| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| debian_hdf5 | Use libhdf5-dev | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| debian_bwa | Use the libbwa-dev package | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| debian_fast5 | Use the libfast5-dev package | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| debian_pybind11 | Use the python3-pybind11 package | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| skip_read_until | Skip unpackaged (and optional) read-util Python module | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| debian_pdqsort | Use the Debian pdqsort-dev package | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| debian_toml11.patch | Use Debian packaged toml11 | Andreas Tille <tille@debian.org> | no | 2022-02-16 | ||
| syntax-warning.patch | Address a couple of Python SyntaxWarnings. Running uncalled with Python 3.13 raises a couple of syntax warning, reproducible for instance by running the example script: . $ cd example $ ./run_example.sh /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' port_re = re.compile("grpc_port = (\d+)") /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' device_re = re.compile("(device_id|instance) = ([^\s,]+)") […] . In addition, Debian bug #1087156 reported also another instance of the issue in the debug.py script: Setting up uncalled (2.3+ds-2) ... /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") . This change adjusts strings to become raw strings, in order to spare Python further attempts to interpret backslashed characters as escape sequences that are invalid. |
Étienne Mollier <emollier@debian.org> | yes | debian | 2024-12-03 |