[Bug 2257524] New: Review Request: python-snakemake-interface-executor-plugins - Stable interface for interactions between Snakemake and its executor plugins
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Bug ID: 2257524 Summary: Review Request: python-snakemake-interface-executor-plugins - Stable interface for interactions between Snakemake and its executor plugins 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,NeuroFedora), 2255578 Target Milestone: --- Classification: Fedora
Spec URL: https://music.fedorapeople.org/python-snakemake-interface-executor-plugins.s... SRPM URL: https://music.fedorapeople.org/python-snakemake-interface-executor-plugins-8...
Description:
This package provides a stable interface for interactions between Snakemake and its executor plugins.
Fedora Account System Username: music
This package is a dependency for Snakemake v8 and is involved in bootstrapping it (due to a set of circular test dependencies). A bootstrap version of this package is uploaded for review that builds as-is. However, I have completed a successful non-bootstrap build (i.e., with tests enabled) in COPR: https://copr.fedorainfracloud.org/coprs/music/snakemake8/build/6877193/
Disabling the bootstrap conditional will require another new package, python-snakemake-executor-plugin-cluster-generic, which I have built in COPR but not yet submitted for review.
This will be a neuro-sig package.
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=2255578 [Bug 2255578] snakemake-8.1.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Fedora Review Service fedora-review-bot@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Keywords| |AutomationTriaged
--- Comment #1 from Fedora Review Service fedora-review-bot@fedoraproject.org --- Copr build: https://copr.fedorainfracloud.org/coprs/build/6877202 (succeeded)
Review template: https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-rev...
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.
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Ben Beasley code@musicinmybrain.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |2257526
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=2257526 [Bug 2257526] Review Request: python-snakemake-executor-plugin-cluster-generic - Generic cluster executor for Snakemake
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Doc Type|--- |If docs needed, set a value CC| |sanjay.ankur@gmail.com Status|NEW |ASSIGNED Flags| |fedora-review?
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+
--- Comment #2 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Looks good. XXX APPROVED XXX
Minor comments:
- `-l` not used in pyproject_save files? - pytest is to be used when not bootstrapped, so the BR can again be moved into the conditional?
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". 27 files have unknown license. Detailed output of licensecheck in /home/asinha/dump/fedora- reviews/2257524-python-snakemake-interface-executor- plugins/licensecheck.txt [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. [x]: Package contains systemd file(s) if in need. [x]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 21480 bytes in 2 files. [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: There are rpmlint messages (see attachment). [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]: 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]: 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. ^ Tests all pass [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: There are rpmlint messages (see attachment). [x]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: python3-snakemake-interface-executor-plugins-8.1.3-1.fc40~bootstrap.noarch.rpm
python-snakemake-interface-executor-plugins-8.1.3-1.fc40~bootstrap.src.rpm =================================================================================== rpmlint session starts =================================================================================== rpmlint: 2.4.0 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/tmp5ssona5r')] checks: 31, packages: 2
python3-snakemake-interface-executor-plugins.noarch: E: non-executable-script /usr/lib/python3.12/site-packages/snakemake_interface_executor_plugins/executors/jobscript.sh 644 /bin/sh ==================================================== 2 packages and 0 specfiles checked; 1 errors, 0 warnings, 1 badness; has taken 0.5 s ====================================================
Rpmlint (installed packages) ---------------------------- ============================ 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
python3-snakemake-interface-executor-plugins.noarch: W: python-missing-require argparse-dataclass python3-snakemake-interface-executor-plugins.noarch: W: python-missing-require snakemake-interface-common python3-snakemake-interface-executor-plugins.noarch: W: python-missing-require throttler python3-snakemake-interface-executor-plugins.noarch: E: non-executable-script /usr/lib/python3.12/site-packages/snakemake_interface_executor_plugins/executors/jobscript.sh 644 /bin/sh 1 packages and 0 specfiles checked; 1 errors, 3 warnings, 4 filtered, 1 badness; has taken 0.1 s
Source checksums ---------------- https://github.com/snakemake/snakemake-interface-executor-plugins/archive/v8... : CHECKSUM(SHA256) this package : 028cdd714b2b60b4102ea626bc19f820dd1c3f2221e71a52db350e8f8b3bf616 CHECKSUM(SHA256) upstream package : 028cdd714b2b60b4102ea626bc19f820dd1c3f2221e71a52db350e8f8b3bf616
Requires -------- python3-snakemake-interface-executor-plugins (rpmlib, GLIBC filtered): (python3.12dist(argparse-dataclass) < 3~~ with python3.12dist(argparse-dataclass) >= 2) (python3.12dist(snakemake-interface-common) < 2~~ with python3.12dist(snakemake-interface-common) >= 1.12) (python3.12dist(throttler) < 2~~ with python3.12dist(throttler) >= 1.2.2) python(abi)
Provides -------- python3-snakemake-interface-executor-plugins: python-snakemake-interface-executor-plugins python3-snakemake-interface-executor-plugins python3.12-snakemake-interface-executor-plugins python3.12dist(snakemake-interface-executor-plugins) python3dist(snakemake-interface-executor-plugins)
Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24 Command line :/usr/bin/fedora-review -b 2257524 Buildroot used: fedora-rawhide-x86_64 Active plugins: Shell-api, Generic, Python Disabled plugins: SugarActivity, PHP, Haskell, fonts, R, Java, Ocaml, C/C++, Perl Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Assignee|nobody@fedoraproject.org |sanjay.ankur@gmail.com
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
--- Comment #3 from Ben Beasley code@musicinmybrain.net --- Thank you for the review!
Same responses as bug 2257676:
(In reply to Ankur Sinha (FranciscoD) from comment #2)
Looks good. XXX APPROVED XXX
Minor comments:
- `-l` not used in pyproject_save files?
Correct, because license files can only be handled automatically in %{pyproject_files} when the build backend marks them as License-File, which comes from draft PEP 639. Since poetry-core doesn’t do that, this package needs a manual %license LICENSE instead. Note that the following does not show the license file in the .dist-info directory:
$ rpm -qL -p results_python-snakemake-interface-executor-plugins/8.1.3/1.fc40/python3-snakemake-interface-executor-plugins-8.1.3-1.fc40~bootstrap.noarch.rpm /usr/share/licenses/python3-snakemake-interface-executor-plugins/LICENSE
- pytest is to be used when not bootstrapped, so the BR can again be moved
into the conditional?
Good catch; thanks. I’ll adjust this on import.
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
--- Comment #4 from Ben Beasley code@musicinmybrain.net --- https://release-monitoring.org/project/370850/
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
--- Comment #5 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-snakemake-interface-executor-plugi...
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |MODIFIED
--- Comment #6 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-3ffc799568 has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2024-3ffc799568
https://bugzilla.redhat.com/show_bug.cgi?id=2257524
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |CLOSED Resolution|--- |ERRATA Last Closed| |2024-01-18 20:27:26
--- Comment #7 from Fedora Update System updates@fedoraproject.org --- FEDORA-2024-3ffc799568 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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