-
Notifications
You must be signed in to change notification settings - Fork 13
396 lines (279 loc) · 13 KB
/
build_on_release.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
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
name: (Release) Build Pipy, Dockerhub image and test
on:
release:
types: [released]
jobs:
build:
name: Build documentation
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@master
- name: Set up Python 3.10.5
uses: actions/setup-python@v2
with:
python-version: 3.10.5
- name: Install dependencies
run: |
pip install -e .[doc]
sudo apt-get install build-essential graphviz libgraphviz-dev
pip install --upgrade pygraphviz graphviz
- name: Test with pytest
run:
py.test --cov macapype --ignore=examples/ --ignore=run_examples/
- name: Build the Doc 🔧
run: |
cd docs
make clean
make html
touch _build/html/.nojekyll
- name: Deploy Github Pages 🚀
uses: JamesIves/github-pages-deploy-action@v4.4.3
with:
branch: gh-pages
folder: docs/_build/html/
clean: true
ssh-key: ${{ secrets.DEPLOY_KEY }}
build-n-publish-pypi:
name: Build and publish Python to PyPI
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@master
- name: Set up Python 3.10.5
uses: actions/setup-python@v2
with:
python-version: 3.10.5
- 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')
uses: pypa/gh-action-pypi-publish@master
with:
password: ${{ secrets.PYPI_API_TOKEN }}
docker-build:
name: Build Docker image and Push to Docker Hub
needs: build-n-publish-pypi
runs-on: ubuntu-latest
steps:
- name: Check out the repo
uses: actions/checkout@v2
- name: Log in to Docker Hub
uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
with:
images: macatools/macapype
- name: Build and push Docker image
uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
with:
context: .
file: Dockerfile_nomcr
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
run-pretest-ants-t1-marmo:
name: Running all existing pipelines in macapype_CI.zip (ANTS marmo T1)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline marmo-marmobrain ANTS_noseg T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-marmo:
name: Running all existing pipelines in macapype_CI.zip (ANTS marmo)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/
run-pretest-ants-t1-baboon:
name: Running all existing pipelines in macapype_CI.zip (ANTS T1 baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-baboon:
name: Running all existing pipelines in macapype_CI.zip (ANTS baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 T2
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/
run-pretest-ants-macaque-t1:
name: Running all existing pipelines in macapype_CI.zip (ANTS macaque T1)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline macaque_prime-de ANTS_prep T1
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/
run-pretest-ants-macaque:
name: Running all existing pipelines in macapype_CI.zip (ANTS macaque)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest
- name: Download dataset
run: |
curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
unzip -o macapype_CI.zip -d macapype_CI
pwd
echo ""
ls macapype_CI
echo ""
ls macapype_CI/macaque_prime-de
echo ""
ls macapype_CI/marmo-marmobrain
echo ""
- name: Running test pipeline macaque_prime-de ANTS_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 -nprocs 1
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/
ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-032140/ses-001/anat/
echo ""
- name: Cleaning dataset
run:
sudo rm -rf macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2