Expanded ensemble

.codecov.yml

@@ -0,0 +1,14 @@
+# Codecov configuration to make it a bit less noisy
+coverage:
+  status:
+    patch: false
+    project:
+      default:
+        threshold: 50%
+comment:
+  layout: "header"
+  require_changes: false
+  branches: null
+  behavior: default
+  flags: null
+  paths: null

.github/CONTRIBUTING.md

@@ -0,0 +1,42 @@
+# How to contribute
+
+We welcome contributions from external contributors, and this document
+describes how to merge code changes into this openmmtools.
+
+## Getting Started
+
+* Make sure you have a [GitHub account](https://github.com/signup/free).
+* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
+* On your local machine,
+  [clone](https://help.github.com/articles/cloning-a-repository/) your fork of
+  the repository.
+
+## Making Changes
+
+* Add some really awesome code to your local fork.  It's usually a [good
+  idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
+  to make changes on a
+  [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
+  with the branch name relating to the feature you are going to add.
+* When you are ready for others to examine and comment on your new feature,
+  navigate to your fork of openmmtools on GitHub and open a [pull
+  request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
+  after you launch a PR from one of your fork's branches, all
+  subsequent commits to that branch will be added to the open pull request
+  automatically.  Each commit added to the PR will be validated for
+  mergability, compilation and test suite compliance; the results of these tests
+  will be visible on the PR page.
+* If you're providing a new feature, you must add test cases and documentation.
+* When the code is ready to go, make sure you run the test suite using pytest.
+* When you're ready to be considered for merging, check the "Ready to go"
+  box on the PR page to let the openmmtools devs know that the changes are complete.
+  The code will not be merged until this box is checked, the continuous
+  integration returns checkmarks,
+  and multiple core developers give "Approved" reviews.
+
+# Additional Resources
+
+* [General GitHub documentation](https://help.github.com/)
+* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
+* [A guide to contributing to software packages](http://www.contribution-guide.org)
+* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,4 +1,11 @@
- - [ ] Implement feature / fix bug
- - [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests)
- - [ ] Update [documentation](https://github.com/choderalab/openmmtools/tree/master/docs) as needed
- - [ ] Update [changelog](https://github.com/choderalab/openmmtools/blob/master/docs/releasehistory.rst)
+## Description
+Provide a brief description of the PR's purpose here.
+
+## Todos
+- [ ] Implement feature / fix bug
+- [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests)
+- [ ] Update [documentation](https://github.com/choderalab/openmmtools/tree/master/docs) as needed
+- [ ] Update [changelog](https://github.com/choderalab/openmmtools/blob/master/docs/releasehistory.rst)Notable points that this PR has either accomplished or will accomplish.
+
+## Status
+- [ ] Ready to go

.gitignore

@@ -1,12 +1,102 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
+*$py.class
 
-openmmtools/version.py
+# C extensions
+*.so
 
-# Packages
-*.egg-info
-dist
-build
-__pycache__
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
 
-# PyCharm
-.idea
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

.lgtm.yml

@@ -0,0 +1,12 @@
+# Configure LGTM for this package
+
+extraction:
+  python:  # Configure Python
+    python_setup:  # Configure the setup
+      version: 3  # Specify Version 3
+path_classifiers:
+  library:
+    - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
+    - devtools/*
+  generated:
+    - openmmtools/_version.py

.travis.yml

@@ -1,46 +1,55 @@
-language: c
-sudo: false
-addons:
-  apt:
-    sources:
-    - ubuntu-toolchain-r-test
+language: python
 
-install:
-  - bash -x devtools/travis-ci/install.sh
-  - export PYTHONUNBUFFERED=true
-  - export PATH=$HOME/miniconda/bin:$PATH
+# Run jobs on container-based infrastructure, can be overridden per job
+
+matrix:
+  include:
+    # Extra includes for OSX since python language is not available by default on OSX
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.6
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.7
 
-script:
-  # Create a test environment
-  - conda create --quiet --yes -n test python=$python
-  # Activate the test environment
-  - source activate test
-  # Add org channel
-  - conda config --add channels ${ORGNAME}
-  # Add omnia dev channels
-  - if [ $DEVOMNIA ]; then conda config --add channels omnia-dev; fi
-  # Add conda-forge channel back to top priority
-  - conda config --add channels conda-forge
-  # Build the recipe
-  - conda build devtools/conda-recipe
-  # Install the package
-  - conda install --yes --quiet --use-local ${PACKAGENAME}-dev
-  # Install testing dependencies. Without specifying the numpy version, numpy
-  # is downgraded to 1.9 and we get a "libgfortran not found" issue.
-  - conda install --yes --quiet nose nose-timer pymbar "numpy>=1.14"
-  # Test the package
-  - cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow' && cd ..
+
+    - os: linux
+      language: generic  # No need to set Python version since its conda
+      env: PYTHON_VER=3.6
+    - os: linux
+      language: generic
+      env: PYTHON_VER=3.7
 
 env:
-  matrix:
-    - python=3.6 CONDA_PY=36
-    - python=3.7 CONDA_PY=37
-    - python=3.7 CONDA_PY=37 DEVOMNIA=true # allowed to fail
   global:
-    - ORGNAME="omnia" # the name of the organization
-    - PACKAGENAME="openmmtools" # the name of your package
     - OPENMM_CPU_THREADS="1" # only use one CPU thread for determinism
 
-matrix:
-  allow_failures:
-  - env: python=3.7 CONDA_PY=37 DEVOMNIA=true
+before_install:
+    # Additional info about the build
+  - uname -a
+  - df -h
+  - ulimit -a
+
+    # Install the Python environment
+  - source devtools/travis-ci/before_install.sh
+  - python -V
+
+install:
+
+    # Create test environment for package
+  - python devtools/scripts/create_conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/test_env.yaml
+    # Activate the test environment
+  - conda activate test
+    # Build and install package
+  - python setup.py develop --no-deps
+
+
+script:
+  #- pytest -v --cov=openmmtools openmmtools/tests/
+  - nosetests openmmtools/tests --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow'
+
+notifications:
+    email: false
+
+after_success:
+  - codecov

CODE_OF_CONDUCT.md

@@ -0,0 +1,77 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Moreover, project maintainers will strive to offer feedback and advice to
+ensure quality and consistency of contributions to the code.  Contributions
+from outside the group of project maintainers are strongly welcomed but the
+final decision as to whether commits are merged into the codebase rests with
+the team of project maintainers.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at '[email protected]'. The project team will
+review and investigate all complaints, and will respond in a way that it deems
+appropriate to the circumstances. The project team is obligated to maintain
+confidentiality with regard to the reporter of an incident. Further details of
+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2015-2017 Chodera lab // Memorial Sloan Kettering Cancer Center
+Copyright (c) 2015-2019 Chodera lab // Memorial Sloan Kettering Cancer Center
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -0,0 +1,6 @@
+include LICENSE
+include MANIFEST.in
+include versioneer.py
+
+graft openmmtools
+global-exclude *.py[cod] __pycache__ *.so