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Bug 2257170 - Review Request: python-bioframe - Operations and utilities for Genomic Interval Dataframes
Summary: Review Request: python-bioframe - Operations and utilities for Genomic Interv...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Michel Lind
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora 2257116
TreeView+ depends on / blocked
 
Reported: 2024-01-07 17:17 UTC by Sandro
Modified: 2024-01-12 20:21 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2024-01-12 20:21:26 UTC
Type: ---
Embargoed:
michel: fedora-review+


Attachments (Terms of Use)

Description Sandro 2024-01-07 17:17:46 UTC
Spec URL: https://download.copr.fedorainfracloud.org/results/gui1ty/reviews/fedora-rawhide-x86_64/06870261-python-bioframe/python-bioframe.spec
SRPM URL: https://download.copr.fedorainfracloud.org/results/gui1ty/reviews/fedora-rawhide-x86_64/06870261-python-bioframe/python-bioframe-0.6.0-1.fc40.src.rpm

Description:
Bioframe enables flexible and scalable operations on genomic interval
dataframes in Python.

Bioframe is built directly on top of Pandas. Bioframe provides:

- A variety of genomic interval operations that work directly on
  dataframes.
- Operations for special classes of genomic intervals, including
  chromosome arms and fixed-size bins.
- Conveniences for diverse tabular genomic data formats and loading
  genome assembly summary information.

Bioframe is an Affiliated Project of NumFOCUS.

Fedora Account System Username: gui1ty

Copr build: https://copr.fedorainfracloud.org/coprs/gui1ty/reviews/build/6870261/

Comment 1 Fedora Review Service 2024-01-07 17:47:04 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/6870295
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2257170-python-bioframe/fedora-rawhide-x86_64/06870295-python-bioframe/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.

Comment 2 Michel Lind 2024-01-12 16:23:34 UTC
Looks fine, APPROVED. Please update to 0.6.1 when importing.

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

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


Issues:
=======
- Dist tag is present.


===== MUST items =====

Generic:
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
     Note: Using prebuilt packages
[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]: 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.
[-]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 26461 bytes in 4 files.
[x]: Package complies to the Packaging Guidelines
[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]: 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]: Packages must not store files under /srv, /opt or /usr/local

Python:
[-]: 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:
[x]: Reviewer should test that the package builds in mock.
[-]: 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).
[?]: 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]: Spec use %global instead of %define unless justified.
     Note: %define requiring justification: %define autorelease(e:s:pb:n)
     %{?-p:0.}%{lua:
[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.

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on all installed packages.
     Note: No rpmlint messages.


Rpmlint
-------
Checking: python3-bioframe-0.6.0-1.fc40.noarch.rpm
          python-bioframe-0.6.0-1.fc40.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/tmpzlb4q5wm')]
checks: 31, packages: 2

 2 packages and 0 specfiles checked; 0 errors, 0 warnings, 0 badness; has taken 0.2 s 




Rpmlint (installed packages)
----------------------------
(none): E: there is no installed rpm "python3-bioframe".
There are no files to process nor additional arguments.
Nothing to do, aborting.
============================ 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
checks: 32, packages: 1

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



Source checksums
----------------
https://github.com/open2c/bioframe/archive/v0.6.0/bioframe-0.6.0.tar.gz :
  CHECKSUM(SHA256) this package     : 81030869c2c4a2e1565c893bbdd869fb55ea7e23b2857f130090d5cab519383d
  CHECKSUM(SHA256) upstream package : 81030869c2c4a2e1565c893bbdd869fb55ea7e23b2857f130090d5cab519383d


Requires
--------
python3-bioframe (rpmlib, GLIBC filtered):
    python(abi)
    python3.12dist(matplotlib)
    python3.12dist(numpy)
    python3.12dist(pandas)
    python3.12dist(pyyaml)
    python3.12dist(requests)



Provides
--------
python3-bioframe:
    python-bioframe
    python3-bioframe
    python3.12-bioframe
    python3.12dist(bioframe)
    python3dist(bioframe)



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/bin/fedora-review --no-colors --prebuilt --rpm-spec --name python-bioframe --mock-config /var/lib/copr-rpmbuild/results/configs/child.cfg
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api
Disabled plugins: SugarActivity, C/C++, R, Java, Perl, PHP, fonts, Haskell, Ocaml
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comment 3 Sandro 2024-01-12 20:03:42 UTC
> Looks fine, APPROVED. Please update to 0.6.1 when importing.

Thanks for the review. I will import version 0.6.1.

Comment 4 Fedora Admin user for bugzilla script actions 2024-01-12 20:05:00 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-bioframe

Comment 5 Fedora Update System 2024-01-12 20:20:08 UTC
FEDORA-2024-08c7f72d0d has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2024-08c7f72d0d

Comment 6 Fedora Update System 2024-01-12 20:21:26 UTC
FEDORA-2024-08c7f72d0d has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.


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