cosmetics for v0.15

Makefile

@@ -3,9 +3,6 @@
 test3:
 	python3 -m pytest -n 3 --disable-warnings --show-capture=no --cov=ngs_toolkit --cov-report xml tests/test_*.py --lf
 
-test2:
-	python2 -m pytest -n 3 --disable-warnings --show-capture=no --cov=ngs_toolkit --cov-report xml tests/test_*.py --lf
-
 test: test3
 
 coverage: test

README.md

@@ -4,7 +4,7 @@
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/30fcafc027e64b21bf9ddfe8d7f0ff3a)](https://app.codacy.com/app/afrendeiro/toolkit?utm_source=github.com&utm_medium=referral&utm_content=afrendeiro/toolkit&utm_campaign=Badge_Grade_Dashboard)
 [![Build Status](https://travis-ci.org/afrendeiro/toolkit.svg?branch=master)](https://travis-ci.org/afrendeiro/toolkit)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
-
+[![Gitter](https://badges.gitter.im/ngs-toolkit/Lobby.svg)](https://gitter.im/ngs-toolkit/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
 [![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/afrendeiro/toolkit)

docs/source/intro.rst

@@ -47,7 +47,7 @@ The following are required only for some data or analysis types:
 
    - `cqn <https://bioconductor.org/packages/release/bioc/html/cqn.html>`_: used for GC-content aware normalization of NGS data.
    - `DESeq2 <https://bioconductor.org/packages/release/bioc/html/DESeq2.html>`_: used for differential testing of genes/regulatory elements.
- - `Kent tools <https://github.com/ENCODE-DCC/kentUtils>`_ (optional): the '2bitToFa' binary from UCSC's Kent bioinformatics toolkit is used to convert between the 2bit and FASTA formats.
+ - `Kent tools <https://github.com/ENCODE-DCC/kentUtils>`_ (optional): the 'twoBitToFa' binary from UCSC's Kent bioinformatics toolkit is used to convert between the 2bit and FASTA formats.
 
 .. note::
 	``bedtools`` version should be below 2.24.0 (2.20.1 is used for testing)

ngs_toolkit/__init__.py

@@ -191,8 +191,10 @@ def setup_timestamping():
             to_csv_timestamped)
         import pandas as pd
 
-        pd.io.parsers.TextFileReader = read_csv_timestamped(pd.io.parsers.TextFileReader)
-        pd.DataFrame.to_csv = to_csv_timestamped(pd.DataFrame.to_csv, exclude_functions=["from_dataframe"])
+        pd.io.parsers.TextFileReader = read_csv_timestamped(
+            pd.io.parsers.TextFileReader)
+        pd.DataFrame.to_csv = to_csv_timestamped(
+            pd.DataFrame.to_csv)
 
 
 # setup

ngs_toolkit/project_manager.py

@@ -152,7 +152,7 @@ def create_project(
     comparison_table = os.path.join(metadata_dir, "comparison_table.csv")
     src_dir = os.path.join(project_dir, "src")
 
-    genome_assemblies = "\n".join(
+    genome_assemblies = "\n            ".join(
         [
             "'{}':\n                genome: '{}'".format(s, g)
             for s, g in genome_assemblies.items()