Merge pull request #264 from ICB-DCM/develop

Release 0.0.12
ICB-DCM · Apr 6, 2020 · f9f4a52 · f9f4a52
2 parents 07fd9da + 9033cbf
commit f9f4a52
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Showing 76 changed files with 4,760 additions and 2,627 deletions.
diff --git a/.gitignore b/.gitignore
@@ -98,6 +98,7 @@ dask-worker-space
 venv/*
 *.tmp
 tmp/*
+*/tmp/*
 amici_models/*
 *.txt
 test/doc/example/tmp/benchmark-models/

diff --git a/.travis.yml b/.travis.yml
@@ -26,18 +26,27 @@ install:
   - mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH
   - pip3 install --upgrade -r ./.travis_pip_reqs.txt
   - pip3 install .
-  - pip3 install https://github.com/petab-dev/petab/archive/develop.zip # REMOVE ME
-  - pip3 install -e git+https://github.com/icb-dcm/amici.git@develop#egg=amici\&subdirectory=python/sdist # REMOVE ME
-  - git clone --depth 1 https://github.com/petab-dev/petab_test_suite tmp/petab_test_suite
+  - pip3 install https://github.com/petab-dev/petab/archive/develop.zip
+  - pip3 install -e
+      git+https://github.com/icb-dcm/amici.git@develop#egg=amici\&subdirectory=python/sdist
+  - git clone --depth 1
+      https://github.com/petab-dev/petab_test_suite tmp/petab_test_suite
   - pip3 install -e tmp/petab_test_suite
 
 # run tests
 script:
-  - python3 -m flake8 --exclude=build,doc,example,tmp,amici_models
+  - python3 -m flake8
+      --exclude=build,doc,example,tmp,amici_models
+      --per-file-ignores='*/__init__.py:F401'
   - travis_wait 20 python3 -m pytest --cov=pypesto ./test/test_*
-  - travis_wait 20 xvfb-run -a python3 -m pytest --cov=pypesto --cov-append ./test/visualize/test_*
-  - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then sphinx-build -W -b html -d doc/_build/html doc/ doc/_build/html; fi
-  - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then test/run_notebook.sh doc/example/; fi
+  - travis_wait 20 xvfb-run -a python3 -m pytest
+      --cov=pypesto --cov-append ./test/visualize/test_*
+  - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+      sphinx-build -W -b html -d doc/_build/html doc/ doc/_build/html;
+    fi
+  - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+      test/run_notebook.sh doc/example/;
+    fi
   - coverage xml
 
 after_success:

diff --git a/README.md b/README.md
@@ -18,9 +18,16 @@ pyPESTO features include:
 * Multi-start local optimization
 * Profile computation
 * Result visualization
-* Interface to [AMICI](https://github.com/ICB-DCM/AMICI/) for efficient simulation and sensitivity analysis of ordinary differential equation (ODE) models
-* Parameter estimation pipeline for systems biology problems specified in [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
-* Parameter estimation with qualitative data as described in [Schmiester et al. (2019)](https://www.biorxiv.org/content/10.1101/848648v1). This is currently implemented in the `feature_ordinal` branch.
+* Interface to [AMICI](https://github.com/ICB-DCM/AMICI/) for efficient
+  simulation and sensitivity analysis of ordinary differential equation (ODE)
+  models
+  ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/boehm_JProteomeRes2014.ipynb))
+* Parameter estimation pipeline for systems biology problems specified in
+  [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
+  ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/petab_import.ipynb))
+* Parameter estimation with qualitative data as described in
+  [Schmiester et al. (2019)](https://www.biorxiv.org/content/10.1101/848648v1).
+  This is currently implemented in the `feature_ordinal` branch.
 
 ## Quick install
 

diff --git a/doc/api_engine.rst b/doc/api_engine.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.engine
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_objective.rst b/doc/api_objective.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.objective
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_optimize.rst b/doc/api_optimize.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.optimize
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_problem.rst b/doc/api_problem.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.problem
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_profile.rst b/doc/api_profile.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.profile
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_result.rst b/doc/api_result.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.result
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_sample.rst b/doc/api_sample.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.sample
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_startpoint.rst b/doc/api_startpoint.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.startpoint
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/api_visualize.rst b/doc/api_visualize.rst
@@ -1,2 +1,4 @@
 .. automodule:: pypesto.visualize
-   :special-members: __init__,__call__
+   :members:
+   :inherited-members:
+   :special-members:
diff --git a/doc/example/conversion_reaction.ipynb b/doc/example/conversion_reaction.ipynb
diff --git a/doc/example/conversion_reaction/model_conversion_reaction.xml b/doc/example/conversion_reaction/model_conversion_reaction.xml
@@ -1,101 +1,77 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by COPASI version 4.23 (Build 184) on 2018-07-25 11:22 with libSBML version 5.16.1. -->
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1" level="3" version="1" layout:required="false" render:required="false">
-  <model metaid="COPASI0" id="New_Model" name="New Model" substanceUnits="substance" timeUnits="time" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="substance">
-    <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>2018-07-25T11:18:28Z</dcterms:W3CDTF>
-              </rdf:Description>
-            </dcterms:created>
-          </rdf:Description>
-        </rdf:RDF>
-      </COPASI>
-    </annotation>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="conversion_reaction_0" name="Conversion Reaction 0">
+
     <listOfUnitDefinitions>
-      <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="-3" multiplier="1"/>
         </listOfUnits>
       </unitDefinition>
-      <unitDefinition id="time" name="time">
-        <listOfUnits>
-          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
-        </listOfUnits>
-      </unitDefinition>
       <unitDefinition id="substance" name="substance">
         <listOfUnits>
           <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
         </listOfUnits>
       </unitDefinition>
     </listOfUnitDefinitions>
+
     <listOfCompartments>
-      <compartment metaid="COPASI1" id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
+      </compartment>
     </listOfCompartments>
+
     <listOfSpecies>
-      <species metaid="COPASI2" id="A" name="A" compartment="compartment" initialConcentration="1" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-      <species metaid="COPASI3" id="B" name="B" compartment="compartment" initialConcentration="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
+      </species>
+      <species id="B" name="B" compartment="compartment" initialConcentration="0" boundaryCondition="false" constant="false">
+      </species>
     </listOfSpecies>
+
+    <listOfParameters>
+      <parameter id="k1" name="k1" value="0" constant="true">
+      </parameter>
+      <parameter id="k2" name="k2" value="0" constant="true">
+      </parameter>
+    </listOfParameters>
+
     <listOfReactions>
-      <reaction metaid="COPASI4" id="R1" name="R1" reversible="true" fast="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>2018-07-25T11:19:13Z</dcterms:W3CDTF>
-                  </rdf:Description>
-                </dcterms:created>
-              </rdf:Description>
-            </rdf:RDF>
-          </COPASI>
-        </annotation>
+      <reaction id="fwd" name="fwd" reversible="false">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="rev" name="rev" reversible="false">
         <listOfReactants>
-          <speciesReference species="A" stoichiometry="1" constant="true"/>
+          <speciesReference species="B" stoichiometry="1"/>
         </listOfReactants>
         <listOfProducts>
-          <speciesReference species="B" stoichiometry="1" constant="true"/>
+          <speciesReference species="A" stoichiometry="1"/>
         </listOfProducts>
         <kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
               <ci> compartment </ci>
-              <apply>
-                <minus/>
-                <apply>
-                  <times/>
-                  <ci> k1 </ci>
-                  <ci> A </ci>
-                </apply>
-                <apply>
-                  <times/>
-                  <ci> k2 </ci>
-                  <ci> B </ci>
-                </apply>
-              </apply>
+              <ci> k2 </ci>
+              <ci> B </ci>
             </apply>
           </math>
-          <listOfLocalParameters>
-            <localParameter id="k1" name="k1" value="0.3"/>
-            <localParameter id="k2" name="k2" value="0.5"/>
-          </listOfLocalParameters>
         </kineticLaw>
       </reaction>
     </listOfReactions>
+
   </model>
 </sbml>
-Original file line number
+Diff line change
@@ Expand Up / @@ -98,6 +98,7 @@ dask-worker-space @@
     venv/*
     *.tmp
     tmp/*
+    */tmp/*
     amici_models/*
     *.txt
     test/doc/example/tmp/benchmark-models/
@@ Expand Down @@