| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 0001-t-test_sequence.py.patch | t/test_sequence.py: 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). |
=?utf-8?q?=C3=89tienne_Mollier?= <emollier@debian.org> | yes | 2022-11-19 | ||
| use_debian_packaged_indexed-gzip.patch | Do not try to download indexed-gzip since it is packagedIn file included from /build/pyfastx-0.9.1/src/fakeys.c:4: /build/pyfastx-0.9.1/src/util.h:7:10: fatal error: zran.h: No such file or directory 7 | #include "zran.h" | ^~~~~~~~ compilation terminated. |
Andreas Tille <tille@debian.org> | not-needed | 2023-02-03 | ||
| use_debian_packaged_zlib.patch | prevent the download of zlib at build time. | Étienne Mollier <emollier@debian.org> | not-needed | 2023-11-28 |