clean up, rerun notebooks

ICB-DCM · Oct 18, 2018 · 6addb8b · 6addb8b
1 parent 77a5d70
commit 6addb8b
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Showing 5 changed files with 226 additions and 216 deletions.
diff --git a/.gitignore b/.gitignore
@@ -80,7 +80,7 @@ data/figures
 coverage_py.xml
 
 # examples
-doc/example/*/*/*
+doc/example/tmp
 
 # general
 data/.snakemake

diff --git a/doc/example/conversion_reaction.ipynb b/doc/example/conversion_reaction.ipynb
diff --git a/doc/example/fixed_parameters.ipynb b/doc/example/fixed_parameters.ipynb
diff --git a/doc/example/rosenbrock.ipynb b/doc/example/rosenbrock.ipynb
diff --git a/test/test_sbml_conversion.py b/test/test_sbml_conversion.py
@@ -84,13 +84,16 @@ def parameter_estimation(
 
 
 def _load_model_objective(example_name):
-    sbml_file = os.path.join('doc', 'example',
-                             'model_' + example_name + '.xml')
     # name of the model that will also be the name of the python module
     model_name = 'model_' + example_name
+
+    # sbml file
+    sbml_file = os.path.join('doc', 'example', 'tmp',
+                             model_name + '.xml')
+
     # directory to which the generated model code is written
-    model_output_dir = os.path.join('doc', 'example',
-                                    example_name)
+    model_output_dir = os.path.join('doc', 'example', 'tmp',
+                                    model_name)
 
     # import sbml model, complile and generate amici module
     sbml_importer = amici.SbmlImporter(sbml_file)