Bug 2270968 - Review Request: python-python-fcl - Python bindings for the Flexible Collision Library
Summary: Review Request: python-python-fcl - Python bindings for the Flexible Collisio...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
unspecified
medium
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2024-03-22 11:24 UTC by Ben Beasley
Modified: 2024-05-30 01:21 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-05-21 17:08:10 UTC
Type: Bug
Embargoed:
sanjay.ankur: fedora-review+


Attachments (Terms of Use)

Description Ben Beasley 2024-03-22 11:24:04 UTC
Spec URL: https://music.fedorapeople.org/python-python-fcl.spec
SRPM URL: https://music.fedorapeople.org/python-python-fcl-0.7.0.6-1.fc39.src.rpm

Description:

Python-FCL is an (unofficial) Python interface for the Flexible Collision
Library (FCL), an excellent C++ library for performing proximity and collision
queries on pairs of geometric models.

This package supports three types of proximity queries for pairs of geometric
models:

  • Collision Detection: Detecting whether two models overlap (and optionally
    where).
  • Distance Computation: Computing the minimum distance between a pair of
    models.
  • Continuous Collision Detection: Detecting whether two models overlap during
    motion (and optionally the time of contact).

This package also supports most of FCL’s object shapes, including:

  • TriangleP
  • Box
  • Sphere
  • Ellipsoid
  • Capsule
  • Cone
  • Convex
  • Cylinder
  • Half-Space
  • Plane
  • Mesh
  • OcTree

Fedora Account System Username: music

The package name is awkward but logical, given this is https://pypi.org/project/python-fcl/; the canonical project name fcl, https://pypi.org/project/fcl/, belongs to a different and apparently defunct project. See https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_library_naming.

This has been patched out of the “recommends” extra of python-trimesh for some time. It will be a neuro-sig package.

Comment 1 Fedora Review Service 2024-03-22 12:03:43 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/7197624
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2270968-python-python-fcl/fedora-rawhide-x86_64/07197624-python-python-fcl/fedora-review/review.txt

Please take a look if any issues were found.


---
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https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
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Comment 2 Ben Beasley 2024-05-18 14:25:35 UTC
Thanks for taking the review. No big hurry on this one, but I wanted to make sure it hadn’t fallen off your radar.

Comment 3 Ankur Sinha (FranciscoD) 2024-05-18 20:32:34 UTC
Sorry Ben, I did run fedora-review on this one, but it erred out and I haven't had the chance to see why. I'll re-run it again on Monday and finish the review manually if I have to.

Comment 4 Ben Beasley 2024-05-19 11:39:20 UTC
I always have to add --mock-options=--dnf to fedora-review now. I don’t know if that will change when I get around to upgrading to F40 or not.

Comment 5 Ankur Sinha (FranciscoD) 2024-05-20 10:38:29 UTC
(Scrubbing my mock chroots fixed it. I should do that more often)

Looks very good. Just a clarification before approving:

- I see this in the build log:

```
[1/1] Cythonizing src/fcl/fcl.pyx
Traceback (most recent call last):
  File "/usr/lib/python3.12/site-packages/setuptools/config/expand.py", line 80, in __getattr__
    return next(
           ^^^^^
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/usr/lib/python3.12/site-packages/setuptools/config/expand.py", line 192, in read_attr
    return getattr(StaticModule(module_name, spec), attr_name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/setuptools/config/expand.py", line 86, in __getattr__
    raise AttributeError(f"{self.name} has no attribute {attr}") from e
AttributeError: fcl has no attribute __version__
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/builddir/build/BUILD/python-fcl-0.7.0.6/src/fcl/__init__.py", line 2, in <module>
    from .fcl import (
ModuleNotFoundError: No module named 'fcl.fcl'
Failed to import fcl.fcl. It is probably not correctly compiled.

```


Is this something to worry about?

- I noticed this in the build log too, but that isn't anything in the package:

```
+ /usr/bin/add-determinism --brp -j8 /builddir/build/BUILDROOT/python-python-fcl-0.7.0.6-1.fc41.x86_64
Cannot initialize handler pyc: ModuleNotFoundError: No module named 'marshalparser'
[src/multiprocess.rs:66:9] &cmd = Command {
    program: "/usr/bin/add-determinism",
    args: [
        "/usr/bin/add-determinism",
        "--socket",
        "3",
        "--brp",
        "--handler",
        "ar,jar,javadoc",
    ],
    env: CommandEnv {
        clear: false,
        vars: {
            "SOURCE_DATE_EPOCH": Some(
                "1716163200",
            ),
        },
    },
    create_pidfd: false,
}
Bye!
Bye!

```


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

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



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

C/C++:
[-]: Provides: bundled(gnulib) in place as required.
     Note: Sources not installed
[x]: Package does not contain kernel modules.
[-]: 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]: Package does not contain any libtool archives (.la)
[x]: Package contains no static executables.
[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", "BSD 3-Clause License", "MIT License",
     "BSD 2-Clause License", "BSD 3-Clause License [generated file]". 52
     files have unknown license. Detailed output of licensecheck in
     /home/asinha/dump/fedora-reviews/2270968-python-python-
     fcl/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[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.
[-]: 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]: Useful -debuginfo package or justification otherwise.
[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 21560 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: No rpmlint messages.
[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 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:
[-]: 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:
[x]: 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]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in
     python3-python-fcl
[x]: Package functions as described.
^
Tests are run

[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.
[-]: 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: No rpmlint messages.
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: python3-python-fcl-0.7.0.6-1.fc41.x86_64.rpm
          python-python-fcl-debugsource-0.7.0.6-1.fc41.x86_64.rpm
          python-python-fcl-0.7.0.6-1.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/tmp5wz9lz8x')]
checks: 32, packages: 3

===================================== 3 packages and 0 specfiles checked; 0 errors, 0 warnings, 13 filtered, 0 badness; has taken 0.9 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: 2

 2 packages and 0 specfiles checked; 0 errors, 0 warnings, 9 filtered, 0 badness; has taken 0.3 s 



Unversioned so-files
--------------------
python3-python-fcl: /usr/lib64/python3.12/site-packages/fcl/fcl.cpython-312-x86_64-linux-gnu.so

Source checksums
----------------
https://github.com/ambi-robotics/fcl/archive/v0.7.0/fcl-0.7.0.6.tar.gz :
  CHECKSUM(SHA256) this package     : 9199e0b7ef3f0556b301f3c449a628ec3455dd4781f9c839cedba1531f3dfa98
  CHECKSUM(SHA256) upstream package : 9199e0b7ef3f0556b301f3c449a628ec3455dd4781f9c839cedba1531f3dfa98
https://github.com/danfis/libccd/archive/v2.1/libccd-0.7.0.6.tar.gz :
  CHECKSUM(SHA256) this package     : 542b6c47f522d581fbf39e51df32c7d1256ac0c626e7c2b41f1040d4b9d50d1e
  CHECKSUM(SHA256) upstream package : 542b6c47f522d581fbf39e51df32c7d1256ac0c626e7c2b41f1040d4b9d50d1e
https://github.com/BerkeleyAutomation/python-fcl/archive/v0.7.0.6/python-fcl-0.7.0.6.tar.gz :
  CHECKSUM(SHA256) this package     : 6940a2baf2bbfd2110304f42fa0bf36c54c8de396d4ccce3aa2d58e1d1a83478
  CHECKSUM(SHA256) upstream package : 6940a2baf2bbfd2110304f42fa0bf36c54c8de396d4ccce3aa2d58e1d1a83478


Requires
--------
python3-python-fcl (rpmlib, GLIBC filtered):
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_3.3.1)(64bit)
    libm.so.6()(64bit)
    liboctomap.so.1.9()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    python(abi)
    python3.12dist(cython)
    python3.12dist(numpy)
    rtld(GNU_HASH)

python-python-fcl-debugsource (rpmlib, GLIBC filtered):



Provides
--------
python3-python-fcl:
    bundled(fcl)
    bundled(libccd)
    python-fcl
    python-python-fcl
    python3-fcl
    python3-python-fcl
    python3-python-fcl(x86-64)
    python3.12-fcl
    python3.12-python-fcl
    python3.12dist(python-fcl)
    python3dist(python-fcl)

python-python-fcl-debugsource:
    python-python-fcl-debugsource
    python-python-fcl-debugsource(x86-64)



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2270968
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, C/C++, Python, Shell-api
Disabled plugins: SugarActivity, Java, PHP, Ocaml, Perl, R, fonts, Haskell
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comment 6 Ben Beasley 2024-05-20 11:28:50 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #5)
> (Scrubbing my mock chroots fixed it. I should do that more often)
> 
> Looks very good. Just a clarification before approving:

Thanks for the review!

> - I see this in the build log:
> 
> ```
> [1/1] Cythonizing src/fcl/fcl.pyx
> […]
> ModuleNotFoundError: No module named 'fcl.fcl'
> Failed to import fcl.fcl. It is probably not correctly compiled.
> ```
> 
> Is this something to worry about?

This appears in %generate_buildrequires and in %build before the compiler is invoked. So I think it is fair to consider it noise. The compiled module imports correctly where it matters, in %check, installing it to a mock chroot and running “python3 -c 'import fcl.fcl'” works fine to, and after all, we should not be able to import the compiled extension until we have compiled it.

The import is attempted at all because of 

  [tool.setuptools.dynamic]
  version = {attr = "fcl.__version__"}

in pyproject.toml, and it succeeds – to the extent it imports the pure-Python portions of the package, which is enough to obtain the version number – just noisily. It would be nice if there were a clean way to silence the expected warning at this point in the build, but I can’t think of a tidy way, since even changing this to

  [tool.setuptools.dynamic]
  version = {attr = "fcl.version.__version__"}

causes fcl/__init__.py to be imported and triggering the message along the way.

> - I noticed this in the build log too, but that isn't anything in the
> package:
> 
> ```
> + /usr/bin/add-determinism --brp -j8
> /builddir/build/BUILDROOT/python-python-fcl-0.7.0.6-1.fc41.x86_64
> Cannot initialize handler pyc: ModuleNotFoundError: No module named
> 'marshalparser'
> […]

Thanks for noticing that. I’ll bring that up with the people working on https://fedoraproject.org/wiki/Changes/ReproduciblePackageBuilds. I don’t think the ModuleNotFoundError is expected.

Comment 7 Ben Beasley 2024-05-20 12:09:48 UTC
(In reply to Ben Beasley from comment #6)
> Thanks for noticing that. I’ll bring that up with the people working on
> https://fedoraproject.org/wiki/Changes/ReproduciblePackageBuilds. I don’t
> think the ModuleNotFoundError is expected.

Fabio Valentini reports, “yeah, marshalparser is not pulled in […] Recommends are not strong enough here,” and Neil Hanlon adds, “AFAIK the intention is for python-devel to declare a dep against Marshallparsher if not in bootstrap mode.” So this is known, and there is a plan to fix it.

Comment 8 Ankur Sinha (FranciscoD) 2024-05-20 12:22:18 UTC
Sounds good. XXX APPROVED XXX

Comment 9 Fedora Admin user for bugzilla script actions 2024-05-20 12:28:38 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/python-python-fcl

Comment 10 Fedora Update System 2024-05-21 17:04:09 UTC
FEDORA-2024-e09a7402b2 (python-python-fcl-0.7.0.6-4.fc41) has been submitted as an update to Fedora 41.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-e09a7402b2

Comment 11 Fedora Update System 2024-05-21 17:08:10 UTC
FEDORA-2024-e09a7402b2 (python-python-fcl-0.7.0.6-4.fc41) has been pushed to the Fedora 41 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 12 Fedora Update System 2024-05-21 21:05:00 UTC
FEDORA-2024-5e0b809a22 (python-python-fcl-0.7.0.6-4.fc40 and python-trimesh-4.4.0-4.fc40) has been submitted as an update to Fedora 40.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-5e0b809a22

Comment 13 Fedora Update System 2024-05-22 01:12:34 UTC
FEDORA-2024-5e0b809a22 has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-5e0b809a22`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-5e0b809a22

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

Comment 14 Fedora Update System 2024-05-30 01:21:54 UTC
FEDORA-2024-5e0b809a22 (python-python-fcl-0.7.0.6-4.fc40 and python-trimesh-4.4.0-4.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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