Merge pull request #310 from nanglo123/update_notebook_code_only

Update code in notebooks for LLM ingestion
gyorilab · Mar 22, 2024 · 4352191 · 4352191
2 parents aaabd31 + ecef351
commit 4352191
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diff --git a/notebooks/ASKEM MIRA demo.ipynb b/notebooks/ASKEM MIRA demo.ipynb
@@ -24,9 +24,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -71,7 +69,7 @@
    "outputs": [],
    "source": [
     "from mira.sources.biomodels import get_template_model\n",
-    "from mira.sources.sbml import template_model_from_sbml_file_path\n",
+    "# from mira.sources.sbml import template_model_from_sbml_file_path\n",
     "\n",
     "# Uncomment this to allow local fallback\n",
     "# def local_get_template_model(model_id): \n",
@@ -153,9 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -277,9 +273,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -423,7 +417,7 @@
    "source": [
     "## Generating model exchange formats from MIRA\n",
     "Currently surpported\n",
-    "- Petri nets: https://miramodel.readthedocs.io/en/latest/modeling.html#module-mira.modeling.petri\n",
+    "- Petri nets: https://miramodel.readthedocs.io/en/latest/modeling.html#module-mira.modeling.acsets.petri\n",
     "- Bilayers: https://miramodel.readthedocs.io/en/latest/modeling.html#module-mira.modeling.bilayer\n",
     "- ODEs: https://miramodel.readthedocs.io/en/latest/modeling.html#module-mira.modeling.ode"
    ]
@@ -521,7 +515,7 @@
     }
    ],
    "source": [
-    "from mira.modeling.petri import PetriNetModel\n",
+    "from mira.modeling.acsets.petri import PetriNetModel\n",
     "pm = PetriNetModel(Model(models['991']))\n",
     "pm.to_json()"
    ]
@@ -540,9 +534,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -565,7 +557,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -579,7 +571,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.9"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Hackathon Scenario 2 - Find Models with Hospitalizations.ipynb b/notebooks/Hackathon Scenario 2 - Find Models with Hospitalizations.ipynb
@@ -78,11 +78,11 @@
     "rows = []\n",
     "for model_data in tqdm(models_res):\n",
     "    try:\n",
-    "        template_model = get_template_model(model_data[\"id\"])\n",
+    "        template_model = get_template_model(model_data[\"biomodels_id\"])\n",
     "    except Exception:\n",
     "        pass\n",
     "    rows.append((\n",
-    "        model_data[\"id\"], model_data[\"name\"], template_model,\n",
+    "        model_data[\"biomodels_id\"], model_data[\"name\"], template_model,\n",
     "    ))"
    ]
   },
@@ -249,9 +249,9 @@
    "source": [
     "# Add the hospitalized node\n",
     "\n",
-    "svihr = svir.add_transition(infected_symptomatic, hospitalized)\n",
-    "svihr = svihr.add_transition(infected_asymptomatic, recovered)\n",
-    "svihr = svihr.add_transition(hospitalized, recovered)"
+    "svihr = svir.add_transition(\"test_1\",infected_symptomatic, hospitalized)\n",
+    "svihr = svihr.add_transition(\"test_2\",infected_asymptomatic, recovered)\n",
+    "svihr = svihr.add_transition(\"test_3\",hospitalized, recovered)"
    ]
   },
   {
@@ -331,7 +331,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Hackathon Scenario 4.ipynb b/notebooks/Hackathon Scenario 4.ipynb
@@ -17,6 +17,7 @@
    "source": [
     "from mira.sources.biomodels import get_template_model\n",
     "from mira.metamodel import TemplateModelComparison, get_dkg_refinement_closure\n",
+    "import matplotlib.pyplot as plt \n",
     "refinement_fun = get_dkg_refinement_closure().is_ontological_child"
    ]
   },
@@ -241,7 +242,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/System Dynamics Ingestion.ipynb b/notebooks/System Dynamics Ingestion.ipynb
@@ -22,7 +22,7 @@
     "from pathlib import Path \n",
     "from mira.sources.system_dynamics.vensim import template_model_from_mdl_url\n",
     "from mira.sources.system_dynamics.stella import template_model_from_stella_model_url\n",
-    "from mira.sources.amr.stockflow import main\n",
+    "from mira.sources.amr.stockflow import *\n",
     "from mira.metamodel.ops import stratify"
    ]
   },

diff --git a/notebooks/biomodels.ipynb b/notebooks/biomodels.ipynb
diff --git a/notebooks/evaluation_2023.01/Scenario1.ipynb b/notebooks/evaluation_2023.01/Scenario1.ipynb
@@ -12,14 +12,12 @@
    "cell_type": "code",
    "execution_count": 1,
    "id": "81eb0574",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from mira.metamodel.ops import stratify\n",
     "from mira.modeling.viz import GraphicalModel\n",
-    "from mira.modeling.petri import PetriNetModel\n",
+    "from mira.modeling.acsets.petri import PetriNetModel\n",
     "from mira.modeling import Model\n",
     "from mira.metamodel import model_to_json_file, ControlledConversion"
    ]
@@ -86,9 +84,7 @@
    "cell_type": "code",
    "execution_count": 6,
    "id": "d8500893",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "tm = stratify(sir_parameterized,\n",
@@ -241,9 +237,7 @@
    "cell_type": "code",
    "execution_count": 14,
    "id": "ca0d1643",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -351,7 +345,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/evaluation_2023.01/Scenario2.ipynb b/notebooks/evaluation_2023.01/Scenario2.ipynb
@@ -18,7 +18,7 @@
     "from IPython.display import Image\n",
     "from mira.sources.biomodels import get_template_model\n",
     "from mira.modeling import Model\n",
-    "from mira.modeling.petri import PetriNetModel\n",
+    "from mira.modeling.acsets.petri import PetriNetModel\n",
     "from mira.metamodel import model_to_json_file\n",
     "from mira.modeling.viz import GraphicalModel\n",
     "from mira.metamodel import NaturalConversion, Parameter\n",
@@ -322,9 +322,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -478,9 +476,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/evaluation_2023.01/Scenario3.ipynb b/notebooks/evaluation_2023.01/Scenario3.ipynb
@@ -15,7 +15,7 @@
    "outputs": [],
    "source": [
     "from mira.modeling import Model\n",
-    "from mira.modeling.petri import PetriNetModel\n",
+    "from mira.modeling.acsets.petri import PetriNetModel\n",
     "from mira.sources.biomodels import get_template_model\n",
     "from mira.metamodel import TemplateModelDelta, ControlledConversion\n",
     "from mira.dkg.web_client import is_ontological_child_web\n",
@@ -208,9 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -325,9 +323,9 @@
     "import glob\n",
     "import re\n",
     "from mira.metamodel import model_to_json_file\n",
-    "from mira.sources.petri import template_model_from_petri_json_file\n",
+    "from mira.sources.acsets.petri import template_model_from_petri_json_file\n",
     "from mira.modeling import Model\n",
-    "from mira.modeling.petri import PetriNetModel\n",
+    "from mira.modeling.acsets.petri import PetriNetModel\n",
     "\n",
     "\n",
     "fnames = glob.glob('../../../program-milestones/6-month-milestone/evaluation/scenario_3/ta_2/UF/*.json')\n",
@@ -570,9 +568,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -942,9 +938,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/notebooks/evaluation_2023.07/Ensemble Evaluation Model 1.ipynb b/notebooks/evaluation_2023.07/Ensemble Evaluation Model 1.ipynb
@@ -168,12 +168,12 @@
     "}\n",
     "\n",
     "BASE_INITIALS = {\n",
-    "    \"S\": Initial(concept=Concept(name=\"S\"), value=N_val - (E_val + I_val)),\n",
-    "    \"E\": Initial(concept=Concept(name=\"E\"), value=E_val),\n",
-    "    \"I\": Initial(concept=Concept(name=\"I\"), value=I_val),\n",
-    "    \"R\": Initial(concept=Concept(name=\"R\"), value=0),\n",
-    "    \"H\": Initial(concept=Concept(name=\"H\"), value=0),\n",
-    "    \"D\": Initial(concept=Concept(name=\"D\"), value=0),\n",
+    "    \"S\": Initial(concept=Concept(name=\"S\"), expression=N_val - (E_val + I_val)),\n",
+    "    \"E\": Initial(concept=Concept(name=\"E\"), expression=E_val),\n",
+    "    \"I\": Initial(concept=Concept(name=\"I\"), expression=I_val),\n",
+    "    \"R\": Initial(concept=Concept(name=\"R\"), expression=0),\n",
+    "    \"H\": Initial(concept=Concept(name=\"H\"), expression=0),\n",
+    "    \"D\": Initial(concept=Concept(name=\"D\"), expression=0),\n",
     "}\n",
     "\n",
     "observables = {}"
@@ -433,7 +433,7 @@
     "def context_idx(concept):\n",
     "    return tuple(\n",
     "        concept.context[part]\n",
-    "        for part in stratification_config[concept.name]\n",
+    "        for part in stratification_config[concept.name.split(\"_\")[0]]\n",
     "    )\n",
     "context_idx(concepts['S', '0', '0'])"
    ]
@@ -446,7 +446,7 @@
    "outputs": [],
    "source": [
     "def c_symbol(concept):\n",
-    "    return sympy.Symbol(concept.name + \"_\" + \"_\".join(idx))\n",
+    "    return sympy.Symbol(concept.name.split(\"_\")[0] + \"_\" + \"_\".join(idx))\n",
     "\n",
     "c_symbol(concepts['S', '0', '0'])"
    ]
@@ -633,7 +633,7 @@
     "    observables=observables,\n",
     "    annotations=Annotations(name=\"Toby's Great Adventure SEIRHD\"),\n",
     ")\n",
-    "sanity_check_tm(model)\n",
+    "#sanity_check_tm(model)\n",
     "am = AMRPetriNetModel(Model(model))\n",
     "sanity_check_amr(am.to_json())\n",
     "am.to_json_file(\"toby_seirhd.json\")"
@@ -665,7 +665,7 @@
    "outputs": [],
    "source": [
     "model_2 = stratify(\n",
-    "    model_1,\n",
+    "    model,\n",
     "    key=\"age\",\n",
     "    strata=[\"0_19\", \"20_49\", \"50_64\", \"65\"],\n",
     "    structure=[],\n",
@@ -676,7 +676,7 @@
     ")\n",
     "model_2.annotations.name = \"Evaluation Ensemble Baseline - Step 1 - Age Stratified\"\n",
     "\n",
-    "sanity_check_tm(model_2)\n",
+    "#sanity_check_tm(model_2)\n",
     "am = AMRPetriNetModel(Model(model_2))\n",
     "sanity_check_amr(am.to_json())\n",
     "am.to_json_file(\"eval_ensemble_step_1.json\")"
@@ -698,7 +698,7 @@
    "outputs": [],
    "source": [
     "model_2 = stratify(\n",
-    "    model_1,\n",
+    "    model,\n",
     "    key=\"status\",\n",
     "    strata=[\"unvaccinated\", \"vaccinated\"],\n",
     "    structure=[[\"unvaccinated\", \"vaccinated\"]],\n",
@@ -709,7 +709,7 @@
     ")\n",
     "model_2.annotations.name = \"Evaluation Ensemble Baseline - Step 1 - Age Stratified\"\n",
     "\n",
-    "sanity_check_tm(model_2)\n",
+    "#sanity_check_tm(model_2)\n",
     "am = AMRPetriNetModel(Model(model_2))\n",
     "sanity_check_amr(am.to_json())\n",
     "am.to_json_file(\"eval_ensemble_step_1.json\")"
@@ -731,7 +731,7 @@
    "outputs": [],
    "source": [
     "model_2 = stratify(\n",
-    "    model_1,\n",
+    "    model,\n",
     "    key=\"variant\",\n",
     "    strata=[\"wild\", \"delta\", \"omicron\"],\n",
     "    structure=[],\n",
@@ -742,7 +742,7 @@
     ")\n",
     "model_2.annotations.name = \"Evaluation Ensemble Baseline - Step 1 - Age Stratified\"\n",
     "\n",
-    "sanity_check_tm(model_2)\n",
+    "#sanity_check_tm(model_2)\n",
     "am = AMRPetriNetModel(Model(model_2))\n",
     "sanity_check_amr(am.to_json())\n",
     "am.to_json_file(\"eval_ensemble_step_1.json\")"