[Bug 2250700] New: Review Request: python-bioread - Utilities to read BIOPAC AcqKnowledge files
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Bug ID: 2250700 Summary: Review Request: python-bioread - Utilities to read BIOPAC AcqKnowledge files Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: code@musicinmybrain.net QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://music.fedorapeople.org/python-bioread.spec SRPM URL: https://music.fedorapeople.org/python-bioread-3.0.1-1.fc39.src.rpm
Description:
Fedora Account System Username: music
Koji scratch builds (forced to build on all architectures to verify there are no arch-dependent build failures):
F40: https://koji.fedoraproject.org/koji/taskinfo?taskID=109305454 F39: https://koji.fedoraproject.org/koji/taskinfo?taskID=109305607 F38: https://koji.fedoraproject.org/koji/taskinfo?taskID=109305635
This will be a neuro-sig package. It is a dependency for (one of the extras of) bidscoin, https://pagure.io/neuro-sig/NeuroFedora/issue/500.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Ben Beasley code@musicinmybrain.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 | |(fedora-neuro,NeuroFedora) Doc Type|--- |If docs needed, set a value
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1276941 [Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #1 from Fedora Review Service fedora-review-bot@fedoraproject.org --- Copr build: https://copr.fedorainfracloud.org/coprs/build/6670537 (failed)
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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
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https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |sanjay.ankur@gmail.com Flags| |fedora-review? Assignee|nobody@fedoraproject.org |sanjay.ankur@gmail.com Status|NEW |ASSIGNED
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #2 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Looks good. My only query is about the extras packages---they're all arched and I don't supposed there's a way of making them noarch? It doesn't really matter, just that rpmlint picks up the lack of binaries in them.
$ ls *rpm python3-bioread-3.0.1-1.fc40.noarch.rpm python3-bioread+hdf5-3.0.1-1.fc40.x86_64.rpm python-bioread-3.0.1-1.fc40.src.rpm python3-bioread+all-3.0.1-1.fc40.x86_64.rpm python3-bioread+mat-3.0.1-1.fc40.x86_64.rpm
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
===== 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. No licenses found. Please check the source files for licenses manually. [x]: License file installed when any subpackage combination is installed. [x]: %build honors applicable compiler flags or justifies otherwise. [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]: Useful -debuginfo package or justification otherwise. [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 must own all directories that it creates. [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]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package must not depend on deprecated() packages. [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 9992 bytes in 2 files. [x]: Packages must not store files under /srv, /opt or /usr/local
Python: [x]: Binary eggs must be removed in %prep Note: Cannot find any build in BUILD directory (--prebuilt option?) [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
===== 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. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python3-bioread , python3-bioread+mat , python3-bioread+hdf5 , python3-bioread+all [x]: Package functions as described. ^ test pass
[x]: 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: [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: python3-bioread-3.0.1-1.fc40.noarch.rpm python3-bioread+mat-3.0.1-1.fc40.x86_64.rpm python3-bioread+hdf5-3.0.1-1.fc40.x86_64.rpm python3-bioread+all-3.0.1-1.fc40.x86_64.rpm python-bioread-3.0.1-1.fc40.src.rpm =========================================================================== rpmlint session starts ========================================================================== rpmlint: 2.4.0 configuration: /usr/lib/python3.12/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/tmpgrrj91lk')] checks: 31, packages: 5
python3-bioread+all.x86_64: W: no-documentation python3-bioread+hdf5.x86_64: W: no-documentation python3-bioread+mat.x86_64: W: no-documentation python3-bioread+all.x86_64: E: no-binary python3-bioread+hdf5.x86_64: E: no-binary python3-bioread+mat.x86_64: E: no-binary ============================================ 5 packages and 0 specfiles checked; 3 errors, 3 warnings, 3 badness; has taken 0.9 s ===========================================
Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.4.0 configuration: /usr/lib/python3.12/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 checks: 31, packages: 4
python3-bioread+mat.x86_64: W: no-documentation python3-bioread+all.x86_64: W: no-documentation python3-bioread+hdf5.x86_64: W: no-documentation python3-bioread+mat.x86_64: E: no-binary python3-bioread+all.x86_64: E: no-binary python3-bioread+hdf5.x86_64: E: no-binary 4 packages and 0 specfiles checked; 3 errors, 3 warnings, 3 badness; has taken 0.1 s
Source checksums ---------------- https://github.com/uwmadison-chm/bioread/archive/v3.0.1/bioread-3.0.1.tar.gz : CHECKSUM(SHA256) this package : 0613f257317857e5c2e8af4bf9715ea4b1b823fe70e3cff70be93ac785e0a7fb CHECKSUM(SHA256) upstream package : 0613f257317857e5c2e8af4bf9715ea4b1b823fe70e3cff70be93ac785e0a7fb
Requires -------- python3-bioread (rpmlib, GLIBC filtered): /usr/bin/python3 python(abi) python3.12dist(docopt) python3.12dist(numpy)
python3-bioread+mat (rpmlib, GLIBC filtered): python(abi) python3-bioread python3.12dist(scipy)
python3-bioread+hdf5 (rpmlib, GLIBC filtered): python(abi) python3-bioread python3.12dist(h5py)
python3-bioread+all (rpmlib, GLIBC filtered): python(abi) python3-bioread python3.12dist(h5py) python3.12dist(scipy)
Provides -------- python3-bioread: python-bioread python3-bioread python3.12-bioread python3.12dist(bioread) python3dist(bioread)
python3-bioread+mat: python-bioread+mat python3-bioread+mat python3-bioread+mat(x86-64) python3.12-bioread+mat python3.12dist(bioread[mat]) python3dist(bioread[mat])
python3-bioread+hdf5: python-bioread+hdf5 python3-bioread+hdf5 python3-bioread+hdf5(x86-64) python3.12-bioread+hdf5 python3.12dist(bioread[hdf5]) python3dist(bioread[hdf5])
python3-bioread+all: python-bioread+all python3-bioread+all python3-bioread+all(x86-64) python3.12-bioread+all python3.12dist(bioread[all]) python3dist(bioread[all])
Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24 Command line :/usr/bin/fedora-review -b 2250700 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api Disabled plugins: PHP, Haskell, Java, fonts, Ocaml, C/C++, SugarActivity, R, Perl Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #3 from Ben Beasley code@musicinmybrain.net --- (In reply to Ankur Sinha (FranciscoD) from comment #2)
Looks good. My only query is about the extras packages---they're all arched and I don't supposed there's a way of making them noarch? It doesn't really matter, just that rpmlint picks up the lack of binaries in them.
I think that there is no way of doing this for an arched base package other than defining them manually without the assistance of %pyproject_extras_subpackage. I’ve sometimes found that necessary in order to do unusual things like adding upgrade paths for old subpackages, but it doesn’t seem worth it just for making them noarch. This limitation is alluded to from a different perspective in https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_extras_ma...:
Due to technical limitations, the macro never generates requirements on the arched BASE_PACKAGE%{?_isa} = %{?epoch:%{epoch}:}%{version}-%{release}. It only adds Requires: BASE_PACKAGE = %{?epoch:%{epoch}:}%{version}-%{release}) because a macro cannot reliably detect if the subpackage is arched or not. So far, this has not been a problem in practice.
However, the fact that the base package is arched is copied from another package I used as a template, and it’s probably unnecessary for this package. Certainly, the comment about endian-dependent test failures is not accurate for this package. Try this:
New Spec URL: https://music.fedorapeople.org/20231121/python-bioread.spec New SRPM URL: https://music.fedorapeople.org/20231121/python-bioread-3.0.1-1.fc39.src.rpm
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #4 from Fedora Review Service fedora-review-bot@fedoraproject.org --- Copr build: https://copr.fedorainfracloud.org/coprs/build/6674477 (succeeded)
Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-rev...
Please take a look if any issues were found.
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https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+ Status|ASSIGNED |POST
--- Comment #5 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com ---
However, the fact that the base package is arched is copied from another package I used as a template, and it’s probably unnecessary for this package. Certainly, the comment about endian-dependent test failures is not accurate for this package. Try this:
New Spec URL: https://music.fedorapeople.org/20231121/python-bioread.spec New SRPM URL: https://music.fedorapeople.org/20231121/python-bioread-3.0.1-1.fc39.src.rpm
Cool, that now also makes rpmlint happy:
Rpmlint ------- Checking: python3-bioread-3.0.1-1.fc40.noarch.rpm python3-bioread+mat-3.0.1-1.fc40.noarch.rpm python3-bioread+hdf5-3.0.1-1.fc40.noarch.rpm python3-bioread+all-3.0.1-1.fc40.noarch.rpm python-bioread-3.0.1-1.fc40.src.rpm =========================================================================== rpmlint session starts ========================================================================== rpmlint: 2.4.0 configuration: /usr/lib/python3.12/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/tmpmrhpt5i6')] checks: 31, packages: 5
python3-bioread+all.noarch: W: no-documentation python3-bioread+hdf5.noarch: W: no-documentation python3-bioread+mat.noarch: W: no-documentation ============================================ 5 packages and 0 specfiles checked; 0 errors, 3 warnings, 0 badness; has taken 0.9 s ===========================================
Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.4.0 configuration: /usr/lib/python3.12/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 checks: 31, packages: 4
python3-bioread+all.noarch: W: no-documentation python3-bioread+hdf5.noarch: W: no-documentation python3-bioread+mat.noarch: W: no-documentation 4 packages and 0 specfiles checked; 0 errors, 3 warnings, 0 badness; has taken 0.1 s
XXX APPROVED XXX
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #6 from Ben Beasley code@musicinmybrain.net --- Thank you for the review!
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #7 from Fedora Admin user for bugzilla script actions fedora-admin-xmlrpc@fedoraproject.org --- The Pagure repository was created at https://src.fedoraproject.org/rpms/python-bioread
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #8 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-a07992920d has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2023-a07992920d
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |CLOSED Resolution|--- |ERRATA Last Closed| |2023-11-22 00:12:38
--- Comment #9 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-a07992920d has been pushed to the Fedora 40 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #10 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-29b67f73a3 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-29b67f73a3
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #11 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-cd0e4b87ad has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2023-cd0e4b87ad
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #12 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-5315aae2c7 has been submitted as an update to Fedora EPEL 9. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2023-5315aae2c7
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #13 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-cd0e4b87ad has been pushed to the Fedora 38 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-cd0e4b87ad *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-cd0e4b87ad
See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #14 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-29b67f73a3 has been pushed to the Fedora 39 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-29b67f73a3 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-29b67f73a3
See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #15 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-5315aae2c7 has been pushed to the Fedora EPEL 9 testing repository.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2023-5315aae2c7
See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #16 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-29b67f73a3 has been pushed to the Fedora 39 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #17 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-cd0e4b87ad has been pushed to the Fedora 38 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2250700
--- Comment #18 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-5315aae2c7 has been pushed to the Fedora EPEL 9 stable repository. If problem still persists, please make note of it in this bug report.
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