Simplify install

.gitignore

@@ -8,6 +8,9 @@
 *.iml
 *.xml
 
+# Ignore PyCharm files
+.idea/*
+
 chemkin_ode/*
 
 *ipynb_checkpoints*

.travis.yml

@@ -16,17 +16,32 @@ before_install:
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
-  - export PYTHONPATH=$TRAVIS_BUILD_DIR/AutoFragmentModeling:$PYTHONPATH
+  - export PYTHONPATH=$TRAVIS_BUILD_DIR:$PYTHONPATH
   # Update conda itself
   - conda update --yes conda
-  - cd ..
-  - cd AutoFragmentModeling
+  - cd $TRAVIS_BUILD_DIR
+  - pwd
 
 install:
-  - conda env create -f envs/environment_linux.yaml
+  - conda env create -q -f envs/environment_linux.yaml
   - source activate afm_env
   - conda list
 
-script: 
-  - make unittests
+jobs:
+  include:
+    - stage: test
+      script:
+        - make unittests
 
+    - script:
+        - conda remove -y -q rmg
+        - conda list
+        - cd ..
+        - git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git --branch afm_latest
+        - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git --branch afm_latest
+        - export PYTHONPATH=$TRAVIS_BUILD_DIR/../RMG-Py:$PYTHONPATH
+        - export PATH=$TRAVIS_BUILD_DIR/../RMG-Py:$PATH
+        - cd RMG-Py
+        - make
+        - cd $TRAVIS_BUILD_DIR
+        - make unittests

afm/canteraModel.py

@@ -395,7 +395,7 @@ def simulate(self):
             while canteraSimulation.time<condition.reactionTime.value_si:
 
                 # Advance the state of the reactor network in time from the current time to time t [s], taking as many integrator timesteps as necessary.
-                canteraSimulation.step(condition.reactionTime.value_si)
+                canteraSimulation.step()
                 times.append(canteraSimulation.time)
                 temperature.append(canteraReactor.T)
                 pressure.append(canteraReactor.thermo.P)