replace deprecated usage of json() with model_dump_json() for pydanti…

…c2 migration
gyorilab · Sep 23, 2024 · 21e7a9c · 21e7a9c
1 parent 8eaab77
commit 21e7a9c
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Showing 6 changed files with 13 additions and 13 deletions.
diff --git a/notebooks/Hackathon Scenario 1.ipynb b/notebooks/Hackathon Scenario 1.ipynb
@@ -2628,7 +2628,7 @@
     }
    ],
    "source": [
-    "print(tc.model_comparison.json(indent=1))"
+    "print(tc.model_comparison.model_dump_json(indent=1))"
    ]
   },
   {
@@ -4710,7 +4710,7 @@
     }
    ],
    "source": [
-    "print(tc.model_comparison.json(indent=1))"
+    "print(tc.model_comparison.model_dump_json(indent=1))"
    ]
   },
   {
@@ -4721,7 +4721,7 @@
    "outputs": [],
    "source": [
     "with open('mira_comparison_threeway.json', 'w') as fh:\n",
-    "    fh.write(tc.model_comparison.json(indent=1))"
+    "    fh.write(tc.model_comparison.model_dump_json(indent=1))"
    ]
   },
   {
@@ -4779,7 +4779,7 @@
    "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
@@ -74,7 +74,7 @@
    "outputs": [],
    "source": [
     "with open('mira_comparison_scenario4.json', 'w') as fh:\n",
-    "    fh.write(tc.model_comparison.json(indent=1))"
+    "    fh.write(tc.model_comparison.model_dump_json(indent=1))"
    ]
   },
   {

diff --git a/notebooks/evaluation_2023.01/Scenario2.ipynb b/notebooks/evaluation_2023.01/Scenario2.ipynb
@@ -456,7 +456,7 @@
    "outputs": [],
    "source": [
     "with open('scenario2_model_comparison.json', 'w') as fh:\n",
-    "    fh.write(tc.model_comparison.json(indent=1))"
+    "    fh.write(tc.model_comparison.model_dump_json(indent=1))"
    ]
   }
  ],

diff --git a/notebooks/evaluation_2023.01/Scenario3.ipynb b/notebooks/evaluation_2023.01/Scenario3.ipynb
@@ -285,9 +285,9 @@
     "    model.to_json_file(mname, indent=1)\n",
     "# Also dump the mira model jsons\n",
     "with open(\"scenario3_biomd958_mira.json\", \"w\") as f:\n",
-    "    f.write(model_958.json(indent=1))\n",
+    "    f.write(model_958.model_dump_json(indent=1))\n",
     "with open(\"scenario3_biomd960_mira.json\", \"w\") as f:\n",
-    "    f.write(model_960.json(indent=1))"
+    "    f.write(model_960.model_dump_json(indent=1))"
    ]
   },
   {
@@ -534,12 +534,12 @@
    "source": [
     "import json\n",
     "res = {\n",
-    "    'graph_comparison_data': json.loads(mc.model_comparison.json()),\n",
+    "    'graph_comparison_data': json.loads(mc.model_comparison.model_dump_json()),\n",
     "    'similarity_scores': mc.model_comparison.get_similarity_scores(),\n",
     "    'model_names': model_names\n",
     "}\n",
     "res_filtered = {\n",
-    "    'graph_comparison_data': json.loads(mc_filtered.model_comparison.json()),\n",
+    "    'graph_comparison_data': json.loads(mc_filtered.model_comparison.model_dump_json()),\n",
     "    'similarity_scores': mc_filtered.model_comparison.get_similarity_scores(),\n",
     "    'model_names': model_names_filtered\n",
     "}"

diff --git a/notebooks/model_api.ipynb b/notebooks/model_api.ipynb
@@ -45,7 +45,7 @@
     "natural_conversion = NaturalConversion(subject=infected, outcome=immune)\n",
     "sir_template_model = TemplateModel(templates=[controlled_conversion, natural_conversion])\n",
     "sir_template_model_dict = sir_template_model.m()\n",
-    "print(sir_template_model.json())"
+    "print(sir_template_model.model_dump_json())"
    ]
   },
   {

diff --git a/notebooks/scenarios_2024.08/eval_202301_scenario2.ipynb b/notebooks/scenarios_2024.08/eval_202301_scenario2.ipynb
@@ -431,7 +431,7 @@
    "outputs": [],
    "source": [
     "with open('eval_202301_scenario2_sidarthe_v_model_comparison.json', 'w') as fh:\n",
-    "    fh.write(tc.model_comparison.json(indent=1))"
+    "    fh.write(tc.model_comparison.model_dump_json(indent=1))"
    ]
   }
  ],
@@ -451,7 +451,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,