RMG-Py v2.3.0 release

meta.yaml → .conda/meta.yaml

@@ -4,7 +4,7 @@ package:
   version: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
 
 source:
-  path: .
+  path: ../
 
 build:
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
@@ -48,6 +48,7 @@ requirements:
     - matplotlib >=1.5
     - mock
     - mopac
+    - mpmath
     - nose
     - {{ pin_compatible('numpy') }}
     - openbabel >=2.4.1
@@ -62,11 +63,12 @@ requirements:
     - pyzmq
     - quantities
     - rdkit >=2015.09.2
-    - rmgdatabase >=2.2.0
+    - rmgdatabase >=2.3.0
     - scipy
     - scoop
     - symmetry
     - xlwt
+    - dde
 
 test:
   source_files:

.coveragerc

@@ -17,6 +17,7 @@ exclude_lines =
     raise NotImplementedError
     if 0:
     if __name__ == .__main__.:
+omit = *Test.py
 
 [html]
 directory = testing/coverage

.github/ISSUE_TEMPLATE/question.md

@@ -11,7 +11,7 @@ General area which your question is related to.
  - [ ] Installation of RMG
  - [ ] Running an RMG job
  - [ ] Using RMG API
- - [ ] CanTherm
+ - [ ] Arkane (formerly CanTherm)
  - [ ] Dependencies
  - [ ] An error message <!-- consider writing a bug report instead -->
 

.gitignore

@@ -39,6 +39,9 @@ nbproject/*
 .pydevproject
 .settings/*
 
+# PyCharm project files
+.idea/*
+
 # Unit test files
 .coverage
 testing/*

.travis.yml

@@ -11,8 +11,10 @@ env:
 
 stages:
   - test
+  - name: documentation
+    if: branch = master AND type = push
   - name: deploy
-    if: branch = stable
+    if: branch = stable AND type = push
 
 before_install:
   - cd ..
@@ -24,6 +26,9 @@ before_install:
   # Update conda
   - conda update --yes conda
   - conda info -a
+  # Set git info
+  - git config --global user.name "Travis Deploy"
+  - git config --global user.email "rmg_dev@mit.edu"
 
 jobs:
   include:
@@ -47,6 +52,21 @@ jobs:
       after_success:
         - codecov
         - bash ./deploy.sh
+    - stage: documentation
+      install:
+        - cd RMG-Py
+        - conda env create -q -f environment_linux.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
+        - make
+        - cd documentation
+        - export COMMITMESSAGE="Automatic documentation rebuild"
+      script:
+        - make travis_setup clean html publish
     - stage: deploy
       install:
         # Setup conda build
@@ -55,7 +75,7 @@ jobs:
         - conda config --add channels rmg
         - conda config --set anaconda_upload yes
       script:
-        - conda build --token $CONDA_TOKEN --user rmg RMG-Py
+        - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda
     - os: osx
       install:
         # Setup conda build
@@ -64,4 +84,4 @@ jobs:
         - conda config --add channels rmg
         - conda config --set anaconda_upload yes
       script:
-        - conda build --token $CONDA_TOKEN --user rmg RMG-Py
+        - conda build --token $CONDA_TOKEN --user rmg RMG-Py/.conda

Makefile

@@ -33,8 +33,8 @@ else
 endif
 	python setup.py build_ext solver --build-lib . --build-temp build --pyrex-c-in-temp
 
-cantherm:
-	python setup.py build_ext cantherm --build-lib . --build-temp build --pyrex-c-in-temp
+arkane:
+	python setup.py build_ext arkane --build-lib . --build-temp build --pyrex-c-in-temp
 
 check:
 	@ python utilities.py check-dependencies
@@ -88,21 +88,21 @@ 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
+	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
 
 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
+	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
 
 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
+	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
 
 test-database:
 	nosetests -v -d testing/databaseTest.py	

cantherm.py → arkane.py

@@ -29,35 +29,35 @@
 ###############################################################################
 
 """
-This is the main executable script for CanTherm, a tool for computing chemical
+This is the main executable script for Arkane, a tool for computing chemical
 reaction rates and other properties used in detailed kinetics models using
-various methodologies and theories. To run CanTherm, use the command ::
+various methodologies and theories. To run Arkane, use the command ::
 
-    $ python cantherm.py FILE
+    $ python arkane.py FILE
 
-where ``FILE`` is the path to a CanTherm input file describing the job to
-execute. CanTherm will run the specified job, writing the output to
-``output.py`` and a log to both the console and to ``cantherm.log``, with both
+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 cantherm.py -h
+    $ python arkane.py -h
 
 for more information.
 """
 
 import os
 import logging
 
-from rmgpy.cantherm.main import *
+from arkane.main import *
 
-cantherm = CanTherm()
+arkane = Arkane()
 
 # Parse and validate the command-line arguments
-cantherm.parseCommandLineArguments()
+arkane.parseCommandLineArguments()
 
 # Execute the job
-cantherm.execute()
+arkane.execute()
 
 try:
     import psutil

rmgpy/cantherm/common.py → arkane/__init__.py

@@ -28,21 +28,8 @@
 #                                                                             #
 ###############################################################################
 
-import numpy
-import os.path
-import logging
-import rmgpy.constants as constants
-################################################################################
-
-def checkConformerEnergy(Vlist,path):
-    """
-    Check to see that the starting energy of the species in the potential energy scan calculation
-    is not 0.5 kcal/mol (or more) higher than any other energies in the scan. If so, print and 
-    log a warning message.  
-    """    
-    Vlist = numpy.array(Vlist, numpy.float64)
-    Vdiff = (Vlist[0] - numpy.min(Vlist))*constants.E_h*constants.Na/1000
-    if Vdiff >= 2: #we choose 2 kJ/mol to be the critical energy
-        logging.warning('the species corresponding to ' + str(os.path.basename(path)) + ' is different in energy from the lowest energy conformer by ' + "%0.2f" % Vdiff + ' kJ/mol. This can cause significant errors in your computed rate constants. ')
-
-
+from arkane.main import Arkane
+from arkane.statmech import StatMechJob
+from arkane.thermo import ThermoJob
+from arkane.kinetics import KineticsJob
+from arkane.pdep import PressureDependenceJob