[Bug 2265851] Review Request: python-trx-python - Experiments with new file format for tractography

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https://bugzilla.redhat.com/show_bug.cgi?id=2265851



--- Comment #2 from Ben Beasley <code@xxxxxxxxxxxxxxxxxx> ---
I have a couple of “non-binding” suggestions, but the one thing I’d really like
to see fixed for approval is proper URLs and better attribution and license
accounting for the test data.

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

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


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

  OK: fedora-review is confused by rpmautospec.

- You might find it nicer to write

   
https://patch-diff.githubusercontent.com/raw/tee-ar-ex/trx-python/pull/75.patch

  as

    https://github.com/tee-ar-ex/trx-python/pull/75.patch

  or

    %{forgeurl}/pull/75.patch

  since it is more succinct and more easily associated with the original
  repository and PR. 

  No change is required.

- If you wanted to make this more concise,

    mkdir tests
    install -m 644 %{SOURCE1} tests
    install -m 644 %{SOURCE2} tests
    install -m 644 %{SOURCE3} tests
    install -m 644 %{SOURCE4} tests

  you could write something like

    install -p -m 644 -D -t tests %{SOURCE1} %{SOURCE2} %{SOURCE3} %{SOURCE4}

  No change is required.

- Since it’s possible to form URLs for the test sources, it would be better to
do so:

    Source1:        https://figshare.com/ndownloader/files/37624154#/DSI.zip
    Source2:       
https://figshare.com/ndownloader/files/37624148#/memmap_test_data.zip
    Source3:       
https://figshare.com/ndownloader/files/37624151#/trx_from_scratch.zip
    Source4:       
https://figshare.com/ndownloader/files/38146098#/gold_standard.zip

  More importantly, we need to audit these files and make sure they are under
  licenses that are allowed for content in Fedora. Something like this seems
  reasonable:

    # https://figshare.com/articles/dataset/DSI_zip/21215549
    # https://doi.org/10.6084/m9.figshare.21215549.v1
    # CC-BY-4.0
    Source1:        https://figshare.com/ndownloader/files/37624154#/DSI.zip
    # https://figshare.com/articles/dataset/memmap_test_data_zip/20020460
    # https://doi.org/10.6084/m9.figshare.20020460.v2
    # CC-BY-4.0
    Source2:       
https://figshare.com/ndownloader/files/37624148#/memmap_test_data.zip
    # https://figshare.com/articles/dataset/trx_from_scratch_zip/20020412
    # https://doi.org/10.6084/m9.figshare.20020412.v2
    # CC-BY-4.0
    Source3:       
https://figshare.com/ndownloader/files/37624151#/trx_from_scratch.zip
    # https://figshare.com/articles/dataset/gold_standard_zip/21520557
    # https://doi.org/10.6084/m9.figshare.21520557.v1
    # CC-BY-4.0
    Source4:       
https://figshare.com/ndownloader/files/38146098#/gold_standard.zip

===== 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: "BSD 2-Clause License", "Unknown or generated". 36 files have
     unknown license. Detailed output of licensecheck in
     /home/ben/Downloads/review/2265851-python-trx-python/licensecheck.txt
[x]: Package requires other packages for directories it uses.
     Note: No known owner of /usr/lib/python3.12, /usr/lib/python3.12/site-
     packages

     Diagnostic is spurious (fedora-review bug).

[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]: 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 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]: 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 1134 bytes in 1 files.
[x]: Packages must not store files under /srv, /opt or /usr/local

Python:
[-]: Binary eggs must be removed in %prep
     Note: Cannot find any build in BUILD directory (--prebuilt option?)
[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

===== 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.

     (tests pass)

[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[!]: SourceX tarball generation or download is documented.
     Note: Package contains tarball without URL, check comments

     Test data sources should be better-documented; see Issues.

[-]: 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.
[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-trx-python-0.2.9-2.fc41.noarch.rpm
          python-trx-python-0.2.9-2.fc41.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/tmp3phrncu8')]
checks: 32, packages: 2

python-trx-python.src: E: spelling-error ('tractography', 'Summary(en_US)
tractography -> cryptography, cartography, chromatography')
python-trx-python.src: E: spelling-error ('tractography', '%description -l
en_US tractography -> cryptography, cartography, chromatography')
python3-trx-python.noarch: E: spelling-error ('tractography', 'Summary(en_US)
tractography -> cryptography, cartography, chromatography')
python3-trx-python.noarch: E: spelling-error ('tractography', '%description -l
en_US tractography -> cryptography, cartography, chromatography')
python-trx-python.spec: W: patch-not-applied Patch0:
https://patch-diff.githubusercontent.com/raw/tee-ar-ex/trx-python/pull/78.patch
python-trx-python.spec: W: invalid-url Source4: gold_standard.zip
python-trx-python.spec: W: invalid-url Source3: trx_from_scratch.zip
python-trx-python.spec: W: invalid-url Source2: memmap_test_data.zip
python-trx-python.spec: W: invalid-url Source1: DSI.zip
===================================================== 2 packages and 0
specfiles checked; 4 errors, 5 warnings, 10 filtered, 4 badness; has taken 1.4
s =====================================================




Rpmlint (installed packages)
----------------------------
============================ 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
checks: 32, packages: 1

python3-trx-python.noarch: E: spelling-error ('tractography', 'Summary(en_US)
tractography -> cryptography, cartography, chromatography')
python3-trx-python.noarch: E: spelling-error ('tractography', '%description -l
en_US tractography -> cryptography, cartography, chromatography')
 1 packages and 0 specfiles checked; 2 errors, 0 warnings, 6 filtered, 2
badness; has taken 0.1 s 



Source checksums
----------------
https://github.com/tee-ar-ex/trx-python/archive/0.2.9/trx-python-0.2.9.tar.gz :
  CHECKSUM(SHA256) this package     :
886a69e1f884536a91dd70ac203561e04eb7dcf3e2d83853cd1a24368499615d
  CHECKSUM(SHA256) upstream package :
886a69e1f884536a91dd70ac203561e04eb7dcf3e2d83853cd1a24368499615d


Requires
--------
python3-trx-python (rpmlib, GLIBC filtered):
    /usr/bin/python3
    python(abi)
    python3.12dist(deepdiff)
    python3.12dist(nibabel)
    python3.12dist(numpy)



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



Diff spec file in url and in SRPM
---------------------------------
---
/home/ben/Downloads/review/2265851-python-trx-python/srpm/python-trx-python.spec
   2024-02-26 13:15:08.256839838 -0500
+++
/home/ben/Downloads/review/2265851-python-trx-python/srpm-unpacked/python-trx-python.spec
  2024-02-23 19:00:00.000000000 -0500
@@ -1,2 +1,12 @@
+## START: Set by rpmautospec
+## (rpmautospec version 0.6.1)
+## 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 pypi_name trx-python
 %global forgeurl https://github.com/tee-ar-ex/trx-python
@@ -113,3 +123,9 @@

 %changelog
-%autochangelog
+## START: Generated by rpmautospec
+* Sat Feb 24 2024 Sandro <devel@xxxxxxxxxxxxx> - 0.2.9-2
+- Add tests and man pages
+
+* Sat Feb 24 2024 Sandro <devel@xxxxxxxxxxxxx> - 0.2.9-1
+- Initial package
+## END: Generated by rpmautospec


Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2265851 --mock-options=--dnf
Buildroot used: fedora-rawhide-x86_64
Active plugins: Shell-api, Generic, Python
Disabled plugins: fonts, Java, Haskell, R, Ocaml, C/C++, SugarActivity, PHP,
Perl
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH


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