Bug 1790838 (libcint) - Re-Review Request: libcint - General Gaussian-type orbitals integrals for quantum chemistry
Summary: Re-Review Request: libcint - General Gaussian-type orbitals integrals for qua...
Keywords:
Status: CLOSED ERRATA
Alias: libcint
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Nobody's working on this, feel free to take it
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: python-pyscf
TreeView+ depends on / blocked
 
Reported: 2020-01-14 11:24 UTC by Susi Lehtola
Modified: 2020-02-02 01:34 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2020-02-01 01:19:56 UTC
Type: ---
Embargoed:
dan.cermak: fedora-review+


Attachments (Terms of Use)

Description Susi Lehtola 2020-01-14 11:24:56 UTC
Spec URL: https://jussilehtola.fedorapeople.org/libcint.spec
SRPM URL: https://jussilehtola.fedorapeople.org/libcint-3.0.19-1.fc31.src.rpm
Fedora Account System Username: jussilehtola

Description:
libcint is an open source library for analytical Gaussian integrals.
It provides C/Fortran API to evaluate one-electron / two-electron
integrals for Cartesian / real-spherical / spinor Gaussian type functions.

This is a re-review request for a package that was retired in August due to FTBFS.

Comment 1 Dan Čermák 2020-01-17 20:37:26 UTC
- %check fails due to a missing numpy dependency:
test 1
    Start 1: cinttest
1: Test command: /usr/bin/python3.8 "/builddir/build/BUILD/libcint-3.0.19/testsuite/test_cint.py" "--quick"
1: Test timeout computed to be: 10000000
1: Traceback (most recent call last):
1:   File "/builddir/build/BUILD/libcint-3.0.19/testsuite/test_cint.py", line 15, in <module>
1:     import numpy
1: ModuleNotFoundError: No module named 'numpy'
1/2 Test #1: cinttest .........................***Failed    0.12 sec
test 2
    Start 2: cint3c2etest
2: Test command: /usr/bin/python3.8 "/builddir/build/BUILD/libcint-3.0.19/testsuite/test_3c2e.py" "--quick"
2: Test timeout computed to be: 10000000
2: Traceback (most recent call last):
2:   File "/builddir/build/BUILD/libcint-3.0.19/testsuite/test_3c2e.py", line 15, in <module>
2:     import numpy
2: ModuleNotFoundError: No module named 'numpy'
2/2 Test #2: cint3c2etest .....................***Failed    0.04 sec
0% tests passed, 2 tests failed out of 2
Total Test time (real) =   0.16 sec
The following tests FAILED:
          1 - cinttest (Failed)
          2 - cint3c2etest (Failed)
Errors while running CTest

- your package explicitly buildrequires python2-devel, which is forbidden

Comment 2 Susi Lehtola 2020-01-18 08:11:46 UTC
Sorry, I only checked that the package built on my workstation and forgot to check mock; the buildrequirements were still in original condition.

Updating br's to python3-devel and python3-numpy fixes the issues.
https://jussilehtola.fedorapeople.org/libcint.spec
https://jussilehtola.fedorapeople.org/libcint-3.0.19-2.fc31.src.rpm

Comment 3 Dan Čermák 2020-01-18 17:02:21 UTC
I'll take a closer look during the weekend.

A few suggestions:
- use %make_build and %make_install instead of manual make invocations
- %ldconfig_scriptlets is obsolete and can be removed
- consider using %autosetup instead of %setup & %patch
- don't bump Release before the package is published
- where does the existing %changelog come from?

Comment 4 Susi Lehtola 2020-01-19 09:54:58 UTC
(In reply to dan.cermak from comment #3)
> I'll take a closer look during the weekend.
> 
> A few suggestions:
> - use %make_build and %make_install instead of manual make invocations
> - %ldconfig_scriptlets is obsolete and can be removed

done

> - consider using %autosetup instead of %setup & %patch

%autosetup doesn't allow patch backups, see https://rpm.org/user_doc/autosetup.html

> - don't bump Release before the package is published

That would go against long-standing, established policy in Fedora package review; how will anyone know what has changed? See https://fedoraproject.org/wiki/FrequentlyMadePackagingMistakes?rd=Packaging:FrequentlyMadeMistakes

> - where does the existing %changelog come from?

See comment 0.

https://jussilehtola.fedorapeople.org/libcint.spec
https://jussilehtola.fedorapeople.org/libcint-3.0.19-3.fc31.src.rpm

Comment 5 Dan Čermák 2020-01-19 23:44:22 UTC
(In reply to Susi Lehtola from comment #4)
> (In reply to dan.cermak from comment #3)
> > I'll take a closer look during the weekend.
> > 
> > A few suggestions:
> > - use %make_build and %make_install instead of manual make invocations
> > - %ldconfig_scriptlets is obsolete and can be removed
> 
> done
> 
> > - consider using %autosetup instead of %setup & %patch
> 
> %autosetup doesn't allow patch backups, see
> https://rpm.org/user_doc/autosetup.html

Fair enough

> 
> > - don't bump Release before the package is published
> 
> That would go against long-standing, established policy in Fedora package
> review; how will anyone know what has changed? See
> https://fedoraproject.org/wiki/FrequentlyMadePackagingMistakes?rd=Packaging:
> FrequentlyMadeMistakes

Huh, didn't know this was recommended. Thanks for the pointer!

> 
> > - where does the existing %changelog come from?
> 
> See comment 0.

Ah, sorry, missed that line.

> 
> https://jussilehtola.fedorapeople.org/libcint.spec
> https://jussilehtola.fedorapeople.org/libcint-3.0.19-3.fc31.src.rpm


This looks overall very good, I have the following two minor issues:
- Patch0 should include a link to https://github.com/sunqm/libcint/pull/33
- Upstream contains a documentation in the doc/ folder, consider building and installing it?


Full review below:


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

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


Issues:
=======
- If your application is a C or C++ application you must list a
  BuildRequires against gcc, gcc-c++ or clang.
  Note: No gcc, gcc-c++ or clang found in BuildRequires
  See: https://docs.fedoraproject.org/en-US/packaging-guidelines/C_and_C++/
- Package does not use a name that already exists.
  Note: A package with this name already exists. Please check
  https://src.fedoraproject.org/rpms/libcint
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/Naming/#_conflicting_package_names


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

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig not called in %post and %postun for Fedora 28 and later.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

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]: License file installed when any subpackage combination is installed.
[x]: %build honors applicable compiler flags or justifies otherwise.
[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.
[x]: 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]: Useful -debuginfo package or justification otherwise.
[!]: 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 20480 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]: 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 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

===== 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.
[!]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[-]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not used.
[-]: Description and summary sections in the package spec file contains
     translations for supported Non-English languages, if available.
[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]: Fully versioned dependency in subpackages if applicable.
[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 debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
[x]: Spec file according to URL is the same as in SRPM.

Comment 6 Susi Lehtola 2020-01-20 11:54:08 UTC
Thanks for the review, the minor issues have been fixed.

https://jussilehtola.fedorapeople.org/libcint.spec
https://jussilehtola.fedorapeople.org/libcint-3.0.19-4.fc31.src.rpm

Comment 7 Dan Čermák 2020-01-20 12:21:50 UTC
Thanks for the fixes, package approved!

Comment 8 Fedora Update System 2020-01-24 19:47:45 UTC
libcint-3.0.19-4.fc30, python-pyscf-1.7.0-4.fc30 has been pushed to the Fedora 30 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-5d3090636b

Comment 9 Fedora Update System 2020-01-25 08:18:37 UTC
libcint-3.0.19-4.fc31, python-pyscf-1.7.0-4.fc31 has been pushed to the Fedora 31 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-75fcd7c6aa

Comment 10 Fedora Update System 2020-02-01 01:19:56 UTC
libcint-3.0.19-4.fc30, python-pyscf-1.7.0-4.fc30 has been pushed to the Fedora 30 stable repository. If problems still persist, please make note of it in this bug report.

Comment 11 Fedora Update System 2020-02-02 01:34:34 UTC
libcint-3.0.19-4.fc31, python-pyscf-1.7.0-4.fc31 has been pushed to the Fedora 31 stable repository. If problems still persist, please make note of it in this bug report.


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