Merge branch 'main' into ruff

* main: [pre-commit.ci] pre-commit autoupdate (SciTools#425) Adopt cython3 (require >=3) (SciTools#460) Add repo-review (SciTools#456) Fully support Python 3.12 (SciTools#461) Bump peter-evans/create-pull-request from 6.0.4 to 7.0.5 (SciTools#459) Fix for bad git path in GHA macos instances. (SciTools#464) test macos wheels (SciTools#458) Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 (SciTools#457) Fixes for CI wheels (SciTools#455) Dependabot check weekly. (SciTools#439) # Conflicts: # .pre-commit-config.yaml # cf_units/tests/test_coding_standards.py # pyproject.toml
rcomer · Sep 24, 2024 · 47592b4 · 47592b4
2 parents 23c47fb + cc0ea12
commit 47592b4
Show file tree

Hide file tree

Showing 24 changed files with 979 additions and 805 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -7,8 +7,12 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      # Check for updates to GitHub Actions every weekday
-      interval: "daily"
+      # Check later in the week - the upstream dependabot check in `workflows` runs deliberately early in the week.
+      #  Therefore allowing time for the `workflows` update to be merged-and-released first.
+      interval: "weekly"
+      day: "thursday"
+      time: "01:00"
+      timezone: "Europe/London"
     labels:
       - "New: Pull Request"
       - "Bot"
diff --git a/.github/workflows/ci-locks.yml b/.github/workflows/ci-locks.yml
@@ -27,7 +27,7 @@ jobs:
       ENV_NAME: "ci-locks"
     strategy:
       matrix:
-        lock: [py39-lock, py310-lock, py311-lock]
+        lock: [py310-lock, py311-lock, py312-lock]
     steps:
     - name: "Checkout"
       uses: actions/checkout@v4
@@ -54,7 +54,7 @@ jobs:
         miniforge-version: latest
         channels: conda-forge,defaults
         activate-environment: ${{ env.ENV_NAME }}
-        auto-update-conda: true 
+        auto-update-conda: true
         use-only-tar-bz2: true
 
     - name: "Conda environment cache"
@@ -122,7 +122,7 @@ jobs:
     - name: "Push pull-request"
       id: cpr
       # v3.12.1 (release date 31 Jan 2022)
-      uses: peter-evans/create-pull-request@9153d834b60caba6d51c9b9510b087acf9f33f83
+      uses: peter-evans/create-pull-request@5e914681df9dc83aa4e4905692ca88beb2f9e91f
       with:
         token: ${{ steps.generate-token.outputs.token }}
         add-paths: ${{ github.workspace }}/requirements/locks/*.txt

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -32,20 +32,26 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        version: [py39, py310, py311]
+        version: [py310, py311, py312]
+        gitpath-prepend: [""]
         include:
           - os: ubuntu-latest
             platform: linux
           - os: ubuntu-latest
-            version: py311
+            version: py312
             posargs: "--cov-report=xml --cov"
             post-command: codecov
           - os: macos-latest
-            version: py311
+            version: py312
             platform: osx
+            # On macos, the up-to-date git may not be first on the path
+            # N.B. setting includes a final ":", to simplify the path setting command
+            gitpath-prepend: "/opt/homebrew/bin:"
     steps:
     - name: "Checkout"
       uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: "Environment configure"
       env:
@@ -106,4 +112,7 @@ jobs:
       env:
         POST_COMMAND: ${{ matrix.post-command }}
       run: |
+        export PATH=${{ matrix.gitpath-prepend }}$PATH
+        which git
+        git --version
         tox -e ${{ matrix.version }}-${{ matrix.platform }}-test -- ${{ matrix.posargs }}
diff --git a/.github/workflows/ci-wheels.yml b/.github/workflows/ci-wheels.yml
@@ -20,45 +20,59 @@ on:
       - "pre-commit-ci-update-config"
       - "dependabot/*"
 
+  workflow_dispatch:
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   build_bdist:
     name: "Build ${{ matrix.os }} (${{ matrix.arch }}) wheels"
+    # TBD: extend to support windows
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        # TBD: extend to support windows
-        os: ["ubuntu-latest", "macos-11", "macos-14"]
+        os: ["ubuntu-latest", "macos-latest", "macos-13"]
+        arch: ["x86_64", "arm64"]
         include:
         - os: ubuntu-latest
           arch: x86_64
           incdir: /usr/include/udunits2
           libdir: /usr/lib64
           xml_path: /usr/share/udunits/udunits2.xml
-        - os: macos-11
+        - os: macos-13
           arch: x86_64
           incdir: /usr/local/Cellar/udunits/2.2.28/include
           libdir: /usr/local/Cellar/udunits/2.2.28/lib
           xml_path: /usr/local/Cellar/udunits/2.2.28/share/udunits/udunits2-common.xml
-        - os: macos-14
+        - os: macos-latest
           arch: arm64
           incdir: /opt/homebrew/Cellar/udunits/2.2.28/include
           libdir: /opt/homebrew/Cellar/udunits/2.2.28/lib
           xml_path: /opt/homebrew/Cellar/udunits/2.2.28/share/udunits/udunits2-common.xml
+        exclude:
+        - os: "ubuntu-latest"
+          arch: "arm64"
+        - os: "macos-latest"
+          arch: "x86_64"
+        - os: "macos-13"
+          arch: "arm64"
 
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
+    - name: "Set MACOSX_DEPLOYMENT_TARGET"
+      if: startsWith(matrix.os, 'macos')
+      run: echo "MACOSX_DEPLOYMENT_TARGET=$([[ ${{ matrix.os }} == 'macos-latest' ]] && echo '14.0' || echo '13.0')" >> $GITHUB_ENV
+
     - name: "Building ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v2.21.1
       env:
-        CIBW_SKIP: "cp36-* cp37-* cp38-* cp312-* pp* *-musllinux*"
+        CIBW_SKIP: "cp39-* cp313-* pp* *-musllinux*"
         CIBW_ARCHS: ${{ matrix.arch }}
         CIBW_BUILD_FRONTEND: build
         CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,5 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# See https://github.com/scientific-python/cookie#sp-repo-review for repo-review
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
@@ -24,6 +25,13 @@ repos:
     -   id: sort-all
         types: [file, python]
 
+-   repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
+    hooks:
+    -   id: sp-repo-review
+        additional_dependencies: ["repo-review[cli]"]   # TODO: Only neededed if extra dependencies are required
+        #args: ["--show=errskip"]  # show everything for the moment
+
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.1.5"
     hooks:

diff --git a/cf_units/_udunits2.pyx b/cf_units/_udunits2.pyx
@@ -19,6 +19,9 @@ import numpy as np
 cimport numpy as np
 from libc cimport errno, string
 
+# Must be called to use the C-API with Numpy
+np.import_array()
+
 
 cdef int _STRING_BUFFER_DEPTH = 128
 cdef list _UT_STATUS = ['UT_SUCCESS', 'UT_BAD_ARG', 'UT_EXISTS', 'UT_NO_UNIT',

diff --git a/cf_units/tests/test_coding_standards.py b/cf_units/tests/test_coding_standards.py
@@ -3,11 +3,10 @@
 # This file is part of cf-units and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
 
-import os
 import subprocess
 from datetime import datetime
 from fnmatch import fnmatch
-from glob import glob
+from pathlib import Path
 
 import pytest
 
@@ -19,21 +18,18 @@
 # See LICENSE in the root of the repository for full licensing details."""
 
 
-# Guess cf_units repo directory of cf_units - realpath is used to mitigate
-# against Python finding the cf_units package via a symlink.
-DIR = os.path.realpath(os.path.dirname(cf_units.__file__))
-REPO_DIR = os.path.dirname(DIR)
-DOCS_DIR = os.path.join(REPO_DIR, "doc")
-DOCS_DIR = cf_units.config.get_option("Resources", "doc_dir", default=DOCS_DIR)
+REPO_DIR = Path(__file__).resolve().parents[2]
+DOCS_DIR = REPO_DIR / "docs"
+DOCS_DIR = Path(
+    cf_units.config.get_option("Resources", "doc_dir", default=DOCS_DIR)
+)
 exclusion = ["Makefile", "make.bat", "build"]
-DOCS_DIRS = glob(os.path.join(DOCS_DIR, "*"))
-DOCS_DIRS = [
-    DOC_DIR
-    for DOC_DIR in DOCS_DIRS
-    if os.path.basename(DOC_DIR) not in exclusion
-]
+DOCS_DIRS = DOCS_DIR.glob("*")
+DOCS_DIRS = [DOC_DIR for DOC_DIR in DOCS_DIRS if DOC_DIR.name not in exclusion]
+IS_GIT_REPO = (REPO_DIR / ".git").is_dir()
 
 
+@pytest.mark.skipif(not IS_GIT_REPO, reason="Not a git repository.")
 class TestLicenseHeaders:
     @staticmethod
     def whatchanged_parse(whatchanged_output):
@@ -73,10 +69,6 @@ def last_change_by_fname():
             or cannot be found by subprocess, an IOError may also be raised.
 
         """
-        # Check the ".git" folder exists at the repo dir.
-        if not os.path.isdir(os.path.join(REPO_DIR, ".git")):
-            raise ValueError(f"{REPO_DIR} is not a git repository.")
-
         # Call "git whatchanged" to get the details of all the files and when
         # they were last changed.
         output = subprocess.check_output(
@@ -100,20 +92,14 @@ def test_license_headers(self):
             "cf_units/_udunits2_parser/parser/*",
         )
 
-        try:
-            last_change_by_fname = self.last_change_by_fname()
-        except ValueError:
-            # Caught the case where this is not a git repo.
-            return pytest.skip(
-                "cf_units installation did not look like a " "git repo."
-            )
+        last_change_by_fname = self.last_change_by_fname()
 
         failed = False
         for fname in sorted(last_change_by_fname):
-            full_fname = os.path.join(REPO_DIR, fname)
+            full_fname = REPO_DIR / fname
             if (
-                full_fname.endswith(".py")
-                and os.path.isfile(full_fname)
+                full_fname.suffix == ".py"
+                and full_fname.is_file()
                 and not any(fnmatch(fname, pat) for pat in exclude_patterns)
             ):
                 with open(full_fname) as fh:
@@ -129,3 +115,93 @@ def test_license_headers(self):
             raise AssertionError(
                 "There were license header failures. See stdout."
             )
+
+
+@pytest.mark.skipif(not IS_GIT_REPO, reason="Not a git repository.")
+def test_python_versions():
+    """Confirm alignment of ALL files listing supported Python versions."""
+    supported = ["3.10", "3.11", "3.12"]
+    supported_strip = [ver.replace(".", "") for ver in supported]
+    supported_latest = supported_strip[-1]
+
+    workflows_dir = REPO_DIR / ".github" / "workflows"
+
+    # Places that are checked:
+    pyproject_toml_file = REPO_DIR / "pyproject.toml"
+    setup_cfg_file = REPO_DIR / "setup.cfg"
+    tox_file = REPO_DIR / "tox.ini"
+    ci_locks_file = workflows_dir / "ci-locks.yml"
+    ci_tests_file = workflows_dir / "ci-tests.yml"
+    ci_wheels_file = workflows_dir / "ci-wheels.yml"
+
+    text_searches: list[tuple[Path, str]] = [
+        (
+            pyproject_toml_file,
+            "target-version = ["
+            + ", ".join([f'"py{p}"' for p in supported_strip])
+            + "]",
+        ),
+        (
+            setup_cfg_file,
+            "\n    ".join(
+                [
+                    f"Programming Language :: Python :: {ver}"
+                    for ver in supported
+                ]
+            ),
+        ),
+        (
+            tox_file,
+            "[testenv:py{" + ",".join(supported_strip) + "}-lock]",
+        ),
+        (
+            tox_file,
+            "[testenv:py{"
+            + ",".join(supported_strip)
+            + "}-{linux,osx,win}-test]",
+        ),
+        (
+            ci_locks_file,
+            "lock: ["
+            + ", ".join([f"py{p}-lock" for p in supported_strip])
+            + "]",
+        ),
+        (
+            ci_tests_file,
+            (
+                f"os: [ubuntu-latest]\n"
+                f"{8*' '}version: ["
+                + ", ".join([f"py{p}" for p in supported_strip])
+                + "]"
+            ),
+        ),
+        (
+            ci_tests_file,
+            (f"os: ubuntu-latest\n" f"{12*' '}version: py{supported_latest}"),
+        ),
+        (
+            ci_tests_file,
+            (f"os: macos-latest\n" f"{12*' '}version: py{supported_latest}"),
+        ),
+    ]
+
+    # This routine will not check for file existence first - if files are
+    #  being added/removed we want developers to be aware that this test will
+    #  need to be updated.
+    for path, search in text_searches:
+        assert search in path.read_text()
+
+    tox_text = tox_file.read_text()
+    for version in supported_strip:
+        # A fairly lazy implementation, but should catch times when the section
+        #  header does not match the conda_spec for the `tests` section.
+        #  (Note that Tox does NOT provide its own helpful error in these cases).
+        py_version = f"py{version}"
+        assert tox_text.count(f"    {py_version}-") == 3
+        assert tox_text.count(f"{py_version}-lock") == 3
+
+    ci_wheels_text = ci_wheels_file.read_text()
+    (cibw_line,) = [
+        line for line in ci_wheels_text.splitlines() if "CIBW_SKIP" in line
+    ]
+    assert all([p not in cibw_line for p in supported_strip])
diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ requires = [
   "setuptools_scm[toml]>=7.0",
   "wheel",
   "oldest-supported-numpy",
-  "Cython"
+  "Cython>=3.0"
 ]
 # Defined by PEP 517
 build-backend = "setuptools.build_meta"
@@ -47,7 +47,7 @@ local_scheme = "dirty-tag"
 
 [tool.ruff]
 line-length = 79
-target-version = "py38"
+target-version = ["py310", "py311", "py312"]
 select = [
     # pyflakes
     "F",
@@ -77,3 +77,26 @@ convention = "numpy"
 [tool.ruff.per-file-ignores]
 # Allow the longer comment lines that the generated code produces.
 "cf_units/_udunits2_parser/parser/*.py" = ["E501"]
+
+[tool.repo-review]
+# These are a list of the currently failing tests:
+ignore = [
+  "PY005",  # Has tests folder
+  "PP003",  # Does not list wheel as a build-dep
+  "PP304",  # Sets the log level in pytest
+  "PP305",  # Specifies xfail_strict
+  "PP306",  # Specifies strict config
+  "PP307",  # Specifies strict markers
+  "PP309",  # Filter warnings specified
+  "GH104",  # Use unique names for upload-artifact
+  "GH212",  # Require GHA update grouping
+  "PC110",  # Uses black or ruff-format
+  "PC140",  # Uses a type checker
+  "PC160",  # Uses a spell checker
+  "PC170",  # Uses PyGrep hooks (only needed if rST present)
+  "PC180",  # Uses a markdown formatter
+  "PC190",  # Uses Ruff
+  "PC901",  # Custom pre-commit CI message
+  "MY100",  # Uses MyPy (pyproject config)
+  "RF001",  # Uses RUFF
+]