Bug 1780849 - Review Request: pymol - PyMOL Molecular Graphics System
Summary: Review Request: pymol - PyMOL Molecular Graphics System
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Sergio Basto
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: 1780848
Blocks: 1597205 1754678
TreeView+ depends on / blocked
 
Reported: 2019-12-07 18:24 UTC by Antonio T. (sagitter)
Modified: 2020-01-05 04:02 UTC (History)
5 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2020-01-05 04:02:20 UTC
Type: ---
Embargoed:
sergio: fedora-review+


Attachments (Terms of Use)
pymol-python3.patch (12.05 KB, patch)
2019-12-31 01:30 UTC, Sergio Basto
no flags Details | Diff

Description Antonio T. (sagitter) 2019-12-07 18:24:19 UTC
Spec URL: https://sagitter.fedorapeople.org/pymol/pymol.spec
SRPM URL: https://sagitter.fedorapeople.org/pymol/pymol-2.3.0-1.fc31.src.rpm

Description: New release of PyMOL software; re-review to resume this package.

Fedora Account System Username: sagitter

Comment 1 Miro Hrončok 2019-12-07 22:17:27 UTC
> # Turn off the brp-python-bytecompile script

1. why is this neeeded
2. there is a newer way to do this described at https://docs.fedoraproject.org/en-US/packaging-guidelines/#_brp_buildroot_policy_scripts


> License: MIT and BSD and ZPLv2.0 and Bitstream Vera and OFL

This needs an explanation in comment.


> Patch0: pymol-setup.py.patch
> Patch1: pymol-wmclass-main.patch
> Patch2: pymol-wmclass-pmgapp.patch
> Patch3: pymol-mmtf.patch

So do those.


> # Fix shebang in individual files to ensure Python 3 dependence
> sed -i '1s=^#!/usr/bin/\(python\|env python\)[0-9.]*=#!%{__python3}=' test/cyg test/run test/show

Consider using pathfix.py from python3-devel.


> echo "%{__python3} %{python3_sitearch}/pymol/__init__.py \"\$@\"" >> pymol

Consider using `exec` here.


> %{python3_sitearch}/*.egg-info

Consider adding trailing slash to ensure this remains a directory (if it is a directory).

Comment 4 Sergio Basto 2019-12-08 17:17:52 UTC
fedora-review 0.7.4 says: 
 No matching package to install: 'mmtf-cpp-devel'
DEBUG util.py:596:  Not all dependencies satisfied

Comment 5 Antonio T. (sagitter) 2019-12-08 18:42:58 UTC
(In reply to Sergio Monteiro Basto from comment #4)
> fedora-review 0.7.4 says: 
>  No matching package to install: 'mmtf-cpp-devel'
> DEBUG util.py:596:  Not all dependencies satisfied

You can't build pymol without mmtf-cpp
In fact, this ticket depends by rhbz #1780848

Comment 6 Antonio T. (sagitter) 2019-12-09 20:28:01 UTC
pymol can be built on Rawhide now.

Comment 7 Robert-André Mauchin 🐧 2019-12-12 15:22:54 UTC
There's some shenanigans with python-pyside2 which break the build in Rawhide.

Comment 8 Sergio Basto 2019-12-18 18:05:50 UTC
Package Review
==============

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


Issues:
=======
- Permissions on files are set properly.
  Note: See rpmlint output
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/#_file_permissions



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

C/C++:
[ ]: Package does not contain kernel modules.
[ ]: Package contains no static executables.
[ ]: Development (unversioned) .so files in -devel subpackage, if present.
     Note: Unversioned so-files in private %_libdir subdirectory (see
     attachment). Verify they are not in ld path.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[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.
[]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "Unknown or generated", "Python Software Foundation License",
     "SIL Open Font License (v1.0)", "Apache License (v2.0)", "BSD 2-clause
     "Simplified" License", "BSD 3-clause "New" or "Revised" License",
     "Expat License". 1260 files have unknown license. Detailed output of
     licensecheck in /home/sergio/fedora-scm/1780849-pymol/licensecheck.txt
[ ]: Package does not own files or directories owned by other packages.
     Note: Dirs in package are owned also by: /usr/lib64/python3.8/site-
     packages/chempy(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/__pycache__(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/bmin(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/bmin/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/champ(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/champ/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/fast(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/fast/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/fragments(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/chempy/fragments/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/mmtf(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/mmtf/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/chempy/tinker(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/chempy/tinker/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_qt(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_qt/__pycache__(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_qt/forms(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_qt/forms/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_qt/syntax(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_qt/syntax/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_tk(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_tk/__pycache__(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_tk/skins(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_tk/skins/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_tk/skins/demo(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pmg_tk/skins/demo/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_tk/skins/normal(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pmg_tk/skins/normal/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pmg_tk/startup(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pmg_tk/startup/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/Qt(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/Qt/__pycache__(locale,, to, Failed, set, defaulting,
     C), /usr/lib64/python3.8/site-packages/pymol/__pycache__(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/contrib(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/contrib/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/chempy(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/chempy/fragments(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/chempy/sidechains(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/chempy/tinker(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/demo(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/pmg_qt(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/pmg_qt/icons(locale,, to, Failed, set, defaulting,
     C), /usr/lib64/python3.8/site-
     packages/pymol/data/pmg_qt/styles(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/pmg_tk(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/pmg_tk/bitmaps(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/pmg_tk/bitmaps/builder(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/pymol(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/pymol/icons(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/pymol/matrices(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/shaders(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/startup(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/startup/lightingsettings_gui(locale,, to, Failed,
     set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/data/test(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/data/tut(locale,, to, Failed,
     set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/embed(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/embed/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/embed/epymol(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pymol/embed/epymol/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/embed/wxpymol(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pymol/embed/wxpymol/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/examples(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/examples/chempy(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/examples/cookbook(locale,, to, Failed, set, defaulting,
     C), /usr/lib64/python3.8/site-packages/pymol/examples/devel(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/examples/launching(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/opengl(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/opengl/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/opengl/gl(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pymol/opengl/gl/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/opengl/glu(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pymol/opengl/glu/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/opengl/glut(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-
     packages/pymol/opengl/glut/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/plugins(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/plugins/__pycache__(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/scripts(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/scripts/metaphorics(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/stereochemistry(locale,, to, Failed, set, defaulting,
     C), /usr/lib64/python3.8/site-
     packages/pymol/stereochemistry/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-packages/pymol/test(locale,,
     to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/test/dat(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/test/inp(locale,, to, Failed,
     set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/test/ref(locale,, to, Failed, set, defaulting, C),
     /usr/lib64/python3.8/site-packages/pymol/wizard(locale,, to, Failed,
     set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol/wizard/__pycache__(locale,, to, Failed, set,
     defaulting, C), /usr/lib64/python3.8/site-packages/pymol2(locale,, to,
     Failed, set, defaulting, C), /usr/lib64/python3.8/site-
     packages/pymol2/__pycache__(locale,, to, Failed, set, defaulting, C),
     /usr/share/doc/pymol(locale,, to, Failed, set, defaulting, C),
     /usr/share/licenses/pymol(locale,, to, Failed, set, defaulting, C)
[ ]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[ ]: Sources contain only permissible code or content.
[ ]: Development files must be in a -devel package
[ ]: Package uses nothing in %doc for runtime.
[ ]: Package consistently uses macros (instead of hard-coded directory
     names).
[ ]: Package is named according to the Package Naming Guidelines.
[ ]: Package does not generate any conflict.
[ ]: 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.
[ ]: Spec file is legible and written in American English.
[ ]: Package contains systemd file(s) if in need.
[ ]: 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 3 files.
[ ]: 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 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 contains desktop file if it is a GUI application.
[x]: Package installs a %{name}.desktop using desktop-file-install or
     desktop-file-validate if there is such a file.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[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

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.
[ ]: 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.
[ ]: Final provides and requires are sane (see attachments).
[ ]: Package functions as described.
[ ]: Latest version is packaged.
[ ]: 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.
[ ]: Package should compile and build into binary rpms on all supported
     architectures.
[ ]: %check is present and all tests pass.
[ ]: Packages should try to preserve timestamps of original installed
     files.
[ ]: Spec use %global instead of %define unless justified.
     Note: %define requiring justification: %define
     __brp_python_bytecompile %{nil}
[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.

===== 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.


Rpmlint
-------
Checking: pymol-2.3.0-3.fc32.x86_64.rpm
          pymol-2.3.0-3.fc32.src.rpm
pymol.x86_64: W: name-repeated-in-summary C PyMOL
pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775
pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775
pymol.x86_64: W: no-manual-page-for-binary pymol
pymol.src: W: name-repeated-in-summary C PyMOL
2 packages and 0 specfiles checked; 2 errors, 3 warnings.




Rpmlint (debuginfo)
-------------------
Checking: pymol-debuginfo-2.3.0-3.fc32.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
pymol.x86_64: W: name-repeated-in-summary C PyMOL
pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775
pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775
pymol.x86_64: W: no-manual-page-for-binary pymol
2 packages and 0 specfiles checked; 2 errors, 2 warnings.



Unversioned so-files
--------------------
pymol: /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so
pymol: /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so

Source checksums
----------------
https://github.com/schrodinger/pymol-open-source/archive/v2.3.0/pymol-open-source-2.3.0.tar.gz :
  CHECKSUM(SHA256) this package     : 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0
  CHECKSUM(SHA256) upstream package : 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0


Requires
--------
pymol (rpmlib, GLIBC filtered):
    /usr/bin/csh
    /usr/bin/python3
    /usr/bin/sh
    apbs(x86-64)
    chemical-mime-data
    libGL.so.1()(64bit)
    libGLEW.so.2.1()(64bit)
    libc.so.6()(64bit)
    libfreetype.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libglut.so.3()(64bit)
    libm.so.6()(64bit)
    libpng16.so.16()(64bit)
    libpng16.so.16(PNG16_0)(64bit)
    libpthread.so.0()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libxml2.so.2()(64bit)
    libxml2.so.2(LIBXML2_2.4.30)(64bit)
    libxml2.so.2(LIBXML2_2.6.0)(64bit)
    libxml2.so.2(LIBXML2_2.6.3)(64bit)
    python(abi)
    python3-PyQt4(x86-64)
    python3-mmtf
    python3-numpy(x86-64)
    python3-pmw
    python3-tkinter(x86-64)
    rtld(GNU_HASH)



Provides
--------
pymol:
    PyMOL(x86-64)
    application()
    application(pymol.desktop)
    metainfo()
    metainfo(pymol.appdata.xml)
    pymol
    pymol(x86-64)
    python3.8dist(pymol)
    python3dist(pymol)



Generated by fedora-review 0.7.4 (54fa030) last change: 2019-12-07
Command line :/usr/bin/fedora-review -b 1780849
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, C/C++, Generic, Shell-api
Disabled plugins: Java, fonts, SugarActivity, Perl, Ruby, Ocaml, PHP, R, Haskell
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Development files must be in a -devel package , I don't know if we need one pymol-devel package but I don't know is unversioned so-files are needed and the non-standard-executable-perm are only thing that I see that needs to be review .

Comment 9 Antonio T. (sagitter) 2019-12-20 09:51:23 UTC
The package needs manual review []

Comment 10 Robert-André Mauchin 🐧 2019-12-20 18:53:35 UTC
> pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775
> pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775

It's a bug with fedora-review/Mock or rpmlint. If you extract the rpm, it has correct 0755 perms.

Comment 11 Sergio Basto 2019-12-27 22:21:57 UTC
 https://sagitter.fedorapeople.org/pymol/pymol.spec is not available anymore

Comment 13 Sergio Basto 2019-12-31 00:26:07 UTC
Rawhide is broken again , please add me on https://src.fedoraproject.org/rpms/mmtf-cpp and or build mmtf-ccp on Fedora 31 , I want bring pymol to F31 anyway I guess .

Comment 14 Sergio Basto 2019-12-31 01:27:47 UTC
I'd would propose all patches be -p1 instead -p0 [1] and use %py3_build  and %py3_install [2].

Also I'd remove "%define __brp_python_bytecompile %{nil}" with next patch in attachment .

Other questions raised on my previous comment one are replied (bug in other place) and Development files must be in a -devel package , for now we can keep it on main package. 

Package APPROVED ! 

Please add me as maintainer and I could do the changes myself


[1]
%autosetup -n pymol-open-source-%{version} -p1


[2]

%build
%py3_build -- --use-msgpackc=c++11 --glut
 
%install
%py3_install -- --use-msgpackc=c++11 --glut --pymol-path=%{python3_sitearch}/pymol

Comment 15 Sergio Basto 2019-12-31 01:30:47 UTC
Created attachment 1648700 [details]
pymol-python3.patch

Applying this patch, fixes brp-python-bytecompile script, i.e. we can remove 
%define __brp_python_bytecompile %{nil}

Comment 16 Antonio T. (sagitter) 2019-12-31 11:12:42 UTC
Thank you Sergio.


Note You need to log in before you can comment on or make changes to this bug.