Spec URL: https://gui1ty.fedorapeople.org/review/python-nipype.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-nipype-1.9.0-2.fc42.src.rpm Description: Current neuroimaging software offer users an incredible opportunity to analyze data using a variety of different algorithms. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., AFNI, ANTS, BRAINS, BrainSuite, Camino, FreeSurfer, FSL, MNE, MRtrix, MNE, Nipy, Slicer, SPM), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. Nipype allows you to: - easily interact with tools from different software packages - combine processing steps from different software packages - develop new workflows faster by reusing common steps from old ones - process data faster by running it in parallel on many cores/machines - make your research easily reproducible - share your processing workflows with the community Fedora Account System Username: gui1ty
Copr build: https://copr.fedorainfracloud.org/coprs/build/8196960 (failed) Build log: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2323073-python-nipype/fedora-rawhide-x86_64/08196960-python-nipype/builder-live.log.gz Please make sure the package builds successfully at least for Fedora Rawhide. - If the build failed for unrelated reasons (e.g. temporary network unavailability), please ignore it. - If the build failed because of missing BuildRequires, please make sure they are listed in the "Depends On" field --- This comment was created by the fedora-review-service https://github.com/FrostyX/fedora-review-service If you want to trigger a new Copr build, add a comment containing new Spec and SRPM URLs or [fedora-review-service-build] string.
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 /usr/lib/python3.13/site-packages/nipype/testing/data/5tt_in.mif 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: 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Thanks for the review. (In reply to Ben Beasley from comment #2) > This looks pretty good. There’s a new release that can be packaged, and > there are some unwanted shebangs that should be removed. I'm aware. I have an update lined up. I was waiting for the dependencies to be reviewed before pushing that. Since that is pretty much a done deal: Spec URL: https://gui1ty.fedorapeople.org/review/python-nipype.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-nipype-1.9.1-3.fc42.src.rpm
Copr build: https://copr.fedorainfracloud.org/coprs/build/8329232 (failed) Build log: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2323073-python-nipype/fedora-rawhide-x86_64/08329232-python-nipype/builder-live.log.gz Please make sure the package builds successfully at least for Fedora Rawhide. - If the build failed for unrelated reasons (e.g. temporary network unavailability), please ignore it. - If the build failed because of missing BuildRequires, please make sure they are listed in the "Depends On" field --- This comment was created by the fedora-review-service https://github.com/FrostyX/fedora-review-service If you want to trigger a new Copr build, add a comment containing new Spec and SRPM URLs or [fedora-review-service-build] string.
[fedora-review-service-build]
Copr build: https://copr.fedorainfracloud.org/coprs/build/8558143 (succeeded) Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2323073-python-nipype/fedora-rawhide-x86_64/08558143-python-nipype/fedora-review/review.txt Found issues: - python3-pytest7 is deprecated, you must not depend on it. Read more: https://docs.fedoraproject.org/en-US/packaging-guidelines/deprecating-packages/ Please know that there can be false-positives. --- This comment was created by the fedora-review-service https://github.com/FrostyX/fedora-review-service If you want to trigger a new Copr build, add a comment containing new Spec and SRPM URLs or [fedora-review-service-build] string.
I haven’t forgotten about this. I’ve just been occupied with a lot of other things.
Overall, this looks fine, and the package is APPROVED. A newer version is available, and I hope you’ll read the notes and discussion below. Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated Notes: ====== - The choices of which extras to include (for BuildRequires generation, and as metapackages) and which to omit (like those that represent documentation and development dependencies) seems reasonable. You *could* include the xvfbwrapper extra, but seeing as we are trying to migrate away from xvfb-run from xorg-x11-server-Xvfb and toward xwfb-run/wlheadless-run from xwayland-run, I think it is reasonable to omit it until/unless a need for it becomes clear. - For packages like this that have many conditional tests, I like to pass -rs to %pytest so that it prints the reasons for skipped tests. Many of these are due to missing optional dependencies that are not and in some cases cannot be pacakged, but there are a handful of tests that could be enabled with additional BuildRequires. For example: SKIPPED [1] nipype/interfaces/tests/test_extra_dcm2nii.py:32: Dcm2niix required It turns out that adding "BuildRequires: dcm2niix" doesn’t actually enable that test, because it also has to fetch test data from the network, but this does reveal that there is some optional functionality that relies on dcm2niix (see nipype/interfaces/dcm2nii.py), suggesting that "Recommends: dcm2niix" might be warranted. I don’t think that this kind of fine-grained picking through the tests should be required for the package to be approved, but should you choose to pursue it, you might learn something useful. I at least recommend adding -rs so you can see the reasons for skipped tests in the build logs. Issues: ======= - Dist tag is present. OK: fedora-review is confused by 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: package built successfully with pytest 8.3.4 - Version 1.9.2 is available, a very small bugfix release compared to the 1.9.1 submitted here. Please update ASAP. https://github.com/nipy/nipype/compare/1.9.1...1.9.2 ===== 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 [x]: License file installed when any subpackage combination is installed. $ rpm -qL -p results/python3-nipype-1.9.1-3.fc42.noarch.rpm /usr/lib/python3.13/site-packages/nipype-1.9.1.dist-info/LICENSE [x]: Package must own all directories that it creates. Note: Directories without known owners: /usr/lib/python3.13/site- packages, /usr/lib/python3.13 (Spurious diagnostics; directories are properly owned by python3-libs.) [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. [x]: 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). [-]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python3-nipype , python3-nipype+data , python3-nipype+duecredit , python3-nipype+nipy , python3-nipype+pybids , python3-nipype+ssh [x]: Package functions as described. (Tests pass) [!]: Latest version is packaged. Please update to 1.9.2. [x]: 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. [x]: Package should compile and build into binary rpms on all supported architectures. https://koji.fedoraproject.org/koji/taskinfo?taskID=128656748 [x]: %check is present and all tests pass. [x]: 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) OK: differences are due to expansion of rpmautospec macros. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). Rpmlint ------- Checking: python3-nipype-1.9.1-3.fc42.noarch.rpm python3-nipype+data-1.9.1-3.fc42.noarch.rpm python3-nipype+duecredit-1.9.1-3.fc42.noarch.rpm python3-nipype+nipy-1.9.1-3.fc42.noarch.rpm python3-nipype+pybids-1.9.1-3.fc42.noarch.rpm python3-nipype+ssh-1.9.1-3.fc42.noarch.rpm python-nipype-1.9.1-3.fc42.src.rpm ============================ rpmlint session starts ============================ rpmlint: 2.6.1 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/tmpxihv0q4l')] checks: 32, packages: 7 python-nipype.src: E: spelling-error ('Neuroimaging', 'Summary(en_US) Neuroimaging -> Neurosurgical') python-nipype.src: E: spelling-error ('neuroimaging', '%description -l en_US neuroimaging -> neurosurgical') python3-nipype+data.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+duecredit.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+nipy.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+pybids.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+ssh.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype.noarch: E: spelling-error ('Neuroimaging', 'Summary(en_US) Neuroimaging -> Neurosurgical') python3-nipype.noarch: E: spelling-error ('neuroimaging', '%description -l en_US neuroimaging -> neurosurgical') python3-nipype.noarch: W: no-manual-page-for-binary nipypecli python3-nipype+data.noarch: W: no-documentation python3-nipype+duecredit.noarch: W: no-documentation python3-nipype+nipy.noarch: W: no-documentation python3-nipype+pybids.noarch: W: no-documentation python3-nipype+ssh.noarch: W: no-documentation python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/sphinxext/__init__.py /usr/lib/python3.13/site-packages/nipype/algorithms/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/afni/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/ants/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/camino/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/dtitk/tests/__init__.py:(and 2 more) python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py 7 packages and 0 specfiles checked; 9 errors, 10 warnings, 102 filtered, 9 badness; has taken 3.3 s Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.6.1 configuration: /usr/lib/python3.13/site-packages/rpmlint/configdefaults.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 checks: 32, packages: 6 python3-nipype+nipy.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+ssh.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+pybids.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype.noarch: E: spelling-error ('Neuroimaging', 'Summary(en_US) Neuroimaging -> Neurosurgical') python3-nipype.noarch: E: spelling-error ('neuroimaging', '%description -l en_US neuroimaging -> neurosurgical') python3-nipype+data.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype+duecredit.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-nipype.noarch: W: no-manual-page-for-binary nipypecli python3-nipype+nipy.noarch: W: no-documentation python3-nipype+ssh.noarch: W: no-documentation python3-nipype+pybids.noarch: W: no-documentation python3-nipype+data.noarch: W: no-documentation python3-nipype+duecredit.noarch: W: no-documentation python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/sphinxext/__init__.py /usr/lib/python3.13/site-packages/nipype/algorithms/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/afni/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/ants/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/camino/tests/__init__.py:/usr/lib/python3.13/site-packages/nipype/interfaces/dtitk/tests/__init__.py:(and 2 more) python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py python3-nipype.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py /usr/lib/python3.13/site-packages/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py 6 packages and 0 specfiles checked; 7 errors, 10 warnings, 98 filtered, 7 badness; has taken 2.3 s Source checksums ---------------- https://github.com/nipy/nipype/archive/1.9.1/nipype-1.9.1.tar.gz : CHECKSUM(SHA256) this package : b8738e31604034b582064fee163af1164b26d7763c39b21e35b5a5a529b511ad CHECKSUM(SHA256) upstream package : b8738e31604034b582064fee163af1164b26d7763c39b21e35b5a5a529b511ad Requires -------- python3-nipype (rpmlib, GLIBC filtered): (python3.13dist(looseversion) < 1.2 or python3.13dist(looseversion) > 1.2) /usr/bin/python3 python(abi) python3.13dist(acres) python3.13dist(click) python3.13dist(etelemetry) python3.13dist(filelock) python3.13dist(networkx) python3.13dist(nibabel) python3.13dist(numpy) python3.13dist(packaging) python3.13dist(prov) python3.13dist(puremagic) python3.13dist(pydot) python3.13dist(python-dateutil) python3.13dist(rdflib) python3.13dist(scipy) python3.13dist(simplejson) python3.13dist(traits) python3-nipype+data (rpmlib, GLIBC filtered): python(abi) python3-nipype python3.13dist(datalad) python3-nipype+duecredit (rpmlib, GLIBC filtered): python(abi) python3-nipype python3.13dist(duecredit) python3-nipype+nipy (rpmlib, GLIBC filtered): python(abi) python3-nipype python3.13dist(dipy) python3.13dist(matplotlib) python3.13dist(nilearn) python3.13dist(nipy) python3.13dist(nitime) python3-nipype+pybids (rpmlib, GLIBC filtered): python(abi) python3-nipype python3.13dist(pybids) python3-nipype+ssh (rpmlib, GLIBC filtered): python(abi) python3-nipype python3.13dist(paramiko) Provides -------- python3-nipype: python-nipype python3-nipype python3.13-nipype python3.13dist(nipype) python3dist(nipype) python3-nipype+data: python-nipype+data python3-nipype+data python3.13-nipype+data python3.13dist(nipype[data]) python3dist(nipype[data]) python3-nipype+duecredit: python-nipype+duecredit python3-nipype+duecredit python3.13-nipype+duecredit python3.13dist(nipype[duecredit]) python3dist(nipype[duecredit]) python3-nipype+nipy: python-nipype+nipy python3-nipype+nipy python3.13-nipype+nipy python3.13dist(nipype[nipy]) python3dist(nipype[nipy]) python3-nipype+pybids: python-nipype+pybids python3-nipype+pybids python3.13-nipype+pybids python3.13dist(nipype[pybids]) python3dist(nipype[pybids]) python3-nipype+ssh: python-nipype+ssh python3-nipype+ssh python3.13-nipype+ssh python3.13dist(nipype[ssh]) python3dist(nipype[ssh]) Diff spec file in url and in SRPM --------------------------------- --- /home/ben/fedora/review/2323073-python-nipype/srpm/python-nipype.spec 2025-01-16 10:40:31.714897662 -0500 +++ /home/ben/fedora/review/2323073-python-nipype/srpm-unpacked/python-nipype.spec 2024-11-22 19:00:00.000000000 -0500 @@ -1,2 +1,12 @@ +## START: Set by rpmautospec +## (rpmautospec version 0.7.3) +## RPMAUTOSPEC: autorelease, autochangelog +%define autorelease(e:s:pb:n) %{?-p:0.}%{lua: + release_number = 3; + base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}")); + print(release_number + base_release_number - 1); +}%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}} +## END: Set by rpmautospec + %global pypi_name nipype @@ -97,3 +107,21 @@ %changelog -%autochangelog +## START: Generated by rpmautospec +* Sat Nov 23 2024 Sandro <devel> - 1.9.1-3 +- Uncommitted changes + +* Sat Nov 23 2024 Sandro <devel> - 1.9.1-2 +- Add extras subpackages + +* Sat Nov 23 2024 Sandro <devel> - 1.9.1-1 +- Update to 1.9.1 + +* Thu Oct 31 2024 Sandro <devel> - 1.9.0-2 +- Disable some failing tests + +* Thu Oct 31 2024 Sandro <devel> - 1.9.0-1 +- Update to 1.9.0 + +* Tue Jul 23 2024 Sandro <devel> - 1.8.6-1 +- Initial package +## END: Generated by rpmautospec Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24 Command line :/usr/bin/fedora-review -b 2323073 -L nipype-deps Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api Disabled plugins: Haskell, fonts, Java, PHP, SugarActivity, Perl, C/C++, Ocaml, R Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH Built with local dependencies: /home/ben/fedora/review/nipype-deps/python3-etelemetry-0.3.1-2.fc42.noarch.rpm
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-nipype
Thanks for the review. I have updated the package to the latest release, added the option to pytest to show the reason for skipping a test. I also enabled the tests requiring xvfbwrapper. Unfortunately that requires specifying xorg-x11-server-Xvfb separately. I believe that should be a dependency pulled in by python3-xvfbwrapper. I'll submit a PR. Regarding xvfb-run vs. xwfbrun, I'll cross that bridge when we get there. Since xvfbwrapper appears to be a test dependency only, I don't think it makes sense to package the extra. I'll consider it if another package comes along requiring nipype[xvfbwrapper], which I think is unlikely. Last but not least I added a recommends for dcm2niix. Thanks for pointing that out.
https://bodhi.fedoraproject.org/updates/FEDORA-2025-24eb518a9d