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Bug 2056447 - Review Request: python-neatdend - NEAT (NEural Analysis Toolkit)
Summary: Review Request: python-neatdend - NEAT (NEural Analysis Toolkit)
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:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
Reported: 2022-02-21 09:30 UTC by Vanessa Christopher
Modified: 2022-07-18 13:20 UTC (History)
2 users (show)

Fixed In Version: python-neatdend-0.9.2-5.fc37
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Last Closed: 2022-07-18 13:20:43 UTC
Type: ---
sanjay.ankur: fedora-review+

Attachments (Terms of Use)

Description Vanessa Christopher 2022-02-21 09:30:45 UTC
Spec URL:
Description: NEAT (NEural Analysis Toolkit) 
Fedora Account System Username: vanessakris

Comment 1 Ankur Sinha (FranciscoD) 2022-03-14 13:13:55 UTC
Sorry, I missed this one Vanessa. I'll review it this week.

Comment 2 Ankur Sinha (FranciscoD) 2022-03-23 18:00:05 UTC
Spec URL:

Vanessa---just a reminder that we need to use the raw URLs for fedora-review to work. 

Reviewing this now.

Comment 3 Vanessa Christopher 2022-03-24 09:35:05 UTC
ohhhh, thank you.

Comment 4 Ankur Sinha (FranciscoD) 2022-04-24 16:41:34 UTC
Hi Vanessa,

Sorry it took so long. There were some fixes that were needed to get this to properly build on all architectures, so I was working on those. Here's the full review now. Please take a look and make the necessary changes (and of course, ping me if anything at all is unclear)

Looks very good, but a few tweaks are needed before we can approve this one.

Package Review

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

- Header files in -devel subpackage, if present.
  Note: python3-NEAT : /usr/lib64/python3.10/site-
  packages/neat/tools/simtools/net/Ionchannels.h python3-NEAT :
  python3-NEAT : /usr/lib64/python3.10/site-

  I'm not sure if these files are used at runtime, but upstream does install them when installing the module using `pip`, so we'll keep them here as they are. So, this is a false positive.

- Dist tag is present.
  False positive, we're using rpmautospec here.

- Some tweaks are needed to get the package to work correctly on all arches. I've submitted a PR to your spec here with the patch and spec updates to make this happen correctly:

- I think we need to name the package python-neatdend to follow what the project is called on pypi. See my comment below for more information.

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

[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.
  False positive, it's the compiled Python module object: 

[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.

[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", "*No copyright* GNU General Public
     License, Version 3", "*No copyright* GNU General Public License". 171
     files have unknown license. Detailed output of licensecheck in
[x]: License file installed when any subpackage combination is installed.
    rpm -ql --licensefiles -p ./python3-NEAT-0.9.2-1.fc37.x86_64.rpm

[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
[!]: Package is named according to the Package Naming Guidelines.

   I see the python naming guidelines suggest lowercase naming, so we should change this to `python-neat` instead of `python-NEAT` I guess. Next, I think we need to use the name the project uses on pypi, which is `neatdend`, so this should probably be `python-neatdend` to match that:

   What do you think, Vanessa?

[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.
[x]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 20480 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]: 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]: 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.
[ ]: Final provides and requires are sane (see attachments).
[-]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in
[!]: Package functions as described.
     We had disabled some tests, I looked into why they weren't running correctly. Opened a PR now with all tests being run and passing:
[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
Scratch build:

[x]: %check is present and all tests pass.
    Some were disabled. I've looked into why they weren't running and opened a PR with fixes:

[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)
False positive---we're using rpmautospec so the spec/srpm differ a little.

[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.

======================================================== rpmlint session starts ========================================================
rpmlint: 2.2.0
checks: 32, packages: 2

python-NEAT.src: W: strange-permission python-NEAT.spec 600
python3-NEAT.x86_64: E: non-executable-script /usr/lib64/python3.10/site-packages/neat/channels/compilechannels 644 /usr/bin/env python3
python3-NEAT.x86_64: W: no-manual-page-for-binary compilechannels
There's no help text for this command from the looks of it, so let's leave it.

python-NEAT.spec:32: W: mixed-use-of-spaces-and-tabs (spaces: line 32, tab: line 10)
Also fixed in PR.

python3-NEAT.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.10/site-packages/neat/tools/simtools/net/Ionchannels.h
python3-NEAT.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.10/site-packages/neat/tools/simtools/net/NETC.h
python3-NEAT.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.10/site-packages/neat/tools/simtools/net/Synapses.h
python3-NEAT.x86_64: W: devel-file-in-non-devel-package /usr/lib64/python3.10/site-packages/neat/tools/simtools/net/netsim.cpp
These are part of the package, and required. We leave them in.
========================= 2 packages and 0 specfiles checked; 1 errors, 7 warnings, 1 badness; has taken 2.6 s =========================

Rpmlint (installed packages)
Cannot parse rpmlint output:
Not sure what to do about this yet (fixed in the new fedora-review release I *think*)

Unversioned so-files
python3-NEAT: /usr/lib64/python3.10/site-packages/neat/

This is the compiled python module, so it's fine.

Source checksums
---------------- :
  CHECKSUM(SHA256) this package     : 3f269c74d3c5c66c06d8eac5400482b577af442f557fb66cc9467533ebcf3687
  CHECKSUM(SHA256) upstream package : 3f269c74d3c5c66c06d8eac5400482b577af442f557fb66cc9467533ebcf3687

python3-NEAT (rpmlib, GLIBC filtered):
    (python3.10dist(cython) >= 0.29.4 with python3.10dist(cython) < 0.30)

python-NEAT-debugsource (rpmlib, GLIBC filtered):



Diff spec file in url and in SRPM
--- /home/asinha/dump/fedora-reviews/2056447-python-NEAT/srpm/python-NEAT.spec	2022-04-22 09:17:14.842975399 +0100
+++ /home/asinha/dump/fedora-reviews/2056447-python-NEAT/srpm-unpacked/python-NEAT.spec	2022-02-17 19:46:14.000000000 +0000
@@ -1,2 +1,11 @@
+## START: Set by rpmautospec
+## (rpmautospec version 0.2.5)
+%define autorelease(e:s:pb:) %{?-p:0.}%{lua:
+    release_number = 1;
+    base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}"));
+    print(release_number + base_release_number - 1);
+## END: Set by rpmautospec
 %bcond_with network
@@ -62,3 +71,3 @@

Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 2056447
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, C/C++, Python, Shell-api
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Comment 6 Ankur Sinha (FranciscoD) 2022-07-05 08:37:20 UTC
Thanks Vanessa. This all looks good! XXX APPROVED XXX

Please continue with requesting repos + branches for F35+, and importing to the SCM as we've noted here:


Comment 7 Gwyn Ciesla 2022-07-05 16:32:51 UTC
(fedscm-admin):  The Pagure repository was created at

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