Please use this ticket to add new software to the NeuroFedora packaging queue.
Short description: BIDScoin converts your source-level neuroimaging data to BIDS
Upstream URL: https://github.com/Donders-Institute/bidscoin
License: GPLv3
Domain: Neuroimaging/Data analysis/Utilities
GUI but written in Python, so should be hopefully straightforward to package.
Paper in Frontiers in Neurinformatics:
https://www.frontiersin.org/articles/10.3389/fninf.2021.770608/full
Missing Python dependencies:
multiecho
pydeface
Additional missing Python dependencies for extras:
bioread
drmaa
spec2nii
Missing Python dependencies: multiecho
https://bugzilla.redhat.com/show_bug.cgi?id=2219161
Upstream made this optional.
Additional missing Python dependencies for extras: bioread drmaa spec2nii
Upstream says:
And it is perhaps also of help to mention that the drmaa dependency is not really important (only for speeding up a few applications), and that the output of the pydeface library can also be generated by the users using a separate application. The spec2nii application is of more importance (similar to dcm2niix)
dcm2niix
Review request for python-nifti-mrs, a spec2nii dependency.
python-nifti-mrs
The optional pydeface dependency will not be packaged because it depends on fsl, which is nonfree.
fsl
I looked at drmaa. The last release was five years ago, the tests require (deprecated) nose, and when I try to run them I get cryptic errors:
nose
+ /usr/bin/python3 -m nose EE....E ====================================================================== ERROR: 'with' statement works with Session ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.12/site-packages/nose/case.py", line 201, in runTest self.test(*self.arg) File "/builddir/build/BUILD/drmaa-0.7.9/test/testcontext.py", line 12, in test_with_session with Session() as s: File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/session.py", line 525, in __enter__ self.initialize(self.contactString) File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) drmaa.errors.InternalException: code 1: pbs-drm: unknown error ====================================================================== ERROR: 'with' statement works with JobTemplate ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.12/site-packages/nose/case.py", line 201, in runTest self.test(*self.arg) File "/builddir/build/BUILD/drmaa-0.7.9/test/testcontext.py", line 22, in test_with_jt s.initialize() File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) drmaa.errors.InternalException: code 1: pbs-drm: unknown error ====================================================================== ERROR: test suite for <module 'testwrap' from '/builddir/build/BUILD/drmaa-0.7.9/test/testwrap.py'> ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.12/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/lib/python3.12/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/lib/python3.12/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/lib/python3.12/site-packages/nose/util.py", line 471, in try_run return func() ^^^^^^ File "/builddir/build/BUILD/drmaa-0.7.9/test/testwrap.py", line 45, in setup Session.initialize() File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/session.py", line 257, in initialize py_drmaa_init(contactString) File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/wrappers.py", line 73, in py_drmaa_init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/drmaa-0.7.9/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) drmaa.errors.InternalException: code 1: pbs-drm: unknown error ---------------------------------------------------------------------- Ran 6 tests in 0.021s FAILED (errors=3)
Since upstream says drmaa is “not really important,” even though it is officially a hard dependency, and given the above, I’ll plan to try patching out the dependency rather than packaging a python-drmaa package.
python-drmaa
This has been done for a while: https://src.fedoraproject.org/rpms/python-multiecho
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
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