https://bugzilla.redhat.com/show_bug.cgi?id=2257170
Bug ID: 2257170 Summary: Review Request: python-bioframe - Operations and utilities for Genomic Interval Dataframes Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: gui1ty@penguinpee.nl QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://download.copr.fedorainfracloud.org/results/gui1ty/reviews/fedora-raw... SRPM URL: https://download.copr.fedorainfracloud.org/results/gui1ty/reviews/fedora-raw...
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/
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
Sandro gui1ty@penguinpee.nl changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 | |(fedora-neuro,NeuroFedora), | |2257116 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=2257116 [Bug 2257116] python-adjustText-1.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
--- Comment #1 from Fedora Review Service fedora-review-bot@fedoraproject.org --- Copr build: https://copr.fedorainfracloud.org/coprs/build/6870295 (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=2257170
Michel Lind michel@michel-slm.name changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |michel@michel-slm.name Assignee|nobody@fedoraproject.org |michel@michel-slm.name
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
Michel Lind michel@michel-slm.name changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+ Status|ASSIGNED |POST
--- Comment #2 from Michel Lind michel@michel-slm.name --- 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
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
--- Comment #3 from Sandro gui1ty@penguinpee.nl ---
Looks fine, APPROVED. Please update to 0.6.1 when importing.
Thanks for the review. I will import version 0.6.1.
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
--- Comment #4 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-bioframe
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |MODIFIED
--- Comment #5 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-08c7f72d0d has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2024-08c7f72d0d
https://bugzilla.redhat.com/show_bug.cgi?id=2257170
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Resolution|--- |ERRATA Status|MODIFIED |CLOSED Last Closed| |2024-01-12 20:21:26
--- Comment #6 from Fedora Update System updates@fedoraproject.org --- 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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