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Package Donders-Institute/bidscoin: BIDScoin converts your source-level neuroimaging data to BIDS #500

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opened 2022-01-17 11:48:19 +00:00 by ankursinha · 8 comments
ankursinha commented 2022-01-17 11:48:19 +00:00
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Please use this ticket to add new software to the NeuroFedora packaging queue.

New software: BIDScoin

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

Additional information

GUI but written in Python, so should be hopefully straightforward to package.

Please use this ticket to add new software to the NeuroFedora packaging queue. #### New software: BIDScoin 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 ##### Additional information GUI but written in Python, so should be hopefully straightforward to package.
ankursinha commented 2022-01-17 11:48:41 +00:00
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Paper in Frontiers in Neurinformatics:

https://www.frontiersin.org/articles/10.3389/fninf.2021.770608/full

Paper in Frontiers in Neurinformatics: https://www.frontiersin.org/articles/10.3389/fninf.2021.770608/full
music commented 2023-06-30 16:32:28 +00:00
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Missing Python dependencies:

Additional missing Python dependencies for extras:

Missing Python dependencies: - [`multiecho`](https://pypi.org/project/multiecho/) - [`pydeface`](https://pypi.org/project/pydeface/) Additional missing Python dependencies for extras: - [`bioread`](https://pypi.org/project/bioread/) - [`drmaa`](https://pypi.org/project/drmaa/) - [`spec2nii`](https://pypi.org/project/spec2nii/)
music commented 2023-07-05 14:14:33 +00:00
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Missing Python dependencies:

https://bugzilla.redhat.com/show_bug.cgi?id=2219161

Upstream made this optional.

Additional missing Python dependencies for extras:

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)

> Missing Python dependencies: > > - [`multiecho`](https://pypi.org/project/multiecho/) https://bugzilla.redhat.com/show_bug.cgi?id=2219161 > - [`pydeface`](https://pypi.org/project/pydeface/) Upstream made this [optional](https://github.com/Donders-Institute/bidscoin/commit/6ca70120caf69350fedc0cce1a1dad79aa4d7c25). > Additional missing Python dependencies for extras: > > - [`bioread`](https://pypi.org/project/bioread/) > - [`drmaa`](https://pypi.org/project/drmaa/) > - [`spec2nii`](https://pypi.org/project/spec2nii/) [Upstream says](https://github.com/Donders-Institute/multiecho/pull/19#issuecomment-1621503955): > 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`)
music commented 2023-11-19 15:24:06 +00:00
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Review request for python-nifti-mrs, a spec2nii dependency.

The optional pydeface dependency will not be packaged because it depends on fsl, which is nonfree.

[Review request for `python-nifti-mrs`](https://bugzilla.redhat.com/show_bug.cgi?id=2250532), a `spec2nii` dependency. The optional [`pydeface`](https://pypi.org/project/pydeface/) dependency will not be packaged because it depends on `fsl`, which is [nonfree](https://docs.fedoraproject.org/en-US/neurofedora/excludedtools/).
music commented 2023-11-20 16:16:15 +00:00
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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:

+ /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.

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: ``` + /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.
music commented 2023-11-20 16:49:25 +00:00
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This has been done for a while: https://src.fedoraproject.org/rpms/python-multiecho

https://bugzilla.redhat.com/show_bug.cgi?id=2250700

> - [`multiecho`](https://pypi.org/project/multiecho/) This has been done for a while: https://src.fedoraproject.org/rpms/python-multiecho > - [`bioread`](https://pypi.org/project/bioread/) https://bugzilla.redhat.com/show_bug.cgi?id=2250700
music commented 2024-07-29 18:57:58 +00:00
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Finally put spec2nii up for review: https://bugzilla.redhat.com/show_bug.cgi?id=2300832

Finally put `spec2nii` up for review: https://bugzilla.redhat.com/show_bug.cgi?id=2300832
music commented 2025-08-05 03:58:19 +00:00
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Review request: https://bugzilla.redhat.com/show_bug.cgi?id=2386481

Review request: https://bugzilla.redhat.com/show_bug.cgi?id=2386481
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