Merge pull request #270 from monarch-initiative/release-0.4.0

Make release `0.4.0`

.gitignore

@@ -1,5 +1,6 @@
 # Cache with transcript/protein pickle files
 .gpsea_cache
+dev/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -3,7 +3,8 @@
 ![PyPi downloads](https://img.shields.io/pypi/dm/gpsea.svg?label=Pypi%20downloads)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gpsea)
 
-GPSEA is a Python library for discovery of genotype-phenotype associations.
+GPSEA (Genotypes and Phenotypes - Statistical Evaluation of Associations, pronounced "G"-"P"-"C") is a Python package designed to support genotype-phenotype correlation analysis.
+
 
 See the [Tutorial](https://monarch-initiative.github.io/gpsea/stable/tutorial.html) 
 and a comprehensive [User guide](https://monarch-initiative.github.io/gpsea/stable/user-guide/index.html)

docs/conf.py

@@ -60,9 +60,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.3'
+version = u'0.4'
 # The full version, including alpha/beta/rc tags.
-release = u'0.3.0'
+release = u'0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -10,8 +10,8 @@ A key question in biology and human genetics concerns the relationships between
 genetics, the focus is generally placed on the study of whether specific disease-causing alleles are associated with specific phenotypic 
 manifestations of the disease. 
 
-`GPSEA`  (genotypes and phenotypes - study and evaluation of associations) is a Python package designed to support genotype-phenotype correlation analysis.
-We pronounce GPSEA as "G"-"P"-"C". The input to `GPSEA` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
+`GPSEA`  (Genotypes and Phenotypes - Statistical Evaluation of Associations, pronounced "G"-"P"-"C") is a Python package designed to support genotype-phenotype correlation analysis.
+The input to `GPSEA` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
 `gpsea` ingests data from these phenopackets and performs analysis of the correlation of specific variants,
 variant types (e.g., missense vs. premature termination codon), or variant location in protein motifs or other features.
 The phenotypic abnormalities are represented by `Human Phenotype Ontology (HPO) <https://hpo.jax.org/app/>`_ terms.