Py3 only fixes breaking Py2 compatibility

.conda/meta.yaml

@@ -34,10 +34,10 @@ requirements:
     - cairo
     - cairocffi
     - cantera >=2.3.0
+    - chemprop
     - coolprop
     - coverage
     - cython >=0.25.2
-    - dde
     - ffmpeg
     - gprof2dot
     - graphviz

.travis.yml

@@ -7,13 +7,6 @@ env:
     - secure: "cfosGf5hvUhIlPoGJu0d/HFddrMwIFU7FfLwd8yRrMGkYv0ePOwAW9kmhFSxUYvuXkxzgD75cIICMFY2fSm6VXBXXzfPQD7vwzoApXf7a8vi0C64XhinXhdEyUYb5/v8fswa0zheUENYhUS1tOqDXT/h8EPNZT5wKizaA3O2Wa8="
     - secure: "QXuqKYuwCocqsTMePBc5OugBbQC4/t+335TYLdkletiateP/rF/eDsVRG792/BVq5gKRZgz3NH9ipTNm5pZoCbAEPt9+eDpfts8WeAbxmjdcEjfBxxwZ69wUTPAVrezTGn2k7W2UBdFrWeUNKPAVCKIkoviXqOHFitqJEC+c6JY="
     - secure: "jIyBEzR10l5SWvY5ouEYzA8YzPHIZNMXMBdcXwuwte8NCU8GBYUqhHA1L67nTaBdLhWbrZ2NireVKPQWJp3ctcI0IB6xZzaYlVpgN/udGPO+1MZd9Xhp9TWuJWrGZ9EoWGB9L5H+O7RYwcDMVH5CUrCIBdsSJuyE8aDpky1/IVE="
-  matrix:
-    - ENV_FILE='environment_linux.yml'
-    - ENV_FILE='environment_py3.yml'
-
-matrix:
-  allow_failures:
-    - env: ENV_FILE='environment_py3.yml'
 
 stages:
   - test
@@ -39,38 +32,36 @@ before_install:
   - git config --global user.name "Travis Deploy"
   - git config --global user.email "rmg_dev@mit.edu"
 
-install:
-  # Clone RMG-database
-  - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
-  - cd RMG-Py
-  # Create and activate environment
-  - conda env create -q -f $ENV_FILE
-  - source activate rmg_env
-  # Install codecov for coverage report
-  - conda install -y -c conda-forge codecov
-  - conda list
-  # Setup MOPAC license key
-  - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
-  # Install Q2DTor
-  - git clone -b arkane https://github.com/mjohnson541/Q2DTor.git external/Q2DTor
-  # Compile RMG
-  - make
-
-script:
-  - make test-unittests
-  - make test-functional
-  - make test-database
-
-after_success:
-  - codecov
-  - bash ./deploy.sh
-
 jobs:
   include:
+    - stage: test
+      install:
+        # Clone RMG-database
+        - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
+        - cd RMG-Py
+        # Create and activate environment
+        - conda env create -q -f environment.yml
+        - source activate rmg_env
+        # Install codecov for coverage report
+        - conda install -y -c conda-forge codecov
+        - conda list
+        # Setup MOPAC license key
+        - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
+        # Install Q2DTor
+        - git clone -b arkanepy3 https://github.com/mjohnson541/Q2DTor.git external/Q2DTor
+        # Compile RMG
+        - make
+      script:
+        - make test-unittests
+        - make test-functional
+        - make test-database
+      after_success:
+        - codecov
+        - bash ./deploy.sh
     - stage: documentation
       install:
         - cd RMG-Py
-        - conda env create -q -f environment_linux.yml
+        - conda env create -q -f environment.yml
         - source activate rmg_env
         # Install sphinx for building documentation
         - conda install -y sphinx
@@ -82,7 +73,6 @@ jobs:
         - export COMMITMESSAGE="Automatic documentation rebuild"
       script:
         - make travis_setup clean html publish
-      after_success: skip
     - stage: deploy
       install:
         # Setup conda build
@@ -95,7 +85,6 @@ jobs:
         - conda config --set anaconda_upload yes
       script:
         - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
-      after_success: skip
     - os: osx
       install:
         # Setup conda build
@@ -108,4 +97,3 @@ jobs:
         - conda config --set anaconda_upload yes
       script:
         - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
-      after_success: skip

Makefile

@@ -4,9 +4,6 @@
 #
 ################################################################################
 
-DASPK=$(shell python -c 'import pydas.daspk; print(pydas.daspk.__file__)')
-DASSL=$(shell python -c 'import pydas.dassl; print(pydas.dassl.__file__)')
-
 .PHONY : all minimal main solver check cantherm clean install decython documentation mopac_travis
 
 all: main solver check
@@ -15,22 +12,10 @@ minimal:
 	python setup.py build_ext minimal --inplace --build-temp .
 
 main:
-	@ echo "Checking you have PyDQED..."
-	@ python -c 'import pydqed; print(pydqed.__file__)'
 	python setup.py build_ext main --inplace --build-temp .
 
 solver:
-
-ifneq ($(DASPK),)
-	@ echo "DASPK solver found. Compiling with DASPK and sensitivity analysis capability..."
-	@ (echo DEF DASPK = 1) > rmgpy/solver/settings.pxi 
-else ifneq ($(DASSL),)
-	@ echo "DASSL solver found. Compiling with DASSL.  Sensitivity analysis capabilities are off..."
-	@ (echo DEF DASPK = 0) > rmgpy/solver/settings.pxi
-else
-	@ echo 'No PyDAS solvers found.  Please check if you have the latest version of PyDAS.'
-	@ python -c 'import pydas.dassl' 
-endif
+	@ python utilities.py check-pydas
 	python setup.py build_ext solver --inplace --build-temp .
 
 arkane:
@@ -73,7 +58,7 @@ q2dtor:
  and HinderedRotor2D within Arkane please cite:  \n\nD. Ferro-Costas, M. N. D. S.Cordeiro, D. G. Truhlar, A.\
 		  Fernández-Ramos, Comput. Phys. Commun. 232, 190-205, 2018.\n"
 	@ read -p "Press ENTER to continue" dummy
-	@ git clone https://github.com/mjohnson541/Q2DTor.git external/Q2DTor --branch arkane
+	@ git clone https://github.com/mjohnson541/Q2DTor.git external/Q2DTor --branch arkanepy3
 
 decython:
 	# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
@@ -99,7 +84,7 @@ ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
 endif
-	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
+	nosetests --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
 
 test-database:
 	nosetests --nocapture --nologcapture --verbose --detailed-errors testing/databaseTest.py

arkane/inputTest.py

@@ -201,8 +201,8 @@ def test_reaction(self):
         self.assertEqual(rxn.label, 'CH2O+H=Methoxy')
         self.assertEqual(len(rxn.reactants), 2)
         self.assertEqual(len(rxn.products), 1)
-        self.assertAlmostEqual(rxn.reactants[0].conformer.E0.value_si, 120038.96)
-        self.assertAlmostEqual(rxn.reactants[1].conformer.E0.value_si, 0)
+        self.assertAlmostEqual(rxn.reactants[0].conformer.E0.value_si, 0)
+        self.assertAlmostEqual(rxn.reactants[1].conformer.E0.value_si, 120038.96)
         self.assertAlmostEqual(rxn.products[0].conformer.E0.value_si, 39496.96)
         self.assertAlmostEqual(rxn.transitionState.conformer.E0.value_si, 142674.4)
         self.assertAlmostEqual(rxn.transitionState.frequency.value_si, -967.0)

arkane/main.py

@@ -221,7 +221,7 @@ def execute(self):
         if supporting_info:
             # write supporting_info.csv for statmech jobs
             supporting_info_file = os.path.join(self.outputDirectory, 'supporting_information.csv')
-            with open(supporting_info_file, 'wb') as csvfile:
+            with open(supporting_info_file, 'w') as csvfile:
                 writer = csv.writer(csvfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
                 writer.writerow(['Label', 'Symmetry Number', 'Number of optical isomers', 'Symmetry Group',
                                  'Rotational constant (cm-1)',
@@ -251,7 +251,7 @@ def execute(self):
             hr_file = os.path.join(self.outputDirectory, 'hindered_rotor_scan_data.csv')
             # find longest length to set column number for energies
             max_energy_length = max([len(hr[4]) for hr in hindered_rotor_info])
-            with open(hr_file, 'wb') as csvfile:
+            with open(hr_file, 'w') as csvfile:
                 writer = csv.writer(csvfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
                 writer.writerow(['species', 'rotor_number', 'symmetry', 'resolution (degrees)',
                                  'pivot_atoms', 'frozen_atoms'] +

arkane/statmech.py

@@ -720,6 +720,7 @@ def create_hindered_rotor_figure(self, angle, v_list, cosineRotor, fourierRotor,
             ['$0$', '$\pi/4$', '$\pi/2$', '$3\pi/4$', '$\pi$', '$5\pi/4$', '$3\pi/2$', '$7\pi/4$', '$2\pi$'])
 
         self.hindered_rotor_plots.append((fig, rotorIndex))
+        fig.close()
 
     def save_hindered_rotor_figures(self, directory):
         """

documentation/source/users/rmg/input.rst

@@ -662,8 +662,8 @@ cyclic species regardless of the ``onlyCyclics`` setting. If ``onlyCyclics`` is
 than zero, RMG will log a warning that ``onlyCyclics`` should also be True and the machine learning estimator will be
 restricted to only cyclic species with the specified minimum cycle overlap.
 
-If the estimated uncertainty of the thermo prediction is greater than any of the ``UncertaintyCutoff`` values, then
-machine learning estimation is not used for that species.
+Note that the current machine learning model is not yet capable of estimating uncertainty so the ``UncertaintyCutoff``
+values do not yet have any effect.
 
 
 .. _pressuredependence:

environment_py3.yml → environment.yml

@@ -4,12 +4,14 @@ channels:
   - rmg
   - rdkit
   - cantera
-  - anaconda
+  - pytorch
+  - conda-forge
 dependencies:
   - cairo
   - cairocffi
   - cantera >=2.3.0
   - cclib
+  - chemprop
   - coolprop
   - coverage
   - cython >=0.25.2