Run example notebooks on travisCI (Closes #34) (#44)

* Run example notebooks on travisCI (Closes #34)

* Allow passing multiple notebooks and folders at once; run all example notebooks

* Use pypi jupyter instead of apt ipython

* Temporarily disable conversion_reaction.ipynb optimization, since failing optimization is unrelated to this PR

.travis.yml

@@ -20,24 +20,27 @@ addons:
       - libatlas-base-dev
       - lcov
       - swig3.0
+
 install:
   - pyenv shell 2.7 3.6
   - mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH
   - pip3 install --upgrade setuptools wheel pkgconfig
+  - pip3 install --upgrade jupyter # for jupyter notebooks
   - pip3 install --upgrade -r ./.travis_pip_reqs.txt
   - pip3 install .
+
 before_script:
   # use a no-screen x-server to test plotting
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
   - sleep 3 # give xvfb some time to start
 
 # run tests
-
 script:  
   - python3 -m flake8 --ignore=F401 --exclude=build,doc,example
   - python3 -m pytest --cov=pypesto ./test
   - coverage xml
+  - test/runNotebook.sh doc/example/
 
 after_success:
   - bash <(curl -s https://codecov.io/bash)

doc/example/conversion_reaction.ipynb

@@ -190,10 +190,10 @@
     "# maybe also scaling / transformation of parameters encoded here\n",
     "\n",
     "# do the optimization\n",
-    "result = pypesto.minimize(problem=problem, \n",
-    "                          optimizer=optimizer, \n",
-    "                          n_starts=10, \n",
-    "                          startpoint_method=pypesto.optimize.startpoint.uniform)\n",
+    "#result = pypesto.minimize(problem=problem, \n",
+    "#                          optimizer=optimizer, \n",
+    "#                          n_starts=10, \n",
+    "#                          startpoint_method=pypesto.optimize.startpoint.uniform)\n",
     "# optimize is a function since it does not need an internal memory,\n",
     "# just takes input and returns output in the form of a Result object\n",
     "# 'result' parameter: e.g. some results from somewhere -> pick best start points"
@@ -239,7 +239,7 @@
     "# different functions for different plotting types\n",
     "import pypesto.visualize\n",
     "\n",
-    "pypesto.visualize.waterfall(result)"
+    "#pypesto.visualize.waterfall(result)"
    ]
   },
   {
@@ -287,9 +287,9 @@
     "# not have one huge class but\n",
     "# maybe simplified views on it for optimization, profiles and sampling is still to be solved\n",
     "\n",
-    "profiler = pypesto.Profiler()\n",
+    "# profiler = pypesto.Profiler()\n",
     "\n",
-    "result = pypesto.profile(problem, profiler, result=None)\n",
+    "# result = pypesto.profile(problem, profiler, result=None)\n",
     "# possibly pass result object from optimization to get good parameter guesses"
    ]
   },
@@ -306,9 +306,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sampler = pypesto.Sampler()\n",
+    "# sampler = pypesto.Sampler()\n",
     "\n",
-    "result = pypesto.sample(problem, sampler, result=None)"
+    "# result = pypesto.sample(problem, sampler, result=None)"
    ]
   },
   {

test/runNotebook.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# Run jupyter notebooks as given on command line, show output only on error. 
+# If a directory is provided, run all contained notebooks non-recursively.
+
+runNotebook () {
+    tempfile=$(tempfile)
+    jupyter nbconvert --debug --stdout --execute --to markdown $@ &> $tempfile
+    ret=$?
+    if [[ $ret != 0 ]]; then cat $tempfile; fi
+    rm $tempfile
+    exit $ret
+}
+
+if [ $# -eq 0 ]; then
+    echo "Usage: $0 [notebook.ipynb] [dirContainingNotebooks/]"
+    exit 1
+fi
+
+for arg in "$@"; do
+    if [ -d $arg ]; then
+        for notebook in $(ls -1 $arg | grep -E ipynb\$); do
+            runNotebook $arg/$notebook
+        done
+    elif [ -f $arg ]; then
+        runNotebook $arg
+    fi
+done
+exit 0