[Bug 2323073] Review Request: python-nipype - Neuroimaging in Python: Pipelines and Interfaces

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https://bugzilla.redhat.com/show_bug.cgi?id=2323073



--- Comment #2 from Ben Beasley <code@xxxxxxxxxxxxxxxxxx> ---
This looks pretty good. There’s a new release that can be packaged, and there
are some unwanted shebangs that should be removed.

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated


Issues:
=======
- Dist tag is present.

  OK: rpmautospec

- Package must not depend on deprecated() packages.
  Note: python3-pytest7 is deprecated, you must not depend on it.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/deprecating-packages/

  OK: spurious, built with pytest 8

- Since this was submitted at version 1.9.0, version 1.9.1 was released. It
  doesn’t look like this should require any packaging changes:
  https://github.com/nipy/nipype/compare/1.9.0...1.9.1 . Please update at your
  earliest convenience.

- Please remove shebangs from test files, which are not script-like and do not
  have executable filesystem permissions; it would make sense to submit this in
  an upstream PR.

    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/algorithms/tests/test_ErrorMap.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/algorithms/tests/test_Overlap.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/algorithms/tests/test_confounds.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/algorithms/tests/test_splitmerge.py
644 /usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/external/fsl_imglob.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/interfaces/base/tests/test_resource_monitor.py
644 /usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/interfaces/fsl/possum.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/pipeline/engine/__init__.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/pipeline/engine/workflows.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/sphinxext/__init__.py 644 /usr/bin/env
python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/sphinxext/plot_workflow.py 644
/usr/bin/env python
    python3-nipype.noarch: E: non-executable-script
/usr/lib/python3.13/site-packages/nipype/utils/tests/test_cmd.py 644
/usr/bin/env python

Notes:
======

- Zero-length files noted by rpmlint are OK (“dummy” test files)

- A man page is always desired for a command-line tool like this, but due to
  the many sub-commands, this isn’t a good fit for help2man, and maintaining
  man pages manually would be a bit fussy.

    python3-nipype.noarch: W: no-manual-page-for-binary nipypecli

- Duplicate files reported by rpmlint are not large enough or numerous enough
  to be worth doing anything about them (like hardlinking).

===== MUST items =====

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "Unknown or generated", "*No copyright* Apache License 2.0",
     "Apache License 2.0", "*No copyright* Apache License". 1465 files have
     unknown license. Detailed output of licensecheck in
     /home/ben/fedora/review/2323073-python-nipype/licensecheck.txt

     From testing/data/README:

       This directory contains empty, dummy files which are meant to be used in
       the doctests of nipype. For version 0.3 of nipype, we're using Traits
       and for input files, the code checks to confirm the assigned files
       actually exist. It doesn't matter what the files are, or even if they
       contain "real data", only that they exist. Again, these files are only
       meant to serve as documentation in the doctests.

     So there are no concerns about possible dubious licensing in the “test
     data,” as this is just a tree of zero-byte files.

[x]: Package must own all directories that it creates.
     Note: Directories without known owners: /usr/lib/python3.13,
     /usr/lib/python3.13/site-packages

     OK: spurious

[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[-]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: If (and only if) the source package includes the text of the
     license(s) in its own file, then that file, containing the text of the
     license(s) for the package is included in %license.
[x]: The License field must be a valid SPDX expression.
[x]: Package requires other packages for directories it uses.
[x]: Package does not own files or directories owned by other packages.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package does not use a name that already exists.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 6648 bytes in 2 files.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: A package which is used by another package via an egg interface should
     provide egg info.
[x]: Package meets the Packaging Guidelines::Python
[x]: Package contains BR: python2-devel or python3-devel
[x]: Packages MUST NOT have dependencies (either build-time or runtime) on
     packages named with the unversioned python- prefix unless no properly
     versioned package exists. Dependencies on Python packages instead MUST
     use names beginning with python2- or python3- as appropriate.
[x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[x]: Package functions as described.

     (tests pass)

[!]: Latest version is packaged.

     Version 1.9.1 is available.

[ ]: Package does not include license text files separate from upstream.
[ ]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not used.
[ ]: Package should compile and build into binary rpms on all supported
     architectures.
[ ]: %check is present and all tests pass.
[ ]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[!]: Spec file according to URL is the same as in SRPM.
     Note: Spec file as given by url is not the same as in SRPM (see
     attached diff).
     See: (this test has no URL)
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).


Rpmlint
-------
Checking: python3-nipype-1.9.0-2.fc42.noarch.rpm
          python-nipype-1.9.0-2.fc42.src.rpm
============================ rpmlint session starts
============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.13/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmpfvjhpux1')]
checks: 32, packages: 2

python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/4d_dwi.nii
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/A.scheme
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/A_qmat.Bdouble
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/A_recon_params.Bdouble
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/BrainSegmentationPrior03.nii.gz
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/FLASH3.mgz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/Fred+orig
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/NWARP
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/PD.mgz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ProbabilityMaskOfStudyTemplate.nii.gz
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/T2.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/TI4D.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/TPM.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/Template_1_IXI550_MNI152.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/Template_6.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/TransformParameters.0.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/afni_output.3D
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/allFA.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/all_FA.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/anat_coreg.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/anatomical.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ants_Affine.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ants_Warp.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ants_deformed.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/aparc+aseg.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/aseg.mgz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/asl.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/atlas.nii.gz
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cont2.nii
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dofrun1
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dofrun2
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ds005/filler.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dteig.Bdouble
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dti.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi.nii.gz
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/usr/lib/python3.13/site-packages/nipype/testing/data/dwi2anat_InverseWarp.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi2anat_Warp.nii.gz
python3-nipype.noarch: E: zero-length
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python3-nipype.noarch: E: zero-length
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/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_FA.mif
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/usr/lib/python3.13/site-packages/nipype/testing/data/converted.trk
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope1.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope1run1.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope1run2.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope2run1.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cope2run2.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cortex.label
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/cov_split.mat
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/csd.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/csffod.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/data.Bfloat
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/db.xml
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/degree.csv
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/degree.mat
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/design.con
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dicomdir/123456-1-1.dcm
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/diffusion.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/diffusion_weighted.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dilated_wm_mask.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dirs.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dofrun1
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dofrun2
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ds005/filler.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dteig.Bdouble
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dti.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi2anat_InverseWarp.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi2anat_Warp.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi2anat_coreg_Affine.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_CSD_tracked.tck
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_FA.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_WMProb.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_evals.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/dwi_tensor.mif
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/elastix.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/encoding.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_acqp.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_index.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_mask.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_phasediff.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_rev.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/epi_slspec.txt
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/f1.1D
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/f2.1D
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fa.nii.gz
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fdir00.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fdir01.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ffra00.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/ffra01.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fieldmap_mag.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fieldmap_mag_brain.nii
python3-nipype.noarch: E: zero-length
/usr/lib/python3.13/site-packages/nipype/testing/data/fieldma


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