| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 0001-t-test_sequence.py.patch | fix test_seq_by_index failure. The way pyfaidx is called to produce the reference object at the negative index is somehow broken (at least with pyfaidx 0.7.1 in Debian sid) and raises a possibly undue test error: . ERROR: test_seq_by_index (tests.test_sequence.SequenceTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/pyfastx-LEa3AU/pyfastx-0.8.4/tests/test_sequence.py", line 54, in test_seq_by_index expect = self.faidx[idx][:] File "/usr/lib/python3/dist-packages/pyfaidx/__init__.py", line 1099, in __getitem__ rname = next(islice(self.records.keys(), rname, None)) ValueError: Indices for islice() must be None or an integer: 0 <= x <= sys.maxsize. . This may be a problem in pyfaidx actually. Manually implementing the negative index wrap around solves the problem and allows us to proceed to the actual negative index test on pyfastx (which works). |
Étienne Mollier <emollier@debian.org> | yes | 2022-11-19 | ||
| use_debian_packaged_components.patch | do not try to download various packaged components. This change is to accomodate Debian specific build context. | Andreas Tille <tille@debian.org> | not-needed | 2025-02-05 | ||
| build-options.patch | facilitate cascading build options. The default behavior of upstream's setup.py causes build options to be dropped. This change facilitates injection of Debian's build options. In the present case, this is notably useful to restore support for debug symbols, but there seems to still be missing items to ensure full source fortification. . Forwarding is deemed not needed as it could be deemed intrusive and error prone outside Debian context. |
Étienne Mollier <emollier@debian.org> | not-needed | 2025-02-05 |