Release 0.14

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,8 +13,8 @@
 ## Checklist
 
 - [ ] Tests added/updated (asserting against a reference value where possible)
-- [ ] `black`, `isort`, `flake8`, and `mypy` pass
-- [ ] `coverage run -m pytest` passes and stays above the coverage gate
+- [ ] `scripts/check.sh` passes (black, isort, flake8, mypy), with the tests of what changed
+- [ ] Anything that must agree with the change is updated with it (see CONTRIBUTING.md, "What must agree")
 - [ ] `CHANGELOG.md` updated under `[Unreleased]`
 - [ ] Any Monte-Carlo tests are seeded (deterministic)
 

.github/workflows/actions.yml

@@ -2,12 +2,18 @@ name: actions
 
 run-name: RePyability CI
 
-on: [push, pull_request]
+# The one automated test run: the full suite on a pull request into master
+# (from dev). Nothing else runs it; release.yml publishes only what it
+# passed.
+on:
+  pull_request:
+    branches: [master]
 
 jobs:
   lint:
     name: lint (black, isort, flake8, mypy)
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - uses: actions/checkout@v5
 
@@ -36,6 +42,7 @@ jobs:
   test:
     name: test (Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
+    timeout-minutes: 120
     strategy:
       fail-fast: false
       matrix:
@@ -53,25 +60,32 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e .[dev]
 
+      - name: pytest
+        # Every version runs the suite on all the runner's cores; coverage is
+        # measured once, on the newest Python (next step).
+        if: matrix.python-version != '3.14'
+        run: python -m pytest -n auto -q --durations=30
+
       - name: pytest (under coverage)
-        # From Python 3.12 coverage can measure through sys.monitoring,
-        # which counts the same lines as its default tracer (sys.settrace)
-        # several times faster: under the tracer, Python 3.12's job took
-        # over an hour. Python 3.11 has no sys.monitoring, and an empty
-        # COVERAGE_CORE leaves it the default tracer.
+        # Coverage is measured on Python 3.14 alone, through sys.monitoring,
+        # which is several times faster than its default tracer
+        # (sys.settrace): under the tracer, Python 3.11's job took an hour.
+        # pytest-cov collects it from each of pytest-xdist's workers.
+        if: matrix.python-version == '3.14'
         env:
-          COVERAGE_CORE: ${{ matrix.python-version != '3.11' && 'sysmon' || '' }}
-        run: coverage run -m pytest
+          COVERAGE_CORE: sysmon
+        run: python -m pytest -n auto -q --durations=30 --cov --cov-report=
 
       - name: coverage report (enforces the fail_under gate)
+        if: matrix.python-version == '3.14'
         run: coverage report
 
       - name: coverage html
-        if: matrix.python-version == '3.11'
+        if: matrix.python-version == '3.14'
         run: coverage html
 
       - name: Upload coverage html report artifact
-        if: matrix.python-version == '3.11'
+        if: matrix.python-version == '3.14'
         uses: actions/upload-artifact@v4
         with:
           name: coverage-html-report
@@ -83,6 +97,7 @@ jobs:
     # the compiled engine runs and its results are checked against Python's.
     name: test (with numba, Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
+    timeout-minutes: 120
     strategy:
       fail-fast: false
       matrix:
@@ -102,13 +117,16 @@ jobs:
           python -c "import numba; print('numba', numba.__version__)"
 
       - name: pytest
-        run: python -m pytest -q
+        run: python -m pytest -n auto -q --durations=30
 
   test-minimum:
-    # CI otherwise installs the newest surpyval, so once surpyval releases,
-    # nothing would test the oldest one pyproject.toml still allows.
-    name: test (minimum surpyval)
+    # The other jobs install the newest of every dependency, so nothing
+    # else tests the oldest that pyproject.toml allows: this one installs
+    # each dependency at its floor (numpy, scipy, networkx, surpyval, tqdm),
+    # on the oldest Python, then the test tools.
+    name: test (minimum dependencies)
     runs-on: ubuntu-latest
+    timeout-minutes: 120
     steps:
       - uses: actions/checkout@v5
 
@@ -117,29 +135,20 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install the package, then the oldest surpyval it allows
+      - name: Install the package at its dependencies' floors
         run: |
-          python -m pip install --upgrade pip
-          pip install -e .[dev]
-          minimum=$(python - <<'EOF'
-          import re
-          import tomllib
-
-          with open("pyproject.toml", "rb") as f:
-              dependencies = tomllib.load(f)["project"]["dependencies"]
-          spec = next(d for d in dependencies if d.startswith("surpyval"))
-          print(re.search(r">=\s*([0-9][0-9.]*)", spec).group(1))
-          EOF
-          )
-          pip install "surpyval==$minimum"
-          python -c "import surpyval; print('surpyval', surpyval.__version__)"
+          python -m pip install --upgrade pip uv
+          uv pip install --system --resolution lowest-direct -e .
+          uv pip install --system "pytest>=7.0" "pytest-xdist>=3.5" "pytest-timeout>=2.3"
+          python -c "import numpy, scipy, networkx, surpyval, tqdm; print('numpy', numpy.__version__, 'scipy', scipy.__version__, 'networkx', networkx.__version__, 'surpyval', surpyval.__version__, 'tqdm', tqdm.__version__)"
 
       - name: pytest
-        run: python -m pytest -q
+        run: python -m pytest -n auto -q --durations=30
 
   docs:
     name: docs (strict build)
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
       - uses: actions/checkout@v5
 

.github/workflows/close-issues.yml

@@ -0,0 +1,56 @@
+name: close issues
+
+# Close the issues a pull request into dev finishes, when it merges.
+# GitHub itself closes an issue only when the pull request that says
+# "Closes #N" merges into the default branch (master), which here happens
+# at a release: this closes them as the work reaches dev, with a comment
+# naming the pull request. It runs no tests (the one automated test run
+# is actions.yml, on the pull request from dev into master).
+
+on:
+  pull_request:
+    types: [closed]
+    branches: [dev]
+
+permissions:
+  issues: write
+  pull-requests: read
+
+jobs:
+  close:
+    name: close the issues the pull request finishes
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/github-script@v7
+        with:
+          script: |
+            const pull = context.payload.pull_request;
+            const body = pull.body || "";
+            // The keywords GitHub takes, in a body line such as "Closes #N".
+            const pattern = /\b(?:close[sd]?|fix(?:e[sd])?|resolve[sd]?)\s+#(\d+)/gi;
+            const numbers = new Set();
+            for (const match of body.matchAll(pattern)) {
+              numbers.add(Number(match[1]));
+            }
+            for (const issue_number of numbers) {
+              const { data: issue } = await github.rest.issues.get({
+                ...context.repo,
+                issue_number,
+              });
+              if (issue.pull_request || issue.state === "closed") {
+                continue;
+              }
+              await github.rest.issues.createComment({
+                ...context.repo,
+                issue_number,
+                body: `Merged into dev by #${pull.number}: it reaches users with the next release.`,
+              });
+              await github.rest.issues.update({
+                ...context.repo,
+                issue_number,
+                state: "closed",
+                state_reason: "completed",
+              });
+              core.info(`Closed #${issue_number}`);
+            }

.github/workflows/release.yml

@@ -6,7 +6,8 @@ name: release
 #    `gh workflow run release.yml --ref master -f version=X.Y`; or the REST
 #    API). It checks that the version typed in matches
 #    repyability/_version.py, that CHANGELOG.md has a dated section for it,
-#    that the tag vX.Y does not exist yet, that CI passed on the commit and
+#    that the tag vX.Y does not exist yet, that the full suite passed on
+#    these files (on the pull request from dev into master) and
 #    that PyPI does not have the version. It then builds, publishes to PyPI,
 #    and last creates the tag vX.Y and a GitHub Release. The release notes
 #    open with the CHANGELOG section's summary, followed by GitHub's
@@ -87,11 +88,26 @@ jobs:
             echo "::error::The tag v$version already exists."
             exit 1
           fi
-          passed=$(gh api "repos/$GITHUB_REPOSITORY/actions/workflows/actions.yml/runs?head_sha=$GITHUB_SHA&status=success" --jq '.total_count')
-          if [ "$passed" -eq 0 ]; then
-            echo "::error::CI (actions.yml) has not passed on $GITHUB_SHA; wait for it, or fix it."
+          # The full suite runs on the pull request from dev into master
+          # (actions.yml), whose run is recorded against dev's commit. The
+          # merge commit on master holds the same files, so a pass on this
+          # commit, or on a parent with the same files, counts.
+          repo="repos/$GITHUB_REPOSITORY"
+          tree=$(gh api "$repo/git/commits/$GITHUB_SHA" --jq '.tree.sha')
+          passed=""
+          for sha in "$GITHUB_SHA" $(gh api "$repo/git/commits/$GITHUB_SHA" --jq '.parents[].sha'); do
+            [ "$(gh api "$repo/git/commits/$sha" --jq '.tree.sha')" = "$tree" ] || continue
+            runs=$(gh api "$repo/actions/workflows/actions.yml/runs?head_sha=$sha&status=success" --jq '.total_count')
+            if [ "$runs" -gt 0 ]; then
+              passed=$sha
+              break
+            fi
+          done
+          if [ -z "$passed" ]; then
+            echo "::error::The full suite (actions.yml) has not passed on these files: on $GITHUB_SHA or the dev commit it merged. Open the pull request from dev into master and wait for it."
             exit 1
           fi
+          echo "The full suite passed on $passed, with the same files as $GITHUB_SHA."
           pypi=$(curl -s -o /dev/null -w '%{http_code}' "https://pypi.org/pypi/repyability/$version/json")
           if [ "$pypi" = 200 ]; then
             echo "::error::repyability $version is already on PyPI."

.pre-commit-config.yaml

@@ -8,17 +8,10 @@
 repos:
   # Organise imports
   - repo: https://github.com/PyCQA/isort
-    rev: "6.0.1"
+    rev: "9.0.1"
     hooks:
       - id: isort
 
-  # Update old python syntax
-  - repo: https://github.com/asottile/pyupgrade
-    rev: "v3.19.1"
-    hooks:
-      - id: pyupgrade
-        args: ["--py310-plus"]
-
   # Format with Black
   - repo: https://github.com/psf/black
     rev: "26.3.1"
@@ -27,18 +20,19 @@ repos:
 
   # Lint with flake8 (reads [tool.flake8] from pyproject via flake8-pyproject)
   - repo: https://github.com/PyCQA/flake8
-    rev: "7.3.0"
+    rev: "7.4.1"
     hooks:
       - id: flake8
         additional_dependencies: ["flake8-pyproject"]
 
   # Uses the locally installed mypy (the mirror uses opinionated args by
-  # default); tests are excluded to match the CI configuration.
+  # default), on the whole package as CI runs it: checking the staged files
+  # alone misses errors their changes cause elsewhere.
   - repo: local
     hooks:
       - id: mypy
         name: mypy
-        entry: mypy
+        entry: mypy repyability
         language: system
-        types: [python]
-        exclude: "^repyability/tests/"
+        pass_filenames: false
+        files: "^repyability/"