Change README and CHANGELOG, prepare for pypi release

Author: Jan Ludwiczak

CHANGELOG.md

@@ -1,6 +1,15 @@
 ## Changelog
 
-### v.1.1
+### v2.0
+- Retrained with the updated dataset based on *[SamCC-Turbo](https://github.com/labstructbioinf/samcc_turbo)* labels.
+- Faster inference time by applying *[SeqVec](https://github.com/rostlab/SeqVec)* embeddings instead of *psiblast* profiles.
+- Heptad register prediction (*a* and *d* core positions).
+- No maximum sequence length limit.
+- Convenient interface for using *DeepCoil* within python scripts.
+- Automated peak detection for improved output readability.
+- Simplified installation with *pip*.
+
+### v1.1
 Added output filtering options <code>-min_residue_score</code> and <code>-min_segment_length</code>.
 
 ### v1.0

README.md

@@ -4,14 +4,15 @@
 
 ## **Fast and accurate prediction of coiled coil domains in protein sequences**
 ### **New in version 2.0** ###
+- Retrained with the updated dataset based on *[SamCC-Turbo](https://github.com/labstructbioinf/samcc_turbo)* labels.
 - Faster inference time by applying *[SeqVec](https://github.com/rostlab/SeqVec)* embeddings instead of *psiblast* profiles.
-- Additional heptad predictions (*a* and *d* core positions).
+- Heptad register prediction (*a* and *d* core positions).
 - No maximum sequence length limit.
 - Convenient interface for using *DeepCoil* within python scripts.
 - Automated peak detection for improved output readability.
 - Simplified installation with *pip*.
 
-Older DeepCoil versions are available [here](https://github.com/labstructbioinf/DeepCoil/releases). 
+**Older DeepCoil versions are available [here](https://github.com/labstructbioinf/DeepCoil/releases).**
 
 ### **Requirements and installation** ###
 DeepCoil requires `python>=3.6.1` and `pip>=19.0`. Other requirements are specified in the `requirements.txt` file.
@@ -40,6 +41,13 @@ deepcoil [-h] -i FILE [-out_path DIR] [-n_cpu NCPU] [--gpu] [--plot]
 
 In a rare case of `deepcoil` being not available in your `PATH` after installation please look in the `$HOME/.local/bin/` or other system specific `pip` directory.
 
+Description of columns in output file:
+- **`aa`** - amino acid in the input protein sequence
+- **`cc`** - sharpened coiled coil propensity
+- **`raw_cc`** - raw coiled coil propensity
+- **`prob_a`** - probability of *a* core position
+- **`prob_d`** - probability of *d* core position
+
 #### Running DeepCoil within script:
 
 ```python

setup.py

@@ -1,12 +1,17 @@
 from setuptools import setup, find_packages
 
-VERSION = '2.0rc1'
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+VERSION = '2.0'
 with open('requirements.txt') as f:
       install_reqs = f.read().splitlines()
 
 setup(name='deepcoil',
       version=VERSION,
-      description='Fast and accurate prediction of coiled coil domains in protein sequences.',
+      description='Fast and accurate prediction of coiled coil domains in protein sequences',
+      long_description=long_description,
+      long_description_content_type="text/markdown",
       author='Jan Ludwiczak',
       author_email='[email protected]',
       url='https://github.com/labstructbioinf/deepcoil',