Merge branch 'master' of https://github.com/openforcefield/smirnoff99…

…Frosst into hydrogen_typo

.gitignore

@@ -20,6 +20,7 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -40,9 +41,10 @@ htmlcov/
 .coverage
 .coverage.*
 .cache
+.pytest_cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
 .hypothesis/
 
 # Translations
@@ -66,7 +68,7 @@ docs/_build/
 # PyBuilder
 target/
 
-# IPython Notebook
+# Jupyter Notebook
 .ipynb_checkpoints
 
 # pyenv
@@ -75,15 +77,26 @@ target/
 # 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/

.travis.yml

@@ -0,0 +1,48 @@
+language: python
+
+# 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
+
+
+    - 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
+
+
+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 smirnoff99Frosst/tests/
+
+notifications:
+    email: false

README.md

@@ -82,3 +82,8 @@ Contributors to the relevant .offxml file include:
 - David L. Mobley (UC Irvine)
 
 Special thanks go to John D. Chodera (MSKCC) for his initial implementation of `openforcefield` toolkits and the SMIRNOFF format.
+
+#### Acknowledgements
+
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.0.

devtools/README.md

@@ -0,0 +1,56 @@
+# Development, testing, and deployment tools
+
+This directory contains a collection of tools for running Continuous Integration (CI) tests, 
+conda installation, and other development tools not directly related to the coding process.
+
+
+## Manifest
+
+### Continuous Integration
+
+* `travis-ci`: Linux and OSX based testing through [Travis-CI](https://about.travis-ci.com/) 
+  * `before_install.sh`: Pip/Miniconda pre-package installation script for Travis
+
+### Conda Environment:
+
+This directory contains the files to setup the Conda environment for testing purposes
+
+* `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's
+  * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration
+
+### Additional Scripts:
+
+This directory contains OS agnostic helper scripts which don't fall in any of the previous categories
+* `scripts`
+  * `create_conda_env.py`: Helper program for spinning up new conda environments based on a starter file with Python Version and Env. Name command-line options
+
+
+## How to contribute changes
+- Clone the repository if you have write access to the main repo, fork the repository if you are a collaborator.
+- Make a new branch with `git checkout -b {your branch name}`
+- Make changes and test your code
+- Ensure that the test environment dependencies (`conda-envs`) line up with the build and deploy dependencies (`conda-recipe/meta.yaml`)
+- Push the branch to the repo (either the main or your fork) with `git push -u origin {your branch name}`
+  * Note that `origin` is the default name assigned to the remote, yours may be different
+- Make a PR on GitHub with your changes
+- We'll review the changes and get your code into the repo after lively discussion!
+
+
+## Checklist for updates
+- [ ] Make sure there is an/are issue(s) opened for your specific update
+- [ ] Create the PR, referencing the issue
+- [ ] Debug the PR as needed until tests pass
+- [ ] Tag the final, debugged version 
+   *  `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags`
+- [ ] Get the PR merged in
+
+## Versioneer Auto-version
+[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version 
+is installed by looking at the `git` tags and how many commits ahead this version is. The format follows 
+[PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of:
+```regexp
+\d+.\d+.\d+(?\+\d+-[a-z0-9]+)
+```
+If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
+e.g. `smirnoff99Frosst-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.

devtools/conda-envs/test_env.yaml

@@ -0,0 +1,16 @@
+name: test
+
+channels:
+  - conda-forge
+  - omnia
+
+dependencies:
+    # Base depends
+  - python
+  - pip
+
+    # Testing
+  - pytest
+
+    # Standard dependencies
+  - openforcefield

devtools/scripts/create_conda_env.py

@@ -0,0 +1,95 @@
+import argparse
+import os
+import re
+import glob
+import shutil
+import subprocess as sp
+from tempfile import TemporaryDirectory
+from contextlib import contextmanager
+# YAML imports
+try:
+    import yaml  # PyYAML
+    loader = yaml.load
+except ImportError:
+    try:
+        import ruamel_yaml as yaml  # Ruamel YAML
+    except ImportError:
+        try:
+            # Load Ruamel YAML from the base conda environment
+            from importlib import util as import_util
+            CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE'])
+            ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..',
+                                                      'lib', 'python*.*', 'site-packages',
+                                                      'ruamel_yaml', '__init__.py'))[0]
+            # Based on importlib example, but only needs to load_module since its the whole package, not just
+            # a module
+            spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path)
+            yaml = spec.loader.load_module()
+        except (KeyError, ImportError, IndexError):
+            raise ImportError("No YAML parser could be found in this or the conda environment. "
+                              "Could not find PyYAML or Ruamel YAML in the current environment, "
+                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " 
+                              "Environment not created!")
+    loader = yaml.YAML(typ="safe").load  # typ="safe" avoids odd typing on output
+
+
+@contextmanager
+def temp_cd():
+    """Temporary CD Helper"""
+    cwd = os.getcwd()
+    with TemporaryDirectory() as td:
+        try:
+            os.chdir(td)
+            yield
+        finally:
+            os.chdir(cwd)
+
+
+# Args
+parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
+parser.add_argument('-n', '--name', type=str,
+                    help='The name of the created Python environment')
+parser.add_argument('-p', '--python', type=str,
+                    help='The version of the created Python environment')
+parser.add_argument('conda_file',
+                    help='The file for the created Python environment')
+
+args = parser.parse_args()
+
+# Open the base file
+with open(args.conda_file, "r") as handle:
+    yaml_script = loader(handle.read())
+
+python_replacement_string = "python {}*".format(args.python)
+
+try:
+    for dep_index, dep_value in enumerate(yaml_script['dependencies']):
+        if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value):  # Match explicitly 'python' and its formats
+            yaml_script['dependencies'].pop(dep_index)
+            break  # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
+except (KeyError, TypeError):
+    # Case of no dependencies key, or dependencies: None
+    yaml_script['dependencies'] = []
+finally:
+    # Ensure the python version is added in. Even if the code does not need it, we assume the env does
+    yaml_script['dependencies'].insert(0, python_replacement_string)
+
+# Figure out conda path
+if "CONDA_EXE" in os.environ:
+    conda_path = os.environ["CONDA_EXE"]
+else:
+    conda_path = shutil.which("conda")
+if conda_path is None:
+    raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path")
+
+print("CONDA ENV NAME  {}".format(args.name))
+print("PYTHON VERSION  {}".format(args.python))
+print("CONDA FILE NAME {}".format(args.conda_file))
+print("CONDA PATH      {}".format(conda_path))
+
+# Write to a temp directory which will always be cleaned up
+with temp_cd():
+    temp_file_name = "temp_script.yaml"
+    with open(temp_file_name, 'w') as f:
+        f.write(yaml.dump(yaml_script))
+    sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True)

devtools/travis-ci/before_install.sh

@@ -0,0 +1,41 @@
+# Temporarily change directory to $HOME to install software
+pushd .
+cd $HOME
+# Make sure some level of pip is installed
+python -m ensurepip
+
+# Install Miniconda
+if [ "$TRAVIS_OS_NAME" == "osx" ]; then
+    # Make OSX md5 mimic md5sum from linux, alias does not work
+    md5sum () {
+        command md5 -r "$@"
+    }
+    MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh
+else
+    MINICONDA=Miniconda3-latest-Linux-x86_64.sh
+fi
+MINICONDA_HOME=$HOME/miniconda
+MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget -q https://repo.continuum.io/miniconda/$MINICONDA
+if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
+    echo "Miniconda MD5 mismatch"
+    exit 1
+fi
+bash $MINICONDA -b -p $MINICONDA_HOME
+
+# Configure miniconda
+export PIP_ARGS="-U"
+# New to conda >=4.4
+echo ". $MINICONDA_HOME/etc/profile.d/conda.sh" >> ~/.bashrc  # Source the profile.d file
+echo "conda activate" >> ~/.bashrc  # Activate conda
+source ~/.bashrc  # source file to get new commands
+#export PATH=$MINICONDA_HOME/bin:$PATH  # Old way, should not be needed anymore
+
+conda config --add channels omnia --add channels conda-forge
+
+conda config --set always_yes yes
+conda install conda conda-build jinja2 anaconda-client
+conda update --quiet --all
+
+# Restore original directory
+popd

setup.cfg

@@ -0,0 +1,30 @@
+# Helper file to handle all configs
+
+[coverage:run]
+# .coveragerc to control coverage.py and pytest-cov
+omit =
+    # Omit the tests
+    */tests/*
+    # Omit generated versioneer
+    smirnoff99Frosst/_version.py
+
+[yapf]
+# YAPF, in .style.yapf files this shows up as "[style]" header
+COLUMN_LIMIT = 119
+INDENT_WIDTH = 4
+USE_TABS = False
+
+[flake8]
+# Flake8, PyFlakes, etc
+max-line-length = 119
+
+[versioneer]
+# Automatic version numbering scheme
+VCS = git
+style = pep440
+versionfile_source = smirnoff99Frosst/_version.py
+versionfile_build = smirnoff99Frosst/_version.py
+tag_prefix = ''
+
+[aliases]
+test = pytest