Merge pull request #87 from EnzymeML/basico-v2-support

Basico v2 support

Author: JR-1991

.github/workflows/unit-tests.yaml

@@ -21,7 +21,7 @@ jobs:
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install pytest-cov openpyxl pytest-httpx  pysces lmfit seaborn numexpr python-libcombine deepdiff deprecation
+          python3 -m pip install pytest-cov openpyxl pytest-httpx  pysces copasi-basico lmfit seaborn numexpr python-libcombine deepdiff deprecation
           pip3 install -e .
 
       - name: Test with pytest

examples/KineticModellingCOPASI.ipynb

@@ -184,4 +184,7 @@ def read_sbml_omex(path: Path | str) -> tuple[TextIO, dict[str, pd.DataFrame]]:
 
         meas_data[entry.location] = df
 
-    return open(omex.get_path(master_file.location)), meas_data
+    return open(
+        omex.get_path(master_file.location),
+        encoding="utf-8",
+    ), meas_data

pyenzyme/sbml/omex.py

@@ -5,4 +5,9 @@
 except ImportError:
     pass
 
-__all__ = ["BaseThinLayer", "ThinLayerPysces"]
+try:
+    from .basico import ThinLayerCopasi
+except ImportError:
+    pass
+
+__all__ = ["BaseThinLayer", "ThinLayerPysces", "ThinLayerCopasi"]