skullTo3d/.github/workflows/build_on_prerelease.yml at main · Macatools/skullTo3d · GitHub

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
name: (Prerelease) Build TestPipy, Dockerhub image and test

on:
  release:
    types: [prereleased]

jobs:


  build-n-publish-testpypi:
    name: Build and publish Python to Test PyPI
    runs-on: ubuntu-latest

    permissions:
      id-token: write

    environment:
      name: testpypi
      url: https://test.pypi.org/p/macapype

    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 Test PyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        repository_url: https://test.pypi.org/legacy/

  docker-build:
    name: Build Docker image and Push to Docker Hub
    needs: build-n-publish-testpypi
    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/skullTo3d

      - name: Build and push Docker image
        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
        with:
          context: .
          file: Dockerfile_testpypi
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}

  run-pretest-ants-macaque-0p5:
    name: Running all existing pipelines in skullTo3d_CI_v2.zip (ANTS macaque 0p5 CT petra)
    needs:  docker-build
    runs-on: ubuntu-latest
    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullto3d:latest

      - name: Download dataset
        run: |

            curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip
            unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

            pwd
            echo ""

            ls skullTo3d_CI_v2
            echo ""

            ls skullTo3d_CI_v2/cerimed_macaque

            ls skullTo3d_CI_v2/cerimed_macaque/sub-Stevie/ses-01/anat

            echo ""

      - name: Running all test pipelines (ANTS cerimed macaque petra CT)
        run: |
            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2:/data macatools/skullto3d:latest segment_skull -data /data/cerimed_macaque -out /data/cerimed_macaque/results -soft ANTS_skullnoisypetra_robustreg_prep -species macaque_0p5 -sub Stevie -ses 01 -brain_dt T1 T2 -skull_dt ct -deriv -pad -nprocs 1

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results/derivatives

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results/derivatives/macapype_ants_skullnoisypetra/sub-Stevie/ses-01/anat

      - name: Cleaning dataset
        run: |
            sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results

  run-pretest-ants-4aniaml-macaque-0p5:
    name: Running all existing pipelines in skullTo3d_CI_v2.zip (ANTS_4animal macaque 0p5 CT petra)
    needs:  docker-build
    runs-on: ubuntu-latest
    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullto3d:latest

      - name: Download dataset
        run: |

            curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip
            unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

            pwd
            echo ""

            ls skullTo3d_CI_v2
            echo ""

            ls skullTo3d_CI_v2/cerimed_macaque

            ls skullTo3d_CI_v2/cerimed_macaque/sub-Stevie/ses-01/anat

            echo ""

      - name: Running all test pipelines (ANTS_4animal cerimed macaque petra CT)
        run: |
            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2:/data macatools/skullto3d:latest segment_skull -data /data/cerimed_macaque -out /data/cerimed_macaque/results -soft ANTS_4animal_skullnoisypetra_robustreg_prep -species macaque_0p5 -sub Stevie -ses 01 -brain_dt T1 T2 -skull_dt ct -deriv -pad -nprocs 1

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results/derivatives

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results/derivatives/macapype_ants_4animal_skullnoisypetra/sub-Stevie/ses-01/anat

      - name: Cleaning dataset
        run: |
            sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_macaque/results

  run-pretest-ants-marmo:
    name: Running all existing pipelines in skullTo3d_CI_v2.zip (ANTS marmo CT)
    needs:  docker-build
    runs-on: ubuntu-latest

    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullto3d:latest

      - name: Download dataset
        run: |

            curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip
            unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

            pwd
            echo ""

            ls skullTo3d_CI_v2
            echo ""

            ls skullTo3d_CI_v2/cerimed_marmo

            ls skullTo3d_CI_v2/cerimed_marmo/sub-Tresor/ses-01/anat

            echo ""


      - name: Running all test pipelines (ANTS cerimed marmo CT)
        run: |
            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2:/data macatools/skullto3d:latest segment_skull -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_skull_robustreg_prep -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt CT -deriv -pad -nprocs 1

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives/macapype_ants_skull/sub-Tresor/ses-01/anat

      - name: Cleaning dataset
        run: |
            sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results

  run-pretest-ants-4animal-marmo:
    name: Running all existing pipelines in skullTo3d_CI_v2.zip (ANTS_4animal marmo CT)
    needs:  docker-build
    runs-on: ubuntu-latest

    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullto3d:latest

      - name: Download dataset
        run: |

            curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip
            unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

            pwd
            echo ""

            ls skullTo3d_CI_v2
            echo ""

            ls skullTo3d_CI_v2/cerimed_marmo

            ls skullTo3d_CI_v2/cerimed_marmo/sub-Tresor/ses-01/anat

            echo ""


      - name: Running all test pipelines (ANTS_4animal cerimed marmo CT)
        run: |
            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2:/data macatools/skullto3d:latest segment_skull -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_4animal_skull_robustreg_prep -species marmo -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt CT -deriv -pad -nprocs 1

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives/macapype_ants_4animal_skull/sub-Tresor/ses-01/anat

      - name: Cleaning dataset
        run: |
            sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results

  run-pretest-ants-marmoT2:
    name: Running all existing pipelines in skullTo3d_CI_v2.zip (ANTS marmoT2 CT)
    needs:  docker-build
    runs-on: ubuntu-latest

    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullto3d:latest

      - name: Download dataset
        run: |

            curl https://amubox.univ-amu.fr/public.php/dav/files/7tf4ooJsyjHfSbG --output skullTo3d_CI_v2.zip
            unzip -o skullTo3d_CI_v2.zip -d skullTo3d_CI_v2

            pwd
            echo ""

            ls skullTo3d_CI_v2
            echo ""

            ls skullTo3d_CI_v2/cerimed_marmo

            ls skullTo3d_CI_v2/cerimed_marmo/sub-Tresor/ses-01/anat

            echo ""


      - name: Running all test pipelines (ANTS cerimed marmoT2 CT)
        run: |
            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2:/data macatools/skullto3d:latest segment_skull -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_skull_robustreg_prep -species marmoT2 -sub Tresor -ses 01 -brain_dt T1 T2 -skull_dt CT -deriv -pad -nprocs 1

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives

            ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results/derivatives/macapype_ants_skull/sub-Tresor/ses-01/anat

      - name: Cleaning dataset
        run: |
            sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI_v2/cerimed_marmo/results