addressing bits of housekeeping

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 ## Version 3.0beta
 
-HistoQC has been nicely packaged thanks to ap--!
+HistoQC has been nicely packaged thanks to [Andreas Poehlmann](https://github.com/ap--) _(Machine Learning Research - Bayer AG)_ !
 
 As a result a lot of quality of live improvements have now been implemented.
 

Readme.md

@@ -111,7 +111,11 @@ optional arguments:
 If you would like, you can install HistoQC into your system by using 
 
 ```
-python setup.py install
+git clone https://github.com/choosehappy/HistoQC.git
+cd HistoQC
+python -m pip install --upgrade pip  # (optional) upgrade pip to newest version
+pip install -r requirements.txt      # install pinned versions of packages
+pip install .
 ```
 
 Installed or simply git-cloned, a typical command line for running the tool thus looks like:

histoqc/__main__.py

@@ -30,7 +30,7 @@ def main(argv=None):
     if argv is None:
         argv = sys.argv[1:]
 
-    parser = argparse.ArgumentParser(description='')
+    parser = argparse.ArgumentParser(prog="histoqc", description='Run HistoQC main quality control pipeline for digital pathology images')
     parser.add_argument('input_pattern',
                         help="input filename pattern (try: *.svs or target_path/*.svs ),"
                              " or tsv file containing list of files to analyze",

histoqc/config/__main__.py

@@ -9,7 +9,7 @@ def main(argv=None):
     if argv is None:
         argv = sys.argv[1:]
 
-    parser = argparse.ArgumentParser(description="show example config")
+    parser = argparse.ArgumentParser(prog="histoqc.config",description="Show example configuration files")
     parser.add_argument('--list',
                         action='store_true',
                         help='list available configs')

histoqc/ui/__main__.py

@@ -11,7 +11,7 @@ def main(argv=None):
     if argv is None:
         argv = sys.argv[1:]
 
-    parser = argparse.ArgumentParser()
+    parser = argparse.ArgumentParser(prog="histoqc.ui",description="launch server for result viewing in user interface")
     parser.add_argument('--bind', '-b', metavar='ADDRESS',
                         default='0.0.0.0',
                         help='Specify alternate bind address '

setup.cfg

@@ -43,6 +43,7 @@ install_requires =
     scikit-learn
     scipy
     openslide-python
+    dill
 
 [options.extras_require]
 tests =