Upstream applied several patches
Andreas Tille
3 years ago
| 0 | Description: fixed a small error with kwargs | |
| 1 | cherry picked from upstream, fixes a crash when running the provided test | |
| 2 | suite: | |
| 3 | plotting in the following window: | |
| 4 | 0 <= Q-score (x-axis) <= 14.0 | |
| 5 | 0 <= length (y-axis) <= 223383 | |
| 6 | . | |
| 7 | Traceback (most recent call last): | |
| 8 | File "/usr/bin/pauvre", line 11, in <module> | |
| 9 | load_entry_point('pauvre==0.1924', 'console_scripts', 'pauvre')() | |
| 10 | File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 630, in main | |
| 11 | args.func(parser, args) | |
| 12 | File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 64, in run_subtool | |
| 13 | submodule.run(args) | |
| 14 | File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 403, in run | |
| 15 | margin_plot(df=df.dropna(), **vars(args)) | |
| 16 | File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 381, in margin_plot | |
| 17 | if kwargs["BASENAME"] is None and not kwargs["path"] is None: | |
| 18 | KeyError: 'path' | |
| 19 | Origin: upstream, https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a | |
| 20 | Forwarded: https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a | |
| 21 | Applied-Upstream: https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a | |
| 22 | Last-Update: 2020-04-28 | |
| 23 | --- | |
| 24 | This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ | |
| 25 | --- python-pauvre.orig/pauvre/marginplot.py | |
| 26 | +++ python-pauvre/pauvre/marginplot.py | |
| 27 | @@ -378,9 +378,7 @@ | |
| 28 | min_plot_qual, max_plot_qual, min_plot_length, max_plot_length), | |
| 29 | file=stderr) | |
| 30 | # Print image(s) | |
| 31 | - if kwargs["BASENAME"] is None and not kwargs["path"] is None: | |
| 32 | - file_base = kwargs["BASENAME"] | |
| 33 | - elif kwargs["BASENAME"] is None: | |
| 34 | + if kwargs["BASENAME"] is None: | |
| 35 | file_base = opath.splitext(opath.basename(kwargs["fastq"]))[0] | |
| 36 | else: | |
| 37 | file_base = kwargs["BASENAME"] |
| 0 | Description: require scikit-learn instead of sklearn | |
| 1 | This fixes a problem in pkg_resource loading when trying to start pauvre with | |
| 2 | the provided command line interface. See the following for more details: | |
| 3 | https://lists.debian.org/debian-python/2020/04/msg00146.html | |
| 4 | Not sure yet if this is Debian specific. If not it might be worth contacting | |
| 5 | upstream. | |
| 6 | Author: Etienne Mollier <etienne.mollier@mailoo.org> | |
| 7 | Forwarded: no | |
| 8 | Last-Update: 2020-04-27 | |
| 9 | --- | |
| 10 | This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ | |
| 11 | --- python-pauvre.orig/setup.py | |
| 12 | +++ python-pauvre/setup.py | |
| 13 | @@ -65,7 +65,7 @@ | |
| 14 | "pandas >= 0.20.1", | |
| 15 | "numpy >= 1.12.1", | |
| 16 | "scipy", | |
| 17 | - "sklearn" | |
| 18 | + "scikit-learn" | |
| 19 | ], | |
| 20 | entry_points={ | |
| 21 | 'console_scripts': ['pauvre=pauvre.pauvre_main:main'], |
| 0 | fix-scikit-learn-resource-load.patch | |
| 1 | 0 | 2to3.patch |
| 2 | typo-redwood.patch | |
| 3 | 1 | lsi-test-args.patch |
| 4 | fix-kwargs.patch |
| 0 | Description: p/redwood.py: fixed what looks like a typo | |
| 1 | this typo issued the following message during byte-compilation: | |
| 2 | . | |
| 3 | byte-compiling /mnt/data/emollier/debian/python-pauvre/debian/python3-pauvre/usr/lib/python3.8/dist-packages/pauvre/redwood.py to redwood.cpython-38.pyc | |
| 4 | File "/usr/lib/python3.8/dist-packages/pauvre/redwood.py", line 706 | |
| 5 | ifargs.BASENAME is None: | |
| 6 | ^ | |
| 7 | SyntaxError: invalid syntax | |
| 8 | Author: Etienne Mollier <etienne.mollier@mailoo.org> | |
| 9 | Bug: https://github.com/conchoecia/pauvre/pull/39 | |
| 10 | Applied-Upstream: https://github.com/conchoecia/pauvre/commit/6d55b8671b2797ae7ffeb8c8e9f2815851a4a3f8 | |
| 11 | Last-Update: 2020-05-01 | |
| 12 | --- | |
| 13 | This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ | |
| 14 | --- python-pauvre.orig/pauvre/redwood.py | |
| 15 | +++ python-pauvre/pauvre/redwood.py | |
| 16 | @@ -703,7 +703,7 @@ | |
| 17 | end = time.time() | |
| 18 | print(end - start) | |
| 19 | # Print image(s) | |
| 20 | - ifargs.BASENAME is None: | |
| 21 | + if args.BASENAME is None: | |
| 22 | file_base = "redwood" | |
| 23 | else: | |
| 24 | file_base = args.BASENAME |