Merge pull request #119 from NeuroML/experimental

Add location of neuron when pip installed on Binder

Author: pgleeson

src/main/java/org/lemsml/export/sedml/SEDMLWriter.java

@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Arrays;
 
 import org.lemsml.export.base.AXMLWriter;
 import org.lemsml.jlems.core.logging.E;
@@ -67,9 +68,18 @@ public String getMainScript() throws ContentError
 
         StringBuilder main = new StringBuilder();
         main.append("<?xml version='1.0' encoding='UTF-8'?>\n");
-        String[] attrs = new String[] { "xmlns=http://sed-ml.org/sed-ml/level"+SEDML_LEVEL+"/version"+SEDML_VERSION, "level="+SEDML_LEVEL, "version="+SEDML_VERSION+"", "xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance",
+        String[] attrs = new String[] { "xmlns=http://sed-ml.org/sed-ml/level"+SEDML_LEVEL+"/version"+SEDML_VERSION, 
+                "level="+SEDML_LEVEL, 
+                "version="+SEDML_VERSION+"", 
+                "xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance",
                 "xsi:schemaLocation=http://sed-ml.org/sed-ml/level"+SEDML_LEVEL+"/version"+SEDML_VERSION+"   " + PREF_SEDML_SCHEMA };
 
+        if(modelFormat == Format.SBML)
+        {
+            attrs = Arrays.copyOf(attrs, attrs.length + 1);
+            attrs[attrs.length-1] = "xmlns:sbml=http://www.sbml.org/sbml/level2/version2";
+        }
+
         startElement(main, "sedML", attrs);
         startElement(main, "notes");
         startElement(main, "p", "xmlns=http://www.w3.org/1999/xhtml");

src/main/java/org/neuroml/export/neuron/ProcessManager.java

@@ -83,6 +83,7 @@ else if (Utils.isLinuxBasedPlatform())
             options.add("/usr");
             options.add("/usr/local");
             options.add("/usr/local/nrn/x86_64");
+            options.add("/srv/conda/envs/notebook/"); // location of neuron when pip installed on Binder... 
         }
 
         for (String option : options)