Merge pull request #9 from brian-team/infra_updates

Infrastructure updates

Author: mstimberg

.github/workflows/publish.yaml

@@ -4,36 +4,19 @@ on:
   push:
     tags:
       - 'v*'
-  pull_request:
-    tags:
-      - 'v*'
 
 jobs:
   pypi-publish:
     name: upload release to PyPI
     runs-on: ubuntu-latest
     environment: release
     permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
         with:
-          python-version: '3.x'
-
-      - name: Install build dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install build
-
-      - name: Build package
-        run: python -m build
-
-      - name: List dist directory contents
-        run: ls -la dist
-
+          fetch-depth: 0  # We need all history to determine the version
+      - uses: pdm-project/setup-pdm@v4
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        run: pdm publish

.github/workflows/pytest-ubuntu.yaml

@@ -1,25 +1,25 @@
-name: Python package
+name: Tests
 
 on: [push, pull_request]
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    name: Run tests
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Check out the repository
       uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Set up PDM
+      uses: pdm-project/setup-pdm@v4
       with:
-        python-version: '3.x'
+        python-version: 3.13
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install .[test]
+        pdm install -G test
 
     - name: Run tests
       run: |
-        pytest --doctest-modules
+        pdm run -v pytest --doctest-modules

.gitignore

@@ -161,3 +161,8 @@ cython_debug/
 
 # version
 _version.py
+
+# pdm
+pdm.lock
+.pdm-*/
+.pdm-*

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: 'ubuntu-20.04'
+  os: 'ubuntu-22.04'
   tools:
-    python: "3.11"
+    python: "3.12"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

README.md

@@ -1,4 +1,2 @@
 # QuantSI
 Work in progress: unit system as used by the Brian2 simulator
-
-We will think of a better name before releasing…

pyproject.toml

@@ -1,17 +1,17 @@
 [project]
 name = "QuantSI"
+description = "unit system as used by the Brian2 simulator"
 authors = [
-    {name = 'Sorin Birchi'},
+    {name = "Sorin Birchi"},
+    {name = "Marcel Stimberg"},
+    {name = "Dan Goodman"},
+    {name = "Romain Brette"},
 ]
-requires-python = '>=3.10'
-dependencies = [
-    'numpy>=1.23.5',
-    'sympy>=1.2',
-    'setuptools>=61'
-]
-dynamic = ["version", "readme"]
-description = 'unit system as used by the Brian2 simulator'
-keywords = ['computational neuroscience', 'simulation', 'system units']
+dependencies = ["numpy>=1.25", "sympy>=1.2"]
+requires-python = ">=3.10"
+readme = "README.md"
+license = {text = "GPLv3"}
+keywords = ['SI', 'SI units', 'unit system', 'physical quantities']
 classifiers = [
     'Development Status :: 4 - Beta',
     'Intended Audience :: Science/Research',
@@ -20,51 +20,34 @@ classifiers = [
     'Operating System :: OS Independent',
     'Programming Language :: Python',
     'Programming Language :: Python :: 3',
-    'Topic :: Scientific/Engineering :: Bio-Informatics'
+    'Topic :: Scientific/Engineering'
 ]
+dynamic = ["version"]
 
 [project.optional-dependencies]
-test = ['pytest', 'pytest-xdist>=1.22.3']
-docs = ['sphinx>=7', 'ipython>=5', 'sphinx-tabs']
-
-[project.urls]
-Documentation ='https://QuantSI.readthedocs.io/en/latest/'
-Source = 'https://github.com/brian-team/QuantSI'
-Tracker = 'https://github.com/brian-team/QuantSI/issues'
-
-[build-system]
-requires = [
-    "setuptools>=61",
-    "numpy>=2.0.0rc1",
-    "wheel",
-    "setuptools_scm[toml]>=6.2"
+test = [
+    "pytest>=8.3.4",
+    "pytest-xdist>=1.22.3",
+    "pdm-backend>=2.4.3",
 ]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools]
-zip-safe = false
-include-package-data = true
-
-[tool.setuptools.packages.find]
-include = ["QuantSI*"]
-
-[tool.setuptools.dynamic]
-readme = {file = 'README.md', content-type = "text/markdown"}
+docs = [
+    "sphinx>=7",
+    "ipython>=5",
+    "sphinx-tabs>=3.4.7",
+]
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
 
-[tool.setuptools_scm]
-version_scheme = 'post-release'
-local_scheme = 'no-local-version'
-write_to = 'QuantSI/_version.py'
-fallback_version = 'unknown'
+[tool.pdm]
+distribution = true
 
-[tool.black]
-target-version = ['py310']
-include = '^/QuantSI/.*\.pyi?$'
+[tool.pdm.version]
+source = "scm"
+tag_filter = "v*"
+version_format = "src.version_helper:format_version"
+write_to = "QuantSI/_version.py"
+write_template = "__version__ = '{}'"
 
-[tool.isort]
-atomic = true
-profile = "black"
-py_version = "311"
-skip_gitignore = true
-# NOTE: isort has no "include" option, only "skip".
-skip_glob = ["docs_sphinx/*"]
+[tool.pytest.ini_options]
+addopts = "-ra"

QuantSI/__init__.py renamed to src/QuantSI/__init__.py

@@ -3,6 +3,7 @@
 """
 
 # isort:skip_file
+from ._version import __version__
 
 from .allunits import (
     # basic units

QuantSI/allunits.py renamed to src/QuantSI/allunits.py

@@ -0,0 +1,11 @@
+from pdm.backend.hooks.version import SCMVersion
+
+def format_version(version) -> str:
+    """
+    Format the version number of the package. This function is only supposed to be
+    called by the pdm-backend to get the version number of the package.
+    """
+    if version.distance is None:
+        return str(version.version)
+    else:
+        return f"{version.version}.post{version.distance}"