Bug 2235132 - Review Request: python-brukerapi - Python package providing I/O interface for Bruker data sets
Summary: Review Request: python-brukerapi - Python package providing I/O interface for...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
unspecified
medium
Target Milestone: ---
Assignee: Benson Muite
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2023-08-26 23:42 UTC by Ben Beasley
Modified: 2023-09-17 01:42 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2023-09-07 12:01:36 UTC
Type: Bug
Embargoed:
benson_muite: fedora-review+


Attachments (Terms of Use)

Description Ben Beasley 2023-08-26 23:42:48 UTC
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.

Comment 1 Benson Muite 2023-09-07 10:06:40 UTC
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-0.1.9.tar.gz :
  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)

Comment 2 Ben Beasley 2023-09-07 11:31:27 UTC
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

Comment 3 Fedora Admin user for bugzilla script actions 2023-09-07 11:32:19 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-brukerapi

Comment 4 Ben Beasley 2023-09-07 11:49:21 UTC
Release monitoring was configured at https://release-monitoring.org/project/141108/.

Comment 5 Fedora Update System 2023-09-07 12:00:02 UTC
FEDORA-2023-4912b8076d has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2023-4912b8076d

Comment 6 Fedora Update System 2023-09-07 12:01:36 UTC
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.

Comment 7 Fedora Update System 2023-09-07 16:31:42 UTC
FEDORA-2023-bc02c4a8b9 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-bc02c4a8b9

Comment 8 Fedora Update System 2023-09-08 00:03:36 UTC
FEDORA-2023-f87b44c4e2 has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2023-f87b44c4e2

Comment 9 Fedora Update System 2023-09-08 01:28:56 UTC
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.

Comment 10 Fedora Update System 2023-09-08 01:37:16 UTC
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.

Comment 11 Fedora Update System 2023-09-08 13:08:55 UTC
FEDORA-2023-dbdd66bf41 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2023-dbdd66bf41

Comment 12 Fedora Update System 2023-09-08 13:23:05 UTC
FEDORA-EPEL-2023-9c1819e640 has been submitted as an update to Fedora EPEL 9. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2023-9c1819e640

Comment 13 Fedora Update System 2023-09-09 02:00:02 UTC
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.

Comment 14 Fedora Update System 2023-09-09 02:34:21 UTC
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.

Comment 15 Fedora Update System 2023-09-15 18:53:57 UTC
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.

Comment 16 Fedora Update System 2023-09-16 01:28:34 UTC
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.

Comment 17 Fedora Update System 2023-09-17 00:36:30 UTC
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.

Comment 18 Fedora Update System 2023-09-17 01:42:48 UTC
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.


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