Upstream applied several patches

4 files changed, 0 insertions, 88 deletions

diff --git a/debian/patches/fix-kwargs.patch b/debian/patches/fix-kwargs.patch
deleted file mode 100644
index ff49ada..0000000
--- a/debian/patches/fix-kwargs.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-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"]
diff --git a/debian/patches/fix-scikit-learn-resource-load.patch b/debian/patches/fix-scikit-learn-resource-load.patch
deleted file mode 100644
index 0cb4c6b..0000000
--- a/debian/patches/fix-scikit-learn-resource-load.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Description: require scikit-learn instead of sklearn
- This fixes a problem in pkg_resource loading when trying to start pauvre with
- the provided command line interface.  See the following for more details:
-     https://lists.debian.org/debian-python/2020/04/msg00146.html
- Not sure yet if this is Debian specific.  If not it might be worth contacting
- upstream.
-Author: Etienne Mollier <etienne.mollier@mailoo.org>
-Forwarded: no
-Last-Update: 2020-04-27
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pauvre.orig/setup.py
-+++ python-pauvre/setup.py
-@@ -65,7 +65,7 @@
-           "pandas >= 0.20.1",
-           "numpy >= 1.12.1",
-           "scipy",
--          "sklearn"
-+          "scikit-learn"
-       ],
-       entry_points={
-           'console_scripts': ['pauvre=pauvre.pauvre_main:main'],
diff --git a/debian/patches/series b/debian/patches/series
index 7421171..c1f6c9b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,2 @@
-fix-scikit-learn-resource-load.patch
 2to3.patch
-typo-redwood.patch
 lsi-test-args.patch
-fix-kwargs.patch
diff --git a/debian/patches/typo-redwood.patch b/debian/patches/typo-redwood.patch
deleted file mode 100644
index 71a33f1..0000000
--- a/debian/patches/typo-redwood.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Description: p/redwood.py: fixed what looks like a typo
- this typo issued the following message during byte-compilation:
- .
-  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
-    File "/usr/lib/python3.8/dist-packages/pauvre/redwood.py", line 706
-      ifargs.BASENAME is None:
-                             ^
-  SyntaxError: invalid syntax
-Author: Etienne Mollier <etienne.mollier@mailoo.org>
-Bug: https://github.com/conchoecia/pauvre/pull/39
-Applied-Upstream: https://github.com/conchoecia/pauvre/commit/6d55b8671b2797ae7ffeb8c8e9f2815851a4a3f8
-Last-Update: 2020-05-01
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-pauvre.orig/pauvre/redwood.py
-+++ python-pauvre/pauvre/redwood.py
-@@ -703,7 +703,7 @@
-     end = time.time()
-     print(end - start)
-     # Print image(s)
--    ifargs.BASENAME is None:
-+    if args.BASENAME is None:
-         file_base = "redwood"
-     else:
-         file_base = args.BASENAME