Debian Patches
Status for scoary/1.6.16-10
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| python3.11.patch | fix invalid argument in open mode past python3.11. Since python3, the universal newline mode 'U' has no effects. Since python3.11, that mode is obsolete and its use raises: Command: scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exa mpledata/Tetracycline_resistance.csv -o Test1 --no-time Traceback (most recent call last): File "/<<PKGBUILDDIR>>/scoary.py", line 25, in <module> methods.main() File "/<<PKGBUILDDIR>>/scoary/methods.py", line 184, in main with open(args.genes, "rU") as genes, \ ^^^^^^^^^^^^^^^^^^^^^^ ValueError: invalid mode: 'rU' |
Étienne Mollier <emollier@debian.org> | yes | 2022-12-07 | ||
| scipy-1.12.0.patch | fix build time test failure with scipy 1.12.0. Deprecated function scipy.stats.binom_test[1] expired in scipy 1.12.0 to be replaced by scipy.stats.binomtest[2]. This patch is a quick fix to port to the newer API. Error handling revolving around the binomial test might make less sense now though, but it's left to keep the change relatively targeted. . [1]: https://docs.scipy.org/doc/scipy-1.11.0/reference/generated/scipy.stats.binom_test.html#scipy.stats.binom_test [2]: https://docs.scipy.org/doc/scipy-1.12.0/reference/generated/scipy.stats.binomtest.html#scipy.stats.binomtest |
Étienne Mollier <emollier@debian.org> | yes | debian | 2024-05-29 | |
| remove_six.patch | ete3 does not need six anymore for a long time | Alexandre Detiste <tchet@debian.org> | yes | |||
| rm-pkg_resources.patch | workaround removal of pkg_resources. | Étienne Mollier <emollier@debian.org> | yes | debian upstream | 2024-10-16 | |
| syntax-warnings.patch | vcf2scoary.py: fix SyntaxWarnings. With contemporary Python versions like 3.13, Scoary emits the following warnings: . /usr/lib/python3/dist-packages/scoary/vcf2scoary.py:94: SyntaxWarning: "is not" with 'str' literal. Did you mean "!="? if args.types is not "ALL": /usr/lib/python3/dist-packages/scoary/vcf2scoary.py:172: SyntaxWarning: "is not" with 'str' literal. Did you mean "!="? if args.types is not "ALL": . Applying the hint resolves the issue. |
Étienne Mollier <emollier@debian.org> | yes | debian | 2024-12-02 |