feat: updated to biosimulators-utils 0.1.102, kisao 2.23; set up matp…

…lotlib config and cache; added validation for symbols of SED-ML variables

Dockerfile

@@ -33,6 +33,12 @@ LABEL \
 ENV PYTHON="OpenCOR -c PythonShell" \
     PIP="${OPENCORDIR}/python/bin/python -m pip"
 
+# setup matplotlib
+RUN mkdir -p /.config/matplotlib \
+    && mkdir -p /.cache/matplotlib \
+    && chmod ugo+rw /.config/matplotlib \
+    && chmod ugo+rw /.cache/matplotlib
+
 # Copy code for command-line interface into image and install it
 COPY . /tmp/Biosimulators_OpenCOR
 RUN $PIP install /tmp/Biosimulators_OpenCOR \

biosimulators_opencor/utils.py

@@ -137,6 +137,10 @@ def validate_variable_xpaths(sed_variables, model_filename):
 
     opencor_variable_names = {}
     for sed_variable in sed_variables:
+        if not sed_variable.target:
+            msg = 'Symbols are not supported.'
+            raise NotImplementedError(msg)
+
         namespaces = copy.copy(sed_variable.target_namespaces)
         namespaces.pop(None, None)
         xml_objs = model_etree.xpath(sed_variable.target, namespaces=namespaces)

requirements.txt

@@ -1,5 +1,5 @@
-biosimulators_utils[cellml,logging] >= 0.1.96
-kisao >= 2.18
+biosimulators_utils[cellml,logging] >= 0.1.102
+kisao >= 2.23
 lxml
 numpy
 # opencor