Update workflow, requirements, ruff (#41)

* Update test/publish workflow * Update pre-commit, replace with ruff. * Rename * Update requirements.txt uv pip compile pyproject.toml -o requirements.txt --upgrade * Update dev requirements Manually. * Use requirements.txt in CI * No numpy 2.0, for now * Python 3.9 requirements.txt
dials · Oct 1, 2024 · 331a8ff · 331a8ff
1 parent 77fb61d
commit 331a8ff
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -1,34 +1,72 @@
-name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+name: Build and Test
 
 on: push
 
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+  build:
     runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+    - name: Install Build
+      run: |
+        python -mpip install --upgrade pip
+        pip install build
+    - name: Build distribution
+      run: |
+        python -mbuild
+        pip install dist/*.whl
+    - uses: actions/upload-artifact@v3
+      with:
+        path: ./dist/*
+  test:
+    needs: build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
 
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest dist/*.whl -r requirements.txt -r requirements_dev.txt pytest-md pytest-emoji
+    - name: Run pytest
+      uses: pavelzw/pytest-action@510c5e90c360a185039bea56ce8b3e7e51a16507   # v2.2.0
+      with:
+        click-to-expand: false
+        emoji: true
+        job-summary: true
+        verbose: false
+        custom-arguments: -v -ra
+        custom-pytest: PYTHONDEVMODE=1 pytest
+        report-title: Test Report
+
+  pypi-publish:
+    name: Upload release to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    environment:
+      name: Release
+      url: https://pypi.org/p/nxmx
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+    - uses: actions/download-artifact@v3
       with:
-        python-version: '3.10'
-    - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
+        name: artifact
+        path: dist
+    - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,35 +1,19 @@
-# Run 'libtbx.precommit install' to enable repository pre-commits.
-repos:
-
-# Bring Python code up to date with pyupgrade
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-  - id: pyupgrade
+ci:
+  autoupdate_schedule: quarterly
+  skip: [poetry-lock]
 
-# Automatically sort imports with isort
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-
-# Automatic source code formatting with Black
-- repo: https://github.com/psf/black
-  rev: 22.12.0
-  hooks:
-  - id: black
-    args: [--safe, --quiet]
+repos:
 
-# Enforce style with Flake8
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.2
   hooks:
-  - id: flake8
-    args: [--max-line-length=88, '--select=E401,E711,E712,E713,E714,E721,E722,E901,F401,F402,F403,F405,F631,F632,F633,F811,F812,F821,F822,F841,F901,W191,W291,W292,W293,W602,W603,W604,W605,W606']
+  - id: ruff
+    args: [--fix, --show-fixes, --exit-non-zero-on-fix]
+  - id: ruff-format
 
 # Format YAML & TOML files prettily
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.6.0
+  rev: v2.14.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, '2']
@@ -38,7 +22,7 @@ repos:
 
 # Syntax check with pre-commit out-of-the-box hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.6.0
   hooks:
   - id: check-ast
   - id: check-json

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,15 +3,8 @@ build-backend = "setuptools.build_meta"
 requires = ["setuptools>=61", "setuptools-scm"]
 
 [project]
-classifiers = [
-  "Programming Language :: Python :: 3"
-]
-dependencies = [
-  "h5py",
-  "pint",
-  "python-dateutil",
-  "scipy"
-]
+classifiers = ["Programming Language :: Python :: 3"]
+dependencies = ["h5py", "pint", "python-dateutil", "scipy", "numpy <2"]
 description = "Read HDF5 data conforming to the NXmx application definition of the NeXus format"
 dynamic = ["version"]
 keywords = ["NeXus", "NXmx"]
@@ -20,6 +13,10 @@ name = "nxmx"
 readme = "README.md"
 requires-python = ">=3.9"
 
+[tool.ruff.lint]
+ignore = ["E501"]
+select = ["E", "F", "UP", "W", "I", "C"]
+
 [tool.setuptools.package-data]
 nxmx = ["py.typed"]
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,28 @@
-h5py==3.9.0
-numpy==1.25.2
-pint==0.22
-python-dateutil==2.8.2
-scipy==1.11.1
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements.txt --python 3.9
+appdirs==1.4.4
+    # via pint
+flexcache==0.3
+    # via pint
+flexparser==0.3.1
+    # via pint
+h5py==3.12.1
+    # via nxmx (pyproject.toml)
+numpy==1.26.4
+    # via
+    #   nxmx (pyproject.toml)
+    #   h5py
+    #   scipy
+pint==0.24.3
+    # via nxmx (pyproject.toml)
+python-dateutil==2.9.0.post0
+    # via nxmx (pyproject.toml)
+scipy==1.13.1
+    # via nxmx (pyproject.toml)
+six==1.16.0
+    # via python-dateutil
+typing-extensions==4.12.2
+    # via
+    #   flexcache
+    #   flexparser
+    #   pint
diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -1,7 +1,2 @@
-h5py==3.9.0
-numpy==1.25.2
-pint==0.22
-pytest==7.4.0
-pytest-cov==4.1.0
-python-dateutil==2.8.2
-scipy==1.11.1
+pytest==8.3.3
+pytest-cov==5.0.0
diff --git a/src/nxmx/__init__.py b/src/nxmx/__init__.py
@@ -5,8 +5,9 @@
 import logging
 import operator
 from collections import abc, namedtuple
+from collections.abc import Iterable, Iterator, Sequence
 from functools import cached_property, reduce
-from typing import Iterable, Iterator, Sequence, Union, overload
+from typing import Union, overload
 
 import dateutil.parser
 import h5py
@@ -266,7 +267,6 @@ def data_scale_factor(self) -> str | None:
         if "data_scale_factor" in self._handle:
             return self._handle["data_scale_factor"][()]
 
-
     @cached_property
     def data_offset(self) -> str | None:
         """
@@ -278,7 +278,6 @@ def data_offset(self) -> str | None:
             return self._handle["data_offset"][()]
 
 
-
 class NXtransformations(H5Mapping):
     """Collection of axis-based translations and rotations to describe a geometry.
 
@@ -1162,12 +1161,10 @@ def __iter__(self) -> Iterator[NXtransformationsAxis]:
         return iter(self.transformations)
 
     @overload
-    def __getitem__(self, idx: int) -> NXtransformationsAxis:
-        ...
+    def __getitem__(self, idx: int) -> NXtransformationsAxis: ...
 
     @overload
-    def __getitem__(self, idx: slice) -> Sequence[NXtransformationsAxis]:
-        ...
+    def __getitem__(self, idx: slice) -> Sequence[NXtransformationsAxis]: ...
 
     def __getitem__(self, idx):
         return self.transformations[idx]

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -79,9 +79,9 @@ def nxmx_example():
             "fast_pixel_direction", data=7.5e-5
         )
         fast_pixel_direction.attrs["transformation_type"] = "translation"
-        fast_pixel_direction.attrs[
-            "depends_on"
-        ] = "/entry/instrument/detector/module/module_offset"
+        fast_pixel_direction.attrs["depends_on"] = (
+            "/entry/instrument/detector/module/module_offset"
+        )
         fast_pixel_direction.attrs["vector"] = np.array([-1.0, 0.0, 0.0])
         fast_pixel_direction.attrs["offset"] = np.array([0.0, 0.0, 0.0])
         fast_pixel_direction.attrs["offset_units"] = b"m"
@@ -91,9 +91,9 @@ def nxmx_example():
             "slow_pixel_direction", data=7.5e-5
         )
         slow_pixel_direction.attrs["transformation_type"] = "translation"
-        slow_pixel_direction.attrs[
-            "depends_on"
-        ] = "/entry/instrument/detector/module/module_offset"
+        slow_pixel_direction.attrs["depends_on"] = (
+            "/entry/instrument/detector/module/module_offset"
+        )
         slow_pixel_direction.attrs["vector"] = np.array([0.0, -1.0, 0.0])
         slow_pixel_direction.attrs["offset"] = np.array([0.0, 0.0, 0.0])
         slow_pixel_direction.attrs["offset_units"] = b"m"

diff --git a/tests/test_nxmx.py b/tests/test_nxmx.py
@@ -263,9 +263,9 @@ def detector_depends_on_example(request):
             "fast_pixel_direction", data=7.5e-5
         )
         fast_pixel_direction.attrs["transformation_type"] = "translation"
-        fast_pixel_direction.attrs[
-            "depends_on"
-        ] = "/entry/instrument/detector/module/module_offset"
+        fast_pixel_direction.attrs["depends_on"] = (
+            "/entry/instrument/detector/module/module_offset"
+        )
         fast_pixel_direction.attrs["vector"] = np.array([-1.0, 0.0, 0.0])
         fast_pixel_direction.attrs["offset"] = np.array([0.0, 0.0, 0.0])
         fast_pixel_direction.attrs["offset_units"] = "m"
@@ -274,13 +274,13 @@ def detector_depends_on_example(request):
         module_offset = module.create_dataset("module_offset", data=0)
         module_offset.attrs["transformation_type"] = "translation"
         if request.param:
-            module_offset.attrs[
-                "depends_on"
-            ] = "/entry/instrument/detector/transformations/det_z_tune"
+            module_offset.attrs["depends_on"] = (
+                "/entry/instrument/detector/transformations/det_z_tune"
+            )
         else:
-            module_offset.attrs[
-                "depends_on"
-            ] = "/entry/instrument/detector/transformations/det_z"
+            module_offset.attrs["depends_on"] = (
+                "/entry/instrument/detector/transformations/det_z"
+            )
         module_offset.attrs["vector"] = np.array([1.0, 0.0, 0.0])
         module_offset.attrs["offset"] = np.array([0.155985, 0.166904, -0])
         module_offset.attrs["offset_units"] = "m"
@@ -291,9 +291,9 @@ def detector_depends_on_example(request):
             det_z_tune = transformations.create_dataset(
                 "det_z_tune", data=np.array([-0.5])
             )
-            det_z_tune.attrs[
-                "depends_on"
-            ] = b"/entry/instrument/detector/transformations/det_z"
+            det_z_tune.attrs["depends_on"] = (
+                b"/entry/instrument/detector/transformations/det_z"
+            )
             det_z_tune.attrs["transformation_type"] = b"translation"
             det_z_tune.attrs["units"] = b"mm"
             det_z_tune.attrs["vector"] = np.array([0.0, 0.0, 1.0])