https://bugzilla.redhat.com/show_bug.cgi?id=2235132
Bug ID: 2235132 Summary: Review Request: python-brukerapi - Python package providing I/O interface for Bruker data sets Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Assignee: nobody@fedoraproject.org Reporter: code@musicinmybrain.net QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Blocks: 1276941 (fedora-neuro) Target Milestone: --- Classification: Fedora
Spec URL: https://music.fedorapeople.org/python-brukerapi.spec SRPM URL: https://music.fedorapeople.org/python-brukerapi-0.1.9-1.fc38.src.rpm
Description:
A Python package providing I/O interface for Bruker data sets.
Fedora Account System Username: music
Koji scratch builds:
F40: https://koji.fedoraproject.org/koji/taskinfo?taskID=105360075 F39: https://koji.fedoraproject.org/koji/taskinfo?taskID=105360244 F38: https://koji.fedoraproject.org/koji/taskinfo?taskID=105360543 F37: https://koji.fedoraproject.org/koji/taskinfo?taskID=105360756
This package is a dependency for spec2nii, which itself is a technically-optional but important dependency for bidscoin, https://pagure.io/neuro-sig/NeuroF edora/issue/500. Accordingly, the neuro-sig packager group will be given commit access.
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=2235132
Benson Muite benson_muite@emailplus.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED Doc Type|--- |If docs needed, set a value CC| |benson_muite@emailplus.org Flags| |fedora-review? Assignee|nobody@fedoraproject.org |benson_muite@emailplus.org
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
Benson Muite benson_muite@emailplus.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST Flags|fedora-review? |fedora-review+
--- Comment #1 from Benson Muite benson_muite@emailplus.org --- 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. Licenses found: "Unknown or generated", "MIT License". 78 files have unknown license. Detailed output of licensecheck in /home/FedoraPackaging/reviews/python-brukerapi/2235132-python- brukerapi/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [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: No rpmlint messages. [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 0 bytes in 0 files. [x]: Packages must not store files under /srv, /opt or /usr/local
Python: [-]: Python eggs must not download any dependencies during the build process. [-]: 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-brukerapi [ ]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: 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: No rpmlint messages. [x]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: python3-brukerapi-0.1.9-1.fc38.noarch.rpm python-brukerapi-doc-0.1.9-1.fc38.noarch.rpm python-brukerapi-0.1.9-1.fc38.src.rpm =========================================== rpmlint session starts ========================================== rpmlint: 2.4.0 configuration: /usr/lib/python3.11/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/tmpf913xsg5')] checks: 31, packages: 3
============ 3 packages and 0 specfiles checked; 0 errors, 0 warnings, 0 badness; has taken 7.0 s ===========
Rpmlint (installed packages) ---------------------------- ============================ rpmlint session starts ============================ rpmlint: 2.4.0 configuration: /usr/lib/python3.11/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: 2
2 packages and 0 specfiles checked; 0 errors, 0 warnings, 0 badness; has taken 0.4 s
Source checksums ---------------- https://github.com/isi-nmr/brukerapi-python/archive/v0.1.9/brukerapi-python-... : CHECKSUM(SHA256) this package : 329c0caecab94dbc04bd628d2db952996b56c587458522d0a76d85a0c924cfe1 CHECKSUM(SHA256) upstream package : 329c0caecab94dbc04bd628d2db952996b56c587458522d0a76d85a0c924cfe1
Requires -------- python3-brukerapi (rpmlib, GLIBC filtered): /usr/bin/python3 python(abi) python3.11dist(numpy) python3.11dist(pyyaml)
python-brukerapi-doc (rpmlib, GLIBC filtered):
Provides -------- python3-brukerapi: python-brukerapi python3-brukerapi python3.11-brukerapi python3.11dist(brukerapi) python3dist(brukerapi)
python-brukerapi-doc: python-brukerapi-doc
Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24 Command line :/usr/bin/fedora-review -b 2235132 -m fedora-38-x86_64 Buildroot used: fedora-38-x86_64 Active plugins: Python, Generic, Shell-api Disabled plugins: Java, Haskell, PHP, Perl, Ruby, R, C/C++, SugarActivity, fonts, Ocaml Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH
Comments: a) Approved b) Distributing PDF seems reasonable. c) Man pages are nice, in addition to pdf Sphinx can generate man pages using: sphinx-build -b man -C source output-man though this may need some cleanup, but in general have found it usable. d) There is a warning in the build log: /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'brukerapi.config' is absent from the `packages` configuration. !!
******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'brukerapi.config' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'brukerapi.config' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'brukerapi.config' to be distributed and are already explicitly excluding 'brukerapi.config' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages.
******************************************************************************** !! check.warn(importable)
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #2 from Ben Beasley code@musicinmybrain.net --- Thank you for the review!
I fixed the warning in [1], which I will add as an additional patch after import.
[1] https://github.com/isi-nmr/brukerapi-python/pull/22
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #3 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-brukerapi
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #4 from Ben Beasley code@musicinmybrain.net --- Release monitoring was configured at https://release-monitoring.org/project/141108/.
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #5 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-4912b8076d has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2023-4912b8076d
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |CLOSED Resolution|--- |ERRATA Last Closed| |2023-09-07 12:01:36
--- Comment #6 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-4912b8076d 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=2235132
--- Comment #7 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-bc02c4a8b9 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-bc02c4a8b9
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #8 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-f87b44c4e2 has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2023-f87b44c4e2
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #9 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-f87b44c4e2 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-f87b44c4e2 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-f87b44c4e2
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=2235132
--- Comment #10 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-bc02c4a8b9 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-bc02c4a8b9 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-bc02c4a8b9
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=2235132
--- Comment #11 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-dbdd66bf41 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2023-dbdd66bf41
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #12 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-9c1819e640 has been submitted as an update to Fedora EPEL 9. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2023-9c1819e640
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #13 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-9c1819e640 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-2023-9c1819e640
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=2235132
--- Comment #14 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-dbdd66bf41 has been pushed to the Fedora 37 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-dbdd66bf41 *` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-dbdd66bf41
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=2235132
--- Comment #15 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-bc02c4a8b9 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=2235132
--- Comment #16 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-f87b44c4e2 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=2235132
--- Comment #17 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2023-9c1819e640 has been pushed to the Fedora EPEL 9 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #18 from Fedora Update System updates@fedoraproject.org --- FEDORA-2023-dbdd66bf41 has been pushed to the Fedora 37 stable repository. If problem still persists, please make note of it in this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #19 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2024-75f6e65fc4 (python-brukerapi-0.1.9-7.el10_0) has been submitted as an update to Fedora EPEL 10.0. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2024-75f6e65fc4
https://bugzilla.redhat.com/show_bug.cgi?id=2235132
--- Comment #20 from Fedora Update System updates@fedoraproject.org --- FEDORA-EPEL-2024-75f6e65fc4 (python-brukerapi-0.1.9-7.el10_0) has been pushed to the Fedora EPEL 10.0 stable repository. If problem still persists, please make note of it in this bug report.
package-review@lists.fedoraproject.org