-
Notifications
You must be signed in to change notification settings - Fork 27
239 lines (210 loc) · 7.53 KB
/
build-test-publish.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
name: CI
on:
push:
pull_request:
schedule:
- cron: 0 0 * * 0
# Allow job to be triggered manually from GitHub interface
workflow_dispatch:
# Force pytest to use color
env:
FORCE_COLOR: true
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
permissions:
contents: read
defaults:
run:
shell: bash -el {0}
jobs:
build-package:
name: Build & inspect package
runs-on: ubuntu-latest
permissions:
attestations: write
id-token: write
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: hynek/build-and-inspect-python-package@v2
test:
if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
runs-on: ubuntu-latest
env:
TEST_DATA_HOME: /home/runner/sdcflows-tests
FSLOUTPUTTYPE: NIFTI_GZ
FSLMULTIFILEQUIT: TRUE
AFNI_HOME: /opt/afni
AFNI_MODELPATH: /opt/afni/models
AFNI_IMSAVE_WARNINGS: NO
AFNI_TTATLAS_DATASET: /opt/afni/atlases
AFNI_PLUGINPATH: /opt/afni/plugins
strategy:
max-parallel: 6
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
marks: ["not slow"]
include:
- python-version: "3.9"
marks: "slow and not veryslow"
- python-version: "3.12"
marks: "veryslow"
steps:
- uses: actions/cache@v4
with:
path: /var/lib/apt
key: apt-cache-v3
restore-keys: |
apt-cache-v3
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y --no-install-recommends \
curl bzip2 ca-certificates \
tcsh gsl-bin netpbm \
libjpeg62 xvfb xterm \
libglu1-mesa-dev libglw1-mesa \
libxm4 build-essential
- uses: actions/cache@v4
with:
path: /opt/afni
key: afni-v1
restore-keys: |
afni-v1
- name: Install AFNI
run: |
if [[ ! -d "${AFNI_HOME}" ]]; then
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
fi
- name: Git settings (pacify DataLad)
run: |
git config --global user.name 'NiPreps Bot'
git config --global user.email '[email protected]'
- name: Set up Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
auto-activate-base: true
python-version: ${{ matrix.python-version }}
channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
- uses: actions/cache@v4
id: conda
env:
CACHE_NUM: v5
with:
path: |
~/conda_pkgs_dir
/home/runner/.cache/pip
key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
restore-keys: |
python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
- name: Install DataLad
run: |
conda install git-annex=*=alldep* pip
pip install datalad datalad-osf
- name: Install fsl and ANTs
run: |
conda install fsl-fugue fsl-topup ants
- uses: actions/checkout@v4
- name: Install dependencies
timeout-minutes: 5
run: |
pip install .[tests]
- uses: actions/cache@v4
with:
path: ~/.cache/templateflow
key: tf-cache-v1
restore-keys: |
tf-cache-
- name: Get TemplateFlow's required objects
run: |
python tools/cache_templateflow.py
- uses: actions/cache@v4
with:
path: ${{ env.TEST_DATA_HOME }}
key: data-cache-v2
restore-keys: |
data-cache-
- name: Install test data
run: |
mkdir -p ${{ env.TEST_DATA_HOME }}
cd ${{ env.TEST_DATA_HOME }}
# ds001600
datalad install -r https://github.com/nipreps-data/ds001600.git
datalad update -r --merge -d ds001600/
datalad get -r -J 2 -d ds001600/ ds001600/sub-1/
# HCP/sub-101006
datalad install -r https://github.com/nipreps-data/HCP101006.git
datalad update -r --merge -d HCP101006/
datalad get -r -J 2 -d HCP101006 HCP101006/*
# ds001771
datalad install -r https://github.com/nipreps-data/ds001771.git
datalad update -r --merge -d ds001771/
datalad get -r -J 2 -d ds001771/ ds001771/sub-36/*
datalad get -r -J 2 -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*
# ds000054
datalad install -r https://github.com/nipreps-data/ds000054.git
datalad update --merge -d ds000054/
datalad get -r -d ds000054/ ds000054/sub-100185/*
datalad get -r -J 2 -d ds000054/ ds000054/derivatives/smriprep-0.6/sub-100185/anat/
# ds000206
datalad install -r https://github.com/nipreps-data/ds000206.git
datalad update -r --merge -d ds000206/
datalad get -r -J 2 -d ds000206/ ds000206/sub-05/
# Brain extraction tests
datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
datalad update --merge -d brain-extraction-tests/
datalad get -r -J 2 -d brain-extraction-tests brain-extraction-tests/*
# HCPH pilot
datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
datalad update -r --merge -d hcph-pilot_fieldmaps/
datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
# ds005250
datalad install -r https://gin.g-node.org/tsalo/ds005250-sdcflows.git
datalad update -r --merge -d ds005250-sdcflows/
datalad get -r -J 2 -d ds005250-sdcflows/ ds005250-sdcflows/sub-04/ses-2/
- name: Set FreeSurfer variables
run: |
echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV
echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV
- name: Install FreeSurfer's mri_robust_template
env:
MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
run: |
curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
sudo install mri_robust_template /usr/local/bin
mkdir -p $( dirname $FS_LICENSE )
echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE
- name: Run pytest with coverage
run: |
export PATH=${AFNI_HOME}:$PATH
export FSLDIR=${CONDA_PREFIX}
pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
--durations=20 --durations-min=10 -m "$MARKS"
env:
MARKS: ${{ matrix.marks }}
- uses: codecov/codecov-action@v4
with:
file: cov.xml
token: ${{ secrets.CODECOV_TOKEN }}
if: ${{ always() }}
publish:
name: Publish released package to pypi.org
environment: release-pypi
if: github.event.action == 'published'
runs-on: ubuntu-latest
needs: [build-package, test]
permissions:
attestations: write
id-token: write
steps:
- name: Download packages built by build-and-inspect-python-package
uses: actions/download-artifact@v4
with:
name: Packages
path: dist
- name: Upload package to PyPI
uses: pypa/gh-action-pypi-publish@release/v1