doc(python) Extend steadystate python-interface example | ci(python) F…

…ixes #348 (#349)

* doc(python) Extend steadystate python-interface example

* feature(python) Add basic plotting functions

* ci(python) python3 instead of python3.6

* ci() Disallow failure on osx; update python path

* doc(python) make doxygen compatible

* ci(osx) add tex path

.travis.yml

@@ -52,35 +52,13 @@ matrix:
         on:
           branch: master
 
-  allow_failures:
-  # allow osx build to fail until symengine/homebrew/python3.7 issue is resolved
-    - os: osx
-      osx_image: xcode9.3
-      compiler: clang
-      before_install: 
-        - brew update # without this homebrew can stumble over wrong ruby version
-        - travis_wait brew install gcc || brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
-        - brew install hdf5 cppcheck swig doxygen ragel graphviz homebrew/cask/mactex
-        - brew upgrade python
-      after_success: 
-        - cd $BASE_DIR # cd to base dir for correct relative path in deploy
-      deploy:
-        provider: pages
-        local-dir: doc
-        skip-cleanup: true
-        github-token: $GITHUB_TOKEN  # Set in the settings page of your repository, as a secure variable
-        keep-history: false
-        verbose: true
-        on:
-          branch: master
-
 install:
     # Python distutils only looks for `swig` and does not find `swig3.0`
     - export BASE_DIR=`pwd`
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH; fi
     - pyenv versions
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv shell 2.7 3.6; fi
-    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Users/travis/Library/Python/3.6/bin:$PATH; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Users/travis/Library/Python/3.7/bin:/Library/TeX/texbin:$PATH; fi
     - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy coverage scipy
     - ./scripts/buildSuiteSparse.sh
     - ./scripts/buildSundials.sh

python/amici/plotting.py

@@ -0,0 +1,52 @@
+"""@package amici.plotting Plotting related functions"""
+
+import matplotlib.pyplot as plt 
+
+def plotStateTrajectories(rdata, state_indices=None, ax = None):
+    """Plot state trajectories
+    
+    Arguments:
+    rdata: AMICI simulation results as returned by amici.getSimulationResults()
+    state_indices: Indices of states for which trajectories are to be plotted
+    ax: matplotlib.axes.Axes instance to plot into
+    
+    Returns:
+
+    Raises:
+
+    """
+    if not ax:
+        fig, ax = plt.subplots()
+    if not state_indices:
+        state_indices = range(rdata['x'].shape[1])
+    for ix in state_indices:
+        ax.plot(rdata['t'], rdata['x'][:, ix], label='$x_%d$' % ix)
+        ax.set_xlabel('$t$ (s)')
+        ax.set_ylabel('$x_i(t)$ (mmol/ml)')
+        ax.legend()
+        ax.set_title('State trajectories')
+
+
+def plotObservableTrajectories(rdata, observable_indices=None, ax = None):
+    """Plot observable trajectories
+    
+    Arguments:
+    rdata: AMICI simulation results as returned by amici.getSimulationResults()
+    observable_indices: Indices of observables for which trajectories are to be plotted
+    ax: matplotlib.axes.Axes instance to plot into
+
+    Returns:
+
+    Raises:
+
+    """
+    if not ax:
+        fig, ax = plt.subplots()
+    if not observable_indices:
+        observable_indices = range(rdata['y'].shape[1])
+    for iy in observable_indices:
+        ax.plot(rdata['t'], rdata['y'][:, iy], label='$y_%d$' % iy)
+        ax.set_xlabel('$t$ (s)')
+        ax.set_ylabel('$y_i(t)$ (AU)')
+        ax.legend()
+        ax.set_title('Observables')