Sci-biology/khmer and friends: version, EAPI, python-targets bumps

[AndrewAmmerlaan]

This is the last one for today 😄

[epsilon-0]

bz2file has a test available which I tried to run with

python_test() {
        distutils_install_for_testing
        ${EPYTHON} test_bz2file.py || die "tests failed for ${EPYTHON}"
}

The tests are failing with

Forcing test.
openpty failed: 'out of pty devices'
 * bz2file-0.98.tar.gz BLAKE2B SHA512 size ;-) ...                                                                                                     [ ok ]
>>> Unpacking source...
>>> Unpacking bz2file-0.98.tar.gz to /var/tmp/portage/dev-python/bz2file-0.98/work
>>> Source unpacked in /var/tmp/portage/dev-python/bz2file-0.98/work
>>> Preparing source in /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98 ...
 * python3_8: running distutils-r1_run_phase distutils-r1_python_compile
python3.8 setup.py build -j 2
running build
running build_py
copying bz2file.py -> /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/lib
warning: build_py: byte-compiling is disabled, skipping.

>>> Source compiled.
>>> Test phase: dev-python/bz2file-0.98
 * python3_8: running distutils-r1_run_phase python_test
python3.8 setup.py install --home=/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/test --install-lib=/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/test/lib --install-scripts=/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/test/scripts
running install
running build
running build_py
warning: build_py: byte-compiling is disabled, skipping.

running install_lib
copying /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/lib/bz2file.py -> /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/test/lib
warning: install_lib: byte-compiling is disabled, skipping.

running install_egg_info
Writing /var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98-python3_8/test/lib/bz2file-0.98-py3.8.egg-info
................................................E.................
======================================================================
ERROR: testWithoutThreading (__main__.BZ2FileTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_bz2file.py", line 504, in testWithoutThreading
    f.write(b"abc")
  File "/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98/bz2file.py", line 391, in write
    return len(data)
  File "/usr/lib/python3.8/_dummy_thread.py", line 129, in __exit__
    self.release()
  File "/usr/lib/python3.8/_dummy_thread.py", line 176, in release
    raise error
RuntimeError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "test_bz2file.py", line 504, in testWithoutThreading
    f.write(b"abc")
  File "/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98/bz2file.py", line 141, in close
    self._buffer_offset = 0
  File "/usr/lib/python3.8/_dummy_thread.py", line 129, in __exit__
    self.release()
  File "/usr/lib/python3.8/_dummy_thread.py", line 176, in release
    raise error
RuntimeError

----------------------------------------------------------------------
Ran 66 tests in 1.088s

FAILED (errors=1)
 * ERROR: dev-python/bz2file-0.98::science failed (test phase):
 *   tests failed for python3.8
 *
 * Call stack:
 *     ebuild.sh, line  125:  Called src_test
 *   environment, line 2968:  Called distutils-r1_src_test
 *   environment, line 1215:  Called _distutils-r1_run_foreach_impl 'python_test'
 *   environment, line  431:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2573:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2055:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2053:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test'
 *   environment, line  788:  Called distutils-r1_run_phase 'python_test'
 *   environment, line 1152:  Called python_test
 *   environment, line 2928:  Called die
 * The specific snippet of code:
 *       ${EPYTHON} test_bz2file.py || die "tests failed for ${EPYTHON}"
 *
 * If you need support, post the output of `emerge --info '=dev-python/bz2file-0.98::science'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/bz2file-0.98::science'`.
 * The complete build log is located at '/var/tmp/portage/dev-python/bz2file-0.98/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/bz2file-0.98/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98'
 * S: '/var/tmp/portage/dev-python/bz2file-0.98/work/bz2file-0.98'

[epsilon-0]

Error has been reported upstream already - nvawda/bz2file#7
Also seems like the package is no longer going to be maintained, which means this is not going to be fixed.
I will merge this with a patch which removes this test.

[AndrewAmmerlaan]

What about:

python_test() {
        distutils_install_for_testing
        pytest test_bz2file.py || die "tests failed for ${EPYTHON}"
}

or

python_test() {
        distutils_install_for_testing
        nosetest test_bz2file.py || die "tests failed for ${EPYTHON}"
}

Sometimes those work, sometimes adding PYTHONPATH="${S}" works. And sometimes the testsuite is just completely broken.

[AndrewAmmerlaan]

Error has been reported upstream already - nvawda/bz2file#7
Also seems like the package is no longer going to be maintained, which means this is not going to be fixed.
I will merge this with a patch which removes this test.

Hmm, that is unfortunate. It is a dependency of the other two packages at the moment, but if it is no longer going to be maintained it will likely not be a dependency in the future (hopefully) and the problem will fix itself.

[epsilon-0]

Thanks a lot :D