Bug 1532082 - Review Request: python-klusta - Spike detection and automatic clustering for spike sorting
Summary: Review Request: python-klusta - Spike detection and automatic clustering for ...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Robert-André Mauchin 🐧
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2018-01-07 23:59 UTC by Ankur Sinha (FranciscoD)
Modified: 2018-01-23 21:45 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2018-01-23 21:17:58 UTC
Type: ---
Embargoed:
zebob.m: fedora-review+


Attachments (Terms of Use)

Description Ankur Sinha (FranciscoD) 2018-01-07 23:59:10 UTC
Spec URL: https://ankursinha.fedorapeople.org/python-klusta/python-klusta.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-klusta/python-klusta-3.0.16-1.fc27.src.rpm


Description:
klusta is an open source package for automatic spike sorting of multielectrode
neurophysiological recordings made with probes containing up to a few dozens of
sites.

klusta implements the following features:

- Kwik: An HDF5-based file format that stores the results of a spike sorting
  session.
- Spike detection (also known as SpikeDetekt): an algorithm designed for probes
  containing tens of channels, based on a flood-fill algorithm in the adjacency
graph formed by the recording sites in the probe.
- Automatic clustering (also known as Masked KlustaKwik): an automatic
  clustering algorithm designed for high-dimensional structured datasets.


Fedora Account System Username: ankursinha

Comment 1 Robert-André Mauchin 🐧 2018-01-09 17:12:48 UTC
 - you could use macros %{py2_dist} and %{py3_dist} for you python BR and R. See https://fedoraproject.org/wiki/Packaging:Python#Requires_and_BuildRequires_with_standardized_names

 - The %{sum} variable is not defined anywhere thus it is not expanded at build time:

Summary:        %{sum}


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

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



===== 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.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "BSD (3 clause)", "Unknown or generated", "*No copyright* BSD
     (unspecified)". 42 files have unknown license. Detailed output of
     licensecheck in /home/bob/packaging/review/python-klusta/review-
     python-klusta/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.
[!]: Macros in Summary, %description expandable at SRPM build time.
     Note: Macros in: python2-klusta (summary), python3-klusta (summary)
[-]: 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]: Package is not known to require an ExcludeArch tag.
[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]: 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 valid UTF-8.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 0 bytes in 0 files.
[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]: 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).
[x]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in
     python2-klusta , python3-klusta
[?]: 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.
[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]: 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: python2-klusta-3.0.16-1.fc28.noarch.rpm
          python3-klusta-3.0.16-1.fc28.noarch.rpm
          python-klusta-3.0.16-1.fc28.src.rpm
python2-klusta.noarch: W: unexpanded-macro Summary(C) %{sum}
python2-klusta.noarch: W: spelling-error %description -l en_US multielectrode -> electromotive
python2-klusta.noarch: W: spelling-error %description -l en_US neurophysiological -> physiological, neurological
python2-klusta.noarch: W: spelling-error %description -l en_US datasets -> data sets, data-sets, databases
python2-klusta.noarch: W: no-documentation
python3-klusta.noarch: W: unexpanded-macro Summary(C) %{sum}
python3-klusta.noarch: W: spelling-error %description -l en_US multielectrode -> electromotive
python3-klusta.noarch: W: spelling-error %description -l en_US neurophysiological -> physiological, neurological
python3-klusta.noarch: W: spelling-error %description -l en_US datasets -> data sets, data-sets, databases
python3-klusta.noarch: W: no-documentation
python3-klusta.noarch: W: no-manual-page-for-binary klusta
python-klusta.src: W: spelling-error %description -l en_US multielectrode -> electromotive
python-klusta.src: W: spelling-error %description -l en_US neurophysiological -> physiological, neurological
python-klusta.src: W: spelling-error %description -l en_US datasets -> data sets, data-sets, databases
3 packages and 0 specfiles checked; 0 errors, 14 warnings.

Comment 2 Ankur Sinha (FranciscoD) 2018-01-09 22:37:16 UTC
Hi!

Thanks for the review! Here is the updated spec/srpm:

Spec URL: https://ankursinha.fedorapeople.org/python-klusta/python-klusta.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-klusta/python-klusta-3.0.16-2.fc27.src.rpm

Update:

* Tue Jan 09 2018 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.0.16-2
- Update based on review comments 1532082
- use py_dist macros


Cheers!

Comment 3 Robert-André Mauchin 🐧 2018-01-09 23:08:50 UTC
All good, package approved.

Comment 4 Ankur Sinha (FranciscoD) 2018-01-10 11:19:10 UTC
Lovely! Thanks very much!

Comment 5 Gwyn Ciesla 2018-01-11 13:57:34 UTC
(fedrepo-req-admin):  The Pagure repository was created at https://src.fedoraproject.org/rpms/python-klusta

Comment 6 Fedora Update System 2018-01-11 18:25:00 UTC
python-klusta-3.0.16-2.fc27 has been submitted as an update to Fedora 27. https://bodhi.fedoraproject.org/updates/FEDORA-2018-6ccd915b6a

Comment 7 Fedora Update System 2018-01-11 18:25:49 UTC
python-klusta-3.0.16-2.fc26 has been submitted as an update to Fedora 26. https://bodhi.fedoraproject.org/updates/FEDORA-2018-f6f388fbb1

Comment 8 Fedora Update System 2018-01-12 15:27:34 UTC
python-klusta-3.0.16-2.fc26 has been pushed to the Fedora 26 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-2018-f6f388fbb1

Comment 9 Fedora Update System 2018-01-12 15:51:03 UTC
python-klusta-3.0.16-2.fc27 has been pushed to the Fedora 27 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-2018-6ccd915b6a

Comment 10 Fedora Update System 2018-01-23 21:17:58 UTC
python-klusta-3.0.16-2.fc26 has been pushed to the Fedora 26 stable repository. If problems still persist, please make note of it in this bug report.

Comment 11 Fedora Update System 2018-01-23 21:45:00 UTC
python-klusta-3.0.16-2.fc27 has been pushed to the Fedora 27 stable repository. If problems still persist, please make note of it in this bug report.


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