[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Susi Lehtola  changed:

   What|Removed |Added

 Blocks|505154 (FE-SCITECH) |




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=505154
[Bug 505154] Tracker: Review Requests for Science and Technology related
packages
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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #52 from Fedora Update System  ---
python-assimulo-2.8-7.el7 has been pushed to the Fedora EPEL 7 stable
repository. If problems still persist, please make note of it in this bug
report.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #51 from Fedora Update System  ---
python-assimulo-2.8-7.fc22 has been pushed to the Fedora 22 stable repository.
If problems still persist, please make note of it in this bug report.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #50 from Fedora Update System  ---
python-assimulo-2.8-7.fc23 has been pushed to the Fedora 23 stable repository.
If problems still persist, please make note of it in this bug report.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA
Last Closed||2015-12-20 01:53:42



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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #49 from Fedora Update System  ---
python-assimulo-2.8-7.el7 has been pushed to the Fedora EPEL 7 testing
repository. If problems still persist, please make note of it in this bug
report.
If you want to test the update, you can install it with
$ su -c 'yum --enablerepo=epel-testing update python-assimulo'
You can provide feedback for this update here:
https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2015-56d4d10de8

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #44 from Antonio Trande  ---
(In reply to Mukundan Ragavan from comment #43)
> Perfect. That fixes it.
> 
> I do not have any further issues. Package APPROVED.

Thank you.

> 
> This being a science package, I would be interested in co-maintaining if you
> do not mind.
> 
> Please request repo on pkgdb.

Yes, of course.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Fedora Update System  changed:

   What|Removed |Added

 Status|ASSIGNED|MODIFIED



--- Comment #45 from Fedora Update System  ---
python-assimulo-2.8-7.fc22 has been submitted as an update to Fedora 22.
https://bodhi.fedoraproject.org/updates/FEDORA-2015-2aa8ee8762

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #45 from Fedora Update System  ---
python-assimulo-2.8-7.fc22 has been submitted as an update to Fedora 22.
https://bodhi.fedoraproject.org/updates/FEDORA-2015-2aa8ee8762

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #46 from Fedora Update System  ---
python-assimulo-2.8-7.el7 has been submitted as an update to Fedora EPEL 7.
https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2015-56d4d10de8

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #41 from Antonio Trande  ---
(In reply to Mukundan Ragavan from comment #40)
> I am fine with approving the package.
> 
> python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
> /usr/lib64/python2.7/site-packages/assimulo/examples/rungekutta34_basic.py
> python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
> /usr/lib64/python2.7/site-packages/assimulo/examples/cvode_with_disc.py
> python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
> /usr/lib64/python2.7/site-packages/assimulo/examples/kinsol_with_jac.py
> 
> ---> I don't really what can be done about this ... Any ideas?

https://fedoraproject.org/wiki/Common_Rpmlint_issues?rd=PackageMaintainers/Common_Rpmlint_Issues#wrong-script-end-of-line-encoding

I will post a new packaging release with these fixes.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Mukundan Ragavan  changed:

   What|Removed |Added

  Flags|fedora-review?  |fedora-review+



--- Comment #43 from Mukundan Ragavan  ---
Perfect. That fixes it.

I do not have any further issues. Package APPROVED.

This being a science package, I would be interested in co-maintaining if you do
not mind.

Please request repo on pkgdb.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #40 from Mukundan Ragavan  ---
I am fine with approving the package.

python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
/usr/lib64/python2.7/site-packages/assimulo/examples/rungekutta34_basic.py
python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
/usr/lib64/python2.7/site-packages/assimulo/examples/cvode_with_disc.py
python-assimulo.x86_64: E: wrong-script-end-of-line-encoding
/usr/lib64/python2.7/site-packages/assimulo/examples/kinsol_with_jac.py

---> I don't really what can be done about this ... Any ideas?

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #39 from Mukundan Ragavan  ---

Package Review
==

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


Issues:
===
- Package installs properly.
  Note: Installation errors (see attachment)
  See: https://fedoraproject.org/wiki/Packaging:Guidelines

---> I can install this on my VM from koji build. I can also install the mock
build. Does not seem to be an issue.


= MUST items =

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: 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.


---> Does not seem to be a problem.

[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.
 Note: Checking patched sources after %prep for licenses. Licenses
 found: "Unknown or generated", "*No copyright* BSD (2 clause)", "*No
 copyright* LGPL (v3)", "BSD (3 clause)", "BSD (2 clause)", "LGPL (v2.1
 or later)", "GPL (v3)", "LGPL (v3)". 72 files have unknown license.
 Detailed output of licensecheck in
 /home/mukundan/ownCloud/misc_pkgs/pkg_reviews/assimulo/1215354-python-
 assimulo/licensecheck.txt

---> Looks fine. As indicated in the previous review, please let upstream know.


[x]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
 must be documented in the spec.

---> Clearly documented.

[x]: Package requires other packages for directories it uses.
 Note: No known owner of /usr/lib64/python3.5/site-packages,
 /usr/lib64/python3.5
[x]: Package must own all directories that it creates.
 Note: Directories without known owners: /usr/lib64/python3.5/site-
 packages, /usr/lib64/python3.5
[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.
[-]: 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.
[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 40960 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]: 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 does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any
 that are listed in the exceptions section of Packaging Guidelines.
[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 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 

[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #37 from Antonio Trande  ---
SPEC: https://sagitter.fedorapeople.org/assimulo/python-assimulo.spec
SRPM:
https://sagitter.fedorapeople.org/assimulo/python-assimulo-2.8-6.fc23.src.rpm


Upstream maintainer does not reply yet, so

- test_dasp3_basic skipped
- Added 'dssp' as additional request

python-assimulo will be built on Fedora and EPEL7.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #33 from Upstream Release Monitoring 
 ---
nonamedotc's scratch build of python-assimulo-2.8-5.fc23.src.rpm for rawhide
failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12105676

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #34 from Mukundan Ragavan  ---
Created attachment 1103422
  --> https://bugzilla.redhat.com/attachment.cgi?id=1103422=edit
build log

I have gone through the package again. It seems fine mostly. Only issue I have
at this point is that the koji does not seem to build ..

http://koji.fedoraproject.org/koji/taskinfo?taskID=12105676

I can build it in mock though (build log from mock attached) - 

$ ls results/
build.log   
python-assimulo-2.8-5.fc23.src.rpm 
python-assimulo-debuginfo-2.8-5.fc23.x86_64.rpm  state.log
python3-assimulo-2.8-5.fc23.x86_64.rpm  
python-assimulo-2.8-5.fc23.x86_64.rpm  
root.log

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #32 from Antonio Trande  ---
SPEC: https://sagitter.fedorapeople.org/assimulo/python-assimulo.spec
SRPM:
https://sagitter.fedorapeople.org/assimulo/python-assimulo-2.8-5.fc23.src.rpm

I've just renamed the package.
Thank you.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #31 from Mukundan Ragavan  ---
@Antonio - do you have an updated SRPM I can use for review?

Is the one on your fedorapeople page good to use?

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Orion Poplawski  changed:

   What|Removed |Added

 CC|or...@cora.nwra.com |



--- Comment #30 from Mukundan Ragavan  ---
Just back from travel. Will try to build with the patch and see ...

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #28 from Antonio Trande  ---
I forgot Path1 included with assimulo, that probably is the real source of this
issue.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #29 from Antonio Trande  ---
Created attachment 1097468
  --> https://bugzilla.redhat.com/attachment.cgi?id=1097468=edit
Numpy patch

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #26 from Antonio Trande  ---
(In reply to Antonio Trande from comment #25)
> An error crops up in rawhide:
> 
> [1/1] Cythonizing assimulo/lib/sundials_kinsol_core.pyx
> Traceback (most recent call last):
>   File "setup.py", line 509, in 
> ext_list += prepare.fortran_extensionlists()
>   File "setup.py", line 427, in fortran_extensionlists
> if StrictVersion(np.version.version) > StrictVersion("1.6.1"): 
>   File "/usr/lib64/python2.7/distutils/version.py", line 40, in __init__
> self.parse(vstring)
>   File "/usr/lib64/python2.7/distutils/version.py", line 107, in parse
> raise ValueError, "invalid version number '%s'" % vstring
> ValueError: invalid version number '1.10.2rc1'
> error: Bad exit status from /var/tmp/rpm-tmp.s0lRAq (%build)
> Bad exit status from /var/tmp/rpm-tmp.s0lRAq (%build)
> 
> I don't know yet from where '1.10.2rc1' comes.
> I'm trying to contact upstream maintainer.
> 
> https://kojipkgs.fedoraproject.org//work/tasks/8811/11838811/build.log

This probably happens (or at least so it seems) because of latest release of
'numpy' (numpy-1.10.2-0.1rc1.fc24); maybe this type of caption (0.1rc1) is not
swallowed by the code. 'assimulo' is rebuilt successfully in a mock
rawhide-tree by downgrading 'numpy' to the 1.10.1-6 release.

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Orion Poplawski  changed:

   What|Removed |Added

 CC||or...@cora.nwra.com



--- Comment #27 from Orion Poplawski  ---
assimulo is using StrictVersion(np.version.version).  StrictVersion does not
allow for "rc" suffixes - see
http://epydoc.sourceforge.net/stdlib/distutils.version.StrictVersion-class.html

But I think this in entirely assimulo's problem for using StrictVersion -
obviously numpy isn't following those rules.  Maybe they should or might like
to, but I don't know.  I've asked:
https://mail.scipy.org/pipermail/numpy-discussion/2015-November/074233.html

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #25 from Antonio Trande  ---
An error crops up in rawhide:

[1/1] Cythonizing assimulo/lib/sundials_kinsol_core.pyx
Traceback (most recent call last):
  File "setup.py", line 509, in 
ext_list += prepare.fortran_extensionlists()
  File "setup.py", line 427, in fortran_extensionlists
if StrictVersion(np.version.version) > StrictVersion("1.6.1"): 
  File "/usr/lib64/python2.7/distutils/version.py", line 40, in __init__
self.parse(vstring)
  File "/usr/lib64/python2.7/distutils/version.py", line 107, in parse
raise ValueError, "invalid version number '%s'" % vstring
ValueError: invalid version number '1.10.2rc1'
error: Bad exit status from /var/tmp/rpm-tmp.s0lRAq (%build)
Bad exit status from /var/tmp/rpm-tmp.s0lRAq (%build)

I don't know yet from where '1.10.2rc1' comes.
I'm trying to contact upstream maintainer.

https://kojipkgs.fedoraproject.org//work/tasks/8811/11838811/build.log

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354



--- Comment #24 from Upstream Release Monitoring 
 ---
sagitter's scratch build of python-assimulo-2.8-5.fc23.src.rpm for rawhide
failed http://koji.fedoraproject.org/koji/taskinfo?taskID=11838809

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[Bug 1215354] Review Request: python-assimulo - Ordinary differential and differential algebraic equations solver

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1215354

Antonio Trande  changed:

   What|Removed |Added

Summary|Review Request: assimulo -  |Review Request:
   |Ordinary differential and   |python-assimulo - Ordinary
   |differential algebraic  |differential and
   |equations solver|differential algebraic
   ||equations solver



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