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Bug 2009827 - Review Request: python-pybv - A lightweight I/O utility for the BrainVision data format
Summary: Review Request: python-pybv - A lightweight I/O utility for the BrainVision d...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Ben Beasley
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2021-10-01 17:24 UTC by Aniket Pradhan
Modified: 2021-11-13 01:13 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2021-11-13 01:06:37 UTC
Type: ---
Embargoed:
code: fedora-review+


Attachments (Terms of Use)

Description Aniket Pradhan 2021-10-01 17:24:44 UTC
Spec URL: https://major.fedorapeople.org/python-pybv/python-pybv.spec
SRPM URL: https://major.fedorapeople.org/python-pybv/python-pybv-0.6.0-1.fc34.src.rpm

Description: pybv is a lightweight exporter to the BrainVision data format. The BrainVision
data format is a recommended data format for use in the Brain Imaging Data
Structure. BrainVision is the name of a file format commonly used for storing
electrophysiology data. Originally, it was put forward by the company Brain
Products, however the simplicity of the format has allowed for a diversity
of tools reading from and writing to the format.

The format consists of three separate files:

* A text header file (.vhdr) containing meta data
* A text marker file (.vmrk) containing information about events in the data
* A binary data file (.eeg) containing the voltage values of the EEG

Fedora Account System Username: major

Koji scratch build: https://koji.fedoraproject.org/koji/taskinfo?taskID=76574341

Comment 1 Ben Beasley 2021-10-01 19:24:22 UTC
Package Review
==============

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

===== Issues =====

- It was recently pointed out that Sphinx-generated HTML documentation contains
  bundled and pre-minified JavaScript that is very difficult to package in
  strict compliance with the relevant guidelines, and that even if these can be
  packaged successfully, they should contribute to the License of the -doc
  subpackage.

  Please see https://bugzilla.redhat.com/show_bug.cgi?id=2006555 and the
  packaging mailing list thread
  https://lists.fedoraproject.org/archives/list/packaging@lists.fedoraproject.org/thread/LLUAURXZVADATHK65HBPPBHKF4EM4UC3/
  for detailed discussion.

  At this time, it seems you have two reasonable choices:

    * The Sphinx-generated PDF documentation *may* be acceptable. (There is an
      open discussion on whether embedded fonts in PDFs should be considered a
      problem.) For the time being, I’ve mostly been switching my existing
      Sphinx-generated (and Doxygen-generated) documentation subpackages to
      PDFs rather than removing them altogether. Here’s an example of how that
      can be done:
      https://src.fedoraproject.org/rpms/python-asyncpg/c/5596d0e7ac63b4c685cd73a991f0e5266759abe4?branch=rawhide

    * You could remove the -doc subpackage entirely, and refrain from packaging
      the documentation—a loss, in my opinion, but an easy solution.

===== 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", "BSD (3 clause)". 23 files have unknown
     license. Detailed output of licensecheck in
     /home/reviewer/2009827-python-pybv/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[!]: Package contains no bundled libraries without FPC exception.

     See notes about Sphinx HTML documentation in Issues.

[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 10240 bytes in 1 files.
[!]: Package complies to the Packaging Guidelines

     See notes about Sphinx HTML documentation in Issues.

[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

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-pybv
[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-pybv-0.6.0-1.fc36.noarch.rpm
          python-pybv-doc-0.6.0-1.fc36.noarch.rpm
          python-pybv-0.6.0-1.fc36.src.rpm
python3-pybv.noarch: W: spelling-error %description -l en_US electrophysiology -> electrocardiography
python3-pybv.noarch: W: spelling-error %description -l en_US vhdr -> HDTV
python3-pybv.noarch: W: spelling-error %description -l en_US vmrk -> murk
python3-pybv.noarch: W: spelling-error %description -l en_US eeg -> EEG, gee, reg
python-pybv-doc.noarch: W: spelling-error %description -l en_US electrophysiology -> electrocardiography
python-pybv-doc.noarch: W: spelling-error %description -l en_US vhdr -> HDTV
python-pybv-doc.noarch: W: spelling-error %description -l en_US vmrk -> murk
python-pybv-doc.noarch: W: spelling-error %description -l en_US eeg -> EEG, gee, reg
python-pybv.src: W: spelling-error %description -l en_US electrophysiology -> electrocardiography
python-pybv.src: W: spelling-error %description -l en_US vhdr -> HDTV
python-pybv.src: W: spelling-error %description -l en_US vmrk -> murk
python-pybv.src: W: spelling-error %description -l en_US eeg -> EEG, gee, reg
3 packages and 0 specfiles checked; 0 errors, 12 warnings.




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


Source checksums
----------------
https://github.com/bids-standard/pybv/archive/v0.6.0/pybv-0.6.0.tar.gz :
  CHECKSUM(SHA256) this package     : 0d0e74479b4d71f928c4c91af8f075cdf66e793959425482da13e4a096f54523
  CHECKSUM(SHA256) upstream package : 0d0e74479b4d71f928c4c91af8f075cdf66e793959425482da13e4a096f54523


Requires
--------
python3-pybv (rpmlib, GLIBC filtered):
    python(abi)
    python3.10dist(numpy)

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



Provides
--------
python3-pybv:
    python-pybv
    python3-pybv
    python3.10-pybv
    python3.10dist(pybv)
    python3dist(pybv)

python-pybv-doc:
    python-pybv-doc
    python3-pybv-doc
    python3.10-pybv-doc



Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 2009827
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Shell-api, Generic
Disabled plugins: Ocaml, Java, SugarActivity, Perl, C/C++, Haskell, fonts, R, PHP
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Comment 2 Aniket Pradhan 2021-10-24 10:38:58 UTC
Hi Ben!

Really sorry for the delay... I had to remove the documentation in all because of issues in the generated tex file. It is not much of a loss, to be frank, since the documentation is generally available online. I have updated the sources in the above links (pasting them below too, for ease).

> Spec URL: https://major.fedorapeople.org/python-pybv/python-pybv.spec
> SRPM URL: https://major.fedorapeople.org/python-pybv/python-pybv-0.6.0-1.fc34.src.rpm

Let me know if other changes are required.

Comment 3 Ben Beasley 2021-10-24 12:48:07 UTC
Looks great! Package approved. Full re-review below.


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

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



===== 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", "BSD (3 clause)", "*No copyright* BSD
     (3 clause)". 19 files have unknown license. Detailed output of
     licensecheck in /home/reviewer/2009827-python-pybv/licensecheck.txt
[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.
[-]: 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
     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

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.
[ ]: 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).
[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-pybv-0.6.0-1.fc36.noarch.rpm
          python-pybv-0.6.0-1.fc36.src.rpm
python3-pybv.noarch: W: spelling-error %description -l en_US electrophysiology -> electrocardiography
python3-pybv.noarch: W: spelling-error %description -l en_US vhdr -> HDTV
python3-pybv.noarch: W: spelling-error %description -l en_US vmrk -> murk
python3-pybv.noarch: W: spelling-error %description -l en_US eeg -> EEG, gee, reg
python-pybv.src: W: spelling-error %description -l en_US electrophysiology -> electrocardiography
python-pybv.src: W: spelling-error %description -l en_US vhdr -> HDTV
python-pybv.src: W: spelling-error %description -l en_US vmrk -> murk
python-pybv.src: W: spelling-error %description -l en_US eeg -> EEG, gee, reg
2 packages and 0 specfiles checked; 0 errors, 8 warnings.




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


Source checksums
----------------
https://github.com/bids-standard/pybv/archive/v0.6.0/pybv-0.6.0.tar.gz :
  CHECKSUM(SHA256) this package     : 0d0e74479b4d71f928c4c91af8f075cdf66e793959425482da13e4a096f54523
  CHECKSUM(SHA256) upstream package : 0d0e74479b4d71f928c4c91af8f075cdf66e793959425482da13e4a096f54523


Requires
--------
python3-pybv (rpmlib, GLIBC filtered):
    python(abi)
    python3.10dist(numpy)



Provides
--------
python3-pybv:
    python-pybv
    python3-pybv
    python3.10-pybv
    python3.10dist(pybv)
    python3dist(pybv)



Generated by fedora-review 0.7.6 (b083f91) last change: 2020-11-10
Command line :/usr/bin/fedora-review -b 2009827
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Generic, Shell-api
Disabled plugins: Java, Haskell, Perl, PHP, C/C++, Ocaml, SugarActivity, fonts, R
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH

Comment 4 Ben Beasley 2021-10-24 12:50:10 UTC
If you’re interested in converting this or any of your other Python packages to the “new guidelines” (pyproject-rpm-macros), I’m happy to help by answering questions or offering a PR.

Comment 5 Aniket Pradhan 2021-10-24 14:37:36 UTC
Ahh, sure... I'll try converting this package to use the pyproject-rpm-macros...

Last I remember they worked only for projects using pyproject.toml file, but I have been out of touch lately, and there has been amazing development on it.

Comment 6 Gwyn Ciesla 2021-10-24 15:45:44 UTC
(fedscm-admin):  The Pagure repository was created at https://src.fedoraproject.org/rpms/python-pybv

Comment 7 Ben Beasley 2021-10-25 20:11:07 UTC
(In reply to Aniket Pradhan from comment #5)
> Ahh, sure... I'll try converting this package to use the
> pyproject-rpm-macros...
> 
> Last I remember they worked only for projects using pyproject.toml file, but
> I have been out of touch lately, and there has been amazing development on
> it.

They work quite well for all but the most exotic Python packages, pyproject.toml or not. The new Python packaging guidelines (https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/) require them. The old Python guidelines (https://docs.fedoraproject.org/en-US/packaging-guidelines/Python_201x/) are considered deprecated, but packaging under them is still allowable.

The few packages I have not yet been able to convert are generally those that build multiple Python packages with distinct metadata from a single source archive (https://src.fedoraproject.org/rpms/python-opentelemetry, https://src.fedoraproject.org/rpms/grpc, https://src.fedoraproject.org/rpms/gaupol). Packages that are still using distutils instead of setuptools or a PEP517 build system like flit/poetry/build are extremely rare now (gaupol is one), but they wouldn’t work either.

Not having to manually update BuildRequires all the time is a great selling point!

Comment 8 Fedora Update System 2021-11-04 17:05:17 UTC
FEDORA-2021-744bd88563 has been submitted as an update to Fedora 35. https://bodhi.fedoraproject.org/updates/FEDORA-2021-744bd88563

Comment 9 Fedora Update System 2021-11-04 17:05:18 UTC
FEDORA-2021-8977ec11b1 has been submitted as an update to Fedora 34. https://bodhi.fedoraproject.org/updates/FEDORA-2021-8977ec11b1

Comment 10 Fedora Update System 2021-11-05 01:22:11 UTC
FEDORA-2021-744bd88563 has been pushed to the Fedora 35 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2021-744bd88563 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-744bd88563

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

Comment 11 Fedora Update System 2021-11-05 01:38:22 UTC
FEDORA-2021-8977ec11b1 has been pushed to the Fedora 34 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2021-8977ec11b1 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-8977ec11b1

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

Comment 12 Fedora Update System 2021-11-13 01:06:37 UTC
FEDORA-2021-744bd88563 has been pushed to the Fedora 35 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 13 Fedora Update System 2021-11-13 01:13:02 UTC
FEDORA-2021-8977ec11b1 has been pushed to the Fedora 34 stable repository.
If problem still persists, please make note of it in this bug report.


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