Bug 1731592 (python-netpyne) - Review Request: python-netpyne - Develop, simulate and analyse biological neuronal networks in NEURON
Summary: Review Request: python-netpyne - Develop, simulate and analyse biological neu...
Keywords:
Status: ASSIGNED
Alias: python-netpyne
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Elliott Sales de Andrade
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: 1731594
Blocks: fedora-neuro
TreeView+ depends on / blocked
 
Reported: 2019-07-19 22:21 UTC by Ankur Sinha (FranciscoD)
Modified: 2019-07-20 10:50 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed:
quantum.analyst: fedora-review?


Attachments (Terms of Use)

Description Ankur Sinha (FranciscoD) 2019-07-19 22:21:14 UTC
Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.2-1.fc30.src.rpm

Description: 
NetPyNE is a python package to facilitate the development, parallel simulation
and analysis of biological neuronal networks using the NEURON simulator.

For more details, installation instructions, documentation, tutorials, forums,
videos and more, please visit: www.netpyne.org

This package is developed and maintained by the Neurosim lab
(www.neurosimlab.org).

Fedora Account System Username: ankursinha

Comment 1 Elliott Sales de Andrade 2019-07-20 08:52:02 UTC
License check shows BSD and GPLv3 licenses. Please correct the License field
and add a comment with the breakdown.

Tests do not pass even with python3-matplotlib-scalebar installed.

There are some hidden files in the docs (see rpmlint output) that you may wish
to remove.

The URL should be https://pypi.org/project/%{pypi_name}

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

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


Issues:
=======
- Header files in -devel subpackage, if present.
  Note: python-netpyne-doc : /usr/share/doc/python-netpyne-
  doc/examples/LFPrecording/mod/misc.h python-netpyne-doc :
  /usr/share/doc/python-netpyne-doc/examples/M1detailed/mod/misc.h python-
  netpyne-doc : /usr/share/doc/python-netpyne-
  doc/examples/PTcell/mod/misc.h python-netpyne-doc :
  /usr/share/doc/python-netpyne-doc/examples/batchCell/misc.h python-
  netpyne-doc : /usr/share/doc/python-netpyne-
  doc/examples/rxd_net/mod/misc.h
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/#_devel_packages


===== 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.
[!]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "Unknown or generated", "Expat License", "BSD 2-clause
     "Simplified" License", "GPL (v3 or later)". 507 files have unknown
     license. Detailed output of licensecheck in
     1731592-python-netpyne/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[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.
[?]: 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.
[x]: 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:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: 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]: Avoid bundling fonts in non-fonts packages.
     Note: Package contains font files
[-]: 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).
[x]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in
     python3-netpyne
[?]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[-]: 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.
[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.
     Note: There are rpmlint messages (see attachment).
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: python3-netpyne-0.9.2-1.fc31.noarch.rpm
          python-netpyne-doc-0.9.2-1.fc31.noarch.rpm
          python-netpyne-0.9.2-1.fc31.src.rpm
python3-netpyne.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze
python3-netpyne.noarch: W: spelling-error %description -l en_US www -> WWW, wow
python3-netpyne.noarch: W: spelling-error %description -l en_US neurosimlab -> neurosis
python-netpyne-doc.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHH.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHHexport.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybrid.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybridexport.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1export.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandbox.omt.broken
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandboxexport.omt.requires05noise
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.import.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.jnmlnetpyne.omt
python-netpyne.src: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze
python-netpyne.src: W: spelling-error %description -l en_US www -> WWW, wow
python-netpyne.src: W: spelling-error %description -l en_US neurosimlab -> neurosis
3 packages and 0 specfiles checked; 0 errors, 17 warnings.




Rpmlint (installed packages)
----------------------------
python3-netpyne.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze
python3-netpyne.noarch: W: spelling-error %description -l en_US www -> WWW, wow
python3-netpyne.noarch: W: spelling-error %description -l en_US neurosimlab -> neurosis
python3-netpyne.noarch: W: invalid-url URL: https://pypi.python.org/pypi/netpyne <urlopen error [Errno -2] Name or service not known>
python-netpyne-doc.noarch: W: spelling-error Summary(en_US) analyse -> analyses, analyst, analyze
python-netpyne-doc.noarch: W: description-shorter-than-summary
python-netpyne-doc.noarch: W: invalid-url URL: https://pypi.python.org/pypi/netpyne <urlopen error [Errno -2] Name or service not known>
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHH.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHHexport.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybrid.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exHybridexport.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exM1export.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandbox.omt.broken
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.exSandboxexport.omt.requires05noise
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.import.omt
python-netpyne-doc.noarch: W: hidden-file-or-dir /usr/share/doc/python-netpyne-doc/examples/NeuroMLImport/test/.test.jnmlnetpyne.omt
2 packages and 0 specfiles checked; 0 errors, 17 warnings.



Source checksums
----------------
https://github.com/Neurosim-lab/netpyne/archive/v0.9.2/netpyne-0.9.2.tar.gz :
  CHECKSUM(SHA256) this package     : 762a2354bdfa9b65488b36db401ca53fe15778159bd1d57f55502a068cf6ba83
  CHECKSUM(SHA256) upstream package : 762a2354bdfa9b65488b36db401ca53fe15778159bd1d57f55502a068cf6ba83


Requires
--------
python3-netpyne (rpmlib, GLIBC filtered):
    python(abi)
    python3.7dist(future)
    python3.7dist(matplotlib)
    python3.7dist(matplotlib-scalebar)
    python3.7dist(numpy)
    python3.7dist(pandas)
    python3.7dist(scipy)

python-netpyne-doc (rpmlib, GLIBC filtered):



Provides
--------
python3-netpyne:
    python-netpyne
    python3-netpyne
    python3.7dist(netpyne)
    python3dist(netpyne)

python-netpyne-doc:
    python-netpyne-doc



Generated by fedora-review 0.7.2 (65d36bb) last change: 2019-04-09
Command line :/usr/bin/fedora-review -b 1731592 -m fedora-rawhide-x86_64 -L scalebar
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Python, Generic
Disabled plugins: C/C++, fonts, Java, Perl, Ocaml, Haskell, PHP, SugarActivity, R
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Built with local dependencies:
    review/scalebar/python3-matplotlib-scalebar-0.6.0-1.fc31.noarch.rpm

Comment 2 Ankur Sinha (FranciscoD) 2019-07-20 10:50:46 UTC
(In reply to Elliott Sales de Andrade from comment #1)
> License check shows BSD and GPLv3 licenses. Please correct the License field
> and add a comment with the breakdown.

Corrected.


> Tests do not pass even with python3-matplotlib-scalebar installed.

Turns out it also needs pyNeuroML which we haven't packaged yet. I'll go work on that now.
https://github.com/Neurosim-lab/netpyne/blob/development/.travis.yml

> 
> There are some hidden files in the docs (see rpmlint output) that you may
> wish
> to remove.

Removed.

> The URL should be https://pypi.org/project/%{pypi_name}

Corrected.


Here's the updated spec/srpm in the meantime, but this review is now blocked until I get pyneuroml in:

Spec URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-netpyne/python-netpyne-0.9.2-1.fc30.src.rpm


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