Bug 2035792 (mrchem) - Review Request: mrchem - A numerical real-space code for molecular electronic structure calculations
Summary: Review Request: mrchem - A numerical real-space code for molecular electronic...
Keywords:
Status: CLOSED ERRATA
Alias: mrchem
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Mark E. Fuller
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: mrcpp
Blocks:
TreeView+ depends on / blocked
 
Reported: 2021-12-27 17:42 UTC by Susi Lehtola
Modified: 2022-02-13 01:15 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2022-02-13 01:06:32 UTC
Type: ---
Embargoed:
mark.e.fuller: fedora-review+


Attachments (Terms of Use)

Description Susi Lehtola 2021-12-27 17:42:17 UTC
Spec URL: https://jussilehtola.fedorapeople.org/mrchem.spec
SRPM URL: https://jussilehtola.fedorapeople.org/mrchem-1.0.2-1.fc35.src.rpm
Fedora Account System Username: jussilehtola

Description:
MRChem is a numerical real-space code for molecular electronic
structure calculations within the self-consistent field (SCF)
approximations of quantum chemistry (Hartree-Fock and Density
Functional Theory).

Comment 2 Mark E. Fuller 2022-01-28 19:32:52 UTC
The initial pass looks very good:
- rpmlint returns 0 errors, 0 warnings, 0 badness
- the automated review returns only one issue:

Issues:
=======
- Static libraries in -static or -devel subpackage, providing -devel if
  present.
  Note: Package has .a files: mrchem-devel. Does not provide -static:
  mrchem-devel.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/#packaging-static-libraries
 
It appears to me that there are no shared libraries in this package, and so it is correct to place the static libraries in -devel with "Provides:       %{name}-static%{?_isa} = %{version}-%{release}" as is the case here


There are some open items which I have found on manual review:

1) Attempting to install mrchem-devel does not pull in the mrchem package automatically, which it must for the license file ("License file installed when any subpackage combination is installed." is a requirement).
Please add "Requires: %{name}%{?_isa} = %{version}-%{release}" in mrchem-devel , mrchem-data

2) Building across architectures, the mrcpp-devel dependency is not built for s390x, so the spec should have an EXCLUDEARCH and BZ# corresponding to this issue (see test builds: https://copr.fedorainfracloud.org/coprs/fuller/cantera-test/build/3258645/)

3a) There is no pypi entry for mrchem: please see https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_pypi_parity as Python interfaces typically must also exist there under the same name
3b) It may also be work splitting the Python interface off into a subpackage "python3-%{name}"

4) Please check and confirm that the package contains no static executables, i.e. that %{_bindir}/mrchem* are not static

5) [suggestion] the "Source0" entry may be simplified to utilize the url macro as "%{url}archive/v%{version}/%{name}-%{version}.tar.gz"



Full review checklist (manually completed):

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

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


Issues:
=======
- Static libraries in -static or -devel subpackage, providing -devel if
  present.
  Note: Package has .a files: mrchem-devel. Does not provide -static:
  mrchem-devel.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/#packaging-static-libraries


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

C/C++:
[x]: Package does not contain kernel modules.
[ ]: Package contains no static executables.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[x]: Header files in -devel subpackage, if present.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.

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.
[!]: 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.
[-]: 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 4 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:
[x]: 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.
[!]: 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:
[-]: 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).
[!]: Fully versioned dependency in subpackages if applicable.
[?]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: 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.
[!]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[?]: 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 debuginfo package(s).
[x]: Rpmlint is run on all installed packages.
[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 3 Susi Lehtola 2022-02-03 20:01:37 UTC
1) Dependencies added on -data and -devel, thanks.
2) excludearch and bz ticket added.
3) mrchem is not a Python package so this is void; it's a C++ program with a Python interface
4) there are no static executables: /usr/bin/mrchem is a Python script. RPM dependency list shows that dependencies are linked in dynamically
5) I like SOURCE0 as it is :)


https://jussilehtola.fedorapeople.org/mrchem.spec
https://jussilehtola.fedorapeople.org/mrchem-1.0.2-3.fc35.src.rpm

Comment 4 Mark E. Fuller 2022-02-04 13:33:04 UTC
Thanks - responses to #3 and #4 are especially helpful for my own knowledge as to these points for the future.

Everything looks great now - approved

Comment 5 Susi Lehtola 2022-02-04 13:57:09 UTC
Thanks!

Comment 6 Gwyn Ciesla 2022-02-04 14:32:07 UTC
(fedscm-admin):  The Pagure repository was created at https://src.fedoraproject.org/rpms/mrchem

Comment 7 Fedora Update System 2022-02-04 15:41:45 UTC
FEDORA-2022-ae769387cb has been submitted as an update to Fedora 34. https://bodhi.fedoraproject.org/updates/FEDORA-2022-ae769387cb

Comment 8 Fedora Update System 2022-02-04 15:41:45 UTC
FEDORA-2022-fd3326f130 has been submitted as an update to Fedora 35. https://bodhi.fedoraproject.org/updates/FEDORA-2022-fd3326f130

Comment 9 Fedora Update System 2022-02-05 01:31:35 UTC
FEDORA-2022-ae769387cb has been pushed to the Fedora 34 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2022-ae769387cb \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-ae769387cb

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

Comment 10 Fedora Update System 2022-02-05 02:12:08 UTC
FEDORA-2022-fd3326f130 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-fd3326f130 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-fd3326f130

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

Comment 11 Fedora Update System 2022-02-13 01:06:32 UTC
FEDORA-2022-ae769387cb has been pushed to the Fedora 34 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 12 Fedora Update System 2022-02-13 01:15:00 UTC
FEDORA-2022-fd3326f130 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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