first commit

CODE_OF_CONDUCT.md

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+# 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

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+
+Copyright 2020 VH Chavez
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
+following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
+disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include LICENSE
+include MANIFEST.in
+include versioneer.py
+
+graft molely
+global-exclude *.py[cod] __pycache__ *.so

README.md

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+molely
+==============================
+[//]: # (Badges)
+[![Travis Build Status](https://travis-ci.com/REPLACE_WITH_OWNER_ACCOUNT/molely.svg?branch=master)](https://travis-ci.com/REPLACE_WITH_OWNER_ACCOUNT/molely)
+[![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/REPLACE_WITH_APPVEYOR_LINK/branch/master?svg=true)](https://ci.appveyor.com/project/REPLACE_WITH_OWNER_ACCOUNT/molely/branch/master)
+[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/molely/branch/master/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/molely/branch/master)
+
+A short description of the project.
+
+### Copyright
+
+Copyright (c) 2020, VH Chavez
+
+
+#### Acknowledgements
+
+Project based on the 
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.

appveyor.yml

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+environment:
+
+  matrix:
+    - PYTHON: "C:\\Miniconda36-x64"
+      PYTHON_VERSION: "3.6"
+      PYTHON_ARCH: "64"
+
+    - PYTHON: "C:\\Miniconda37-x64"
+      PYTHON_VERSION: "3.7"
+      PYTHON_ARCH: "64"
+
+
+install:
+    # Make sure pip is around
+  - python -m ensurepip
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+    # Add conda-forge channel
+  - conda config --add channels conda-forge
+
+
+    # Always run commands without asking
+  - conda config --set always_yes yes
+
+    # Try to update conda first to avoid odd dependency clashes
+  - conda update --all
+
+    # Create test environment for package
+  - python devtools\\scripts\\create_conda_env.py -n=test -p=%PYTHON_VERSION% devtools\\conda-envs\\test_env.yaml
+
+    # Activate the test environment
+  - activate test
+
+    # Build and install package
+  - python setup.py develop --no-deps
+
+
+build: false
+
+test_script:
+  - pytest -v --cov=molely molely\\tests
+
+on_success:
+  - codecov

devtools/README.md

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+# 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
+
+You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and 
+Windows testing if you only plan to deploy on specific platforms. These are just to help you get started
+
+* `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 
+* `appveyor`: Windows based testing through [AppVeyor](https://www.appveyor.com/) (there are no files directly related to this)
+
+### 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. `molely-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

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+name: test
+channels:
+dependencies:
+    # Base depends
+  - python
+  - pip
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+
+    # Pip-only installs
+  #- pip:
+  #  - codecov
+

devtools/scripts/create_conda_env.py

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+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

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+# 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 conda-forge
+
+conda config --set always_yes yes
+conda install conda conda-build jinja2 anaconda-client
+conda update --quiet --all
+
+# Restore original directory
+popd