From 93723f0535eb3683662bab0ccfe525e6474c5482 Mon Sep 17 00:00:00 2001
From: "Janne H. Korhonen" <janne.h.korhonen@gmail.com>
Date: Fri, 10 May 2019 15:51:52 +0200
Subject: [PATCH] tweaks to python setup, readme; need to test that the scripts
 offered by the pypi package work correctly

---
 python/readme.MD | 30 ++++++++++++++++++++++++------
 python/setup.py  | 12 ++++++++++++
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/python/readme.MD b/python/readme.MD
index 44fd77d..d94edde 100644
--- a/python/readme.MD
+++ b/python/readme.MD
@@ -6,11 +6,29 @@ Motif Occurrence Detection Suite
 https://www.cs.helsinki.fi/group/pssmfind/
 
 
-Getting Started
----------------
+Installing from PyPi
+--------------------
 
-Start by compiling the MOODS extensions and optionally installing
-the MOODS module to Python library path. Do one of the following:
+The easiest way to install MOODS is using pip:
+
+(a) Install the module to your local Python library path:
+
+    pip install --user moods-python
+
+(b) Install the module for all users:
+
+    pip install moods-python
+
+Installing the MOODS package from PyPi installs the `moods-dna` command to you
+Python path. Test it by running:
+
+    moods-dna --help
+
+
+Installing from Source
+----------------------
+
+Alternatively, you can install MOODS from the source package:
 
 (a) Compile the extensions in place and create a symlink under `scripts/`
 (if you just want to test things without installing to Python library path,
@@ -29,8 +47,8 @@ analysis):
 
     sudo python setup.py install
 
-In all cases, you can test MOODS by running the `moods_dna.py` script
-with the example data provided with the package:
+You can test MOODS by running the `moods_dna.py` script with
+the example data provided with the package:
 
     cd scripts/
     python moods_dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001
diff --git a/python/setup.py b/python/setup.py
index be7f054..a287250 100755
--- a/python/setup.py
+++ b/python/setup.py
@@ -5,6 +5,7 @@
 """
 
 from distutils.core import setup, Extension
+from os import path
 
 common_includes = ["core/"]
 common_compile_args = ['-march=native', '-O3', '-fPIC', '--std=c++11']
@@ -42,13 +43,24 @@
                            extra_compile_args=common_compile_args,
                            )
 
+
+
+this_directory = path.abspath(path.dirname(__file__))
+with open(path.join(this_directory, 'readme.MD'), encoding='utf-8') as f:
+    long_description = f.read()
+
 setup (name = 'MOODS-python',
        version = '1.9.4',
        description = 'MOODS: Motif Occurrence Detection Suite',
+       long_description = long_description,
+       long_description_content_type="text/markdown",
        maintainer = "Janne H. Korhonen",
        maintainer_email = "janne.h.korhonen@gmail.com",
        url='https://www.cs.helsinki.fi/group/pssmfind/',
        license = "GPLv3 / Biopython license",
        ext_modules = [tools_mod, scan_mod, parsers_mod],
        packages = ["MOODS"],
+       scripts=['scripts/moods-dna.py'],
+       classifiers=["Topic :: Scientific/Engineering :: Bio-Informatics"]
+       keywords="PWM, PSSM, motif scan"
 )
\ No newline at end of file