Bug 2307489 - Review Request: python-snakemake-executor-plugin-flux - A snakemake executor plugin for the Flux scheduler
Summary: Review Request: python-snakemake-executor-plugin-flux - A snakemake executor ...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: Trivial
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2024-08-23 04:13 UTC by Ben Beasley
Modified: 2024-10-08 03:07 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2024-10-07 14:20:44 UTC
Type: ---
Embargoed:
sanjay.ankur: fedora-review+


Attachments (Terms of Use)

Description Ben Beasley 2024-08-23 04:13:41 UTC
Spec URL: https://music.fedorapeople.org/python-snakemake-executor-plugin-flux.spec
SRPM URL: https://music.fedorapeople.org/python-snakemake-executor-plugin-flux-0.1.1-1.fc40.src.rpm

Description:

This serves both as an example implementation for an external snakemake plugin
and as a usable executor plugin for the Flux scheduler.

Fedora Account System Username: music

This will be a neuro-sig package.

https://release-monitoring.org/project/374009/

Comment 1 Ankur Sinha (FranciscoD) 2024-10-07 13:51:15 UTC
XXX Looks good XXX APPROVED XXX

The only thing that I found was that the LICENSE may have been included twice---please do check that before importing.


Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- 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/

^ false positive

- LICENSE seems to be included already---no need to re-include it explicitly in %files?


===== 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* MIT License", "MIT
     License". 19 files have unknown license. Detailed output of
     licensecheck in /home/asinha/dump/fedora-reviews/2307489-python-
     snakemake-executor-plugin-flux/licensecheck.txt
[x]: Package must own all directories that it creates.
     Note: Directories without known owners: /usr/lib/python3.13/site-
     packages, /usr/lib/python3.13
[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 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 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 5597 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.
^
Import checks are run

[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: No rpmlint messages.
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: python3-snakemake-executor-plugin-flux-0.1.1-1.fc42.noarch.rpm
          python-snakemake-executor-plugin-flux-0.1.1-1.fc42.src.rpm
=================================================================================== rpmlint session starts ===================================================================================
rpmlint: 2.5.0
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/tmpuepwbanr')]
checks: 32, packages: 2

============================================== 2 packages and 0 specfiles checked; 0 errors, 0 warnings, 9 filtered, 0 badness; has taken 0.3 s ==============================================




Rpmlint (installed packages)
----------------------------
============================ rpmlint session starts ============================
rpmlint: 2.5.0
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: 1

 1 packages and 0 specfiles checked; 0 errors, 0 warnings, 5 filtered, 0 badness; has taken 0.0 s 



Source checksums
----------------
https://github.com/snakemake/snakemake-executor-plugin-flux/archive/v0.1.1/snakemake-executor-plugin-flux-0.1.1.tar.gz :
  CHECKSUM(SHA256) this package     : 1a8797053017da280a0ae17c80dcedef1c82b8d855e195b758cb1640e43e8eee
  CHECKSUM(SHA256) upstream package : 1a8797053017da280a0ae17c80dcedef1c82b8d855e195b758cb1640e43e8eee


Requires
--------
python3-snakemake-executor-plugin-flux (rpmlib, GLIBC filtered):
    (python3.13dist(snakemake-interface-common) < 2~~ with python3.13dist(snakemake-interface-common) >= 1.14)
    (python3.13dist(snakemake-interface-executor-plugins) < 10~~ with python3.13dist(snakemake-interface-executor-plugins) >= 9)
    python(abi)



Provides
--------
python3-snakemake-executor-plugin-flux:
    python-snakemake-executor-plugin-flux
    python3-snakemake-executor-plugin-flux
    python3.13-snakemake-executor-plugin-flux
    python3.13dist(snakemake-executor-plugin-flux)
    python3dist(snakemake-executor-plugin-flux)



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2307489
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, Shell-api, Python
Disabled plugins: Ocaml, Haskell, SugarActivity, C/C++, fonts, Perl, PHP, Java, R
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comment 2 Ben Beasley 2024-10-07 13:58:45 UTC
Thank you for the review!

(In reply to Ankur Sinha (FranciscoD) from comment #1)
> XXX Looks good XXX APPROVED XXX
> 
> The only thing that I found was that the LICENSE may have been included
> twice---please do check that before importing.
> 
> - LICENSE seems to be included already---no need to re-include it explicitly
> in %files?

In cases were the build backend doesn’t declare license files via the PEP 639 License-File field, the license file in the .dist-infor field doesn’t get automatically marked with %license:

  /usr/lib/python3.13/site-packages/snakemake_executor_plugin_flux-0.1.1.dist-info/LICENSE

This package uses poetry-core, which is one such build backend.

The usual practice is just to write

  %license LICENSE

which gives an additional (properly indicated) license file

  /usr/share/licenses/python3-snakemake-executor-plugin-flux/LICENSE

We can see that there is only one properly marked license file:

  $ rpm -qL -p /path/to/python3-snakemake-executor-plugin-flux-0.1.1-1.fc42.noarch.rpm
  /usr/share/licenses/python3-snakemake-executor-plugin-flux/LICENSE

It’s technically possible to modify %{pyproject_files} using something like sed to add the annotation to the file in dist-info, but I have never seen it done, and I don’t think it would be a good practice. It would be too messy, with too much risk of error, for the tiny gain of avoiding one small duplicate file.

Comment 3 Fedora Admin user for bugzilla script actions 2024-10-07 13:59:42 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-snakemake-executor-plugin-flux

Comment 4 Fedora Update System 2024-10-07 14:18:27 UTC
FEDORA-2024-b44c8cb2e7 (python-snakemake-executor-plugin-flux-0.1.1-1.fc42) has been submitted as an update to Fedora 42.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-b44c8cb2e7

Comment 5 Fedora Update System 2024-10-07 14:20:44 UTC
FEDORA-2024-b44c8cb2e7 (python-snakemake-executor-plugin-flux-0.1.1-1.fc42) has been pushed to the Fedora 42 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 6 Fedora Update System 2024-10-07 14:29:04 UTC
FEDORA-2024-60b3263362 (python-snakemake-executor-plugin-flux-0.1.1-1.fc41) has been submitted as an update to Fedora 41.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-60b3263362

Comment 7 Fedora Update System 2024-10-07 14:52:28 UTC
FEDORA-2024-a367bbfb97 (python-snakemake-executor-plugin-flux-0.1.1-1.fc40) has been submitted as an update to Fedora 40.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-a367bbfb97

Comment 8 Fedora Update System 2024-10-08 01:45:36 UTC
FEDORA-2024-60b3263362 has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-60b3263362 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-60b3263362

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 9 Fedora Update System 2024-10-08 03:07:28 UTC
FEDORA-2024-a367bbfb97 has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-a367bbfb97 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-a367bbfb97

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.


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