[med-svn] [Git][med-team/python-pauvre][upstream] New upstream version 0.2.1
Andreas Tille
gitlab at salsa.debian.org
Sat May 2 10:26:26 BST 2020
Andreas Tille pushed to branch upstream at Debian Med / python-pauvre
Commits:
5b36a488 by Andreas Tille at 2020-05-02T10:04:18+02:00
New upstream version 0.2.1
- - - - -
10 changed files:
- PKG-INFO
- README.md
- 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:
=====================================
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/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc
--
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc
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