add vcell api client

.github/workflows/main.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     defaults:
       run:

.gitignore

@@ -169,3 +169,7 @@ cython_debug/
 .idea/
 
 test_output_1/
+
+.python-version
+
+**/.DS_Store

.pre-commit-config.yaml

@@ -14,6 +14,7 @@ repos:
     hooks:
       - id: ruff
         args: [--exit-non-zero-on-fix]
+        exclude: 'pyvcell/api/.*\.py'
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-prettier

Makefile

@@ -14,7 +14,7 @@ check: ## Run code quality tools.
 	@echo "🚀 Static type checking: Running mypy"
 	@poetry run mypy
 	@echo "🚀 Checking for obsolete dependencies: Running deptry"
-	@poetry run deptry .
+	@poetry run deptry --exclude .venv .
 
 .PHONY: test
 test: ## Test the code with pytest

docs/modules.md

@@ -1 +1,10 @@
-::: pyvcell.foo
+# Modules
+
+## pyvcell
+
+::: pyvcell
+handler: python
+options:
+show_root_heading: true
+show_source: true
+show_signature_annotations: true

examples/vcell_publications.ipynb

@@ -0,0 +1,216 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "source": [
+    "from pyvcell.api.vcell_client import ApiClient, Configuration, PublicationResourceApi\n",
+    "from pyvcell.api.vcell_client.auth.auth_utils import login_interactive\n",
+    "from pyvcell.api.vcell_client.models import Publication"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:37.703710Z",
+     "start_time": "2025-01-23T07:43:37.701027Z"
+    }
+   },
+   "id": "5e183b4a68315dfe",
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# VCell API Client usage\n",
+    "1. as a public user (no authentication)\n",
+    "2. as an authenticated user (with authentication)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "d11f5830839dbfb4"
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 1) Create anonymous API Client - access to public resources"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "524d1696c6c50b83"
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "api_url: str = \"https://vcell-dev.cam.uchc.edu\"  # vcell base url\n",
+    "\n",
+    "public_client = ApiClient(configuration=Configuration(host=api_url))"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:37.725514Z",
+     "start_time": "2025-01-23T07:43:37.723335Z"
+    }
+   },
+   "id": "902c6d3a8dc70af",
+   "outputs": [],
+   "execution_count": 3
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### Test Publication API - without authentication\n",
+    "1. get publications - doesn't need authentication/authorization"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "b12dfb281d589869"
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "public_publication_api = PublicationResourceApi(public_client)\n",
+    "pubs: list[Publication] = public_publication_api.get_publications()\n",
+    "display(pubs[0])"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:38.028844Z",
+     "start_time": "2025-01-23T07:43:37.735773Z"
+    }
+   },
+   "id": "9ba5b1ac2df17231",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 4
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## 2) invoke VCell API as an authenticated user\n",
+    "This will open a browser window to login into VCell using Auth0.  After login, the browser will redirect to the VCell webapp '/success_login'.  `api_client` will be authenticated for VCell API requests.  "
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6444e342beaccd4d"
+  },
+  {
+   "cell_type": "code",
+   "id": "f56d96abf59682dd",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:46.823079Z",
+     "start_time": "2025-01-23T07:43:38.037782Z"
+    }
+   },
+   "source": [
+    "client_id: str = 'cjoWhd7W8A8znf7Z7vizyvKJCiqTgRtf' # default client id for standalone VCell clients\n",
+    "issuer_url: str = 'https://dev-dzhx7i2db3x3kkvq.us.auth0.com' # Auth0 issuer url for VCell\n",
+    "\n",
+    "authenticated_client = login_interactive(api_base_url=api_url, client_id=client_id, issuer_url=issuer_url)\n",
+    "display(\"may loose focus to the browser window for login, switch back to this notebook after login.\")"
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'may loose focus to the browser window for login, switch back to this notebook after login.'"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 5
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a0e558b807038809",
+   "metadata": {
+    "collapsed": false
+   },
+   "source": [
+    "### Test Publication API\n",
+    "1. get publications - also doesn't need authentication/authorization"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "id": "8f95b36e4437ccbb",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:47.020349Z",
+     "start_time": "2025-01-23T07:43:46.852654Z"
+    }
+   },
+   "source": [
+    "publication_api = PublicationResourceApi(authenticated_client)\n",
+    "pubs: list[Publication] = publication_api.get_publications()\n",
+    "display(pubs[0])"
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "execution_count": 6
+  },
+  {
+   "cell_type": "code",
+   "id": "ed266f9194abb748",
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2025-01-23T07:43:47.026801Z",
+     "start_time": "2025-01-23T07:43:47.025477Z"
+    }
+   },
+   "source": [],
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}