Spec URL: https://gui1ty.fedorapeople.org/review/python-vascpy.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-vascpy-0.1.1-1.fc41.src.rpm Description: vascpy is a python library for reading, writing, and manipulating large-scale vasculature graphs. There are two alternative graph representations available: a section-centered and an edge-centered one. It supports the following respective formats: - H5 Morphology - SONATA node population of edges The vascpy library provides two classes: `PointVasculature` and `SectionVasculature` that allow for reading and writing edge-centered and section-centered datasets respectively, as well as converting between them. Fedora Account System Username: gui1ty
Copr build: https://copr.fedorainfracloud.org/coprs/build/7484543 (succeeded) Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2283110-python-vascpy/fedora-rawhide-x86_64/07484543-python-vascpy/fedora-review/review.txt Please take a look if any issues were found. --- 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.
It doesn’t look like this builds in Rawhide anymore: tests/test_point_vasculature.py::test_file_formats Fatal Python error: Segmentation fault Current thread 0x00007f42e6a65740 (most recent call first): File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 1316 in create_module File "<frozen importlib._bootstrap>", line 813 in module_from_spec File "<frozen importlib._bootstrap>", line 921 in _load_unlocked File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1360 in _find_and_load File "/usr/lib64/python3.13/site-packages/vtk.py", line 4 in <module> File "<frozen importlib._bootstrap>", line 488 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 1022 in exec_module File "<frozen importlib._bootstrap>", line 935 in _load_unlocked File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1360 in _find_and_load File "/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/lib/python3.13/site-packages/vascpy/point_graph/io.py", line 237 in write File "/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/lib/python3.13/site-packages/vascpy/point_vasculature.py", line 119 in save_vtk File "/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/lib/python3.13/site-packages/vascpy/point_vasculature.py", line 241 in save File "/builddir/build/BUILD/python-vascpy-0.1.1-build/vascpy-0.1.1/tests/test_point_vasculature.py", line 523 in test_file_formats File "/usr/lib/python3.13/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/python.py", line 1792 in runtest File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 169 in pytest_runtest_call File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 262 in <lambda> File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 341 in from_call File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 261 in call_runtest_hook File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 222 in call_and_report File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 133 in runtestprotocol File "/usr/lib/python3.13/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 350 in pytest_runtestloop File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 325 in _main File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 271 in wrap_session File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 350 in pytest_runtestloop File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 325 in _main File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 271 in wrap_session File "/usr/lib/python3.13/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main File "/usr/lib/python3.13/site-packages/pluggy/_callers.py", line 77 in _multicall File "/usr/lib/python3.13/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/usr/lib/python3.13/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/usr/lib/python3.13/site-packages/_pytest/config/__init__.py", line 169 in main File "/usr/lib/python3.13/site-packages/_pytest/config/__init__.py", line 192 in console_main File "/usr/bin/pytest", line 8 in <module> Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5o, h5py.h5l, h5py._selector, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering (total: 107) /var/tmp/rpm-tmp.NQZpV0: line 53: 423 Segmentation fault (core dumped) CFLAGS="${CFLAGS:-${RPM_OPT_FLAGS}}" LDFLAGS="${LDFLAGS:-${RPM_LD_FLAGS}}" PATH="/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/bin:$PATH" PYTHONPATH="${PYTHONPATH:-/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-vascpy-0.1.1-build/BUILDROOT/usr/lib/python3.13/site-packages}" PYTHONDONTWRITEBYTECODE=1 PYTEST_ADDOPTS="${PYTEST_ADDOPTS:-} --ignore=/builddir/build/BUILD/python-vascpy-0.1.1-build/vascpy-0.1.1/.pyproject-builddir" PYTEST_XDIST_AUTO_NUM_WORKERS="${PYTEST_XDIST_AUTO_NUM_WORKERS:-16}" /usr/bin/pytest -v
I can reproduce this error in a local mock build with Python 3.13. I'm not sure what's causing it, though. But it seems specific to rawhide / Python 3.13. For F40 all tests succeed. I'll investigate...
It turns out this fails due to `vtk` segfaulting on import as reported in bug 2310520. When I submitted this package it was build with Python 3.12 as can be verified looking ad the Fedora Review Service build logs.
[fedora-review-service-build]
Copr build: https://copr.fedorainfracloud.org/coprs/build/8148477 (succeeded) Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2283110-python-vascpy/fedora-rawhide-x86_64/08148477-python-vascpy/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.
Issues: ======= - Remove markup from description - Update latest 0.1.2: https://github.com/BlueBrain/vascpy/releases ===== 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. [-]: License file installed when any subpackage combination is installed. [x]: Package must own all directories that it creates. [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 [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. [!]: 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 2910 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]: Fully versioned dependency in subpackages if applicable. [x]: Package functions as described. [!]: Latest version is packaged. [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. [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) [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). Rpmlint ------- Checking: python3-vascpy-0.1.1-1.fc42.noarch.rpm python3-vascpy+all-0.1.1-1.fc42.noarch.rpm python-vascpy-0.1.1-1.fc42.src.rpm ============================ rpmlint session starts ============================ rpmlint: 2.5.0 python-vascpy.src: E: spelling-error ('Vasculature', 'Summary(en_US) Vasculature -> Musculature, Curvature') python-vascpy.src: E: spelling-error ('vasculature', '%description -l en_US vasculature -> musculature, curvature') python3-vascpy+all.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage') python3-vascpy+all.noarch: E: spelling-error ('metapackage', '%description -l en_US metapackage -> meta package, meta-package, prepackage') python3-vascpy.noarch: E: spelling-error ('Vasculature', 'Summary(en_US) Vasculature -> Musculature, Curvature') python3-vascpy.noarch: E: spelling-error ('vasculature', '%description -l en_US vasculature -> musculature, curvature') python3-vascpy.noarch: W: no-manual-page-for-binary vascpy python3-vascpy+all.noarch: W: no-documentation python3-vascpy.noarch: W: files-duplicate /usr/lib/python3.13/site-packages/vascpy/utils/__init__.py /usr/lib/python3.13/site-packages/vascpy/section_graph/__init__.py 3 packages and 0 specfiles checked; 6 errors, 3 warnings, 34 filtered, 6 badness; has taken 0.6 s Seem to be harmless Source checksums ---------------- https://github.com/BlueBrain/vascpy/archive/v0.1.1/vascpy-0.1.1.tar.gz : CHECKSUM(SHA256) this package : 536f69a6b0888d99050f778ff27c97ce440f0c02622b11e9e21c4aa8f2c7dee1 CHECKSUM(SHA256) upstream package : 536f69a6b0888d99050f778ff27c97ce440f0c02622b11e9e21c4aa8f2c7dee1 Requires -------- python3-vascpy (rpmlib, GLIBC filtered): /usr/bin/python3 python(abi) python3.13dist(click) python3.13dist(h5py) python3.13dist(libsonata) python3.13dist(morphio) python3.13dist(numpy) python3.13dist(pandas) python3.13dist(scipy) python3-vascpy+all (rpmlib, GLIBC filtered): python(abi) python3-vascpy python3.13dist(igraph) python3.13dist(vtk) Provides -------- python3-vascpy: python-vascpy python3-vascpy python3.13-vascpy python3.13dist(vascpy) python3dist(vascpy) python3-vascpy+all: python-vascpy+all python3-vascpy+all python3.13-vascpy+all python3.13dist(vascpy[all]) python3dist(vascpy[all]) Diff spec file in url and in SRPM --------------------------------- --- /review/2283110-python-vascpy/srpm/python-vascpy.spec 2024-11-17 10:49:45.386077943 +0100 +++ /review/2283110-python-vascpy/srpm-unpacked/python-vascpy.spec 2024-05-23 02:00:00.000000000 +0200 @@ -1,2 +1,12 @@ +## START: Set by rpmautospec +## (rpmautospec version 0.6.3) +## RPMAUTOSPEC: autorelease, autochangelog
(In reply to Terje Rosten from comment #8) > Issues: > ======= > - Remove markup from description > - Update latest 0.1.2: > https://github.com/BlueBrain/vascpy/releases Thank you again! I have updated the package to the latest release. I'm not sure why you would like to see the markup removed. It may not be parsed, but it certainly doesn't hurt either. Though, I believe it makes the description easier to parse. As for `puremagic` this is just copied from upstream's README file. Spec URL: https://gui1ty.fedorapeople.org/review/python-vascpy.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-vascpy-0.1.2-1.fc41.src.rpm
There seems to be some problem with the following file. SRPM URL: https://gui1ty.fedorapeople.org/review/python-vascpy-0.1.2-1.fc41.src.rpm Fetching it results in a 404 Not Found error. Please make sure the URL is correct and publicly available. --- 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 made a typo in the updated SRPM URL. Spec URL: https://gui1ty.fedorapeople.org/review/python-vascpy.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-vascpy-0.1.2-1.fc42.src.rpm
Created attachment 2058564 [details] The .spec file difference from Copr build 8148477 to 8277212
Copr build: https://copr.fedorainfracloud.org/coprs/build/8277212 (succeeded) Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2283110-python-vascpy/fedora-rawhide-x86_64/08277212-python-vascpy/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'm not sure why you would like to see the markup removed. It's just noise in context used.
(In reply to Terje Rosten from comment #14) > > I'm not sure why you would like to see the markup removed. > > It's just noise in context used. That's a debate on opinions or a matter of taste. Nothing in the packaging guidelines forbids (MUST NOT) or recommends to avoid (SHOULD NOT) it. Regardless, I removed it: Spec URL: https://gui1ty.fedorapeople.org/review/python-vascpy.spec SRPM URL: https://gui1ty.fedorapeople.org/review/python-vascpy-0.1.2-2.fc42.src.rpm
Created attachment 2059374 [details] The .spec file difference from Copr build 8277212 to 8302288
Copr build: https://copr.fedorainfracloud.org/coprs/build/8302288 (succeeded) Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2283110-python-vascpy/fedora-rawhide-x86_64/08302288-python-vascpy/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.
Package is APPROVED.
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-vascpy