Specify openbabel >= 3 in environment.yml

.github/workflows/cont_int.yml

@@ -1,37 +1,38 @@
 name: continuous integration
 
-on: [push]
+on:
+  push:
+  pull_request:
+    branches:
+      - master
+    types: [opened, synchronize, reopened, ready_for_review, review_requested]
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up miniconda Python ${{ matrix.python-version }}
+    - name: Set up miniconda Python 3.7
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: t3_env
         environment-file: environment.yml
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.7
         auto-activate-base: false
 
-    - name: Install dependencies
+    - name: Install codecov
+      run: conda install -y -c conda-forge codecov
+
+    - name: Install dependencies and test with PyTest
       shell: bash -l {0}
       run: |
         export PYTHONPATH=$PYTHONPATH:$(pwd)
         conda activate t3_env
         make install
         echo $(pwd)
         conda list
-
-    - name: Test with nosetests
-      shell: bash -l {0}
-      run: |
         cd ..
         cd RMG-Py
         export PYTHONPATH=$PYTHONPATH:$(pwd)

devtools/install_pyrms.sh

@@ -12,10 +12,3 @@ julia devtools/install_pycall.jl
 
 echo installing pyrms, RMS, and all required Julia packages...
 python -c "import pyrms; pyrms.install()"
-
-# the above line installs RMS v0.2.1
-# v0.3.2 is needed to use the latest SA features
-# once there is a functional package for v0.3.2, 
-# the line below can be deleted since pyrms.install() will pull the latest version
-echo installing RMS v0.3.2...
-julia devtools/install_RMS_v032.jl

environment.yml

@@ -2,61 +2,60 @@ name: t3_env
 channels:
   - defaults
   - rmg
-  - anaconda
-  - omnia
   - conda-forge
-  - mjohnson541
 dependencies:
-  - ase >=3.15.0
   - cairo
   - cairocffi
   - rmg::cantera >=2.3.0
-  - cclib >=1.6
+  - conda-forge::cclib >=1.6.3
   - rmg::chemprop
-  - codecov
   - coolprop
   - coverage
   - cython >=0.25.2
   - ffmpeg
   - rmg::gprof2dot
   - graphviz
   - h5py
-  - ipython
   - jinja2
   - jupyter
   - rmg::lpsolve55
-  - mako
   - markupsafe
-  - matplotlib >=2.2.2
-  - mkdocs-material >=5.1.7
-  - mkdocs-material-extensions
-  - mock
+  - matplotlib >=1.5
   - rmg::mopac
   - mpmath
+  - rmg::muq2
   - networkx
-  - nose
   - rmg::numdifftools
-  - numpy >=1.15.4
-  - openbabel
-  - paramiko >=2.6.0
+  - numpy >=1.10.0
+  - conda-forge::openbabel >= 3
   - pandas
   - psutil
-  - py3dmol >= 0.8.0
   - rmg::pydas >=1.0.2
   - pydot
   - rmg::pydqed >=1.0.1
   - pymongo
   - pyparsing
   - rmg::pyrdl
-  - pyrms
-  - python >=3.7
   - pytest
+  - python >=3.7
   - pyyaml
-  - qcelemental
   - rmg::quantities
   - rmg::rdkit >=2020.03.3.0
   - scikit-learn
   - scipy
-  - sphinx
   - rmg::symmetry
+  - xlrd
   - xlwt
+  - anaconda::sphinx_rtd_theme
+  - anaconda::paramiko >=2.6.0
+  - conda-forge::py3dmol >= 0.8.0
+  - conda-forge::ase >=3.15.0
+  - anaconda::ipython
+  - anaconda::sphinx
+  - conda-forge::qcelemental
+  - mako
+  - conda-forge::mkdocs-material >=5.1.7
+  - conda-forge::mkdocs-material-extensions
+  - conda-forge::mock
+  - mjohnson541::pyrms
+  - mjohnson541::julia >= 1.6

t3/simulate/rms_constantHP.py

@@ -12,13 +12,12 @@
 from t3.simulate.adapter import SimulateAdapter
 from t3.simulate.factory import register_simulate_adapter
 
-HAS_RMS = True
 try:
     from diffeqpy import de
     from pyrms import rms
 except (ImportError, ModuleNotFoundError):
     # diffeqpy and/or pyrms are missing
-    HAS_RMS = False
+    Logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were correctly installed.')
 
 
 class RMSConstantHP(SimulateAdapter):
@@ -147,10 +146,6 @@ def simulate(self):
         """
         Simulate the mechanism with RMS
         """
-        if not HAS_RMS:
-            self.logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were'
-                              'correctly installed.')
-
         if len(self.observable_list):
             self.logger.info('Running a simulation with SA using RMSConstantHP...')
         else:

t3/simulate/rms_constantTP.py

@@ -11,13 +11,12 @@
 from t3.simulate.adapter import SimulateAdapter
 from t3.simulate.factory import register_simulate_adapter
 
-HAS_RMS = True
 try:
     from diffeqpy import de
     from pyrms import rms
 except (ImportError, ModuleNotFoundError):
     # diffeqpy and/or pyrms are missing
-    HAS_RMS = False
+    Logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were correctly installed.')
 
 
 class RMSConstantTP(SimulateAdapter):
@@ -146,10 +145,6 @@ def simulate(self):
         """
         Simulate the mechanism with RMS
         """
-        if not HAS_RMS:
-            self.logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were'
-                              'correctly installed.')
-
         if len(self.observable_list):
             self.logger.info('Running a simulation with SA using RMSConstantTP...')
         else:

t3/simulate/rms_constantUV.py

@@ -12,13 +12,12 @@
 from t3.simulate.adapter import SimulateAdapter
 from t3.simulate.factory import register_simulate_adapter
 
-HAS_RMS = True
 try:
     from diffeqpy import de
     from pyrms import rms
 except (ImportError, ModuleNotFoundError):
     # diffeqpy and/or pyrms are missing
-    HAS_RMS = False
+    Logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were correctly installed.')
 
 
 class RMSConstantUV(SimulateAdapter):
@@ -147,10 +146,6 @@ def simulate(self):
         """
         Simulate the mechanism with RMS
         """
-        if not HAS_RMS:
-            self.logger.error('Missing diffeqpy and/or pyrms. Please ensure these dependencies were'
-                              'correctly installed.')
-
         if len(self.observable_list):
             self.logger.info('Running a simulation with SA using RMSConstantUV...')
         else: