Maint/pre commit (mosdef-hub#417)

* Include pre-commit configuration files

Foyer currently lacks an automated way to enforce a style guide and
basic docstring formatting that is easily distributed to other
developers.

An example of this is mBuild, which now uses the `pre-commit` framework
to automate this during pull-requests as well as an installable git
commit hook.
This commit adds the initial configuration files for pre-commit setup.

* Inital pre-commit, formatting, docstyle, blackening, etc.

* Include blurb about pre-commit

* Include note section for networkX graph objects

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix docstring in topology_graph.py

* minor style fix

* more style fix

* add precommit hooks installation instruction

Co-authored-by: Co Quach <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Co Quach <[email protected]>

.gitignore

@@ -1,4 +1,6 @@
+test-output.xml
 *.py[cod]
+*.ipynb_checkpoints
 
 # C extensions
 *.so

.landscape.yaml

@@ -11,4 +11,4 @@ ignore-patterns:
   - __init__.py
 python-targets:
   - 2
-  - 3
+  - 3

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.4.0
+  hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 21.4b2
+  hooks:
+    - id: black
+      args: [--line-length=80]
+- repo: https://github.com/pycqa/isort
+  rev: 5.8.0
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: [--profile=black, --line-length=80]
+- repo: https://github.com/pycqa/pydocstyle
+  rev: '6.0.0'
+  hooks:
+    - id: pydocstyle
+      exclude: ^(foyer/tests/|docs/|devtools/|setup.py)
+      args: [--convention=numpy]

.readthedocs.yml

@@ -7,4 +7,4 @@ conda:
 sphinx:
   builder: html
   configuration: docs/conf.py
-  fail_on_warning: false
+  fail_on_warning: false

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-Contributions are welcomed via [pull requests on GitHub](https://github.com/mosdef-hub/foyer/pulls). Developers and/or 
+Contributions are welcomed via [pull requests on GitHub](https://github.com/mosdef-hub/foyer/pulls). Developers and/or
 users will review requested changes and make comments. The rest of this file will serve as a set of general guidelines
 for contributors.
 
@@ -18,7 +18,7 @@ Please try to keep the `master` branch of your fork up-to-date with the `master`
 
 ## Propose a single set of related changes
 
-Small changes are preferred over large changes. A major contribution can often be broken down into smaller PRs. Large PRs that 
+Small changes are preferred over large changes. A major contribution can often be broken down into smaller PRs. Large PRs that
 affect many parts of the codebase can be harder to review and are more likely to cause merge conflicts.
 
 # Source code
@@ -32,7 +32,11 @@ It is important to have a consistent style throughout the source code. The follo
 * Lines do not end with whitespace
 * For other details, refer to [PEP8](https://www.python.org/dev/peps/pep-0008)
 
-To help with the above, there are tools such as [flake8](https://pypi.org/project/flake8/) and [Black](https://github.com/ambv/black).
+We use [pre-commit](https://pre-commit.com/) to automatically check our code style. Pre-commit is included in the dev environment and its git hooks can be installed using:
+
+```bash
+pre-commit install
+```
 
 ## Document code with comments
 
@@ -45,8 +49,8 @@ can have simple one-liner docstrings.
 
 ## Write unit tests
 
-All new functionality in Foyer should be tested with automatic unit tests that execute in a few seconds. These tests 
-should attempt to cover all options that the user can select. All or most of the added lines of source code should be 
+All new functionality in Foyer should be tested with automatic unit tests that execute in a few seconds. These tests
+should attempt to cover all options that the user can select. All or most of the added lines of source code should be
 covered by unit test(s). We currently use [pytest](https://docs.pytest.org/en/latest/), which can be executed simply by calling
-`pytest` from the root directory of the package. Additions to force field files should include test molecules that encompass 
+`pytest` from the root directory of the package. Additions to force field files should include test molecules that encompass
 the added or modified atom types or functionality.

README.md

@@ -10,7 +10,7 @@
 
 ## Overview
 Foyer is an open-source Python tool for defining and applying force field atom-typing
-rules in a format that is both human- and machine-readable.  It parametrizes chemical topologies, 
+rules in a format that is both human- and machine-readable.  It parametrizes chemical topologies,
 generating, syntactically correct input files for various simulation engines. Foyer provides a framework for force field
 dissemination, helping to eliminate ambiguity in atom-typing and improving reproducibility
 (for more information, see [our paper](https://www.sciencedirect.com/science/article/pii/S0927025619303040) or its corresponding [pre-print](https://arxiv.org/pdf/1812.06779.pdf)).
@@ -50,10 +50,10 @@ ethane.save('ethane.top')
 ethane.save('ethane.gro')
 ```
 
-The `Foyer` package is part of the [Molecular Simulation Design Framework (MoSDeF) project](http://mosdef.org/). 
-Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline 
+The `Foyer` package is part of the [Molecular Simulation Design Framework (MoSDeF) project](http://mosdef.org/).
+Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline
 a researcher's simulation workflow. When setting up simulation studies,
-we also recommend users to follow the [TRUE](https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938)  
+we also recommend users to follow the [TRUE](https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938)
 (Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common
 practices meant to improve the reproducibility of computational simulation research.
 
@@ -110,7 +110,7 @@ Example template for disseminating force fields:
 * [Installation instructions](docs/installation.rst)
 
 ### Citing Foyer:
-* If you use this package, please cite [our paper](https://www.sciencedirect.com/science/article/pii/S0927025619303040) published in [Computational Materials Science](https://www.journals.elsevier.com/computational-materials-science). 
+* If you use this package, please cite [our paper](https://www.sciencedirect.com/science/article/pii/S0927025619303040) published in [Computational Materials Science](https://www.journals.elsevier.com/computational-materials-science).
 * This manuscript is also available in its pre-print form on [arxiv](https://arxiv.org/pdf/1812.06779.pdf)
 * The paper and examples in this work were developed for tag [paper_COMMAT_2019](https://github.com/mosdef-hub/foyer/tree/paper_COMMAT_2019)
 

devtools/README.md

@@ -11,7 +11,7 @@ License
 Copyright (c) 2012-2015 Stanford University and the Authors
 All rights reserved.
 
-Redistribution and use of all files in this folder (devtools) and (../basesetup.py, 
+Redistribution and use of all files in this folder (devtools) and (../basesetup.py,
 ../setup.py) files in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:
 

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = 
+SPHINXPROJ    =
 BUILDDIR      = _build
 
 # User-friendly check for sphinx-build

docs/_templates/footer.html

@@ -21,4 +21,4 @@
     }
   </script>
 {{ super() }}
-{% endblock %}
+{% endblock %}

docs/atom-typing_options.rst

@@ -13,4 +13,3 @@ Forcefield
 
 .. autoclass:: foyer.forcefield.Forcefield
     :members:
-