-
Notifications
You must be signed in to change notification settings - Fork 182
320 lines (311 loc) · 10.9 KB
/
python.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
name: Python
on:
push:
branches: [main]
tags: ["*"]
pull_request:
branches: [main]
permissions:
contents: read
env:
PYTHONUNBUFFERED: 1
jobs:
pre-commit:
name: Rerun pre-commit checks
runs-on: ubuntu-latest
outputs:
dist-base: ${{ steps.paths.outputs.dist }}
docs-base: ${{ steps.paths.outputs.docs }}
steps:
- name: Check out repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
- name: Run pre-commit hooks
uses: pre-commit/[email protected]
- name: Define artifact paths
id: paths
run: |
suffix="$GITHUB_RUN_NUMBER-$(echo $GITHUB_SHA | cut -c-10)"
echo "dist=openslide-python-dist-$suffix" >> $GITHUB_OUTPUT
echo "docs=openslide-python-docs-$suffix" >> $GITHUB_OUTPUT
tests:
name: Tests
needs: pre-commit
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, ubuntu-24.04-aarch64, macos-latest]
python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"]
openslide: [system, wheel]
include:
- os: ubuntu-latest
python-version: "3.13"
openslide: system
sdist: sdist
# Python 3.8 is too old to support universal binaries, and
# setup-python's Python 3.9 and 3.10 won't build them. Use the
# last upstream patch releases that ship with installers.
# https://github.com/actions/setup-python/issues/439#issuecomment-1247646682
- os: macos-latest
python-version: "3.9"
upstream-python: 3.9.13
- os: macos-latest
python-version: "3.10"
upstream-python: 3.10.11
steps:
- name: Check out repo
uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
if: matrix.upstream-python == null
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Set up Python ${{ matrix.python-version }} (macOS fallback)
if: matrix.upstream-python != null
run: |
pkgdir="${{ runner.temp }}/python"
mkdir -p "$pkgdir/bin"
pkg="$pkgdir/python.pkg"
curl -Lfo "$pkg" \
"https://www.python.org/ftp/python/${{ matrix.upstream-python }}/python-${{ matrix.upstream-python }}-macos11.pkg"
sudo installer -pkg "$pkg" -target /
for bin in python pip; do
ln -s /usr/local/bin/${bin}3 $pkgdir/bin/${bin}
done
export PATH="$pkgdir/bin:$PATH"
echo "PATH=$PATH" >> $GITHUB_ENV
python -V
pip -V
- name: Install Python tools
run: |
python -m pip install --upgrade pip
pip install auditwheel build jinja2 pytest
- name: Install OpenSlide (system)
if: matrix.openslide == 'system'
run: |
case "${{ matrix.os }}" in
ubuntu-latest)
echo OS_ARCH_TAG=linux-x86_64 >> $GITHUB_ENV
sudo apt-get install libopenslide0
;;
ubuntu-24.04-aarch64)
echo OS_ARCH_TAG=linux-aarch64 >> $GITHUB_ENV
sudo apt-get install libopenslide0
;;
macos-latest)
echo OS_ARCH_TAG=macos-arm64-x86_64 >> $GITHUB_ENV
echo DYLD_LIBRARY_PATH=/opt/homebrew/lib >> $GITHUB_ENV
brew install openslide
;;
esac
- name: Install OpenSlide (wheel)
if: matrix.openslide == 'wheel'
run: pip install openslide-bin
- name: Build dist
run: |
if [ -z "${{ matrix.sdist }}" ]; then
wheel_only=-w
fi
python -m build $wheel_only
case "${{ matrix.os }}" in
ubuntu-*)
mkdir old
mv dist/*.whl old/
auditwheel repair --only-plat -w dist old/*whl
;;
macos-*)
if [ "${{ matrix.python-version }}" != 3.8 -a ! -e dist/*universal2* ]; then
echo "Wheel is not universal:"
ls dist
exit 1
fi
esac
if [ -z "$wheel_only" ]; then
mkdir -p "artifacts/src/${{ needs.pre-commit.outputs.dist-base }}"
mv dist/*.tar.gz "artifacts/src/${{ needs.pre-commit.outputs.dist-base }}"
fi
mkdir -p "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}"
mv dist/* "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}"
# from system builds, save version-specific wheels and oldest abi3 wheel
python -c 'import sys
if sys.version_info < (3, 12) and "${{ matrix.openslide }}" == "system":
print("archive_wheel=1")' >> $GITHUB_ENV
- name: Install
run: pip install artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}/*.whl
- name: Run tests
run: pytest -v
- name: Tile slide
run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs
- name: Archive sdist
if: matrix.sdist
uses: actions/upload-artifact@v4
with:
name: ${{ needs.pre-commit.outputs.dist-base }}-source
path: artifacts/src
compression-level: 0
- name: Archive wheel
if: env.archive_wheel
uses: actions/upload-artifact@v4
with:
name: ${{ needs.pre-commit.outputs.dist-base }}-${{ env.OS_ARCH_TAG }}-${{ matrix.python-version }}
path: artifacts/whl
compression-level: 0
windows:
name: Windows
needs: pre-commit
runs-on: windows-latest
defaults:
run:
shell: bash
strategy:
matrix:
python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"]
openslide: [zip, wheel]
steps:
- name: Check out repo
uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install Python tools
run: |
python -m pip install --upgrade pip
pip install build flask pytest
- name: Install OpenSlide (zip)
if: matrix.openslide == 'zip'
env:
GH_TOKEN: ${{ github.token }}
run: |
mkdir -p c:\\openslide
cd c:\\openslide
release=$(gh release list -R openslide/openslide-bin -L 1 \
--json tagName --exclude-drafts --exclude-pre-releases | \
jq -r .[0].tagName | \
tr -d v)
zipname="openslide-bin-${release}-windows-x64"
gh release download -R openslide/openslide-bin "v${release}" \
--pattern "${zipname}.zip"
7z x ${zipname}.zip
echo "OPENSLIDE_PATH=c:\\openslide\\${zipname}\\bin" >> $GITHUB_ENV
- name: Install OpenSlide (wheel)
if: matrix.openslide == 'wheel'
run: pip install openslide-bin
- name: Build wheel
run: |
python -m build -w
mkdir -p "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}"
mv dist/*.whl "artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}"
# from zip builds, save version-specific wheels and oldest abi3 wheel
python -c 'import sys
if sys.version_info < (3, 12) and "${{ matrix.openslide }}" == "zip":
print("archive_wheel=1")' >> $GITHUB_ENV
- name: Install
run: pip install artifacts/whl/${{ needs.pre-commit.outputs.dist-base }}/*.whl
- name: Run tests
# Reads OPENSLIDE_PATH
run: pytest -v
- name: Test library loading in examples
# Reads OPENSLIDE_PATH
run: |
python examples/deepzoom/deepzoom_multiserver.py -h >/dev/null
python examples/deepzoom/deepzoom_server.py -h >/dev/null
python examples/deepzoom/deepzoom_tile.py -h >/dev/null
- name: Tile slide
# Reads OPENSLIDE_PATH
run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs
- name: Archive wheel
if: env.archive_wheel
uses: actions/upload-artifact@v4
with:
name: ${{ needs.pre-commit.outputs.dist-base }}-windows-x64-${{ matrix.python-version }}
path: artifacts/whl
compression-level: 0
setuptools:
name: Setuptools install
needs: pre-commit
runs-on: ubuntu-20.04
steps:
- name: Check out repo
uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y libopenslide0 python3-pil
pip install pytest
- name: Install OpenSlide Python
run: sudo python setup.py install
- name: Run tests
run: pytest -v
- name: Tile slide
run: python examples/deepzoom/deepzoom_tile.py --viewer -o tiled tests/fixtures/small.svs
docs:
name: Docs
needs: pre-commit
runs-on: ubuntu-latest
steps:
- name: Check out repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
- name: Install Python tools
run: |
python -m pip install --upgrade pip
pip install sphinx
- name: Build
run: sphinx-build -d doctrees doc artifact/${{ needs.pre-commit.outputs.docs-base }}
- name: Archive
uses: actions/upload-artifact@v4
with:
name: ${{ needs.pre-commit.outputs.docs-base }}
path: artifact
release:
name: Release
if: github.ref_type == 'tag'
environment:
name: pypi
url: https://pypi.org/p/openslide-python
needs: [pre-commit, tests, windows]
runs-on: ubuntu-latest
concurrency: release-${{ github.ref }}
permissions:
contents: write
id-token: write
steps:
- name: Download artifacts
uses: actions/download-artifact@v4
with:
pattern: "${{ needs.pre-commit.outputs.dist-base }}-*"
merge-multiple: true
- name: Release to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
packages-dir: ${{ needs.pre-commit.outputs.dist-base }}
repository-url: ${{ vars.PYPI_URL }}
- name: Release to GitHub
env:
GITHUB_TOKEN: ${{ github.token }}
run: |
version=$(echo "${{ github.ref_name }}" | sed "s/^v//")
# recompress tarball with xz
gunzip -k "${{ needs.pre-commit.outputs.dist-base }}/openslide_python-${version}.tar.gz"
tar xf "${{ needs.pre-commit.outputs.dist-base }}/openslide_python-${version}.tar"
xz -9 "${{ needs.pre-commit.outputs.dist-base }}/openslide_python-${version}.tar"
# extract changelog
awk -e '/^## / && ok {exit}' \
-e '/^## / {ok=1; next}' \
-e 'ok {print}' \
"openslide_python-$version/CHANGELOG.md" > changes
# create release; upload artifacts but not *.publish.attestation
# files created by gh-action-pypi-publish
gh release create --latest --verify-tag \
--repo "${{ github.repository }}" \
--title "OpenSlide Python $version" \
--notes-file changes \
"${{ github.ref_name }}" \
"${{ needs.pre-commit.outputs.dist-base }}/"*.{tar.gz,tar.xz,whl}