[Bug 2005105] Review Request: python-exdir - Directory structure standard for experimental pipelines

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https://bugzilla.redhat.com/show_bug.cgi?id=2005105



--- Comment #2 from Ben Beasley <code@xxxxxxxxxxxxxxxxxx> ---
Package Review
==============

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


Issues:
=======
- Dist tag is present.

  (This is just fedora-review not understanding rpmautospec.)

- You don’t need the manual BR’s for testing. Since setup.py has:

    install_requires=[
        "numpy>=1.20",
        "ruamel.yaml>=0.16",
        "six>=1.15",
    ],

  you can remove

    BuildRequires:  %{py3_dist numpy}
    BuildRequires:  %{py3_dist ruamel-yaml}

  and change

    %pyproject_buildrequires

  to

    %pyproject_buildrequires %{?with_tests:-r}

  Furthermore, since %pyproject_buildrequires can now read requirements.txt
  format files, you can remove

    BuildRequires:  %{py3_dist h5py}
    BuildRequires:  %{py3_dist pytest}
    BuildRequires:  %{py3_dist quantities}

  and update to

    %pyproject_buildrequires %{?with_tests:-r requirements.in}

  Finally,

    BuildRequires:  %{py3_dist attrs}

  appears to be spurious, and

    BuildRequires:  %{py3_dist iniconfig}

  is in requirements.txt only as an indirect dependency via pytest, so you
  don’t need to BR it directly either.

  The net result is that this block:

    %if %{with tests}
    BuildRequires:  %{py3_dist attrs}
    BuildRequires:  %{py3_dist h5py}
    BuildRequires:  %{py3_dist iniconfig}
    BuildRequires:  %{py3_dist numpy}
    BuildRequires:  %{py3_dist pytest}
    BuildRequires:  %{py3_dist quantities}
    BuildRequires:  %{py3_dist ruamel-yaml}
    %endif

  is entirely removed.

- You can remove

    BuildRequires:  pyproject-rpm-macros

  since python3-devel now requires it. This changed only a couple of months
  ago, and there was no big announcement that I know of, but it’s now true for
  all Fedora releases.

- You can parallelize the Sphinx documentation build by changing

    PYTHONPATH=".:.." make -C docs SPHINXBUILD=sphinx-build-3 html

  to

    PYTHONPATH=".:.." make -C docs html SPHINXOPTS=%{?_smp_mflags}

  This parallelizes (certain parts of) Sphinx itself. The only time it’s not
  possible is when the Sphinx configuration uses plugins that haven’t
  explicitly marked themselves as parallel-safe, and you’ll get a clear error
  message on projects where that is the case.

  I dropped the SPHINXBUILD=sphinx-build-3 since that’s only needed on EPEL7
  where “sphinx-build” is Python 2, or where upstream has some weird default in
  the Makefile.

  You *can* use “%make_build” in place of “make” here, and I usually do, but it
  makes little difference. In fact, if you were building multiple Sphinx
  targets (like “html latex”) it would be counterproductive, as these generated
  Sphinx Makefiles are typically not safe for parallel make, and you would have
  to add -j1 to override %{?_smp_mflags}.

- Since there is an “artificial filesystem package” for Jupyter-related
  directories, these should not be co-owned under
 
https://docs.fedoraproject.org/en-US/packaging-guidelines/#_the_directory_is_owned_by_a_package_which_is_not_required_for_your_package_to_function.

  Instead, add:

    # %%dir %%{_sysconfdir}/jupyter
    # %%dir %%{_sysconfdir}/jupyter/jupyter_notebook_config.d
    # %%dir %%{_sysconfdir}/jupyter/nbconfig
    # %%dir %%{_sysconfdir}/jupyter/nbconfig/notebook.d
    # %%dir %%{_datadir}/jupyter
    # %%dir %%{_datadir}/jupyter/nbextensions
    Requires:       python-jupyter-filesystem

  and change

    %{_datadir}/jupyter
    %config(noreplace) %{_sysconfdir}/jupyter

  to

    %{_datadir}/jupyter/nbextensions/exdir
    %config(noreplace)
%{_sysconfdir}/jupyter/jupyter_notebook_config.d/exdir.json
    %config(noreplace) %{_sysconfdir}/jupyter/nbconfig/notebook.d/exdir.json

- There is a bundled JavaScript library at exdir/static/index.js that must be
  handled according to
  https://docs.fedoraproject.org/en-US/packaging-guidelines/#bundling.

  It’s a fork that can’t be unbundled. It’s otherwise compliant with
  https://docs.fedoraproject.org/en-US/packaging-guidelines/JavaScript/ (e.g.
  it isn’t pre-minified). Thus I recommend something like:

    # The included copy is a fork and therefore can’t be unbundled. The
    # original can be found at
    # https://code.iamkate.com/javascript/collapsible-lists/ and was never
    # versioned nor committed to version control.
    Provides:       bundled(js-collapsible-lists)

===== 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: "Unknown or generated", "MIT License", "*No copyright*
     [generated file]", "*No copyright* Creative Commons CC0 Universal 1.0
     Public Domain Dedication". 80 files have unknown license. Detailed
     output of licensecheck in /home/reviewer/2005105-python-
     exdir/licensecheck.txt

     The file exdir/static/index.js is CC0. I think the overall “MIT” license
     is correct under
    
https://fedoraproject.org/wiki/Licensing:FAQ#What_is_.22effective_license.22_and_do_I_need_to_know_that_for_the_License:_tag.3F.

[x]: License file installed when any subpackage combination is installed.

    $ rpm -qL -p results/python3-exdir-0.4.2-1.fc36.noarch.rpm 
    /usr/lib/python3.10/site-packages/exdir-0.4.2.dist-info/LICENSE

    $ rpm -qL -p results/python-exdir-doc-0.4.2-1.fc36.noarch.rpm
    /usr/share/licenses/python-exdir-doc/LICENSE

[!]: Package does not own files or directories owned by other packages.
     Note: Dirs in package are owned also by: /etc/jupyter(python-jupyter-
     filesystem), /etc/jupyter/jupyter_notebook_config.d(python-jupyter-
     filesystem), /etc/jupyter/nbconfig(python-jupyter-filesystem),
     /etc/jupyter/nbconfig/notebook.d(python-jupyter-filesystem),
     /usr/share/jupyter(python-jupyter-filesystem),
     /usr/share/jupyter/nbextensions(python-jupyter-filesystem)

     Add a dependency on python-jupyter-filesystem instead.

[!]: Package contains no bundled libraries without FPC exception.

     Virtual Provides for forked and bundled JavaScript library should be
     added.

[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.
[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]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 20480 bytes in 1 files.
[x]: Package complies to the Packaging Guidelines

     (except as noted)

[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 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]: %config files are marked noreplace or the reason is justified.
[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
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: No %config files under /usr.
[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

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]: 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 =====

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
     python3-exdir
[x]: Package functions as described.

     (based on tests 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
     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: python3-exdir-0.4.2-1.fc36.noarch.rpm
          python-exdir-doc-0.4.2-1.fc36.noarch.rpm
          python-exdir-0.4.2-1.fc36.src.rpm
python3-exdir.noarch: W: spelling-error %description -l en_US assosciated ->
associated, dissociated, associate
python3-exdir.noarch: W: spelling-error %description -l en_US neuroscience ->
pseudoscience
python-exdir-doc.noarch: W: wrong-file-end-of-line-encoding
/usr/share/doc/python-exdir-doc/html/objects.inv
python-exdir-doc.noarch: W: file-not-utf8
/usr/share/doc/python-exdir-doc/html/objects.inv
python-exdir.src: W: spelling-error %description -l en_US assosciated ->
associated, dissociated, associate
python-exdir.src: W: spelling-error %description -l en_US neuroscience ->
pseudoscience
python-exdir.src:97: W: macro-in-%changelog %autochangelog
3 packages and 0 specfiles checked; 0 errors, 7 warnings.




Rpmlint (installed packages)
----------------------------
Cannot parse rpmlint output:


Source checksums
----------------
https://github.com/CINPLA/exdir/archive/v0.4.2/exdir-0.4.2.tar.gz :
  CHECKSUM(SHA256) this package     :
8cf7c3b2b98f615ad46efeefc734b796e5a4ee47f8e634235b94c712cc7070ef
  CHECKSUM(SHA256) upstream package :
8cf7c3b2b98f615ad46efeefc734b796e5a4ee47f8e634235b94c712cc7070ef


Requires
--------
python3-exdir (rpmlib, GLIBC filtered):
    config(python3-exdir)
    python(abi)
    python3.10dist(numpy)
    python3.10dist(ruamel-yaml)
    python3.10dist(six)

python-exdir-doc (rpmlib, GLIBC filtered):



Provides
--------
python3-exdir:
    config(python3-exdir)
    python-exdir
    python3-exdir
    python3.10-exdir
    python3.10dist(exdir)
    python3dist(exdir)

python-exdir-doc:
    python-exdir-doc



Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 2005105
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Generic, Python
Disabled plugins: Perl, fonts, Haskell, R, SugarActivity, C/C++, Ocaml, Java,
PHP
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH


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