Bug 2303543 - Review Request: bids-schema - BIDS schema description
Summary: Review Request: bids-schema - BIDS schema description
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora 2303188
TreeView+ depends on / blocked
 
Reported: 2024-08-07 18:40 UTC by Ben Beasley
Modified: 2024-09-23 01:24 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-09-14 17:32:20 UTC
Type: ---
Embargoed:
sanjay.ankur: fedora-review+


Attachments (Terms of Use)

Description Ben Beasley 2024-08-07 18:40:03 UTC
Spec URL: https://music.fedorapeople.org/bids-schema.spec
SRPM URL: https://music.fedorapeople.org/bids-schema-0.10.0-1.fc40.src.rpm

Description:

Portions of the BIDS specification are defined using YAML files in order to
make the specification machine-readable.

Currently the portions of the specification that rely on this schema are:

  • the entity tables,
  • entity definitions,
  • filename templates,
  • metadata tables.

Any changes to the specification should be mirrored in the schema.

Fedora Account System Username: music

This also ships a Python library as python3-bidsschematools. I decided that the *schema*, not the Python library, was the “main” part of the package, which is why the source package is called bids-schema rather than python-bidsschematools. The Python library is shipped from the same source RPM because it is jointly versioned with the schema, the PyPI wheel bundles data from the schema, and both are released from the same git repo. Even if these were separate source packages, they would need to be carefully maintained as one. Shipping them from a single source package is easier and less error-prone.

This will be a neuro-sig package and is a dependency for the latest python-bids-validator, bug 2303188.

Comment 1 Ben Beasley 2024-08-07 18:53:34 UTC
This is spurious:

- Package must not depend on deprecated() packages.
  Note: python3-pytest7 is deprecated, you must not depend on it.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/deprecating-packages/

The diagnostic appears because python3-pytest and python3-pytest7 both Provide python3dist(pytest), and this package depends on python3dist(pytest) – but not specifically on python3-pytest7 or on pytest<8, so there is no problem.

Comment 2 Ben Beasley 2024-08-07 18:56:40 UTC
python3-bidsschematools.noarch: W: dangling-relative-symlink /usr/lib/python3.13/site-packages/bidsschematools/data/0.10.0 ../../../../../share/bids-schema/versions/0.10.0

This is OK because the symlink target is provided by the base bids-schema package, and python3-bidsschematools does have a fully-versioned dependency on that. If we install both packages in the mock chroot, we can see that the symbolic link does not dangle.

Comment 3 Ankur Sinha (FranciscoD) 2024-09-11 10:39:27 UTC
Looks very good. A few things that need tweaking perhaps:


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

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


Issues:
=======
- Package must not depend on deprecated() packages.
  Note: python3-pytest7 is deprecated, you must not depend on it.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/deprecating-packages/
^
This must be a false positive, the pacakge does not explicitly depend on pytest7

- Does the python3-bidsschematools sub-package need the MIT license tag added to it?

- A couple of the directories are perhaps unowned (see below).

- Upstream has made new releases :(

===== 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.
[?]: 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* Creative Commons
     Attribution 4.0", "MIT License", "*No copyright* MIT License". 488
     files have unknown license. Detailed output of licensecheck in
     /home/asinha/dump/fedora-reviews/2303543-bids-schema/licensecheck.txt

^
- Does the python3-bidsschematools sub-package need the MIT license tag added to it?

[x]: License file installed when any subpackage combination is installed.
[?]: Package requires other packages for directories it uses.
     Note: No known owner of /usr/share/doc/python3-bidsschematools,
     /usr/share/doc/bids-schema
^
I reckon we need to own the directories too?

[?]: Package must own all directories that it creates.
     Note: Directories without known owners: /usr/lib/python3.13/site-
     packages, /usr/lib/python3.13, /usr/share/doc/python3-bidsschematools,
     /usr/share/doc/bids-schema

^
See above

[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.
[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 51355 bytes in 2 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]: The License field must be a valid SPDX expression.
[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 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-bidsschematools+render , python3-bidsschematools+expressions
[x]: Package functions as described.

^
Tests all pass, imports all pass.

[?]: Latest version is packaged.
^
Upstream seems to have made a number of new releases---3 in one week :)
https://pypi.org/project/bidsschematools/#history

[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.
[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: bids-schema-0.10.0-1.fc42.noarch.rpm
          python3-bidsschematools-0.10.0-1.fc42.noarch.rpm
          python3-bidsschematools+render-0.10.0-1.fc42.noarch.rpm
          python3-bidsschematools+expressions-0.10.0-1.fc42.noarch.rpm
          bids-schema-0.10.0-1.fc42.src.rpm
=================================================================================== rpmlint session starts ===================================================================================
rpmlint: 2.5.0
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
rpmlintrc: [PosixPath('/tmp/tmphutrzjfe')]
checks: 32, packages: 5

python3-bidsschematools+expressions.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage')
python3-bidsschematools+expressions.noarch: E: spelling-error ('metapackage', '%description -l en_US metapackage -> meta package, meta-package, prepackage')
python3-bidsschematools+render.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage')
python3-bidsschematools+render.noarch: E: spelling-error ('metapackage', '%description -l en_US metapackage -> meta package, meta-package, prepackage')
python3-bidsschematools+expressions.noarch: W: no-documentation
python3-bidsschematools+render.noarch: W: no-documentation
bids-schema.spec:177: W: macro-in-comment %doc
bids-schema.spec: W: invalid-url Source3: bids-error-examples-ac0a2f58f34ce284847dde5bd3b90d7ea048c141-filtered.tar.zst
bids-schema.spec: W: invalid-url Source2: bids-examples-ad9db4bbae20f76ff9512932940a719b865e3d50-filtered.tar.zst
bids-schema.src: W: inconsistent-file-extension bids-error-examples-ac0a2f58f34ce284847dde5bd3b90d7ea048c141-filtered.tar.zst
bids-schema.src: W: inconsistent-file-extension bids-examples-ad9db4bbae20f76ff9512932940a719b865e3d50-filtered.tar.zst
python3-bidsschematools.noarch: W: dangling-relative-symlink /usr/lib/python3.13/site-packages/bidsschematools/data/0.10.0 ../../../../../share/bids-schema/versions/0.10.0
============================================= 5 packages and 0 specfiles checked; 4 errors, 8 warnings, 50 filtered, 4 badness; has taken 0.6 s ==============================================




Rpmlint (installed packages)
----------------------------
============================ rpmlint session starts ============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.13/site-packages/rpmlint/configdefaults.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: 32, packages: 4

python3-bidsschematools+render.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage')
python3-bidsschematools+render.noarch: E: spelling-error ('metapackage', '%description -l en_US metapackage -> meta package, meta-package, prepackage')
python3-bidsschematools+expressions.noarch: E: spelling-error ('Metapackage', 'Summary(en_US) Metapackage -> Meta package, Meta-package, Prepackage')
python3-bidsschematools+expressions.noarch: E: spelling-error ('metapackage', '%description -l en_US metapackage -> meta package, meta-package, prepackage')
python3-bidsschematools+render.noarch: W: no-documentation
python3-bidsschematools+expressions.noarch: W: no-documentation
python3-bidsschematools.noarch: W: dangling-relative-symlink /usr/lib/python3.13/site-packages/bidsschematools/data/0.10.0 ../../../../../share/bids-schema/versions/0.10.0
 4 packages and 0 specfiles checked; 4 errors, 3 warnings, 46 filtered, 4 badness; has taken 0.2 s 



Source checksums
----------------
https://github.com/bids-standard/bids-specification/archive/schema-0.10.0/bids-specification-schema-0.10.0.tar.gz :
  CHECKSUM(SHA256) this package     : 94bc203917b29e0de41a9aab326336134f20d44861ea8a043d42334e059076fd
  CHECKSUM(SHA256) upstream package : 94bc203917b29e0de41a9aab326336134f20d44861ea8a043d42334e059076fd


Requires
--------
bids-schema (rpmlib, GLIBC filtered):

python3-bidsschematools (rpmlib, GLIBC filtered):
    /usr/bin/python3
    bids-schema
    python(abi)
    python3.13dist(click)
    python3.13dist(jsonschema)
    python3.13dist(pyyaml)

python3-bidsschematools+render (rpmlib, GLIBC filtered):
    python(abi)
    python3-bidsschematools
    python3.13dist(markdown-it-py)
    python3.13dist(pandas)
    python3.13dist(tabulate)

python3-bidsschematools+expressions (rpmlib, GLIBC filtered):
    python(abi)
    python3-bidsschematools
    python3.13dist(pyparsing)



Provides
--------
bids-schema:
    bids-schema

python3-bidsschematools:
    python-bidsschematools
    python3-bidsschematools
    python3.13-bidsschematools
    python3.13dist(bidsschematools)
    python3dist(bidsschematools)

python3-bidsschematools+render:
    python-bidsschematools+render
    python3-bidsschematools+render
    python3.13-bidsschematools+render
    python3.13dist(bidsschematools[render])
    python3dist(bidsschematools[render])

python3-bidsschematools+expressions:
    python-bidsschematools+expressions
    python3-bidsschematools+expressions
    python3.13-bidsschematools+expressions
    python3.13dist(bidsschematools[expressions])
    python3dist(bidsschematools[expressions])



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2303543
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, Shell-api, Generic
Disabled plugins: C/C++, Haskell, Perl, SugarActivity, Java, Ocaml, R, PHP, fonts
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comment 4 Ben Beasley 2024-09-11 14:49:59 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #3)
> Looks very good. A few things that need tweaking perhaps:

Thanks for the review!

> Issues:
> =======
> - Package must not depend on deprecated() packages.
>   Note: python3-pytest7 is deprecated, you must not depend on it.
>   See: https://docs.fedoraproject.org/en-US/packaging-
>   guidelines/deprecating-packages/
> ^
> This must be a false positive, the pacakge does not explicitly depend on
> pytest7

Agreed.

> - Does the python3-bidsschematools sub-package need the MIT license tag
> added to it?

Definitely. Thanks for catching that.

> - A couple of the directories are perhaps unowned (see below).

Yes, I guess I need to explicitly own /usr/share/doc/python3-bidsschematools
and /usr/share/doc/bids-schema. /usr/lib/python3.13/site-packages and
/usr/lib/python3.13 are clearly false positives.

> - Upstream has made new releases :(

Will update.

Comment 7 Fedora Review Service 2024-09-12 00:44:39 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/8010425
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2303543-bids-schema/fedora-rawhide-x86_64/08010425-bids-schema/fedora-review/review.txt

Found issues:

- python3-pytest7 is deprecated, you must not depend on it.
  Read more: https://docs.fedoraproject.org/en-US/packaging-guidelines/deprecating-packages/

Please know that there can be false-positives.

---
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 8 Ankur Sinha (FranciscoD) 2024-09-14 11:58:55 UTC
Looks good XXX APPROVED XXX

Comment 9 Ben Beasley 2024-09-14 16:56:33 UTC
Thank you for the review!

https://release-monitoring.org/project/277776/

Comment 10 Fedora Admin user for bugzilla script actions 2024-09-14 16:57:05 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/bids-schema

Comment 11 Fedora Update System 2024-09-14 17:28:14 UTC
FEDORA-2024-d01e0e6459 (bids-schema-0.11.3-1.fc42) has been submitted as an update to Fedora 42.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-d01e0e6459

Comment 12 Fedora Update System 2024-09-14 17:32:20 UTC
FEDORA-2024-d01e0e6459 (bids-schema-0.11.3-1.fc42) has been pushed to the Fedora 42 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 13 Fedora Update System 2024-09-14 17:39:54 UTC
FEDORA-2024-d6d720c792 (bids-schema-0.11.3-1.fc41) has been submitted as an update to Fedora 41.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-d6d720c792

Comment 14 Fedora Update System 2024-09-14 17:58:22 UTC
FEDORA-2024-bfe18f6130 (bids-schema-0.11.3-1.fc40) has been submitted as an update to Fedora 40.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-bfe18f6130

Comment 15 Fedora Update System 2024-09-14 18:25:53 UTC
FEDORA-2024-e0851a691a (bids-schema-0.11.3-1.fc39) has been submitted as an update to Fedora 39.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-e0851a691a

Comment 16 Fedora Update System 2024-09-15 02:16:46 UTC
FEDORA-2024-d6d720c792 has been pushed to the Fedora 41 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-d6d720c792 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-d6d720c792

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

Comment 17 Fedora Update System 2024-09-15 12:14:15 UTC
FEDORA-2024-bfe18f6130 has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-bfe18f6130 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-bfe18f6130

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

Comment 18 Fedora Update System 2024-09-15 12:42:40 UTC
FEDORA-2024-e0851a691a 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-2024-e0851a691a \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-e0851a691a

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

Comment 19 Fedora Update System 2024-09-23 00:16:14 UTC
FEDORA-2024-d6d720c792 (bids-schema-0.11.3-1.fc41) has been pushed to the Fedora 41 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 20 Fedora Update System 2024-09-23 01:02:16 UTC
FEDORA-2024-e0851a691a (bids-schema-0.11.3-1.fc39) has been pushed to the Fedora 39 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 21 Fedora Update System 2024-09-23 01:24:27 UTC
FEDORA-2024-bfe18f6130 (bids-schema-0.11.3-1.fc40) has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.


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