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Bug 1931183 - Review Request: python-spikeextractors - Python module for extracting recorded and spike sorted extracellular data from different file types and formats
Summary: Review Request: python-spikeextractors - Python module for extracting recorde...
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
Depends On: 1948573
Blocks: fedora-neuro
TreeView+ depends on / blocked
Reported: 2021-02-21 11:17 UTC by Andy Mender
Modified: 2021-04-19 17:38 UTC (History)
2 users (show)

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

Attachments (Terms of Use)

Description Andy Mender 2021-02-21 11:17:02 UTC
Spec URL:
Description: SpikeExtractors attempts to standardize data retrieval rather than data storage. This eliminates the need for shared file formats and allows 
for the creation of new tools built off of our data retrieval guidelines.

In addition to implementing multi-format I/O for various formats, the framework makes it possible to develop software tools that are agnostic 
to the underlying formats by working with the standardized python objects (recording and sorting extractors). 
These include processing routines (filters, sorting algorithms, downstream processing), and visualization widgets.
It also provides mechanisms for lazy manipulation of recordings and sortings (concatenation, combination, subset extraction).

Fedora Account System Username: andymenderunix

python-spikeextractors actually covers a lot more extra dependencies than is listed in the of the project and these are tested in the unit test suite, however one of the tests currently fails:

I marked unit tests as optional, but that doesn't solve the problem.

Comment 1 Andy Mender 2021-02-21 11:19:41 UTC
This is a resubmission of

Comment 2 Andy Mender 2021-02-21 11:21:22 UTC
Koji build:

Comment 3 Ankur Sinha (FranciscoD) 2021-02-23 21:09:12 UTC
Thanks very much Andy! I'll have a look at this in the next day or two.

Comment 5 Ankur Sinha (FranciscoD) 2021-02-27 17:29:00 UTC
Looks very good.

A few comments below.

Package Review

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

- Can you please regenerate the srpm from the latest version of the spec?

- You don't need explicit Requires. It should be done automatically nowadays:

  Only the ones that aren't mentioned in the need to be included in the spec.

- the %description bit for the python3 subpackage is missing the text.

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

[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
[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", "Expat License", "*No copyright* Apache
     License". 88 files have unknown license. Detailed output of
     licensecheck in /home/asinha/dump/fedora-reviews/1931183-python-
[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
[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.
See note about automated generated requires.

[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.
[-]: 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
[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
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

[x]: Python eggs must not download any dependencies during the build
[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 =====

[-]: 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).
[?]: Package functions as described.
Not tested this out.

[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[-]: 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.
[x]: Package should compile and build into binary rpms on all supported
[?]: %check is present and all tests pass.
The issue is reported upstream. We'll need to follow that up and enable the tests when possible.

[x]: Packages should try to preserve timestamps of original installed
[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
[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 =====

[!]: Spec file according to URL is the same as in SRPM.
     Note: Spec file as given by url is not the same as in SRPM (see
     attached diff).
     See: (this test has no URL)
Can you regenerate the SRPM from the latest version of the spec please?

[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).

Checking: python3-spikeextractors-0.9.0-1.fc35.noarch.rpm
python3-spikeextractors.noarch: E: no-description-tag
python-spikeextractors.src: W: spelling-error %description -l en_US sortings -> sorting, sorting s, sortieing
2 packages and 0 specfiles checked; 1 errors, 1 warnings.

Rpmlint (installed packages)
python3-spikeextractors.noarch: E: no-description-tag
1 packages and 0 specfiles checked; 1 errors, 0 warnings.

Source checksums
---------------- :
  CHECKSUM(SHA256) this package     : f3008d1e4b5ec0da9a480f04f5601b7dc88ede9270deae8e6c8e806006b12168
  CHECKSUM(SHA256) upstream package : f3008d1e4b5ec0da9a480f04f5601b7dc88ede9270deae8e6c8e806006b12168

python3-spikeextractors (rpmlib, GLIBC filtered):


Diff spec file in url and in SRPM
--- /home/asinha/dump/fedora-reviews/1931183-python-spikeextractors/srpm/python-spikeextractors.spec	2021-02-27 16:57:21.825993228 +0000
+++ /home/asinha/dump/fedora-reviews/1931183-python-spikeextractors/srpm-unpacked/python-spikeextractors.spec	2021-02-21 10:54:14.000000000 +0000
@@ -71,2 +71,3 @@
 * Sun Feb 21 2021 Andy Mender <andymenderunix> - 0.9.0-1
 - Initial submission

Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 1931183
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Generic, Python
Disabled plugins: Haskell, Perl, fonts, Java, PHP, C/C++, R, SugarActivity, Ocaml

Comment 6 Andy Mender 2021-03-07 09:06:25 UTC
> - Can you please regenerate the srpm from the latest version of the spec?

Done! Here are the new links:
Koji build:

> - You don't need explicit Requires. It should be done automatically nowadays:

Right, done!

> - the %description bit for the python3 subpackage is missing the text.

Done! Sorry for that.

Comment 8 Ankur Sinha (FranciscoD) 2021-04-19 17:28:54 UTC
It won't build because pynwb is FTBFS at the moment. I'll see if I can fix that so we can proceed here.

Comment 9 Ankur Sinha (FranciscoD) 2021-04-19 17:38:28 UTC
We're going to have to wait till hdmf supports h5py version 3.0. It's being worked on here, and will hopefully be merged soon:

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