Merge branch 'main' into split-gks-common-models

Makefile

@@ -57,6 +57,14 @@ devready:
 	@echo '###  Do not forget to `source ${VEDIR}/bin/activate` to use this environment  ###'
 	@echo '#################################################################################'
 
+#=> nbready: create venv, install prerequisites, install pkg in notebook mode
+.PHONY: nbready
+nbready:
+	make ${VEDIR} && source ${VEDIR}/bin/activate && pip install -e '.[extras,notebooks]'
+	@echo '#################################################################################'
+	@echo '###  Do not forget to `source ${VEDIR}/bin/activate` to use this environment  ###'
+	@echo '#################################################################################'
+
 #=> install: install package
 .PHONY: install-extras
 install-extras:

notebooks/getting_started/README.md

@@ -16,8 +16,8 @@ The following software packages must exist in your execution environment before
 From a terminal window, run the following commands:
 * git clone --recurse-submodules https://github.com/ga4gh/vrs-python
 * cd vrs-python
-* make devready
-* source venv/3.10/bin/activate
+* make nbready
+* source venv/3.12/bin/activate
 * cd notebooks/getting_started
 * jupyter notebook notebook_name.ipynb
 

notebooks/t.ipynb

@@ -0,0 +1,88 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ga4gh.core"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Gene(id=None, type=<CommonDomainType.GENE: 'Gene'>, label=None, description=None, alternativeLabels=None, extensions=None, mappings=None)"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ga4gh.core.domain_models.Gene()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Document(id='d', type=<CommonEntityType.DOCUMENT: 'Document'>, label=None, description=None, alternativeLabels=None, extensions=None, specifiedBy=None, contributions=None, isReportedIn=None, dateAuthored=None, derivedFrom=None, recordMetadata=None, subtype=None, title=None, url=None, doi=None, pmid=None)"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ga4gh.core.entity_models.Document(id=\"d\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "3.12",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}