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RMG-Py v2.2.0 release
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‎.github/ISSUE_TEMPLATE/bug-report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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---
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<!--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. -->
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### Bug Description
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A clear and concise description of what the bug is.
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### How To Reproduce
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Steps to reproduce the behavior.
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### Expected Behavior
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A clear and concise description of what you expected to happen.
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### Installation Information
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Describe your installation method and system information.
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- OS (include version if known): (e.g. Windows 10, Ubuntu 18, macOS 10.13, etc.)
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- Installation method: (e.g. installation from binary or source, with or without anaconda)
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- RMG version information:
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<!--
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For binary installation, get version number using `conda list -f rmg`
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For installation from source, get git commit using `git describe --tags`
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-->
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- RMG-Py:
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- RMG-database:
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### Additional Context
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature.md‎

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---
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name: Feature suggestion
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about: Suggest an idea for RMG
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---
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<!-- 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. -->
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### Motivation or Problem
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A clear and concise description of what the problem is.
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### Desired Solution
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A clear and concise description of what you want to happen.
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### Potential Alternatives
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A clear and concise description of any alternative solutions or features you've considered.
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### Additional Context
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Add any other context or screenshots about the feature request here.

‎.github/ISSUE_TEMPLATE/question.md‎

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---
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name: Question
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about: Ask a question about RMG
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---
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<!-- 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. -->
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### Topic
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General area which your question is related to.
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- [ ] Installation of RMG
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- [ ] Running an RMG job
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- [ ] Using RMG API
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- [ ] CanTherm
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- [ ] Dependencies
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- [ ] An error message <!-- consider writing a bug report instead -->
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### Context
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A clear and concise description what you're trying to do.
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### Question
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Write your question here.
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### Installation Information
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Describe your installation method and system information if applicable.
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- OS (include version if known): (e.g. Windows 10, Ubuntu 18, macOS 10.13, etc.)
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- Installation method: (e.g. installation from binary or source, with or without anaconda)
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- RMG version information:
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<!--
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For binary installation, get version number using `conda list -f rmg`
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For installation from source, get git commit using `git describe --tags`
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-->
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- RMG-Py:
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- RMG-database:

‎.github/PULL_REQUEST_TEMPLATE.md‎

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

‎.travis.yml‎

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

‎Makefile‎

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DASPK=$(shell python -c 'import pydas.daspk; print pydas.daspk.__file__')
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DASSL=$(shell python -c 'import pydas.dassl; print pydas.dassl.__file__')
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.PHONY : all minimal main solver check cantherm clean decython documentation mopac_travis
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.PHONY : all minimal main solver check cantherm clean install decython documentation mopac_travis
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all: main solver check
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@ python utilities.py clean-solver
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@ echo "Cleanup completed."
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install:
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@ echo "Checking you have PyDQED..."
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@ python -c 'import pydqed; print pydqed.__file__'
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ifneq ($(DASPK),)
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@ echo "DASPK solver found. Compiling with DASPK and sensitivity analysis capability..."
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@ (echo DEF DASPK = 1) > rmgpy/solver/settings.pxi
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else ifneq ($(DASSL),)
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@ echo "DASSL solver found. Compiling with DASSL. Sensitivity analysis capabilities are off..."
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@ (echo DEF DASPK = 0) > rmgpy/solver/settings.pxi
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else
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@ echo 'No PyDAS solvers found. Please check if you have the latest version of PyDAS.'
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@ python -c 'import pydas.dassl'
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endif
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python setup.py install
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decython:
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# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
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find . -name *.so ! \( -name _statmech.so -o -name quantity.so -o -regex '.*rmgpy/solver/.*' \) -exec rm -f '{}' \;
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endif
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nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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test-unittests:
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test test-unittests:
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ifneq ($(OS),Windows_NT)
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mkdir -p testing/coverage
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rm -rf testing/coverage/*
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endif
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nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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test test-unittests-non-auth:
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ifneq ($(OS),Windows_NT)
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mkdir -p testing/coverage
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rm -rf testing/coverage/*
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endif
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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
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‎bld.bat‎

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

‎build.sh‎

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

‎cantherm.py‎

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"""
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import os
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import os.path
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import logging
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from rmgpy.cantherm.main import *

‎documentation/RMG-Py_API_Reference.pdf‎

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