Feature/67 update test suite results (#74)

Compatibility processing - reformat compatibility message (remove colour coding of text) - In addition to recognizing .sbml and .sedml files as SBML and SED-ML format, .xml files with 'sedml' + 'sbml' or 'sbml' but not 'sedml' in their filename are recognized as SBML and SED-ML files. Other file types are not recognized but this can be extended in the future. - Instead of ❌ FAIL, unrecognized filetypes will marked as ❓UNSURE (this hasn't happened so far). At the moment all engines that do not support SBML/SED-ML are still marked as⚠ XFAIL. Test suite - Updated the results table of case 00001 - Added a table of case 01186 (steady state Flux Balance Analysis) Add back foldout menu in Engines column (went lost with the previous PR when the engine names were reformated)
OpenSourceBrain · Nov 11, 2024 · 9cd561b · 9cd561b
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diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
diff --git a/test_suite/README.md b/test_suite/README.md
@@ -47,6 +47,12 @@ The `process_test_suite.py` script provides various command-line options to cust
   **Usage:** `--limit <number>`  
   **Default:** `0` (no limit)
 
+ `--cases`  
+  **Description:** list specific cases to process
+  **Usage:** `--cases <list>`  
+  **Default:** `[]` (no limit)
+
+
 - `--suite-path`  
   **Description:** Specifies the path to the directory containing the test suite files.  
   **Usage:** `--suite-path <path>`  

diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py
@@ -45,6 +45,15 @@ def parse_arguments():
         help="Limit to the first n test cases, 0 means no limit",
     )
 
+    parser.add_argument(
+        "--cases",
+        action="extend",
+        nargs="+",
+        type=str,
+        default=[],
+        help="Limit to the cases listed in the file. Empty list means no limit",
+    )
+
     parser.add_argument(
         "--suite-path",
         action="store",
@@ -116,8 +125,8 @@ def process_cases(args):
     matplotlib.use("agg") 
     # Suppress specific UserWarning caused by matplotlib (required to suppress interactive plots)
     warnings.filterwarnings("ignore", category=UserWarning, message="FigureCanvasAgg is non-interactive, and thus cannot be shown")
-    subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit]    
-    
+    subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit]   
+
     for subfolder in subfolders:
         # if sbml_level_version is empty string (default), find the highest level and version in the folder
         if args.sbml_level_version == "highest":

diff --git a/test_suite/test_00001/00001-sbml-l3v2-sedml.omex b/test_suite/test_00001/00001-sbml-l3v2-sedml.omex
diff --git a/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf
diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md
diff --git a/test_suite/test_00001/tests/results_local.json b/test_suite/test_00001/tests/results_local.json
@@ -0,0 +1,107 @@
+{
+    "amici": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "brian2": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "bionetgen": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "boolnet": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "cbmpy": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "cobrapy": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "copasi": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "gillespy2": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "ginsim": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "libsbmlsim": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "masspy": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "netpyne": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "neuron": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "opencor": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "pyneuroml": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "pysces": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "rbapy": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "smoldyn": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "tellurium": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "vcell": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    },
+    "xpp": {
+        "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')",
+        "log_yml": {},
+        "detailed_error_log": {}
+    }
+}