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Bug 2244809 - Review Request: python-lqrt - Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test
Summary: Review Request: python-lqrt - Robust Hypothesis Testing of Location Parameter...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Sandro
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2023-10-18 11:40 UTC by Ankur Sinha (FranciscoD)
Modified: 2023-12-02 02:43 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2023-11-23 12:36:39 UTC
Type: ---
Embargoed:
gui1ty: fedora-review+


Attachments (Terms of Use)

Description Ankur Sinha (FranciscoD) 2023-10-18 11:40:46 UTC
Spec URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt-0.3.3-2.20231018gite2c250d.fc40.src.rpm

Description:
This package implements a robust hypothesis testing procedure: the
Lq-likelihood-ratio-type test (LqRT), introduced in Qin and Priebe (2017). The
code replicates and extends the R package which can be found here:
http://homepages.uc.edu/~qinyn/LqLR/

The paper supporting this package is currently in review; a preprint can be
found here:
https://arxiv.org/abs/1911.11922

Fedora Account System Username: ankursinha

Comment 1 Ankur Sinha (FranciscoD) 2023-10-18 11:40:49 UTC
This package built on koji:  https://koji.fedoraproject.org/koji/taskinfo?taskID=107701958

Comment 2 Fedora Review Service 2023-10-18 11:45:00 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/6543438
(failed)

Build log:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2244809-python-lqrt/srpm-builds/06543438/builder-live.log.gz

Please make sure the package builds successfully at least for Fedora Rawhide.

- If the build failed for unrelated reasons (e.g. temporary network
  unavailability), please ignore it.
- If the build failed because of missing BuildRequires, please make sure they
  are listed in the "Depends On" field


---
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If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 3 Sandro 2023-10-19 13:13:17 UTC
Issues
======

[!]: Spec file is legible and written in American English.

=> rpmlint reports: E: summary-too-long Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test

[x]: Latest version is packaged.

=> Building from master. I suppose the actual release happens after the paper is published / approved?

python3-lqrt.noarch: W: no-documentation

=> Please include README.md as %doc.

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

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



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

Generic:
[ ]: 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. No licenses
     found. Please check the source files for licenses manually.
[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.
[!]: 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]: The License field must be a valid SPDX expression.
[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]: 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:
[-]: Binary eggs must be removed in %prep
[-]: Python eggs must not download any dependencies during the build
     process.
[-]: 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

===== 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).
[?]: Package functions as described.
[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.
[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:
[!]: 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)
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).


Rpmlint
-------
Checking: python3-lqrt-0.3.3-2.20231018gite2c250d.fc40.noarch.rpm
          python-lqrt-0.3.3-2.20231018gite2c250d.fc40.src.rpm
============================================================================================================================ rpmlint session starts ============================================================================================================================
rpmlint: 2.4.0
configuration:
    /usr/lib/python3.11/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmpu0z54d2z')]
checks: 31, packages: 2

python-lqrt.src: E: summary-too-long Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test
python3-lqrt.noarch: E: summary-too-long Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test
python-lqrt.src: W: strange-permission python-lqrt.spec 600
python3-lqrt.noarch: W: no-documentation
============================================================================================= 2 packages and 0 specfiles checked; 2 errors, 2 warnings, 2 badness; has taken 1.7 s =============================================================================================




Rpmlint (installed packages)
----------------------------
============================ rpmlint session starts ============================
rpmlint: 2.4.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
checks: 31, packages: 1

python3-lqrt.noarch: E: summary-too-long Robust Hypothesis Testing of Location Parameters using Lq-Likelihood-Ratio-Type Test
python3-lqrt.noarch: W: no-documentation
 1 packages and 0 specfiles checked; 1 errors, 1 warnings, 1 badness; has taken 0.0 s 



Source checksums
----------------
https://github.com/alyakin314/lqrt/archive/e2c250d46669bea7d294c514b407631027ae015e/lqrt-e2c250d46669bea7d294c514b407631027ae015e.tar.gz :
  CHECKSUM(SHA256) this package     : e43d878128c5a17df530adb9a9243338575729b200dbc1c4bd1dac05d92303e7
  CHECKSUM(SHA256) upstream package : e43d878128c5a17df530adb9a9243338575729b200dbc1c4bd1dac05d92303e7


Requires
--------
python3-lqrt (rpmlib, GLIBC filtered):
    python(abi)
    python3.12dist(numpy)
    python3.12dist(scipy)



Provides
--------
python3-lqrt:
    python-lqrt
    python3-lqrt
    python3.12-lqrt
    python3.12dist(lqrt)
    python3dist(lqrt)



Diff spec file in url and in SRPM
---------------------------------
--- /home/sandro/devel/fedora/fedora-review/2244809-python-lqrt/srpm/python-lqrt.spec	2023-10-19 14:06:56.090796706 +0200
+++ /home/sandro/devel/fedora/fedora-review/2244809-python-lqrt/srpm-unpacked/python-lqrt.spec	2023-10-18 02:00:00.000000000 +0200
@@ -1,2 +1,12 @@
+## START: Set by rpmautospec
+## (rpmautospec version 0.3.5)
+## RPMAUTOSPEC: autorelease, autochangelog
+%define autorelease(e:s:pb:n) %{?-p:0.}%{lua:
+    release_number = 2;
+    base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}"));
+    print(release_number + base_release_number - 1);
+}%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}}
+## END: Set by rpmautospec
+
 %global forgeurl https://github.com/alyakin314/lqrt
 # No tag on GitHub, and no sources on Pypi
@@ -56,3 +66,7 @@
 
 %changelog
-%autochangelog
+* Wed Oct 18 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur> - 0.3.3-2
+- feat: ready for review
+
+* Wed Oct 18 2023 Ankur Sinha (Ankur Sinha Gmail) <sanjay.ankur> - 0.3.3-1
+- init


Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2244809
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Python, Generic
Disabled plugins: SugarActivity, PHP, fonts, Ocaml, R, Haskell, C/C++, Java, Perl
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comment 4 Sandro 2023-10-27 14:07:59 UTC
Oops. It looks like I set myself as QA contact instead of assigning to me. Fixed!

Comment 5 Ankur Sinha (FranciscoD) 2023-11-21 06:13:11 UTC
Sorry for the delay! Here's the updated spec/srpm:

Spec URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt-0.3.3-2.20231018gite2c250d.fc40.src.rpm

> => Building from master. I suppose the actual release happens after the paper is published / approved?

This isn't compulsory, but it depends on the individual here. They have versioning in the code, they just haven't tagged on git/pypi somehow.

Comment 6 Fedora Review Service 2023-11-21 06:13:53 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/6672407
(failed)

Build log:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2244809-python-lqrt/srpm-builds/06672407/builder-live.log.gz

Please make sure the package builds successfully at least for Fedora Rawhide.

- If the build failed for unrelated reasons (e.g. temporary network
  unavailability), please ignore it.
- If the build failed because of missing BuildRequires, please make sure they
  are listed in the "Depends On" field


---
This comment was created by the fedora-review-service
https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 7 Sandro 2023-11-21 11:41:36 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #5)
> Sorry for the delay! Here's the updated spec/srpm:
> 
> Spec URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt.spec
> SRPM URL:
> https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt-0.3.3-2.
> 20231018gite2c250d.fc40.src.rpm

The SRPM URL is a 404. That's why the the Fedora Review Service build failed.

> > => Building from master. I suppose the actual release happens after the paper is published / approved?
> 
> This isn't compulsory, but it depends on the individual here. They have
> versioning in the code, they just haven't tagged on git/pypi somehow.

I was just curious. But since you are using a commit, I have the following to remark:

Version 0.3.3, as published on PyPI, appears to be commit d5ec8cd0530967b9281af4ea17a00ecd68d20c88 [1] looking at what changed and the date of publication. Since this is then the same as version 0.3.3 on PyPI, you probably wanna add the following to the spec file:

# Don't use commit in dist tag
%global distprefix %{nil}

That will get rid of the commit in %dist. That's what I've been doing for `autograd` [2] as well, where the PyPI sdist is missing stuff.

[1] https://github.com/alyakin314/lqrt/commit/d5ec8cd0530967b9281af4ea17a00ecd68d20c88
[2] https://src.fedoraproject.org/rpms/python-autograd/pull-request/5#request_diff

Comment 8 Ankur Sinha (FranciscoD) 2023-11-21 17:07:47 UTC
> I was just curious. But since you are using a commit, I have the following to remark:
> Version 0.3.3, as published on PyPI, appears to be commit d5ec8cd0530967b9281af4ea17a00ecd68d20c88 [1] looking at what changed and the date of publication. 

It depends. The usual suggested practice is to make a release, and then immediately bump the version so that if someone installs from source, they get the new unreleased version that doesn't clash with the pypi released version. So, it's hard to tell what commit they've released from here---it could be any commit after they bumped to 0.3.3. Luckily, there's only one commit after the one that bumps the release, and it's a cosmetic change to the readme, so no harm including it too.

https://github.com/alyakin314/lqrt/commits/master

> Since this is then the same as version 0.3.3 on PyPI, you probably wanna add the following to the spec file:
> # Don't use commit in dist tag
> %global distprefix %{nil}

> That will get rid of the commit in %dist. That's what I've been doing for `autograd` [2] as well, where the PyPI sdist is missing stuff.


Oo, nice! Used that now. Updated spec/srpm:

Spec URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt.spec
SRPM URL: https://ankursinha.fedorapeople.org/python-lqrt/python-lqrt-0.3.3-4.fc40.src.rpm

Comment 9 Fedora Review Service 2023-11-21 17:15:41 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/6675318
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2244809-python-lqrt/fedora-rawhide-x86_64/06675318-python-lqrt/fedora-review/review.txt

Please take a look if any issues were found.


---
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https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 10 Sandro 2023-11-23 11:39:01 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #8)
> > I was just curious. But since you are using a commit, I have the following to remark:
> > Version 0.3.3, as published on PyPI, appears to be commit d5ec8cd0530967b9281af4ea17a00ecd68d20c88 [1] looking at what changed and the date of publication. 
> 
> It depends. The usual suggested practice is to make a release, and then
> immediately bump the version so that if someone installs from source, they
> get the new unreleased version that doesn't clash with the pypi released
> version. So, it's hard to tell what commit they've released from here---it
> could be any commit after they bumped to 0.3.3. Luckily, there's only one
> commit after the one that bumps the release, and it's a cosmetic change to
> the readme, so no harm including it too.
> 
> https://github.com/alyakin314/lqrt/commits/master

Okay. It wasn't a blocker to begin with. I suppose you are right. There are different strategies to approaching the version bump and without a specific tag that can be distilled from the PyPI release, we just don't know for sure.


Package looks good now. APPROVED!

Comment 11 Fedora Admin user for bugzilla script actions 2023-11-23 12:10:49 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-lqrt

Comment 12 Fedora Update System 2023-11-23 12:34:45 UTC
FEDORA-2023-ee2598755f has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2023-ee2598755f

Comment 13 Fedora Update System 2023-11-23 12:36:29 UTC
FEDORA-2023-a33aeedef4 has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-a33aeedef4

Comment 14 Fedora Update System 2023-11-23 12:36:39 UTC
FEDORA-2023-ee2598755f has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 15 Fedora Update System 2023-11-23 12:44:51 UTC
FEDORA-2023-b28d5c655b has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2023-b28d5c655b

Comment 16 Fedora Update System 2023-11-24 01:43:54 UTC
FEDORA-2023-a33aeedef4 has been pushed to the Fedora 39 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-a33aeedef4 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-a33aeedef4

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 17 Fedora Update System 2023-11-24 02:18:55 UTC
FEDORA-2023-b28d5c655b has been pushed to the Fedora 38 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-b28d5c655b \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-b28d5c655b

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 18 Fedora Update System 2023-12-02 01:24:21 UTC
FEDORA-2023-a33aeedef4 has been pushed to the Fedora 39 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 19 Fedora Update System 2023-12-02 02:43:23 UTC
FEDORA-2023-b28d5c655b has been pushed to the Fedora 38 stable repository.
If problem still persists, please make note of it in this bug report.


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