Merge pull request #246 from monarch-initiative/release-0.3.0

Make release `0.3.0`
monarch-initiative · Sep 4, 2024 · f23741a · f23741a
2 parents 8505fbf + 140a8f0
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diff --git a/README.md b/README.md
@@ -5,46 +5,11 @@
 
 GPSEA is a Python library for discovery of genotype-phenotype associations.
 
-An example of simple genotype-phenotype association 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)
+for more information.
 
-```python
-# Load HPO
-import hpotk
-
-store = hpotk.configure_ontology_store()
-hpo = store.load_minimal_hpo()
-
-# Load a cohort of phenopackets
-from gpsea.data import get_toy_cohort
-
-cohort = get_toy_cohort()
-
-# Analyze genotype-phenotype associations
-from gpsea.analysis import configure_cohort_analysis
-from gpsea.analysis.predicate import PatientCategories
-
-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')
-
-frameshift.summarize(hpo, category=PatientCategories.YES)
-```
-
-provides a pandas data frame with genotype-phenotype correlations:
-
-```text
-FRAMESHIFT_VARIANT on NM_1234.5                                    No                Yes
-                                                                Count   Percent    Count   Percent    p value    Corrected p value
-    Arachnodactyly [HP:0001166]                                  1/10       10%    13/16       81%   0.000781             0.020299
-    Abnormality of the musculature [HP:0003011]                   6/6      100%    11/11      100%   1.000000             1.000000
-    Abnormal nervous system physiology [HP:0012638]               9/9      100%    15/15      100%   1.000000             1.000000
-    ...                                                           ...       ...      ...       ...        ...                  ...
-```
-
-## Documentation
-
-Check out the User guide and the API reference for more info:
+The documentation comes in two flavors:
 
 - [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)