Merge pull request #230 from monarch-initiative/rebrand-to-gpsea

Change the project name to GPSEA

.github/workflows/pages.yml

@@ -32,8 +32,8 @@ jobs:
         touch gh-pages/.nojekyll
         
         function build_docs {
-          # The function will checkout a branch and build the Javadoc & documentation 
-          # into provided documentation directory.
+          # The function will checkout a branch and build the API docs & documentation 
+          # into provided directory.
           BRANCH=${1}
           DOCDIR=${2}
         
@@ -50,7 +50,7 @@ jobs:
           printf "Building the %s documentation\n" ${DOCDIR}
 
           cd docs
-          sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/genophenocorr
+          sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/gpsea
           make clean html
           
           mv _build/html/* ../gh-pages/${DOCDIR}

.github/workflows/python_ci.yml

@@ -25,4 +25,5 @@ jobs:
         - name: Run pytest tests
           run: |
             export MPLBACKEND=Agg
+            export GPSEA_CACHEDIR=.gpsea_ci_cachedir
             pytest

.gitignore

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

HOW_TO_RELEASE.md

@@ -1,6 +1,6 @@
 # How to release
 
-The document describes how to release `genophenocorr` to *PyPi*.
+The document describes how to release `gpsea` to *PyPi*.
 
 ## Release checklist
 
@@ -9,7 +9,7 @@ The document describes how to release `genophenocorr` to *PyPi*.
 - remove deprecated methods targeted for removal in this version. The `TODO` markers are labeled using 
   the target version (e.g. `TODO[v0.3.0]`)
 - bump versions to a release:
-  - `src/genophenocorr/__init__.py`
+  - `src/gpsea/__init__.py`
   - `docs/conf.py`
 - ensure the CI passes
 - deploy to PyPi (described below)
@@ -52,11 +52,11 @@ Store the token into `$HOME/.pypirc` file with `-rw-------` permissions. The fil
 Now we're ready to publish packages!
 
 ### Deploy
-Run the following to deploy `genophenocorr` to PyPi:  
+Run the following to deploy `gpsea` to PyPi:  
 
 ```bash
 # Ensure you're on the release branch
-cd genophenocorr
+cd gpsea
 
 # Build the package
 python3 -m build

MANIFEST.in

@@ -1,2 +1,2 @@
-include src/genophenocorr/model/genome/GCF_*.tsv
-include src/genophenocorr/view/templates/*.html
+include src/gpsea/model/genome/GCF_*.tsv
+include src/gpsea/view/templates/*.html

README.md

@@ -1,9 +1,9 @@
-[![Build status](https://github.com/monarch-initiative/genophenocorr/workflows/CI/badge.svg)](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)
-[![GitHub release](https://img.shields.io/github/release/monarch-initiative/genophenocorr.svg)](https://github.com/monarch-initiative/genophenocorr/releases)
-![PyPi downloads](https://img.shields.io/pypi/dm/genophenocorr.svg?label=Pypi%20downloads)
-![PyPI - Python Version](https://img.shields.io/pypi/pyversions/genophenocorr)
+[![Build status](https://github.com/monarch-initiative/gpsea/workflows/CI/badge.svg)](https://github.com/monarch-initiative/gpsea/actions/workflows/python_ci.yml)
+[![GitHub release](https://img.shields.io/github/release/monarch-initiative/gpsea.svg)](https://github.com/monarch-initiative/gpsea/releases)
+![PyPi downloads](https://img.shields.io/pypi/dm/gpsea.svg?label=Pypi%20downloads)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gpsea)
 
-Genophenocorr is a Python library for genotype-phenotype association analysis.
+GPSEA is a Python library for discovery of genotype-phenotype associations.
 
 An example of simple genotype-phenotype association analysis
 
@@ -15,15 +15,15 @@ store = hpotk.configure_ontology_store()
 hpo = store.load_minimal_hpo()
 
 # Load a cohort of phenopackets
-from genophenocorr.data import get_toy_cohort
+from gpsea.data import get_toy_cohort
 
 cohort = get_toy_cohort()
 
 # Analyze genotype-phenotype associations
-from genophenocorr.analysis import configure_cohort_analysis
-from genophenocorr.analysis.predicate import PatientCategories
+from gpsea.analysis import configure_cohort_analysis
+from gpsea.analysis.predicate import PatientCategories
 
-from genophenocorr.model import VariantEffect
+from gpsea.model import VariantEffect
 
 cohort_analysis = configure_cohort_analysis(cohort, hpo)
 frameshift = cohort_analysis.compare_by_variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id='NM_1234.5')
@@ -46,5 +46,5 @@ FRAMESHIFT_VARIANT on NM_1234.5                                    No
 
 Check out the User guide and the API reference for more info:
 
-- [Stable documentation](https://monarch-initiative.github.io/genophenocorr/stable/) (last release on `main` branch)
-- [Latest documentation](https://monarch-initiative.github.io/genophenocorr/latest) (bleeding edge, latest commit on `development` branch)
+- [Stable documentation](https://monarch-initiative.github.io/gpsea/stable/) (last release on `main` branch)
+- [Latest documentation](https://monarch-initiative.github.io/gpsea/latest) (bleeding edge, latest commit on `develop` branch)

docs/conf.py

@@ -15,8 +15,8 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-genophenocorr_src = os.path.abspath(os.path.join('..', 'src'))
-sys.path.insert(0, genophenocorr_src)
+src_dir = os.path.abspath(os.path.join('..', 'src'))
+sys.path.insert(0, src_dir)
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
@@ -51,7 +51,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'genophenocorr'
+project = u'GPSEA'
 copyright = u'2024'
 author = u'Lauren Rekerle, Daniel Danis, Peter N Robinson'
 
@@ -103,7 +103,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
-html_css_files = ['genophenocorr.css']
+html_css_files = ['gpsea.css']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -124,7 +124,7 @@
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'genophenocorr'
+htmlhelp_basename = 'GPSEA'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -151,7 +151,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'genophenocorr.tex', u'genophenocorr Documentation',
+    (master_doc, 'gpsea.tex', u'GPSEA Documentation',
      u'Lauren Rekerle, Peter Robinson', 'manual'),
 ]
 
@@ -161,7 +161,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'genophenocorr', u'genophenocorr Documentation',
+    (master_doc, 'gpsea', u'GPSEA Documentation',
      [author], 1)
 ]
 
@@ -172,8 +172,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'genophenocorr', u'genophenocorr Documentation',
-     author, 'genophenocorr', 'genotype phenotype correlations with GA4GH Phenopackets',
+    (master_doc, 'gpsea', u'GPSEA Documentation',
+     author, 'gpsea', 'Genotype phenotype correlations with GA4GH Phenopackets',
      'Miscellaneous'),
 ]
 
@@ -183,7 +183,7 @@
 
 # -- Doctest setup ------------------------------------------------------------
 
-doctest_path = [genophenocorr_src]
+doctest_path = [src_dir]
 doctest_test_doctest_blocks = ""
 
 doctest_global_setup = """
@@ -200,8 +200,7 @@
 # -- Intersphinx setup --------------------------------------------------------
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    # TODO - change to stable when we arrive there
-    "hpotk": ("https://ielis.github.io/hpo-toolkit/latest/", None),
+    "hpotk": ("https://ielis.github.io/hpo-toolkit/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/version/2.0.0/", None),
     "requests": ("https://docs.python-requests.org/en/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy-1.11.0/", None),