Bug#996921: Please help fixing build time test (Was: Bug#996921: RFA: unifrac)
Hi Andreas, Andreas Tille, on 2022-11-16: > Ahhh, that's a different one and should be fixed now. The real issue > with autopkgtest is: > > autopkgtest [20:00:40]: test run-unit-test: [--- > Test 4 -- Unifrac python tests > unifrac (unittest.loader._FailedTest.unifrac) ... ERROR > > == > ERROR: unifrac (unittest.loader._FailedTest.unifrac) > -- > ImportError: Failed to import test module: unifrac > Traceback (most recent call last): > File "/usr/lib/python3.11/unittest/loader.py", line 440, in _find_test_path > package = self._get_module_from_name(name) > > File "/usr/lib/python3.11/unittest/loader.py", line 350, in > _get_module_from_name > __import__(name) > File "/tmp/autopkgtest.FVEVf1/tree/unifrac/__init__.py", line 30, in > > from unifrac._api import ssu, faith_pd, ssu_to_file, ssu_inmem > ModuleNotFoundError: No module named 'unifrac._api' This one looks to have been caused by python3 grabbing the unifrac/ directory instead of fetching the module from its /usr/lib location. I have pushed a fix on salsa. Have a good evening, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. On air: Bjørn Riis - Lay Me Down signature.asc Description: PGP signature
Bug#996921: Please help fixing build time test (Was: Bug#996921: RFA: unifrac)
Am Wed, Nov 16, 2022 at 08:25:29PM +0100 schrieb Étienne Mollier: > ModuleNotFoundError: No module named 'bp._bp' > > looks to be caused by python3-iow not being built for python3.11 > yet: > > $ python3.10 -c 'import bp' ; echo $? > 0 > > $ python3.11 -c 'import bp' ; echo $? > Traceback (most recent call last): > File "", line 1, in > File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in > > from ._bp import BP > ModuleNotFoundError: No module named 'bp._bp' > 1 Ahhh, that's a different one and should be fixed now. The real issue with autopkgtest is: autopkgtest [20:00:40]: test run-unit-test: [--- Test 4 -- Unifrac python tests unifrac (unittest.loader._FailedTest.unifrac) ... ERROR == ERROR: unifrac (unittest.loader._FailedTest.unifrac) -- ImportError: Failed to import test module: unifrac Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 440, in _find_test_path package = self._get_module_from_name(name) File "/usr/lib/python3.11/unittest/loader.py", line 350, in _get_module_from_name __import__(name) File "/tmp/autopkgtest.FVEVf1/tree/unifrac/__init__.py", line 30, in from unifrac._api import ssu, faith_pd, ssu_to_file, ssu_inmem ModuleNotFoundError: No module named 'unifrac._api' -- Ran 1 test in 0.000s FAILED (errors=1) autopkgtest [20:00:42]: test run-unit-test: ---] Kind regards Andreas. -- http://fam-tille.de
Bug#996921: Please help fixing build time test (Was: Bug#996921: RFA: unifrac)
Hi Andreas, Andreas Tille, on 2022-11-16: > Am Thu, Oct 21, 2021 at 01:25:52AM +0530 schrieb Nilesh Patra: > > I currently have no interest in maintaining unifrac, which > > is a bit cumbersome to maintain (the new update being an example) > > and it doesn't motivate me enough to keep maintaining it. > > > > Should you feel motivated, feel free to adopt this one. > > Adopted and provided all new dependencies. Unfortunately there > is some remaining issue with the build time test I would welcome > some help[1] This: ModuleNotFoundError: No module named 'bp._bp' looks to be caused by python3-iow not being built for python3.11 yet: $ python3.10 -c 'import bp' ; echo $? 0 $ python3.11 -c 'import bp' ; echo $? Traceback (most recent call last): File "", line 1, in File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in from ._bp import BP ModuleNotFoundError: No module named 'bp._bp' 1 > [1] https://salsa.debian.org/med-team/unifrac/-/jobs/3523436 Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. signature.asc Description: PGP signature
Bug#996921: Please help fixing build time test (Was: Bug#996921: RFA: unifrac)
Hi, Am Thu, Oct 21, 2021 at 01:25:52AM +0530 schrieb Nilesh Patra: > I currently have no interest in maintaining unifrac, which > is a bit cumbersome to maintain (the new update being an example) > and it doesn't motivate me enough to keep maintaining it. > > Should you feel motivated, feel free to adopt this one. Adopted and provided all new dependencies. Unfortunately there is some remaining issue with the build time test I would welcome some help[1] Kind regards Andreas. [1] https://salsa.debian.org/med-team/unifrac/-/jobs/3523436 -- http://fam-tille.de
Bug#996921: RFA: unifrac
Package: wnpp Severity: normal X-Debbugs-Cc: debian-...@lists.debian.org Hi, I currently have no interest in maintaining unifrac, which is a bit cumbersome to maintain (the new update being an example) and it doesn't motivate me enough to keep maintaining it. Should you feel motivated, feel free to adopt this one. Package Description: --- High-performance phylogenetic diversity calculations --- The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac. This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation. Nilesh
