RMG-Py v3.0.0 Release

Author: mliu49

.conda/conda_build_config.yaml

@@ -1,5 +1,5 @@
 python:
-  - 2.7
+  - 3.7
 numpy:
   - 1.15
 

.conda/meta.yaml

@@ -12,62 +12,60 @@ build:
 requirements:
   build:
     - {{ compiler('c') }} # [unix]
-    - mingwpy # [win]
   host:
-    - boost ==1.56.0
     - cython >=0.25.2
-    - jinja2
     - lpsolve55
     - numpy
-    - openbabel >=2.4.1
+    - openbabel
     - pydas >=1.0.2
     - pydqed >=1.0.1
     - pyrdl
     - python
-    - pyzmq
     - quantities
     - rdkit >=2018
     - scipy
     - setuptools
   run:
-    - argparse # [py26]
     - cairo
     - cairocffi
     - cantera >=2.3.0
+    - cclib
+    - chemprop
     - coolprop
     - coverage
     - cython >=0.25.2
-    - dde
     - ffmpeg
     - gprof2dot
     - graphviz
-    - guppy
+    - h5py
     - jinja2
+    - jupyter
     - lpsolve55
     - markupsafe
     - matplotlib >=1.5
-    - mock
     - mopac
     - mpmath
+    - networkx
     - nose
+    - numdifftools
     - {{ pin_compatible('numpy') }}
-    - openbabel >=2.4.1
+    - openbabel
     - psutil
     - pydas >=1.0.2
-    - pydot ==1.2.2
+    - pydot
     - pydqed >=1.0.1
     - pymongo
     - pyparsing
     - pyrdl
     - python
+    - pyyaml
     - pyzmq
     - quantities
     - rdkit >=2018
-    - rmgdatabase >=2.4.0
+    - rmgdatabase >=3.0.0
     - scikit-learn
     - scipy
     - symmetry
-    - textgenrnn
     - xlwt
 test:
   source_files:

.coveragerc

@@ -3,9 +3,14 @@
 plugins = Cython.Coverage
 branch = True
 source =
+    arkane
+    Arkane.py
     rmgpy
     rmg.py
-omit = *Test.py
+omit =
+    *Test.py
+    */test_data/*
+    arkane/data/*
 
 [report]
 show_missing = False
@@ -18,7 +23,13 @@ exclude_lines =
     raise NotImplementedError
     if 0:
     if __name__ == .__main__.:
-omit = *Test.py
+include =
+    arkane/*
+    rmgpy/*
+omit =
+    *Test.py
+    */test_data/*
+    arkane/data/*
 
 [html]
 directory = testing/coverage

.gitignore

@@ -68,4 +68,7 @@ bin/symmetry
 
 # ipython folder except for notebooks
 ipython/*
-!ipython/*.ipynb
+!ipython/*.ipynb
+
+# Q2DTor
+external/Q2DTor

.travis.yml

@@ -1,5 +1,4 @@
-language: c
-sudo: false
+language: minimal
 
 env:
   global:
@@ -18,6 +17,9 @@ stages:
 
 before_install:
   - cd ..
+  # Display CPU and memory information on the Linux builds
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then lscpu; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then free -m; fi
   # Install miniconda
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
@@ -37,13 +39,17 @@ jobs:
         # Clone RMG-database
         - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
         - cd RMG-Py
-        - conda env create -q -f environment_linux.yml
+        # 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
@@ -55,13 +61,13 @@ jobs:
     - 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
         - conda list
         # Modify setup.py
-        - sed -i '/embedsignature/s/^#//g' setup.py
+        - sed -i '/embedsignature/s/# //g' setup.py
         - make
         - cd documentation
         - export COMMITMESSAGE="Automatic documentation rebuild"
@@ -75,7 +81,8 @@ jobs:
         - conda config --append channels rmg
         - conda config --append channels rdkit
         - conda config --append channels cantera
-        - conda config --append channels anaconda
+        - conda config --append channels pytorch
+        - conda config --append channels conda-forge
         - conda config --set anaconda_upload yes
       script:
         - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
@@ -87,7 +94,8 @@ jobs:
         - conda config --append channels rmg
         - conda config --append channels rdkit
         - conda config --append channels cantera
-        - conda config --append channels anaconda
+        - conda config --append channels pytorch
+        - conda config --append channels conda-forge
         - conda config --set anaconda_upload yes
       script:
         - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda

Arkane.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python3
 
 ###############################################################################
 #                                                                             #
@@ -33,34 +32,35 @@
 reaction rates and other properties used in detailed kinetics models using
 various methodologies and theories. To run Arkane, use the command ::
 
-    $ python arkane.py FILE
+    $ python Arkane.py FILE
 
 where ``FILE`` is the path to an Arkane input file describing the job to
 execute. Arkane will run the specified job, writing the output to
 ``output.py`` and a log to both the console and to ``Arkane.log``, with both
 files appearing in the same directory as the input file. Some additional
 command-line arguments are available; run the command ::
 
-    $ python arkane.py -h
+    $ python Arkane.py -h
 
 for more information.
 """
 
 import os
 import logging
 
-from arkane.main import *
+from arkane.main import Arkane
 
 arkane = Arkane()
 
 # Parse and validate the command-line arguments
-arkane.parseCommandLineArguments()
+arkane.parse_command_line_arguments()
 
 # Execute the job
 arkane.execute()
 
 try:
     import psutil
+
     process = psutil.Process(os.getpid())
     memory_info = process.memory_info()
     logging.info('Memory used: %.2f MB' % (memory_info.rss / 1024.0 / 1024.0))

Makefile

@@ -4,80 +4,54 @@
 #
 ################################################################################
 
-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 pycheck arkane clean install decython documentation mopac_travis
 
-.PHONY : all minimal main solver check cantherm clean install decython documentation mopac_travis
-
-all: main solver check
+all: pycheck main solver check
 
 minimal:
-	python setup.py build_ext minimal --build-lib . --build-temp build --pyrex-c-in-temp
+	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 --build-lib . --build-temp build --pyrex-c-in-temp
+	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 setup.py build_ext solver --build-lib . --build-temp build --pyrex-c-in-temp
+	@ python utilities.py check-pydas
+	python setup.py build_ext solver --inplace --build-temp .
 
 arkane:
-	python setup.py build_ext arkane --build-lib . --build-temp build --pyrex-c-in-temp
+	python setup.py build_ext arkane --inplace --build-temp .
 
 check:
 	@ python utilities.py check-dependencies
 
+pycheck:
+	@ python utilities.py check-python
+
 documentation:
 	$(MAKE) -C documentation html
 	@ echo "Start at: documentation/build/html/index.html"
 
 clean:
-	@ echo "Removing build directory..."
-	@ python setup.py clean --build-temp build
-	@ echo "Removing compiled files..."
 	@ python utilities.py clean
-	@ echo "Cleanup completed."
 
 clean-solver:
-	@ echo "Removing solver build directories..."
-ifeq ($(OS),Windows_NT)
-	@ -rd /s /q build\pyrex\rmgpy\solver
-	@ -rd /s /q build\build\pyrex\rmgpy\solver
-else
-	@ -rm -r build/pyrex/rmgpy/solver/
-	@ -rm -r build/build/pyrex/rmgpy/solver/
-endif
-	@ echo "Removing compiled files..."
 	@ python utilities.py clean-solver
-	@ echo "Cleanup completed."
 
 install:
-	@ echo "Checking you have PyDQED..."
-	@ python -c 'import pydqed; print pydqed.__file__'
-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 install
 
+q2dtor:
+	@ echo "\nInstalling Q2DTor...\n"
+	@ echo "Q2DTor is a software for calculating the partition functions and themodynamic properties\
+	of molecular systems with two or more torsional modes developed by David Ferro Costas ([email protected])\
+	 and Antonio Fernandez Ramos ([email protected]) at the Universidade de Santiago de Compostela. Arkane can\
+	  integrate Q2DTor to compute the quantum mechanical partition function of 2D rotors.  \n\nFor use of 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 arkanepy3
+	
 decython:
 	# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
 	find . -name *.so ! \( -name _statmech.so -o -name quantity.so -o -regex '.*rmgpy/solver/.*' \) -exec rm -f '{}' \;
@@ -88,21 +62,21 @@ ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
 endif
-	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
+	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
 
 test test-unittests:
 ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
 endif
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
+	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
 
 test-functional:
 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/__init__.py

@@ -1,9 +1,4 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-initialize imports
-"""
+#!/usr/bin/env python3
 
 ###############################################################################
 #                                                                             #
@@ -32,9 +27,14 @@
 #                                                                             #
 ###############################################################################
 
+"""
+initialize imports
+"""
+
+from arkane.common import ArkaneSpecies
+from arkane.explorer import ExplorerJob
+from arkane.kinetics import KineticsJob
 from arkane.main import Arkane
+from arkane.pdep import PressureDependenceJob
 from arkane.statmech import StatMechJob
 from arkane.thermo import ThermoJob
-from arkane.kinetics import KineticsJob
-from arkane.pdep import PressureDependenceJob
-from arkane.common import ArkaneSpecies