fixes for webapp

sbml4humans/README.md

@@ -14,7 +14,7 @@ Alternatively the backend and frontend can be run directly on the machine. This
 ### Start backend API (local)
 Create Python virtual environment and install sbml4humans
 ```bash
-mkvirtualenv sbml4humans --python=python3.10
+mkvirtualenv sbml4humans --python=python3.12
 pip install -e .[sbml4humans,development] --upgrade
 ``` 
 

setup.cfg

@@ -70,10 +70,8 @@ install_requires =
 	openpyxl>=3.1.5
 	xmlschema>=3.3.2
     uvicorn>=0.30.6
-
-	matplotlib>=3.5
+	matplotlib>=3.9
 	py4cytoscape>=1.9.0
-
 	libroadrunner>=1.26.4
 tests_require =
 	tox>=3.24.3
@@ -94,9 +92,9 @@ where = src
 [options.extras_require]
 sbml4humans =
 	fastapi>=0.112.0
-	python-multipart>=0.0.6
+	python-multipart>=0.0.9
 development =
-	pip-tools>7.4.1
+	pip-tools>=7.4.1
 	black>=24.8.0
 	bump2version>=1.0.1
 	isort>=5.12.0

src/sbmlutils/cytoscape.py

@@ -1,5 +1,8 @@
 """Module for visualiation in Cytoscape."""
+import os
 import tempfile
+os.environ["PY4CYTOSCAPE_DETAIL_LOGGER_DIR"] = str(tempfile.gettempdir())
+
 from pathlib import Path
 from typing import Any, Union
 

src/sbmlutils/report/api_examples.py

@@ -76,9 +76,9 @@ def biomodels_examples() -> List[ExampleMetaData]:
             omex_path = BIOMODELS_CURATED_PATH / f"{biomodel_id}.omex"
             omex = Omex.from_omex(omex_path)
             sbml_entries = omex.entries_by_format(format_key="sbml")
-            print(biomodel_id)
-            print(omex)
-            print(sbml_entries)
+            # print(biomodel_id)
+            # print(omex)
+            # print(sbml_entries)
             biomodel_path = omex.get_path(sbml_entries[0].location)
             example = create_models_metadata(biomodel_path)
             example.id = biomodel_id