Merge pull request #156 from khaeru/ci/2025-w03

Miscellaneous CI updates

.github/workflows/publish.yaml

@@ -1,21 +1,42 @@
 name: Build package / publish
 
 on:
+  pull_request:
+    branches: [ main ]
   push:
     branches: [ main ]
     tags: [ "v*" ]
   release:
     types: [ published ]
-  # Check that package can be built even on PRs
-  pull_request:
-    branches: [ main ]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  python-version: "3.13"
+  # Uncomment for testing
+  # UV_PUBLISH_URL: https://test.pypi.org/legacy/
+
+
 jobs:
   publish:
-    uses: iiasa/actions/.github/workflows/publish.yaml@main
-    secrets:
-      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+    environment:
+      name: publish
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v5
+      with:
+        cache-dependency-glob: "**/pyproject.toml"
+        python-version: ${{ env.python-version }}
+    - run: uv build
+    - run: uv publish --trusted-publishing=always
+      if: >-
+        github.event_name == 'release' || (
+          github.event_name == 'push'
+          && startsWith(github.ref, 'refs/tags')
+        )

.github/workflows/pytest.yaml

@@ -8,8 +8,7 @@ on:
   schedule:
   - cron: "0 5 * * *"
 
-# Cancel previous runs that have not completed
-concurrency:
+concurrency:  # Cancel previous runs that have not completed
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
@@ -51,31 +50,30 @@ jobs:
       with:
         fetch-depth: ${{ env.depth }}
 
-    - uses: actions/setup-python@v5
+    - name: Set up uv, Python
+      uses: astral-sh/setup-uv@v5
       with:
+        cache-dependency-glob: "**/pyproject.toml"
         python-version: ${{ matrix.python.version }}
-        cache: pip
-        cache-dependency-path: "**/pyproject.toml"
 
     - uses: ts-graphviz/setup-graphviz@v2
       with:
         macos-skip-brew-update: true
 
-    - name: Install the Python package and dependencies
-      run: pip install --upgrade --upgrade-strategy=eager .[tests] ${{ matrix.python.extras }}
+    - name: Install the package and dependencies
+      run: uv pip install .[tests] ${{ matrix.python.extras }}
 
-    - name: Run test suite using pytest
+    - name: Run tests
       run: |
-        pytest genno \
-          --trace-config --color=yes --verbose \
+        uv run --no-sync \
+          pytest \
+          --trace-config --color=yes --durations=20 -ra --verbose \
           --cov-report=xml --cov-report=term \
-          --numprocesses auto
+          --numprocesses=auto
       shell: bash
 
     - name: Upload test coverage to Codecov.io
       uses: codecov/codecov-action@v5
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
 
   pre-commit:
     name: Code quality
@@ -84,14 +82,13 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with: { python-version: 3.x }
-    - run: python -m pip install pre-commit && python -m pip freeze --local
+    - uses: astral-sh/setup-uv@v5
+      with:
+        cache-dependency-glob: "**/pyproject.toml"
+        python-version: "3.12"  # TEMPORARY work around https://github.com/python/mypy/issues/18216
     - uses: actions/cache@v4
       with:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
-    - name: Force recreation of pre-commit virtual environment for mypy
-      if: github.event_name == 'schedule'  # Comment this line to run on a PR
-      run: pre-commit clean
-    - run: pre-commit run --all-files --color=always --show-diff-on-failure
+        lookup-only: ${{ github.event_name == 'schedule' }}  # Set 'true' to recreate cache
+    - run: uvx pre-commit run --all-files --color=always --show-diff-on-failure

.pre-commit-config.yaml

@@ -1,8 +1,9 @@
 repos:
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.1
+  rev: v1.14.1
   hooks:
   - id: mypy
+    pass_filenames: false
     additional_dependencies:
     - importlib_resources
     - lxml-stubs
@@ -18,9 +19,8 @@ repos:
     - types-python-dateutil
     - types-requests
     - xarray
-    args: []
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.7
+  rev: v0.9.1
   hooks:
   - id: ruff
   - id: ruff-format

README.rst

@@ -13,7 +13,7 @@ The package name is warning, by reference, to the adage “When you hold a hamme
 License
 =======
 
-Copyright © 2018–2024 genno contributors.
+Copyright © 2018–2025 genno contributors.
 
 Licensed under the GNU General Public License, version 3.0.
 

doc/conf.py

@@ -7,7 +7,7 @@
 # -- Project information ---------------------------------------------------------------
 
 project = "genno"
-copyright = "2018–2024, Genno contributors"
+copyright = "2018–%Y, Genno contributors"
 author = "Genno contributors"
 
 

doc/index.rst

@@ -60,7 +60,7 @@ Packages that extend :mod:`genno` include:
 License
 =======
 
-Copyright © 2018–2024 genno contributors.
+Copyright © 2018–2025 genno contributors.
 
 Licensed under the GNU General Public License, version 3.0.
 

genno/config.py

@@ -249,7 +249,7 @@ def _log_or_raise(exc: Exception, default_level: str, message: str):
             _log_or_raise(e, "warning", repr(e))
         else:
             if keys := list(iter_keys(result)):
-                log.info(f"Add {repr(keys[0])} + {len(keys)-1} partial sums")
+                log.info(f"Add {repr(keys[0])} + {len(keys) - 1} partial sums")
 
 
 @handles("alias")
@@ -288,7 +288,7 @@ def combine(c: Computer, info):
 
     added = iter_keys(c.add(key, task, strict=True, sums=True))
 
-    log.info(f"Add {repr(key)} + {len(list(added))-1} partial sums")
+    log.info(f"Add {repr(key)} + {len(list(added)) - 1} partial sums")
     log.debug("    as combination of")
     log.debug(f"    {repr(quantities)}")
 
@@ -354,7 +354,7 @@ def general(c: Computer, info):
         added = c.add(key, _seq(task), strict=True, sums=info.get("sums", False))
 
         if isinstance(added, tuple):
-            log.info(f"    + {len(added)-1} partial sums")
+            log.info(f"    + {len(added) - 1} partial sums")
 
 
 @handles("report")

genno/core/quantity.py

@@ -20,7 +20,7 @@ def assert_quantity(*args):
     for i, arg in enumerate(args):
         if not isinstance(arg, BaseQuantity):
             raise TypeError(
-                f"arg #{i+1} ({repr(arg)[:20]}) is not Quantity; likely an incorrect key"
+                f"arg #{i + 1} ({repr(arg)[:20]}) is not Quantity; likely an incorrect key"
             )
 
 

genno/core/sparsedataarray.py

@@ -139,9 +139,9 @@ def __init__(
 
         attrs = collect_attrs(data, attrs, kwargs)
 
-        assert 0 == len(
-            kwargs
-        ), f"Unrecognized kwargs {kwargs.keys()} to SparseDataArray()"
+        assert 0 == len(kwargs), (
+            f"Unrecognized kwargs {kwargs.keys()} to SparseDataArray()"
+        )
 
         if isinstance(data, int):
             data = float(data)

genno/testing/__init__.py

@@ -412,9 +412,9 @@ def assert_qty_allclose(
 
 def assert_units(qty: "AnyQuantity", exp: str) -> None:
     """Assert that `qty` has units `exp`."""
-    assert (
-        qty.units / qty.units._REGISTRY(exp)
-    ).dimensionless, f"Units '{qty.units:~}'; expected {repr(exp)}"
+    assert (qty.units / qty.units._REGISTRY(exp)).dimensionless, (
+        f"Units '{qty.units:~}'; expected {repr(exp)}"
+    )
 
 
 def random_qty(shape: dict[str, int], **kwargs) -> "AnyQuantity":

genno/tests/core/test_exceptions.py

@@ -48,9 +48,10 @@ def test_computationerror_format(caplog):
 Use Computer.describe\(...\) to trace the computation\.
 
 Computation traceback:
-  File ".*", line 4, in fail
-    'x' \+ 3.4  # Raises TypeError(\n.*)?
-TypeError: can only concatenate str \(not "float"\) to str.*"""
+  File ".*", line 5, in fail
+    "x" \+ 3.4  # Raises TypeError.*
+TypeError: can only concatenate str \(not "float"\) to str.*""",
+    re.DOTALL,
 )
 
 

genno/tests/data/exceptions.ipynb

@@ -8,12 +8,14 @@
    "source": [
     "import genno\n",
     "\n",
+    "\n",
     "def fail():\n",
-    "    'x' + 3.4  # Raises TypeError\n",
+    "    \"x\" + 3.4  # Raises TypeError\n",
+    "\n",
     "\n",
     "c = genno.Computer()\n",
-    "c.add('test', (fail,))\n",
-    "c.get('test')"
+    "c.add(\"test\", (fail,))\n",
+    "c.get(\"test\")"
    ]
   }
  ],

pyproject.toml

@@ -1,5 +1,6 @@
 [build-system]
-requires = ["build", "setuptools-scm"]
+requires = ["hatchling", "versioningit"]
+build-backend = "hatchling.build"
 
 [project]
 dynamic = ["version"]
@@ -56,7 +57,10 @@ tests = [
   "pytest-rerunfailures",
   "pytest-xdist",
 ]
-sparse = ["sparse >= 0.12"]
+sparse = [
+  "numba >= 0.54",  # Override >= 0.49 as of sparse 0.15.4
+  "sparse >= 0.12",
+]
 
 [project.urls]
 homepage = "https://github.com/khaeru/genno"
@@ -75,6 +79,16 @@ exclude_also = [
   "return NotImplemented",
 ]
 
+[tool.hatch]
+version.source = "versioningit"
+
+[tool.mypy]
+files = [
+  "conftest.py",
+  "doc",
+  "genno",
+]
+
 [[tool.mypy.overrides]]
 # Packages/modules for which no type hints are available
 module = [
@@ -111,7 +125,5 @@ ignore = ["E501", "W191"]
 # - .core.computer.add_queue: 11
 mccabe.max-complexity = 10
 
-[tool.setuptools.packages]
-find = {}
-
-[tool.setuptools_scm]
+[tool.versioningit]
+default-version = "0.1.dev1"  # Match setuptools-scm