build: explicit interpreter, drop --find-interpreter

.github/workflows/test_pytest.yml

@@ -33,6 +33,7 @@ jobs:
         name: Test on Linux
         runs-on: ubuntu-latest
         strategy:
+            fail-fast: false
             matrix:
                 pixi-env: [py312, py313, py314]
         steps:
@@ -54,6 +55,7 @@ jobs:
         name: Test on OSX
         runs-on: macOS-latest
         strategy:
+            fail-fast: false
             matrix:
                 pixi-env: [py312, py313, py314]
         steps:

.github/workflows/wheels-preview.yml

@@ -44,7 +44,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
+                  args: --release --out dist -i python3.12 python3.13 python3.14
                   manylinux: 2_28
                   before-script-linux: |
                       set -ex
@@ -101,7 +101,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
+                  args: --release --out dist -i python3.12 python3.13 python3.14
                   manylinux: musllinux_1_2
                   before-script-linux: |
                       apt-get update
@@ -149,7 +149,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
+                  args: --release --out dist -i python3.12 python3.13 python3.14
             - name: Upload wheels
               uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
               with:
@@ -194,6 +194,9 @@ jobs:
         name: Publish preview to TestPyPI
         runs-on: ubuntu-latest
         needs: [linux, musllinux, macos, sdist]
+        environment: testpypi
+        permissions:
+            id-token: write
         steps:
             - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
               with:
@@ -204,6 +207,5 @@ jobs:
               uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3
               with:
                   repository-url: https://test.pypi.org/legacy/
-                  password: ${{ secrets.TESTPYPI_API_TOKEN }}
                   packages-dir: dist
                   skip-existing: true

.github/workflows/wheels.yml

@@ -29,8 +29,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
-                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+                  args: --release --out dist -i python3.12 python3.13 python3.14
                   manylinux: 2_28
                   before-script-linux: |
                       set -ex
@@ -87,8 +86,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
-                  # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
+                  args: --release --out dist -i python3.12 python3.13 python3.14
                   manylinux: musllinux_1_2
                   before-script-linux: |
                       apt-get update
@@ -122,7 +120,7 @@ jobs:
               uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1.51.0
               with:
                   target: ${{ matrix.platform.target }}
-                  args: --release --out dist --find-interpreter
+                  args: --release --out dist -i python3.12 python3.13 python3.14
             - name: Upload wheels
               uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
               with:
@@ -151,6 +149,7 @@ jobs:
         runs-on: ubuntu-latest
         if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
         needs: [linux, musllinux, macos, sdist]
+        environment: pypi
         permissions:
             id-token: write
             contents: write
@@ -169,6 +168,5 @@ jobs:
               if: ${{ startsWith(github.ref, 'refs/tags/') }}
               uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3
               with:
-                  password: ${{ secrets.PYPI_API_TOKEN }}
                   packages-dir: dist
                   skip-existing: true

.pre-commit-config.yaml

@@ -6,10 +6,10 @@ repos:
   - repo: local
     hooks:
       - id: check-version-sync
-        name: check Rust versions (docs - toml) and deeptools versions (toml - galaxy) to stay in sync
+        name: check Rust, Python and deeptools versions to stay in sync
         entry: python scripts/check_version_sync.py
         language: system
-        files: ^(Cargo\.toml|pyproject\.toml|\.readthedocs\.yaml|galaxy/wrapper/deepTools_macros\.xml)$
+        files: ^(Cargo\.toml|pyproject\.toml|\.readthedocs\.yaml|galaxy/wrapper/deepTools_macros\.xml|\.github/workflows/(test_pytest|test_planemo|wheels|wheels-preview)\.yml|scripts/check_version_sync\.py)$
         pass_filenames: false
   - repo: local
     hooks:

pyproject.toml

@@ -49,7 +49,11 @@ description = "Useful tools for exploring deep sequencing data."
 license = {file = "LICENSE.txt"}
 classifiers = [
     "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering :: Bio-Informatics"
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    # Supported Python versions:
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14"
 ]
 readme = "README.md"
 [project.optional-dependencies]
@@ -75,9 +79,6 @@ repository = "https://github.com/deeptools/deepTools"
 [tool.setuptools]
 packages = ["deeptools"]
 
-[tool.ruff]
-target-version = "py312"
-
 [tool.ruff.lint]
 ignore = [
     "N999", #invalid module name

scripts/check_version_sync.py

@@ -99,9 +99,49 @@ def galaxy_tool_version() -> str:
     return match.group(1)
 
 
+def _grep(path: str, pattern: str) -> list[str]:
+    return re.findall(pattern, (REPO_ROOT / path).read_text(), re.MULTILINE)
+
+
+def python_version_mismatches() -> dict[str, tuple[object, object]]:
+    """Check every hardcoded Python version against the pyproject.toml classifiers."""
+    project = tomllib.loads((REPO_ROOT / "pyproject.toml").read_text())
+    classifiers = project["project"]["classifiers"]
+    versions = [c.rsplit(" ", 1)[1] for c in classifiers
+                if re.fullmatch(r"Programming Language :: Python :: 3\.\d+", c)]
+    if not versions:
+        sys.exit("pyproject.toml: no 'Programming Language :: Python :: 3.X' classifiers found")
+    if any(c.startswith("Programming Language :: Python :: Free Threading") for c in classifiers):
+        versions += [f"{v}t" for v in versions if _version_tuple(v) >= (3, 14)]
+    envs = [f"py{v.replace('.', '')}" for v in versions]
+    interpreters = [f"python{v}" for v in versions]
+
+    pixi_envs = [name for name in project["tool"]["pixi"]["environments"] if name.startswith("py3")]
+    rtd = _grep(".readthedocs.yaml", r'^\s*python:\s*"([\d.]+)"')
+    checks = {
+        "pyproject.toml requires-python": (f">= {versions[0]}", project["project"]["requires-python"]),
+        "pyproject.toml pixi environments": (envs, pixi_envs),
+        "test_planemo.yml python-version (lowest)": (
+            [versions[0]],
+            _grep(".github/workflows/test_planemo.yml", r'python-version:\s*"([\d.]+)"'),
+        ),
+        ".readthedocs.yaml python (any supported)": (True, bool(rtd) and rtd[0] in versions),
+    }
+    # Files with several matrices / build steps: every one of them must match.
+    matrices = [[e.strip() for e in m.split(",")]
+                for m in _grep(".github/workflows/test_pytest.yml", r"pixi-env:\s*\[([^\]]*)\]")]
+    checks["test_pytest.yml pixi-env matrices"] = ([envs] * max(len(matrices), 1), matrices)
+    for workflow in ("wheels.yml", "wheels-preview.yml"):
+        # a wheel build without `-i` (e.g. --find-interpreter) yields an empty list
+        builds = [args.split() for args in
+                  _grep(f".github/workflows/{workflow}", r"^\s*args:\s*--release(?:.*?\s-i\s+(.*))?.*$")]
+        checks[f"{workflow} maturin -i"] = ([interpreters] * max(len(builds), 1), builds)
+    return {name: pair for name, pair in checks.items() if pair[0] != pair[1]}
+
+
 def main() -> None:
     cargo_version = cargo_rust_version()
-    mismatches: dict[str, tuple[str, str]] = {}
+    mismatches: dict[str, tuple[object, object]] = {}
 
     pixi_version = pixi_rust_version()
     if pixi_version != cargo_version:
@@ -117,6 +157,10 @@ def main() -> None:
     elif rtd_version != "latest" and _version_tuple(rtd_version) < _version_tuple(cargo_version):
         mismatches["rust: .readthedocs.yaml build.tools.rust"] = (f">= {cargo_version}", rtd_version)
 
+    mismatches.update(
+        {f"python: {name}": pair for name, pair in python_version_mismatches().items()}
+    )
+
     pkg_version = deeptools_version()
     galaxy_version = galaxy_tool_version()
     if galaxy_version != pkg_version: