Merge pull request #10 from biosimulators/update-docker

Fix CI

.github/workflows/ci.yml

@@ -73,7 +73,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v3
         with:
-          python-version: '3.9'
+          python-version: '3.11'
 
       - name: Setup pip cache
         uses: actions/cache@v3

Dockerfile

@@ -1,5 +1,5 @@
 # Base OS
-FROM python:3.9-slim-buster
+FROM python:3.11-slim-bookworm
 
 ARG VERSION="0.1.22"
 ARG SIMULATOR_VERSION="0.11.25"
@@ -45,9 +45,11 @@ RUN apt-get update -y \
 
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_AMICI
-RUN pip install /root/Biosimulators_AMICI \
+RUN pip install pip==23.0.1
+RUN pip install sympy /root/Biosimulators_AMICI \
     && rm -rf /root/Biosimulators_AMICI
-RUN pip install amici==${SIMULATOR_VERSION}
+#RUN pip install sympy /root/Biosimulators_AMICI amici==${SIMULATOR_VERSION} \
+#    && rm -rf /root/Biosimulators_AMICI
 ENV VERBOSE=0 \
     MPLBACKEND=PDF
 

biosimulators_amici/core.py

@@ -280,7 +280,7 @@ def import_model_from_sbml(filename, variables):
     model_dir = tempfile.mkdtemp()
     model_name = 'biosimulators_amici_model_' + os.path.basename(model_dir)
     constant_parameters = [param.getId() for param in sbml_model.parameters if param.constant]
-    observables = {var: {'name': var, 'formula': var} for var in variables}
+    observables = {variable_id_to_observable_id(var): {'name': var, 'formula': var} for var in variables}
     sbml_importer.sbml2amici(model_name,
                              model_dir,
                              observables=observables,
@@ -456,7 +456,7 @@ def validate_variables(model, variables, variable_target_sbml_id_map):
     unpredicted_symbols = []
     unpredicted_targets = []
 
-    sbml_id_to_obs_index = {id: index for index, id in enumerate(model.getObservableIds())}
+    obs_id_to_obs_index = {id: index for index, id in enumerate(model.getObservableIds())}
 
     for variable in variables:
         if variable.symbol:
@@ -467,7 +467,7 @@ def validate_variables(model, variables, variable_target_sbml_id_map):
 
         else:
             sbml_id = variable_target_sbml_id_map.get(variable.target, None)
-            i_obs = sbml_id_to_obs_index.get(sbml_id, None)
+            i_obs = obs_id_to_obs_index.get(variable_id_to_observable_id(sbml_id), None)
             if i_obs is None:
                 unpredicted_targets.append(variable.target)
             else:
@@ -566,3 +566,12 @@ def preprocess_sed_task(task, variables, config=None):
             }
         },
     }
+
+
+def variable_id_to_observable_id(variable_id: str) -> str:
+    """Convert a variable ID to an observable ID.
+
+    In AMICI, identifiers need to be globally unique. Therefore, we cannot use a species ID as an observable ID.
+    Let's hope that this alias does not already exist in the model...
+    """
+    return f"___{variable_id}"

docs-src/conf.py

@@ -42,7 +42,6 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.linkcode',
     'sphinx.ext.napoleon',
-    'sphinxprettysearchresults',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs-src/requirements.txt

@@ -1,3 +1,2 @@
 pydata-sphinx-theme
 sphinx >= 1.8
-sphinxprettysearchresults

tests/test_core_main.py

@@ -251,7 +251,7 @@ def test_exec_sed_task_with_changes(self):
             model.changes.append(sedml_data_model.ModelAttributeChange(
                 target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{}']".format(variable_id),
                 target_namespaces=self.NAMESPACES,
-                new_value=None))
+                new_value=1.3))
             variables.append(sedml_data_model.Variable(
                 id=variable_id,
                 target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{}']".format(variable_id),
@@ -287,7 +287,7 @@ def test_exec_sed_task_with_changes(self):
         for variable_id in variable_ids:
             numpy.testing.assert_allclose(
                 results3[variable_id],
-                results[variable_id][-int(sim.number_of_points + 1):],
+                results[variable_id][-int(sim.number_of_points + 1):], rtol=1e-5, atol=1e-4
             )
 
         task.model.changes = [
@@ -673,3 +673,6 @@ def test_exec_sedml_docs_in_combine_archive_with_docker_image(self):
             archive_filename, out_dir, docker_image, environment=env, pull_docker_image=False)
 
         self._assert_combine_archive_outputs(doc, out_dir)
+
+if __name__ == "__main__":
+    unittest.main()