[med-svn] [Git][med-team/python-pauvre][master] 5 commits: New upstream version 0.2.1
Andreas Tille
gitlab at salsa.debian.org
Sat May 2 10:26:21 BST 2020
Andreas Tille pushed to branch master at Debian Med / python-pauvre
Commits:
5b36a488 by Andreas Tille at 2020-05-02T10:04:18+02:00
New upstream version 0.2.1
- - - - -
3be6eb9b by Andreas Tille at 2020-05-02T10:04:19+02:00
Update upstream source from tag 'upstream/0.2.1'
Update to upstream version '0.2.1'
with Debian dir 4c2ee76539cbe432bd883b9e52341cf2c652328c
- - - - -
69dce03b by Andreas Tille at 2020-05-02T10:04:39+02:00
Import new upstream version
- - - - -
cbdef0f1 by Andreas Tille at 2020-05-02T10:08:39+02:00
Upstream applied several patches
- - - - -
a64c7f8c by Andreas Tille at 2020-05-02T10:12:23+02:00
Upload to unstable
- - - - -
15 changed files:
- PKG-INFO
- README.md
- debian/changelog
- − debian/patches/fix-kwargs.patch
- − debian/patches/fix-scikit-learn-resource-load.patch
- debian/patches/series
- − debian/patches/typo-redwood.patch
- pauvre.egg-info/PKG-INFO
- pauvre.egg-info/requires.txt
- pauvre.egg-info/top_level.txt
- pauvre/marginplot.py
- pauvre/rcparams.py
- pauvre/redwood.py
- pauvre/version.py
- setup.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,11 +1,11 @@
Metadata-Version: 1.2
Name: pauvre
-Version: 0.1924
+Version: 0.2.1
Summary: Tools for plotting Oxford Nanopore and other long-read data.
Home-page: https://github.com/conchoecia/pauvre
Author: Darrin Schultz
Author-email: dts at ucsc.edu
-License: GPLv3
+License: UNKNOWN
Description:
'pauvre' is a package for plotting Oxford Nanopore and other long read data.
The name means 'poor' in French, a play on words to the oft-used 'pore' prefix
@@ -17,10 +17,9 @@ Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
-Requires: python (>3.0)
-Provides: pauvre
Requires-Python: >=3
=====================================
README.md
=====================================
@@ -24,45 +24,6 @@ This package currently hosts four scripts for plotting and/or printing stats.
genomes with the fewest crossings-over. Input is one `.gff` file
per circular genome and one directory of gene alignments.
-## Updates:
-- 20200215 - v0.1.924 - Made some minor updates to work with python 3.7 and the latest version of pandas,
-- 20171130 - v0.1.86 - some changes by @wdecoster to integrate `pauvre` into [nanoplot](https://github.com/wdecoster/NanoPlot),
- as well as some formatting changes that *may* make `pauvre` work better with python2.7. Adding Travis-CI functionality.
-- 20171025 - v0.1.83 - added some changes to make marginplot interface
- with @wdecoster's [nanoPlot](https://github.com/wdecoster/NanoPlot)
- package, and made `pauvre stats` only output data tables for
- filtered reads. `pauvre stats` also now has the `--filt_maxlen`,
- `--filt_maxqual`, `--filt_minlen`, and `--filt_minqual` options.
-- 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window.
- [See below for a demonstration.](#filter-reads-and-adjust-viewing-window) I added the following options:
-
-```
- --filt_maxlen FILT_MAXLEN
- This sets the max read length filter reads.
- --filt_maxqual FILT_MAXQUAL
- This sets the max mean read quality to filter reads.
- --filt_minlen FILT_MINLEN
- This sets the min read length to filter reads.
- --filt_minqual FILT_MINQUAL
- This sets the min mean read quality to filter reads.
- --plot_maxlen PLOT_MAXLEN
- Sets the maximum viewing area in the length dimension.
- --plot_maxqual PLOT_MAXQUAL
- Sets the maximum viewing area in the quality
- dimension.
- --plot_minlen PLOT_MINLEN
- Sets the minimum viewing area in the length dimension.
- --plot_minqual PLOT_MINQUAL
- Sets the minimum viewing area in the quality
- dimension.
-```
-- 20171014 - uploading information on `pauvre redwood` and `pauvre synteny` usage.
-- 20171012 - made `pauvre stats` more consistently produce useful histograms.
- `pauvre stats` now also calculates some statistics for different size ranges.
-- 20170529 - added automatic scaling to the input fastq file. It
- scales to show the highest read quality and the top 99th percentile
- of reads by length.
-
# Requirements
- You must have the following installed on your system to install this software:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-python-pauvre (0.1.924-1) unstable; urgency=medium
+python-pauvre (0.2.1-1) unstable; urgency=medium
* Initial release (Closes: #958951)
- -- Andreas Tille <tille at debian.org> Wed, 29 Apr 2020 08:39:50 +0200
+ -- Andreas Tille <tille at debian.org> Sat, 02 May 2020 10:08:54 +0200
=====================================
debian/patches/fix-kwargs.patch deleted
=====================================
@@ -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"]
=====================================
debian/patches/fix-scikit-learn-resource-load.patch deleted
=====================================
@@ -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 at 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'],
=====================================
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
=====================================
debian/patches/typo-redwood.patch deleted
=====================================
@@ -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 at 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
=====================================
pauvre.egg-info/PKG-INFO
=====================================
@@ -1,11 +1,11 @@
Metadata-Version: 1.2
Name: pauvre
-Version: 0.1924
+Version: 0.2.1
Summary: Tools for plotting Oxford Nanopore and other long-read data.
Home-page: https://github.com/conchoecia/pauvre
Author: Darrin Schultz
Author-email: dts at ucsc.edu
-License: GPLv3
+License: UNKNOWN
Description:
'pauvre' is a package for plotting Oxford Nanopore and other long read data.
The name means 'poor' in French, a play on words to the oft-used 'pore' prefix
@@ -17,10 +17,9 @@ Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
-Requires: python (>3.0)
-Provides: pauvre
Requires-Python: >=3
=====================================
pauvre.egg-info/requires.txt
=====================================
@@ -3,4 +3,4 @@ biopython>=1.68
pandas>=0.20.1
numpy>=1.12.1
scipy
-sklearn
+scikit-learn
=====================================
pauvre.egg-info/top_level.txt
=====================================
@@ -1,2 +1 @@
pauvre
-scripts
=====================================
pauvre/marginplot.py
=====================================
@@ -378,9 +378,7 @@ def margin_plot(df, **kwargs):
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"]
=====================================
pauvre/rcparams.py
=====================================
@@ -5,21 +5,24 @@ from matplotlib import rcParams
def update_rcParams():
# This mpl style is from the UCSC BME163 class.
rcParams.update({
- 'font.size' : 8.0 ,
- 'font.sans-serif' : 'Arial' ,
- 'xtick.major.size' : 2 ,
- 'xtick.major.width' : 0.75 ,
- 'xtick.labelsize' : 8.0 ,
- 'xtick.direction' : 'out' ,
- 'ytick.major.size' : 2 ,
- 'ytick.major.width' : 0.75 ,
- 'ytick.labelsize' : 8.0 ,
- 'ytick.direction' : 'out' ,
- 'xtick.major.pad' : 2 ,
- 'xtick.minor.pad' : 2 ,
- 'ytick.major.pad' : 2 ,
- 'ytick.minor.pad' : 2 ,
- 'savefig.dpi' : 601 ,
- 'axes.linewidth' : 0.75 ,
- 'text.usetex' : False ,
- 'text.latex.unicode' : False })
+ 'font.size' : 8.0 ,
+ 'font.sans-serif' : 'Arial' ,
+ 'xtick.major.size' : 2 ,
+ 'xtick.major.width' : 0.75 ,
+ 'xtick.labelsize' : 8.0 ,
+ 'xtick.direction' : 'out' ,
+ 'ytick.major.size' : 2 ,
+ 'ytick.major.width' : 0.75 ,
+ 'ytick.labelsize' : 8.0 ,
+ 'ytick.direction' : 'out' ,
+ 'xtick.major.pad' : 2 ,
+ 'xtick.minor.pad' : 2 ,
+ 'ytick.major.pad' : 2 ,
+ 'ytick.minor.pad' : 2 ,
+ 'savefig.dpi' : 601 ,
+ 'axes.linewidth' : 0.75 ,
+ 'text.usetex' : False ,
+ "image.composite_image": False ,
+ "pdf.fonttype" : 42,
+ "ps.fonttype" : 42 })
+
=====================================
pauvre/redwood.py
=====================================
@@ -703,7 +703,7 @@ def redwood(args):
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
=====================================
pauvre/version.py
=====================================
@@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
-__version__ = "0.1924"
+__version__ = "0.2.1"
+
=====================================
setup.py
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
-# pauvre
+# pauvre
# Copyright (c) 2016-2020 Darrin T. Schultz.
#
# This file is part of pauvre.
@@ -28,11 +28,9 @@ from setuptools import setup, find_packages
version_py = os.path.join(os.path.dirname(__file__), 'pauvre', 'version.py')
version = open(version_py).read().strip().split('=')[-1].replace('"', '').strip()
-print(version)
setup(name='pauvre',
- requires=['python (>3.0)'],
version=version,
description='Tools for plotting Oxford Nanopore and other long-read data.',
long_description="""
@@ -42,7 +40,6 @@ setup(name='pauvre',
python 2. You can visit the gitub page for more detailed information here:
https://github.com/conchoecia/pauvre
""",
-
url='https://github.com/conchoecia/pauvre',
author='Darrin Schultz',
author_email='dts at ucsc.edu',
@@ -50,14 +47,13 @@ setup(name='pauvre',
'Development Status :: 2 - Pre-Alpha',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Programming Language :: Python :: 3',
- 'Programming Language :: Python :: 3.5',
+ 'Programming Language :: Python :: 3.6',
+ 'Programming Language :: Python :: 3.7',
'Operating System :: POSIX :: Linux',
'Topic :: Scientific/Engineering :: Bio-Informatics',
- 'Intended Audience :: Science/Research'
+ 'Intended Audience :: Science/Research',
],
- license='GPLv3',
- provides=['pauvre'],
- packages=find_packages() + ['scripts'],
+ packages=find_packages(),
python_requires='>=3',
install_requires=[
"matplotlib >= 2.0.2",
@@ -65,7 +61,7 @@ setup(name='pauvre',
"pandas >= 0.20.1",
"numpy >= 1.12.1",
"scipy",
- "sklearn"
+ "scikit-learn",
],
entry_points={
'console_scripts': ['pauvre=pauvre.pauvre_main:main'],
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/compare/76d4bedb92589a92b723b8f9483722845e85aab2...a64c7f8ce7a2f0d8947c1cc6606aea7e2ef21881
--
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/compare/76d4bedb92589a92b723b8f9483722845e85aab2...a64c7f8ce7a2f0d8947c1cc6606aea7e2ef21881
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