Add basico-copasi model interface (#531)

* Add basico-copasi model interface * fix docs * fixup
ICB-DCM · Jun 30, 2022 · 89727c3 · 89727c3
1 parent 1f5467c
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diff --git a/doc/api.rst b/doc/api.rst
@@ -23,5 +23,7 @@ API reference
    api_random_variables
    api_sge
    api_external
+   api_petab
+   api_copasi
    api_visualization
    api_weightedstatistics
diff --git a/doc/api_copasi.rst b/doc/api_copasi.rst
@@ -0,0 +1,4 @@
+.. _api_copasi:
+
+.. automodule:: pyabc.copasi
+   :imported-members:
diff --git a/doc/api_petab.rst b/doc/api_petab.rst
@@ -0,0 +1,4 @@
+.. _api_petab:
+
+.. automodule:: pyabc.petab
+   :imported-members:
diff --git a/doc/examples.rst b/doc/examples.rst
@@ -45,8 +45,8 @@ Algorithms and features
    examples/discrete_parameters.ipynb
    examples/look_ahead.ipynb
 
-Languages
----------
+External interfaces
+-------------------
 
 .. toctree::
    :maxdepth: 2
@@ -55,6 +55,7 @@ Languages
    examples/using_julia.ipynb
    examples/external_simulators.ipynb
    examples/petab_yaml2sbml.ipynb
+   examples/using_copasi.ipynb
 
 Application examples
 --------------------
@@ -75,8 +76,9 @@ Download the examples as notebooks
 * :download:`Model selection <examples/model_selection.ipynb>`
 * :download:`Early stopping of model simulations <examples/early_stopping.ipynb>`
 * :download:`Resuming stored ABC runs <examples/resuming.ipynb>`
-* :download:`Using R with pyABC <examples/using_R.ipynb>`
-* :download:`Using Julia with pyABC <examples/using_julia.ipynb>`
+* :download:`Using R via rpy2 <examples/using_R.ipynb>`
+* :download:`Using Julia via pyjulia <examples/using_julia.ipynb>`
+* :download:`Using COPASI via BasiCO <examples/using_copasi.ipynb>`
 * :download:`Ordinary differential equations: Conversion reaction <examples/conversion_reaction.ipynb>`
 * :download:`Markov jump process: Reaction network <examples/chemical_reaction.ipynb>`
 * :download:`Multi-scale model: Tumor spheroid growth <examples/multiscale_agent_based.ipynb>`

diff --git a/doc/examples/models/model1.xml b/doc/examples/models/model1.xml
@@ -0,0 +1,154 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by COPASI version 4.30 (Build 240) on 2021-03-03 15:27 with libSBML version 5.19.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model metaid="COPASI0" id="ABC_Example" name="ABC Example">
+    <notes>
+      <body xmlns="http://www.w3.org/1999/xhtml">
+        <pre>Example from:
+
+https://pyabc.readthedocs.io/en/latest/examples/chemical_reaction.html</pre>
+      </body>
+    </notes>
+    <annotation>
+      <COPASI xmlns="http://www.copasi.org/static/sbml">
+        <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+          <rdf:Description rdf:about="#COPASI0">
+            <dcterms:created>
+              <rdf:Description>
+                <dcterms:W3CDTF>2021-03-03T11:20:00Z</dcterms:W3CDTF>
+              </rdf:Description>
+            </dcterms:created>
+          </rdf:Description>
+        </rdf:RDF>
+      </COPASI>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="length" name="length">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area" name="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time" name="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment metaid="COPASI1" id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
+        <annotation>
+          <COPASI xmlns="http://www.copasi.org/static/sbml">
+            <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+              <rdf:Description rdf:about="#COPASI1">
+                <dcterms:created>
+                  <rdf:Description>
+                    <dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
+                  </rdf:Description>
+                </dcterms:created>
+              </rdf:Description>
+            </rdf:RDF>
+          </COPASI>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species metaid="COPASI2" id="X" name="X" compartment="compartment" initialConcentration="40" boundaryCondition="false" constant="false">
+        <annotation>
+          <COPASI xmlns="http://www.copasi.org/static/sbml">
+            <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+              <rdf:Description rdf:about="#COPASI2">
+                <dcterms:created>
+                  <rdf:Description>
+                    <dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
+                  </rdf:Description>
+                </dcterms:created>
+              </rdf:Description>
+            </rdf:RDF>
+          </COPASI>
+        </annotation>
+      </species>
+      <species metaid="COPASI3" id="Y" name="Y" compartment="compartment" initialConcentration="3" boundaryCondition="false" constant="false">
+        <annotation>
+          <COPASI xmlns="http://www.copasi.org/static/sbml">
+            <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+              <rdf:Description rdf:about="#Metabolite_0">
+                <dcterms:created>
+                  <rdf:Description>
+                    <dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
+                  </rdf:Description>
+                </dcterms:created>
+              </rdf:Description>
+            </rdf:RDF>
+          </COPASI>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="COPASI5" id="rate" name="rate" value="2.3" constant="true">
+        <annotation>
+          <COPASI xmlns="http://www.copasi.org/static/sbml">
+            <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+              <rdf:Description rdf:about="#COPASI5">
+                <dcterms:created>
+                  <rdf:Description>
+                    <dcterms:W3CDTF>2021-03-03T14:26:22Z</dcterms:W3CDTF>
+                  </rdf:Description>
+                </dcterms:created>
+              </rdf:Description>
+            </rdf:RDF>
+          </COPASI>
+        </annotation>
+      </parameter>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="COPASI4" id="reaction" name="R1" reversible="false">
+        <annotation>
+          <COPASI xmlns="http://www.copasi.org/static/sbml">
+            <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+              <rdf:Description rdf:about="#COPASI4">
+                <dcterms:created>
+                  <rdf:Description>
+                    <dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
+                  </rdf:Description>
+                </dcterms:created>
+              </rdf:Description>
+            </rdf:RDF>
+          </COPASI>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1"/>
+          <speciesReference species="Y" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Y" stoichiometry="2"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> rate </ci>
+              <ci> X </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/doc/examples/using_R.ipynb b/doc/examples/using_R.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Using R with pyABC"
+    "# Using R via rpy2"
    ]
   },
   {

diff --git a/doc/examples/using_copasi.ipynb b/doc/examples/using_copasi.ipynb
diff --git a/doc/examples/using_julia.ipynb b/doc/examples/using_julia.ipynb
@@ -5,7 +5,7 @@
    "id": "11bed717-fd94-4e66-a839-285e30377757",
    "metadata": {},
    "source": [
-    "# Using Julia with pyABC"
+    "# Using Julia via pyjulia"
    ]
   },
   {

diff --git a/pyabc/acceptor/__init__.py b/pyabc/acceptor/__init__.py
@@ -3,7 +3,6 @@
 =========
 
 Acceptors handle the acceptance step.
-
 """
 
 

diff --git a/pyabc/copasi/__init__.py b/pyabc/copasi/__init__.py
@@ -0,0 +1,8 @@
+"""
+Copasi
+======
+
+Simulations via COPASI (http://copasi.org).
+"""
+
+from .model import BasicoModel