Bug 2029677 - Review Request: sep - Astronomical source extraction and photometry in Python and C
Summary: Review Request: sep - Astronomical source extraction and photometry in Python...
Keywords:
Status: NEW
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Nobody's working on this, feel free to take it
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On: 2038164
Blocks: 1938451
TreeView+ depends on / blocked
 
Reported: 2021-12-07 02:25 UTC by Petr Menšík
Modified: 2024-07-15 14:28 UTC (History)
5 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed:
Type: ---
Embargoed:


Attachments (Terms of Use)

Description Petr Menšík 2021-12-07 02:25:28 UTC
Spec URL: https://pemensik.fedorapeople.org/sep.spec
SRPM URL: https://pemensik.fedorapeople.org/sep-1.2.0-1.fc36.src.rpm

Description:

SEP makes available some of the astronomical source extraction and
photometry algorithms in Source Extractor as stand-alone
functions and classes. These operate directly on in-memory numpy arrays
(no FITS files, configuration files, etc). It’s derived directly from
(and tested against) the Source Extractor code base.

Native code shared library.

Fedora Account System Username: pemensik

Comment 1 Petr Menšík 2021-12-07 02:25:31 UTC
This package built on koji:  https://koji.fedoraproject.org/koji/taskinfo?taskID=79666000

Comment 2 Petr Menšík 2021-12-07 02:29:54 UTC
Hello Sergio. I would like to provide also native C library to sep package, which you maitain in python-sep. Would you like to co-maintain it? I have used your spec of python-sep as a template and added cmake parts with native. I think it should eventually replace python-sep, because it provides python code from github repository.

Are you interested?

Comment 3 Petr Menšík 2021-12-07 09:27:49 UTC
This package is sort of modified python-sep package [1], where also native library export is done. It provides both native and python parts taken from authoritative source. I think it should replace python-sep.

It is a library, which is used in modified form in stellarsolver, bug #1938451. It cannot be used straight away because stellarsolver's code is modified an incompatible. But should be ready once that is possible.

1. https://src.fedoraproject.org/rpms/python-sep

Comment 4 Mattia Verga 2021-12-07 11:11:03 UTC
So, both this new package and python-sep are going to provide python3-sep... I think it's wrong.

I think the only way to handle this is to bump this new package to a version greater than python-sep and retire python-sep.

Comment 5 Petr Menšík 2022-01-07 13:51:34 UTC
(In reply to Mattia Verga from comment #4)
> So, both this new package and python-sep are going to provide python3-sep...
> I think it's wrong.
> 
> I think the only way to handle this is to bump this new package to a version
> greater than python-sep and retire python-sep.

Of course, something like that is expected. This package can provide both python and native library from single source. Moreover it does not use python site to proxy releases, but uses what I believe is original author's repository.

Because I am using %autorelease macro, raising release above current 3 would be just matter of 3 commits. I think Obsoletes is not necessary if the new python3-sep package has the same name, just is built from different source.

Comment 6 Mattia Verga 2022-01-07 17:48:42 UTC
(In reply to Petr Menšík from comment #5)
> (In reply to Mattia Verga from comment #4)
> > So, both this new package and python-sep are going to provide python3-sep...
> > I think it's wrong.
> > 
> > I think the only way to handle this is to bump this new package to a version
> > greater than python-sep and retire python-sep.
> 
> Of course, something like that is expected. This package can provide both
> python and native library from single source. Moreover it does not use
> python site to proxy releases, but uses what I believe is original author's
> repository.
> 
> Because I am using %autorelease macro, raising release above current 3 would
> be just matter of 3 commits.

...or just use the `-b` parameter.

>I think Obsoletes is not necessary if the new
> python3-sep package has the same name, just is built from different source.

Having two packages providing the same file (not only just the same name package/subpackage) would cause a conflict, which is not allowed:
https://docs.fedoraproject.org/en-US/packaging-guidelines/Conflicts/

I think we should handle this like a package renaming, thus the new package should provide appropriate Obsoletes and Provides and everything should be synchronized with Sergio retiring the old package (obviously if he accepts to do this change).

I'm willing to perform this review, but I'd like to hear Sergio's opinion...

Comment 7 Package Review 2023-01-08 00:45:26 UTC
This is an automatic check from review-stats script.

This review request ticket hasn't been updated for some time. We're sorry
it is taking so long. If you're still interested in packaging this software
into Fedora repositories, please respond to this comment clearing the
NEEDINFO flag.

You may want to update the specfile and the src.rpm to the latest version
available and to propose a review swap on Fedora devel mailing list to increase
chances to have your package reviewed. If this is your first package and you
need a sponsor, you may want to post some informal reviews. Read more at
https://fedoraproject.org/wiki/How_to_get_sponsored_into_the_packager_group.

Without any reply, this request will shortly be considered abandoned
and will be closed.
Thank you for your patience.

Comment 8 Petr Menšík 2023-01-18 10:15:07 UTC
Still interested in review. Updated to following release.

Spec URL: https://pemensik.fedorapeople.org/srpm/sep.spec
SRPM URL: https://pemensik.fedorapeople.org/srpm/sep-1.2.1-4.fc36.src.rpm

Comment 9 Jakub Kadlčík 2023-01-18 10:23:18 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/5242832
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2029677-sep/fedora-rawhide-x86_64/05242832-sep/fedora-review/review.txt

Please take a look if any issues were found.

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

Comment 10 Benson Muite 2023-06-22 07:13:31 UTC
Package Review
==============

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



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

C/C++:
[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.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig not called in %post and %postun for Fedora 28 and later.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.

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: "Unknown or generated", "*No copyright* GNU Lesser General
     Public License, Version 3", "*No copyright* GNU Lesser General Public
     License v3.0 or later", "BSD 3-Clause License", "GNU Lesser General
     Public License, Version 3", "MIT License", "GNU Lesser General Public
     License v3.0 or later". 39 files have unknown license. Detailed output
     of licensecheck in
     /home/FedoraPackaging/reviews/sep/2029677-sep/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[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.
[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.
[ ]: Useful -debuginfo package or justification otherwise.
[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 40960 bytes in 6 files.
[ ]: 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

===== 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).
[ ]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in sep-
     devel , python3-sep
[ ]: 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.
     Note: gpgverify is not used.
[ ]: 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:
[!]: 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 debuginfo package(s).
     Note: No rpmlint messages.
[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
-------
Checking: sep-1.2.1-4.fc39.x86_64.rpm
          sep-devel-1.2.1-4.fc39.x86_64.rpm
          python3-sep-1.2.1-4.fc39.x86_64.rpm
          sep-debuginfo-1.2.1-4.fc39.x86_64.rpm
          sep-debugsource-1.2.1-4.fc39.x86_64.rpm
          sep-1.2.1-4.fc39.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/tmpnk07vg1i')]
checks: 31, packages: 6

sep.src: W: strange-permission sep.spec 600
sep-devel.x86_64: W: no-documentation
======================== 6 packages and 0 specfiles checked; 0 errors, 2 warnings, 0 badness; has taken 3.4 s ========================




Rpmlint (debuginfo)
-------------------
Checking: sep-debuginfo-1.2.1-4.fc39.x86_64.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/tmphoj_5ful')]
checks: 31, packages: 1

======================== 1 packages and 0 specfiles checked; 0 errors, 0 warnings, 0 badness; has taken 0.8 s ========================





Rpmlint (installed packages)
----------------------------
============================ 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
checks: 31, packages: 5

sep-devel.x86_64: W: no-documentation
 5 packages and 0 specfiles checked; 0 errors, 1 warnings, 0 badness; has taken 2.5 s 



Unversioned so-files
--------------------
python3-sep: /usr/lib64/python3.11/site-packages/sep.cpython-311-x86_64-linux-gnu.so

Source checksums
----------------
https://github.com/kbarbary/sep/archive/v1.2.1/sep-1.2.1.tar.gz :
  CHECKSUM(SHA256) this package     : 746223ff6cba9a2e32312be3e549c95d14f286d1a77871fedfe282a13c7f45e8
  CHECKSUM(SHA256) upstream package : 746223ff6cba9a2e32312be3e549c95d14f286d1a77871fedfe282a13c7f45e8


Requires
--------
sep (rpmlib, GLIBC filtered):
    glibc
    ld-linux-x86-64.so.2()(64bit)
    libc.so.6()(64bit)
    libm.so.6()(64bit)
    rtld(GNU_HASH)

sep-devel (rpmlib, GLIBC filtered):
    libsep.so.0()(64bit)
    sep(x86-64)

python3-sep (rpmlib, GLIBC filtered):
    ld-linux-x86-64.so.2()(64bit)
    libc.so.6()(64bit)
    python(abi)
    python3.11dist(numpy)
    rtld(GNU_HASH)

sep-debuginfo (rpmlib, GLIBC filtered):

sep-debugsource (rpmlib, GLIBC filtered):



Provides
--------
sep:
    libsep.so.0()(64bit)
    sep
    sep(x86-64)

sep-devel:
    sep-devel
    sep-devel(x86-64)

python3-sep:
    python-sep
    python3-sep
    python3-sep(x86-64)
    python3.11-sep
    python3.11dist(sep)
    python3dist(sep)

sep-debuginfo:
    debuginfo(build-id)
    libsep.so.0.6.0-1.2.1-4.fc39.x86_64.debug()(64bit)
    sep-debuginfo
    sep-debuginfo(x86-64)

sep-debugsource:
    sep-debugsource
    sep-debugsource(x86-64)



Diff spec file in url and in SRPM
---------------------------------
--- /home/benson/Projects/FedoraPackaging/reviews/sep/2029677-sep/srpm/sep.spec 2023-06-20 13:38:40.705014960 +0300
+++ /home/benson/Projects/FedoraPackaging/reviews/sep/2029677-sep/srpm-unpacked/sep.spec 2023-01-18 13:10:08.000000000 +0300
@@ -1,2 +1,12 @@
+## START: Set by rpmautospec
+## (rpmautospec version 0.3.1)
+## RPMAUTOSPEC: autorelease, autochangelog
+%define autorelease(e:s:pb:n) %{?-p:0.}%{lua:
+    release_number = 1;
+    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 forgeurl0 https://github.com/kbarbary/sep
 
@@ -82,3 +92,13 @@
 
 %changelog
-%autochangelog
+* Wed Jan 18 2023 Petr Menšík <pemensik> - 1.2.1-4
+- Uncommitted changes
+
+* Tue Jan 11 2022 Petr Menšík <pemensik> - 1.2.0-5
+- Ensure higher version than the last build of python-sep is used
+
+* Tue Dec 07 2021 Petr Menšík <pemensik> - 1.2.0-1
+- Native package sep
+
+* Mon Apr 19 2021 Ingvar Stepanyan <me>
+- RPMAUTOSPEC: unresolvable merge


Generated by fedora-review 0.9.0 (6761b6c) last change: 2022-08-23
Command line :/usr/bin/fedora-review -b 2029677
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, C/C++, Shell-api
Disabled plugins: Python, Haskell, Perl, PHP, fonts, Ruby, Ocaml, Java, R, SugarActivity
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Comments:
a) Please use SPDX expressions for licenses
b) Can tests be run using tox?

Comment 11 Package Review 2024-06-22 00:45:29 UTC
This is an automatic check from review-stats script.

This review request ticket hasn't been updated for some time. We're sorry
it is taking so long. If you're still interested in packaging this software
into Fedora repositories, please respond to this comment clearing the
NEEDINFO flag.

You may want to update the specfile and the src.rpm to the latest version
available and to propose a review swap on Fedora devel mailing list to increase
chances to have your package reviewed. If this is your first package and you
need a sponsor, you may want to post some informal reviews. Read more at
https://fedoraproject.org/wiki/How_to_get_sponsored_into_the_packager_group.

Without any reply, this request will shortly be considered abandoned
and will be closed.
Thank you for your patience.

Comment 12 Petr Menšík 2024-07-15 14:26:29 UTC
Made a modernized python version, including tox and SPDX tags.

Spec URL: https://pemensik.fedorapeople.org/srpm/sep.spec
SRPM URL: https://pemensik.fedorapeople.org/srpm/sep-1.2.1-5.fc41.src.rpm

Comment 13 Petr Menšík 2024-07-15 14:28:32 UTC
There will be probably some issues once numpy is upgraded to version 2. Not yet on rawhide though. That fails when tox run is used from command line.

Upstream issue reported:
https://github.com/kbarbary/sep/issues/157


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