Update upstream source from tag 'upstream/0.2.1'

Update to upstream version '0.2.1'
with Debian dir 4c2ee76539cbe432bd883b9e52341cf2c652328c

10 files changed, 40 insertions, 84 deletions

diff --git a/PKG-INFO b/PKG-INFO
index 043b040..99c527a 100644
--- a/PKG-INFO
+++ b/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@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
diff --git a/README.md b/README.md
index f16c7b2..0122fc3 100644
--- a/README.md
+++ b/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:
diff --git a/pauvre.egg-info/PKG-INFO b/pauvre.egg-info/PKG-INFO
index 043b040..99c527a 100644
--- a/pauvre.egg-info/PKG-INFO
+++ b/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@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
diff --git a/pauvre.egg-info/requires.txt b/pauvre.egg-info/requires.txt
index f2e372a..2df747c 100644
--- a/pauvre.egg-info/requires.txt
+++ b/pauvre.egg-info/requires.txt
@@ -3,4 +3,4 @@ biopython>=1.68
 pandas>=0.20.1
 numpy>=1.12.1
 scipy
-sklearn
+scikit-learn
diff --git a/pauvre.egg-info/top_level.txt b/pauvre.egg-info/top_level.txt
index 68ebe9c..57f5848 100644
--- a/pauvre.egg-info/top_level.txt
+++ b/pauvre.egg-info/top_level.txt
@@ -1,2 +1 @@
 pauvre
-scripts
diff --git a/pauvre/marginplot.py b/pauvre/marginplot.py
index 1c24e57..53da1ae 100644
--- a/pauvre/marginplot.py
+++ b/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"]
diff --git a/pauvre/rcparams.py b/pauvre/rcparams.py
index fac7145..89a4b9e 100644
--- a/pauvre/rcparams.py
+++ b/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  })
+
diff --git a/pauvre/redwood.py b/pauvre/redwood.py
index 277a608..059440d 100644
--- a/pauvre/redwood.py
+++ b/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
diff --git a/pauvre/version.py b/pauvre/version.py
index 22ea753..200a6d2 100644
--- a/pauvre/version.py
+++ b/pauvre/version.py
@@ -1,3 +1,4 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "0.1924"
+__version__ = "0.2.1"
+
diff --git a/setup.py b/setup.py
index 3da3e10..7e38014 100755
--- a/setup.py
+++ b/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@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'],