.6.0',
-]
-style = [
-  'bibclean',
-  'codespell[toml]>=2.2.4',
-  'pre-commit',
-  'ruff>=0.6.0',
-  'toml-sort',
-  'yamllint',
-]
-test = [
-  'pytest-cov',
-  'pytest-timeout',
-  'pytest>=8.0',
-]
+requires-python = '>=3.11'
 
 [project.scripts]
-template = 'template.commands.main:run'
+template = 'template._commands.main:run'
 
 [project.urls]
 documentation = 'https://github.com/mscheltienne/template-python'
@@ -166,3 +157,6 @@ all = true
 ignore_case = true
 spaces_before_inline_comment = 2
 trailing_comma_inline_array = true
+
+[tool.uv]
+default-groups = "all"

template/commands/__init__.py template/_commands/__init__.pytemplate/commands/__init__.py renamed to template/_commands/__init__.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+
+import click
+
+from .. import sys_info
+
+
+@click.command(name="sys-info")
+@click.option(
+    "--extra",
+    help="Display information for optional dependencies.",
+    is_flag=True,
+)
+@click.option(
+    "--developer",
+    help="Display information for developer dependencies.",
+    is_flag=True,
+)
+@click.option(
+    "--package",
+    help="The package to display information about.",
+    type=str,
+)
+def run(extra: bool, developer: bool, package: str | None) -> None:
+    """Run sys_info() command."""
+    sys_info(extra=extra, developer=developer, package=package)