Merge pull request #42 from dstansby/composite-actions

Use brainglobe/actions composite actions for GH actions

.github/workflows/test_and_deploy.yml

@@ -6,33 +6,7 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - name: checkout source
-        uses: actions/checkout@v2
-      - name: set up python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: set PY
-        run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
-      - name: cache stuff
-        uses: actions/cache@v2
-        with:
-          path: |
-            ${{ env.pythonLocation }}
-            ~/.cache/pre-commit
-          key: |
-            pre-commit-${{ env.PY }}-${{ hashFiles('.pre-commit-config.yaml') }}
-      - name: install dependencies
-        run: pip install pre-commit
-      - name: Install pre-commit hooks
-        run: pre-commit install
-      # This will run on all files in the repo not just those that have been
-      # committed. Once formatting has been applied once globally, from then on
-      # the files being changed by pre-commit should be just those that are
-      # being committed - provided that people are using the pre-commit hook to
-      # format their code.
-      - name: run pre-commit
-        run: pre-commit run --all-files --color always
+      - uses: brainglobe/actions/lint@main
 
   test:
     needs: linting
@@ -51,23 +25,9 @@ jobs:
           - os: windows-latest
             python-version: 3.8
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - uses: brainglobe/actions/test@main
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .[dev]
-      - name: Test
-        run: pytest
-      - name: Coveralls
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-            pip install coveralls
-            coveralls --service=github
 
   deploy-source:
     needs: test

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
       hooks:
           - id: flake8
     - repo: https://github.com/psf/black
-      rev: 22.1.0
+      rev: 22.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy

MANIFEST.in

@@ -1,5 +1,3 @@
-include cellfinder_core/config/*
+include src/cellfinder_core/config/*
 global-include *.pxd
-prune tests
-prune resources
-prune .github
+global-include *.pyx

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ['setuptools', 'wheel', 'cython']
+build-backend = 'setuptools.build_meta'
+
 [tool.black]
 target-version = ['py36', 'py37', 'py38']
 skip-string-normalization = false

setup.cfg

@@ -1,3 +1,11 @@
+[options]
+package_dir =
+    =src
+packages = find:
+
+[options.packages.find]
+where = src
+
 [bumpversion]
 current_version = 0.2.8
 commit = True

setup.py

@@ -1,81 +1,55 @@
-import platform
 from os import path
 
-from setuptools import Extension, find_packages, setup
+import Cython.Build
+from setuptools import Extension, setup
 
 this_directory = path.abspath(path.dirname(__file__))
 with open(path.join(this_directory, "README.md"), encoding="utf-8") as f:
     long_description = f.read()
 
 requirements = [
+    "dask[array]",
+    "fancylog>=0.0.7",
+    "imlib>=0.0.26",
+    "natsort",
     "numpy",
-    "scikit-learn",
-    "configparser",
-    "pandas",
-    "packaging",
     "scikit-image",
-    "tifffile",
-    "natsort",
-    "tqdm",
-    "multiprocessing-logging",
-    "psutil",
-    "configobj",
+    "scikit-learn",
     "tensorflow>=2.5.0; "
     + "platform_system!='Darwin' or "
     + "platform_machine!='arm64'",
     "tensorflow-macos>=2.5.0; "
     + "platform_system=='Darwin' and "
     + "platform_machine=='arm64'",
-    "fancylog>=0.0.7",
-    "imlib>=0.0.26",
-    "slurmio>=0.0.4",
-    "imio",
-    "dask[array]",
+    "tifffile",
+    "tqdm",
 ]
 
 
-if platform.system() == "Windows":
-    # FIXME: There must be a better way of doing this.
-    base_tile_filter_extension = Extension(
-        name="cellfinder_core.detect.filters.plane.base_tile_filter",
-        sources=["cellfinder_core/detect/filters/plane/base_tile_filter.pyx"],
-        language="c++",
-    )
-
-    ball_filter_extension = Extension(
-        name="cellfinder_core.detect.filters.volume.ball_filter",
-        sources=["cellfinder_core/detect/filters/volume/ball_filter.pyx"],
-    )
+base_tile_filter_extension = Extension(
+    name="cellfinder_core.detect.filters.plane.base_tile_filter",
+    sources=["src/cellfinder_core/detect/filters/plane/base_tile_filter.pyx"],
+    language="c++",
+)
 
-    structure_detection_extension = Extension(
-        name="cellfinder_core.detect.filters.volume.structure_detection",
-        sources=[
-            "cellfinder_core/detect/filters/volume/structure_detection.pyx"
-        ],
-        language="c++",
-    )
-else:
-    base_tile_filter_extension = Extension(
-        name="cellfinder_core.detect.filters.plane.base_tile_filter",
-        sources=["cellfinder_core/detect/filters/plane/base_tile_filter.pyx"],
-        libraries=["m"],
-        language="c++",
-    )
+ball_filter_extension = Extension(
+    name="cellfinder_core.detect.filters.volume.ball_filter",
+    sources=["src/cellfinder_core/detect/filters/volume/ball_filter.pyx"],
+)
 
-    ball_filter_extension = Extension(
-        name="cellfinder_core.detect.filters.volume.ball_filter",
-        sources=["cellfinder_core/detect/filters/volume/ball_filter.pyx"],
-        libraries=["m"],
-    )
+structure_detection_extension = Extension(
+    name="cellfinder_core.detect.filters.volume.structure_detection",
+    sources=[
+        "src/cellfinder_core/detect/filters/volume/structure_detection.pyx"
+    ],
+    language="c++",
+)
 
-    structure_detection_extension = Extension(
-        name="cellfinder_core.detect.filters.volume.structure_detection",
-        sources=[
-            "cellfinder_core/detect/filters/volume/structure_detection.pyx"
-        ],
-        libraries=["m"],
-        language="c++",
-    )
+extensions = [
+    base_tile_filter_extension,
+    ball_filter_extension,
+    structure_detection_extension,
+]
 
 
 setup(
@@ -99,13 +73,8 @@
     },
     setup_requires=["cython"],
     python_requires=">=3.7",
-    packages=find_packages(),
     include_package_data=True,
-    ext_modules=[
-        ball_filter_extension,
-        structure_detection_extension,
-        base_tile_filter_extension,
-    ],
+    ext_modules=Cython.Build.cythonize(extensions),
     entry_points={
         "console_scripts": [
             "cellfinder_download = cellfinder_core.download.cli:main",

cellfinder_core/detect/filters/plane/classical_filter.py → src/cellfinder_core/detect/filters/plane/classical_filter.py

@@ -1,5 +1,5 @@
 import numpy as np
-from scipy.ndimage.filters import gaussian_filter, laplace
+from scipy.ndimage import gaussian_filter, laplace
 from scipy.signal import medfilt2d
 
 

cellfinder_core/detect/filters/plane/tile_walker.py → src/cellfinder_core/detect/filters/plane/tile_walker.py

@@ -19,7 +19,7 @@ def __init__(self, img, soma_diameter):
         n_tiles_width = math.ceil(self.img_width / self.tile_width)
         n_tiles_height = math.ceil(self.img_height / self.tile_height)
         self.good_tiles_mask = np.zeros(
-            (n_tiles_width, n_tiles_height), dtype=np.bool
+            (n_tiles_width, n_tiles_height), dtype=bool
         )
 
         self.x = 0

cellfinder_core/tools/geometry.py → src/cellfinder_core/tools/geometry.py

@@ -30,4 +30,4 @@ def make_sphere(ball_shape, radius, position):
 
 
 def four_connected_kernel():
-    return np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=np.bool)
+    return np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]], dtype=bool)

tox.ini

@@ -1,19 +1,16 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{37,38}-{linux,windows}
+envlist = py{37,38,39}
+isolated_build = true
 
 [gh-actions]
 python =
     3.7: py37
     3.8: py38
-
-[gh-actions:env]
-PLATFORM =
-    ubuntu-latest: linux
-    windows-latest: windows
+    3.9: py39
 
 [testenv]
-commands = pytest -v --cov=./ --cov-report=xml
+commands = python -m pytest -v --color=yes --cov --cov-report=xml
 deps =
     pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
     pytest  # https://docs.pytest.org/en/latest/contents.html