Bug 2048507 - Review Request: python-molmass - calculate molecular mass properties from elemental composition
Summary: Review Request: python-molmass - calculate molecular mass properties from ele...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Susi Lehtola
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: Trivial
Depends On:
Blocks: FE-SCITECH
TreeView+ depends on / blocked
 
Reported: 2022-01-31 11:56 UTC by Mark E. Fuller
Modified: 2022-06-30 02:17 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2022-06-30 01:17:57 UTC
Type: ---
Embargoed:
susi.lehtola: fedora-review+


Attachments (Terms of Use)

Description Mark E. Fuller 2022-01-31 11:56:42 UTC
Spec URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/03268910-python-molmass/python-molmass.spec
SRPM URL: https://download.copr.fedorainfracloud.org/results/fuller/test-builds/fedora-rawhide-x86_64/03268910-python-molmass/python-molmass-2021.6.18-1.fc36.src.rpm
Description: Molmass is a Python library and console script to calculate the molecular mass (average, nominal, and isotopic pure), the elemental composition, and the mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.
Fedora Account System Username: fuller

Comment 1 Susi Lehtola 2022-06-09 20:45:35 UTC
The spec and srpm are missing.

Comment 2 Mark E. Fuller 2022-06-12 18:50:23 UTC
Sorry about that:

SPEC: https://fuller.fedorapeople.org/python-molmass.spec
SRPM: https://fuller.fedorapeople.org/python-molmass-2021.6.18-1.fc36.src.rpm

Thank you very much for taking the review

Comment 3 Susi Lehtola 2022-06-15 19:48:56 UTC
The LICENSE file is missing from the rpm. Please add it as %license.

Also, fix the rpmlint issues:

python3-molmass.noarch: W: wrong-file-end-of-line-encoding /usr/share/doc/python3-molmass/README.rst
python3-molmass.noarch: E: non-executable-script /usr/lib/python3.10/site-packages/molmass/molmass_web.py 644 /usr/bin/env python3
python3-molmass.noarch: W: no-manual-page-for-binary elements_gui
python3-molmass.noarch: W: no-manual-page-for-binary molmass
python3-molmass.noarch: W: no-manual-page-for-binary molmass_web
python3-molmass.noarch: E: description-line-too-long Molmass is a Python library and console script to calculate the molecular mass (average, nominal, and isotopic pure), the elemental composition, and the mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.
 1 packages and 0 specfiles checked; 2 errors, 4 warnings, 2 badness; has taken 0.1 s 

You can fix the end of line encodings with e.g. dos2unix, just remember to preserve the time stamps in that operation.

The problem with non-executable script can be addressed just by removing the shebang from the Python libraries, which aren't meant to be executed.

The description should be line-wrapped.

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

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

===== 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.
[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 10240 bytes in 1 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]: 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:
[-]: 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:
[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).
[?]: Package functions as described.
[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.
[?]: Package should compile and build into binary rpms on all supported
     architectures.
[-]: %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.
[x]: Spec file according to URL is the same as in SRPM.

Source checksums
----------------
https://files.pythonhosted.org/packages/source/m/molmass/molmass-2021.6.18.tar.gz :
  CHECKSUM(SHA256) this package     : b011fda8875249042ff8cc2e22d8033c833717994d46f2c894738bba51be4470
  CHECKSUM(SHA256) upstream package : b011fda8875249042ff8cc2e22d8033c833717994d46f2c894738bba51be4470


Requires
--------
python3-molmass (rpmlib, GLIBC filtered):
    /usr/bin/python3
    python(abi)

Provides
--------
python3-molmass:
    python-molmass
    python3-molmass
    python3.10-molmass
    python3.10dist(molmass)
    python3dist(molmass)


Generated by fedora-review 0.8.0 (e988316) last change: 2022-04-07
Command line :/usr/bin/fedora-review -b 2048507
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Shell-api, Generic
Disabled plugins: Ocaml, R, C/C++, PHP, Haskell, Java, SugarActivity, fonts, Perl
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Comment 4 Mark E. Fuller 2022-06-15 21:15:07 UTC
Thank you for the review - here are the updated files:
SPEC: https://fuller.fedorapeople.org/python-molmass.spec
SRPM: https://fuller.fedorapeople.org/python-molmass-2021.6.18-1.fc36.src.rpm

I corrected the line endings and also removed the shebang inside the spec with dos2unix and sed (added to BuildRequires)
Is this an acceptable approach over using patching?

Comment 5 Susi Lehtola 2022-06-15 21:57:47 UTC
(In reply to Mark E. Fuller from comment #4)
> Thank you for the review - here are the updated files:
> SPEC: https://fuller.fedorapeople.org/python-molmass.spec
> SRPM: https://fuller.fedorapeople.org/python-molmass-2021.6.18-1.fc36.src.rpm
> 
> I corrected the line endings and also removed the shebang inside the spec
> with dos2unix and sed (added to BuildRequires)
> Is this an acceptable approach over using patching?

Yes. The problem with sed is that you won't get notified if the command stops working with a new release; however, line endings and shebangs aren't critical issues and sed is fine.

To keep the time stamp of molmass_web, use e.g.

sed s/#!.*$// molmass/molmass_web.py > molmass/molmass_web.py.noenv && touch -r molmass/molmass_web.py molmass/molmass_web.py.noenv && mv molmass/molmass_web.py.noenv molmass/molmass_web.py

With this change, the package has been

APPROVED

by jussilehtola.

Comment 6 Mark E. Fuller 2022-06-18 16:41:27 UTC
Thank you very much!

Comment 7 Kevin Fenzi 2022-06-19 22:52:38 UTC
(fedscm-admin):  The Pagure repository was created at https://src.fedoraproject.org/rpms/python-molmass

Comment 8 Fedora Update System 2022-06-21 19:15:56 UTC
FEDORA-2022-6db4a91175 has been submitted as an update to Fedora 35. https://bodhi.fedoraproject.org/updates/FEDORA-2022-6db4a91175

Comment 9 Fedora Update System 2022-06-21 19:16:22 UTC
FEDORA-2022-cc4f9dc161 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-cc4f9dc161

Comment 10 Fedora Update System 2022-06-22 02:01:53 UTC
FEDORA-2022-cc4f9dc161 has been pushed to the Fedora 36 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2022-cc4f9dc161 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-cc4f9dc161

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

Comment 11 Fedora Update System 2022-06-22 02:20:57 UTC
FEDORA-2022-6db4a91175 has been pushed to the Fedora 35 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2022-6db4a91175 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-6db4a91175

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

Comment 12 Fedora Update System 2022-06-30 01:17:57 UTC
FEDORA-2022-cc4f9dc161 has been pushed to the Fedora 36 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 13 Fedora Update System 2022-06-30 02:17:43 UTC
FEDORA-2022-6db4a91175 has been pushed to the Fedora 35 stable repository.
If problem still persists, please make note of it in this bug report.


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