[med-svn] [Git][med-team/python-pauvre][master] upstream patch fix kwargs

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / python-pauvre


Commits:
99a99a4a by Etienne Mollier at 2020-04-28T21:42:37+02:00
upstream patch fix kwargs

- - - - -


2 changed files:

- + debian/patches/fix-kwargs.patch
- debian/patches/series


Changes:

=====================================
debian/patches/fix-kwargs.patch
=====================================
@@ -0,0 +1,38 @@
+Description: fixed a small error with kwargs 
+ cherry picked from upstream, fixes a crash when running the provided test
+ suite:
+  plotting in the following window:
+          0 <= Q-score (x-axis) <= 14.0
+          0 <= length  (y-axis) <= 223383
+ .
+  Traceback (most recent call last):
+    File "/usr/bin/pauvre", line 11, in <module>
+      load_entry_point('pauvre==0.1924', 'console_scripts', 'pauvre')()
+    File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 630, in main
+      args.func(parser, args)
+    File "/usr/lib/python3/dist-packages/pauvre/pauvre_main.py", line 64, in run_subtool
+      submodule.run(args)
+    File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 403, in run
+      margin_plot(df=df.dropna(), **vars(args))
+    File "/usr/lib/python3/dist-packages/pauvre/marginplot.py", line 381, in margin_plot
+      if kwargs["BASENAME"] is None and not kwargs["path"] is None:
+  KeyError: 'path'
+Origin: upstream, https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a
+Forwarded: https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a
+Applied-Upstream: https://github.com/conchoecia/pauvre/commit/90fbe2f4c190ff897dfc8ae12971d5865682fc8a
+Last-Update: 2020-04-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pauvre.orig/pauvre/marginplot.py
++++ python-pauvre/pauvre/marginplot.py
+@@ -378,9 +378,7 @@
+             min_plot_qual, max_plot_qual, min_plot_length, max_plot_length),
+             file=stderr)
+     # Print image(s)
+-    if kwargs["BASENAME"] is None and not kwargs["path"] is None:
+-        file_base = kwargs["BASENAME"]
+-    elif kwargs["BASENAME"] is None:
++    if kwargs["BASENAME"] is None:
+         file_base = opath.splitext(opath.basename(kwargs["fastq"]))[0]
+     else:
+         file_base = kwargs["BASENAME"]


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ fix-scikit-learn-resource-load.patch
 2to3.patch
 typo-redwood.patch
 lsi-test-args.patch
+fix-kwargs.patch



View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/commit/99a99a4a6ebf702a7dfe355e621ba397a7bfdad0

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View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/commit/99a99a4a6ebf702a7dfe355e621ba397a7bfdad0
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