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📦️ Fix packaging bugs from #1971 #1981
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& double up on until #1974 is resolved [rebuild base-ABCD-HCP] [rebuild base-fMRIPrep-LTS] [rebuild base-lite] [rebuild base-standard]
…lution more robust
I see there are merge conflicts. I'll fix those next week |
e-kenneally
approved these changes
Aug 28, 2023
8 tasks
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Fixes
Fixes #1971 by @shnizzedy
Fixes cmi-cnl#cpac/p1691439898750679 by @nx10
Fixes cmi-cnl#cpac/p1691686240018959 by @e-kenneally
Fixes #1983 by @e-kenneally
Restores 42962c1 by @anibalsolon
Description
bc
to images with FreeSurferxvfbwrapper
from OS base image installation into C-PAC dependenciesxvfbwrapper
)FSLDIR
paths (e.g.,/usr/share/fsl/5.0
) to use environment variable$FSLDIR
C-PAC/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml
Line 293 in dd2b3ab
C-PAC/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml
Line 274 in eb39a16
Technical details
MNI152_T1_2mm_eye_mask.nii.gz
is the only resolution prepackaged here, which was causing a problem if the output resolution wasn't 2mm.coverage
to capture tests.pylintrc
re: several deprecated-option warningsTests
bc
C-PAC/CPAC/surface/tests/test_installation.py
Lines 23 to 29 in eb39a16
Coverage for CPAC/surface/tests/test_installation.py: 100%
package installation permissions
C-PAC/CPAC/unet/tests/test_torch.py
Lines 18 to 27 in eb39a16
Coverage for CPAC/unet/tests/test_torch.py: 100%
preconfig templates
C-PAC/CPAC/resources/tests/test_templates.py
Lines 26 to 42 in eb39a16
Additional details
Rodent pipeline
C-PAC/CPAC/resources/configs/pipeline_config_rodent.yml
Lines 103 to 109 in fe0cb0f
C-PAC/CPAC/resources/configs/pipeline_config_rodent.yml
Lines 320 to 339 in fe0cb0f
C-PAC/CPAC/resources/tests/test_templates.py
Lines 38 to 39 in fe0cb0f
Updated
resolve_resolution
These are both described above, but I want to highlight them to make sure
C-PAC/CPAC/utils/datasource.py
Lines 906 to 908 in fe0cb0f
MNI152_T1_2mm_eye_mask.nii.gz
is the only resolution prepackaged here, which was causing a problem if the output resolution wasn't 2mm.C-PAC/CPAC/resources/tests/test_templates.py
Line 37 in 051220a
C-PAC/CPAC/utils/datasource.py
Line 905 in 051220a
aws s3 ls
for s3 files so we wouldn't have to download (and potentially resample) each oneChecklist
Update index.md
).develop
branch of the repository.Developer Certificate of Origin
Developer Certificate of Origin