RMG-Py v2.2.0 release

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+<!--Thanks for creating this bug report! Please try to provide as much information as possible so we can recreate the bug. This template is provided as a guide, which you can adjust based on your issue. Also, try searching GitHub issues to see if someone has previously posted a similar bug. -->
+
+### Bug Description
+A clear and concise description of what the bug is.
+
+### How To Reproduce
+Steps to reproduce the behavior.
+
+### Expected Behavior
+A clear and concise description of what you expected to happen.
+
+### Installation Information
+Describe your installation method and system information.
+ - OS (include version if known): (e.g. Windows 10, Ubuntu 18, macOS 10.13, etc.)
+ - Installation method: (e.g. installation from binary or source, with or without anaconda)
+ - RMG version information:
+   <!--
+   For binary installation, get version number using `conda list -f rmg`
+   For installation from source, get git commit using `git describe --tags`
+   -->
+   - RMG-Py: 
+   - RMG-database: 
+
+### Additional Context
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature.md

@@ -0,0 +1,19 @@
+---
+name: Feature suggestion
+about: Suggest an idea for RMG
+
+---
+
+<!-- Thanks for contributing a feature suggestion! Please try to provide as much detail as possible. This template is provided as a guide, which you can modify as needed. Also, try searching GitHub issues to see if someone has previously suggested a similar feature. -->
+
+### Motivation or Problem
+A clear and concise description of what the problem is.
+
+### Desired Solution
+A clear and concise description of what you want to happen.
+
+### Potential Alternatives
+A clear and concise description of any alternative solutions or features you've considered.
+
+### Additional Context
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,34 @@
+---
+name: Question
+about: Ask a question about RMG
+
+---
+
+<!-- Thanks for your interest in RMG! Please first check the online documentation at reactionmechanismgenerator.github.io/RMG-Py to see if it answers your question. Also, try searching GitHub issues to see if someone has asked your question before. This template is provided as a guide, which you can adjust based on your question. -->
+
+### Topic
+General area which your question is related to.
+ - [ ] Installation of RMG
+ - [ ] Running an RMG job
+ - [ ] Using RMG API
+ - [ ] CanTherm
+ - [ ] Dependencies
+ - [ ] An error message <!-- consider writing a bug report instead -->
+
+### Context
+A clear and concise description what you're trying to do.
+
+### Question
+Write your question here.
+
+### Installation Information
+Describe your installation method and system information if applicable.
+ - OS (include version if known): (e.g. Windows 10, Ubuntu 18, macOS 10.13, etc.)
+ - Installation method: (e.g. installation from binary or source, with or without anaconda)
+ - RMG version information:
+   <!--
+   For binary installation, get version number using `conda list -f rmg`
+   For installation from source, get git commit using `git describe --tags`
+   -->
+   - RMG-Py: 
+   - RMG-database: 

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,26 @@
+<!--
+Thanks for contributing a pull request! Please try to provide as much detail as possible to help the reviewer understand your work.
+You can also add the appropriate labels to describe the topic of the pull request and the type of changes you're making.
+-->
+
+### Motivation or Problem
+A clear and concise description of what what you're trying to fix or improve. Please reference any issues that this addresses.
+
+### Description of Changes
+A clear and concise description of what what you've changed or added.
+
+### Testing
+A clear and concise description of testing that you've done or plan to do.
+
+### Reviewer Tips
+Suggestions for verifying that this PR works or other notes for the reviewer.
+
+<!--
+Checklist before submission:
+ - Have you added appropriate unit tests?
+ - Have you checked that all unit tests pass?
+ - Is your code commented and understandable?
+ - Have you updated related documentation?
+ - Are the commits logically organized and informative?
+ - Is your branch up to date with master?
+-->

.travis.yml

@@ -1,41 +1,67 @@
-language: python
+language: c
 sudo: false
-python:
-  - "2.7"
+
 env:
   global:
     - secure: "L2ja+ZnV83w4qG3E8FwTjm0D6IWNOnj5wuFOjYTwbzQP4OAgLAWBzCMtxzWy5sMxFLtRgkswBH1d5f5kg8Ab7GIyAMFgQwe8UFqMJ+N05QNszE1mJkAvJtv2XN7669XXQhTt5EXfHrCcGZaODVnI2CEA8GB5DxiHO2Lcqf/xvgE="
-    - secure: "Fa/qcHKKkTzgNanhgz+XWXg5K+uae5Ukxd0hfzYaiOI4+ldFbyMrYbPpxxoYVXw1SSO0psSupLfPfXzHwyJpFOyc46P+fo+R3YgNTJwr2VfdvSC0bp9K01nlRJ/z62IpMwmDwR2UH5xnfTeB9nhtzviFNKZoDZ/GR7F1Wqd/nnU="
     - secure: "dkhvrkbNEHv55q3NU+lNJ0SqaNG0/vPMsG3X2eQvYjFsq/e8EliILtEtjrugSgeFohxqms0F+sSyDpw46mtn+jukYejdywLVL7w8o9pxlkHv8uEqYhNiwCD8RjNyRPQAS9jL+sAJiqdqUWR6AzjwaLproCe6rFzzGe7Io5oDLMg="
     - secure: "cfosGf5hvUhIlPoGJu0d/HFddrMwIFU7FfLwd8yRrMGkYv0ePOwAW9kmhFSxUYvuXkxzgD75cIICMFY2fSm6VXBXXzfPQD7vwzoApXf7a8vi0C64XhinXhdEyUYb5/v8fswa0zheUENYhUS1tOqDXT/h8EPNZT5wKizaA3O2Wa8="
     - secure: "QXuqKYuwCocqsTMePBc5OugBbQC4/t+335TYLdkletiateP/rF/eDsVRG792/BVq5gKRZgz3NH9ipTNm5pZoCbAEPt9+eDpfts8WeAbxmjdcEjfBxxwZ69wUTPAVrezTGn2k7W2UBdFrWeUNKPAVCKIkoviXqOHFitqJEC+c6JY="
     - secure: "jIyBEzR10l5SWvY5ouEYzA8YzPHIZNMXMBdcXwuwte8NCU8GBYUqhHA1L67nTaBdLhWbrZ2NireVKPQWJp3ctcI0IB6xZzaYlVpgN/udGPO+1MZd9Xhp9TWuJWrGZ9EoWGB9L5H+O7RYwcDMVH5CUrCIBdsSJuyE8aDpky1/IVE="
 
+stages:
+  - test
+  - name: deploy
+    if: branch = stable
+
 before_install:
   - cd ..
   # Install miniconda
-  - wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
+  - 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
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH=$HOME/miniconda/bin:$PATH
+  # Update conda
   - conda update --yes conda
   - conda info -a
-  # Clone RMG-database
-  - git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
-  - cd RMG-Py
-
-install:
-  - conda env create -q -f environment_linux.yml
-  - source activate rmg_env
-  - conda install -y -c conda-forge codecov
-  - conda list
-  - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
-  - 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
+        - conda env create -q -f environment_linux.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
+        - make
+      script:
+        - make test-unittests
+        - make test-functional
+        - make test-database
+      after_success:
+        - codecov
+        - bash ./deploy.sh
+    - stage: deploy
+      install:
+        # Setup conda build
+        - conda install -y conda-build
+        - conda install -y anaconda-client
+        - conda config --add channels rmg
+        - conda config --set anaconda_upload yes
+      script:
+        - conda build --token $CONDA_TOKEN --user rmg RMG-Py
+    - os: osx
+      install:
+        # Setup conda build
+        - conda install -y conda-build
+        - conda install -y anaconda-client
+        - conda config --add channels rmg
+        - conda config --set anaconda_upload yes
+      script:
+        - conda build --token $CONDA_TOKEN --user rmg RMG-Py

Makefile

@@ -7,7 +7,7 @@
 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 decython documentation mopac_travis
+.PHONY : all minimal main solver check cantherm clean install decython documentation mopac_travis
 
 all: main solver check
 
@@ -63,6 +63,21 @@ endif
 	@ 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 setup.py install
+
 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 '{}' \;
@@ -75,20 +90,13 @@ ifneq ($(OS),Windows_NT)
 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
 
-test-unittests:
+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
 
-test test-unittests-non-auth:
-ifneq ($(OS),Windows_NT)
-	mkdir -p testing/coverage
-	rm -rf testing/coverage/*
-endif
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-
 test-functional:
 ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage

bld.bat

@@ -1,8 +1,5 @@
-:: Compile RMG
-mingw32-make -j%CPU_COUNT%
-
 :: Install RMG
-%PYTHON% setup.py install
+mingw32-make install
 
 :: lazy "install" of everything in our 'external' folder.
 :: most of which should probably be elsewhere

build.sh

@@ -1,8 +1,5 @@
-# Compile RMG
-make -j${CPU_COUNT}
-
 # Install RMG
-$PYTHON setup.py install
+make install
 
 # lazy "install" of everything in our 'external' folder.
 # most of which should probably be elsewhere

cantherm.py

@@ -47,7 +47,6 @@
 """
 
 import os
-import os.path
 import logging
 
 from rmgpy.cantherm.main import *

documentation/source/_static/custom.css

@@ -1,5 +1,11 @@
 @import url("classic.css");
 
+/* ----- overall styles ----- */
+
+div.body {
+    max-width: none;
+}
+
 /* ----- sidebar styles ----- */
 
 div.sidebarlogo {

documentation/source/conf.py

@@ -227,24 +227,24 @@
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-latex_logo = '_static/rmg-logo-big.pdf'
+latex_logo = '_static/rmg-logo-medium.pdf'
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 #latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
-latex_preamble = """
-\\usepackage[scaled]{beramono}
-\\usepackage[version=3]{mhchem}
-\\DeclareUnicodeCharacter{0394}{\\ensuremath{\\Delta}}
-\\renewcommand{\\vector}[1]{\\ensuremath{\\boldsymbol{\\mathbf{#1}}}}
-\\renewcommand{\\matrix}[1]{\\ensuremath{\\boldsymbol{\\mathbf{#1}}}}
-"""
+latex_elements = {
+    'preamble': r"""
+\usepackage[scaled]{beramono}
+\usepackage[version=3]{mhchem}
+\DeclareUnicodeCharacter{0394}{\ensuremath{\\Delta}}
+\renewcommand{\vector}[1]{\ensuremath{\boldsymbol{\mathbf{#1}}}}
+\renewcommand{\matrix}[1]{\ensuremath{\boldsymbol{\mathbf{#1}}}}
+""",
+}
 # See also the extrahead block in the layout.html template for mathjax extenions!
 
-pngmath_latex_preamble = latex_preamble
-
 # If true, show page references after internal links.
 #latex_show_pagerefs = False
 

documentation/source/latex-rmg.rst

@@ -9,13 +9,13 @@ steps using a general understanding of how molecules react. This documentation i
 +---------------------------------------------+----------------------------------------------------------------------------------------+
 | I want to...                                | Resource                                                                               |
 +=============================================+========================================================================================+
-| analyze models & search databases           | `RMG website resources <http://rmg.mit.edu/>`__  (no download needed                   |
+| analyze models & search databases           | `RMG website resources <http://rmg.mit.edu/>`__  (no download needed)                  |
 +---------------------------------------------+----------------------------------------------------------------------------------------+
 | make transition state theory calculations   | Run Cantherm with the Canterm User's Guide                                             |
 +---------------------------------------------+----------------------------------------------------------------------------------------+
 | create mechanisms automatically             | Download RMG with the RMG User's Guide                                                 |
 +---------------------------------------------+----------------------------------------------------------------------------------------+
-| post an issue with RMG                      | `github issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__   |
+| post an issue with RMG                      | `GitHub issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__   |
 +---------------------------------------------+----------------------------------------------------------------------------------------+
 | contribute to RMG project                   | `RMG developer's wiki <https://github.com/ReactionMechanismGenerator/RMG-Py/wiki>`__   |
 +---------------------------------------------+----------------------------------------------------------------------------------------+