Merge pull request #50 from marjanAlbouye/docstrings

Complete docstrings

.gitignore

@@ -134,3 +134,7 @@ dmypy.json
 
 # IDE files
 .idea/
+
+# emacs backup saves
+*.~
+*.#

.pre-commit-config.yaml

@@ -1,47 +1,47 @@
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit.com hooks
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
 
-        for more information, see https://pre-commit.ci
-    autofix_prs: true
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: weekly
-    skip: []
-    submodules: false
+    for more information, see https://pre-commit.ci
+  autofix_prs: true
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: [ ]
+  submodules: false
 
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-    - id: check-yaml
-    - id: end-of-file-fixer
-    - id: trailing-whitespace
-      exclude: 'hoomd_organics/tests/assets/.* | hoomd_organics/assets/.*'
-- repo: https://github.com/psf/black
-  rev: 23.9.1
-  hooks:
-    - id: black
-      args: [--line-length=80]
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args:
-        [--profile=black, --line-length=80]
-      exclude: 'cmeuitls/tests/assets/.* '
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: 'hoomd_organics/tests/assets/.* | hoomd_organics/assets/.*'
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+        args: [ --line-length=80 ]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        args:
+          [ --profile=black, --line-length=80 ]
+        exclude: 'cmeuitls/tests/assets/.* '
 
-- repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
-  hooks:
-    - id: flake8
-      args:
-        - --max-line-length=80
-      exclude: '__init__.py'
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        args:
+          - --max-line-length=80
+        exclude: '__init__.py'
 
-#- repo: https://github.com/pycqa/pydocstyle
-#  rev: '6.3.0'
-#  hooks:
-#    - id: pydocstyle
-#      exclude: ^(cmeuitls/tests/|setup.py)
-#      args: [--convention=numpy]
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: '6.3.0'
+    hooks:
+      - id: pydocstyle
+        exclude: ^(hoomd_organics/tests/|hoomd_organics/utils/|setup.py|hoomd_organics/__version__.py|docs/)
+        args: [ --convention=numpy ]

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "miniconda3-4.7"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+conda:
+    environment: environment-readthedocs.yml

README.md

@@ -1,9 +1,19 @@
 [![pytest](https://github.com/cmelab/hoomd-organics/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/hoomd-organics/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/hoomd-organics/branch/main/graph/badge.svg?token=86LY9WHSH6)](https://codecov.io/gh/cmelab/hoomd-organics)
-## About
+## HOOMD-Organics
+HOOMD-Organics is a modular “wrapper” package for molecular dynamics (MD)
+simulation pipeline development, designed to enable fast, reproducible,
+end-to- end simulation workflows with minimal user effort. This package is a
+wrapper for [MoSDeF](https://github.com/mosdef-hub) packages and
+[Hoomd-Blue](https://github.com/glotzerlab/hoomd-blue) with a focus on
+simulating soft matter systems.
+
+An object-oriented design makes HOOMD-Organics extensible and highly flexible.
+This is bolstered by a library-based approach to system initialization, making
+HOOMD-Organics agnostic to system identity, forcefield, and thermodynamic
+ensemble, and allowing for growth on an as-needed basis.
+
 
-Wrapper for [MoSDeF](https://github.com/mosdef-hub) packages and [Hoomd-Blue](https://github.com/glotzerlab/hoomd-blue) with
-a focus on simulating soft matter systems.
 
 ## Installation
 
@@ -23,5 +33,12 @@ python -m pip install .
 ```
 
 ## Basic Usage
-#### Using the built in molecules, systems and forcefields:
-README, documentation and tutorials are a work in progress.
+Please checkout the [tutorials](tutorials) for a detailed description of
+how to use HOOMD-Organics and what functionalities it provides.
+
+## Documentation
+Documentation is available at [(path to readthedocs)]()
+
+[//]: # (#### Using the built in molecules, systems and forcefields:)
+
+[//]: # (README, documentation and tutorials are a work in progress.)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/base.rst

@@ -0,0 +1,19 @@
+Base
+=====
+
+.. rubric:: Overview
+
+.. py:currentmodule:: hoomd_organics.base
+
+.. rubric:: Details
+
+.. automodule:: hoomd_organics.base
+
+.. rubric:: Modules
+
+.. toctree::
+   :maxdepth: 1
+
+   molecule
+   system
+   simulation

docs/source/conf.py

@@ -0,0 +1,53 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+
+project = "hoomd-organics"
+copyright = (
+    "2023, Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
+)
+author = "Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["nbsphinx", "sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+autodoc_mock_imports = [
+    "cmeutils",
+    "forcefield_utilities",
+    "foyer",
+    "freud",
+    "gmso",
+    "grits",
+    "gsd",
+    "hoomd",
+    "mbuild",
+    "numpy",
+    "openbabel",
+    "py3Dmol",
+    "pydantic",
+    "symengine",
+    "sympy",
+    "unyt",
+    "jupyter",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+nbsphinx_execute = "never"
+nbsphinx_allow_errors = True
+source_suffix = [".rst"]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/forcefields.rst

@@ -0,0 +1,9 @@
+forcefields
+-----------
+
+.. py:currentmodule:hoomd_organics.library
+
+.. rubric:: Details
+
+.. automodule:: hoomd_organics.library.forcefields
+    :members:

docs/source/index.rst

@@ -0,0 +1,43 @@
+Welcome to hoomd-organics's documentation!
+==========================================
+
+
+HOOMD-Organics is a modular “wrapper” package for molecular dynamics (MD)
+simulation pipeline development, designed to enable fast, reproducible, end-to-
+end simulation workflows with minimal user effort. An object-oriented design
+makes HOOMD-Organics extensible and highly flexible. This is bolstered by a
+library-based approach to system initialization, making HOOMD-Organics agnostic
+to system identity, forcefield, and thermodynamic ensemble, and allowing
+for growth on an as-needed basis.
+
+Quick start
+===========
+.. toctree::
+    installation
+
+
+Resources
+=========
+
+`GitHub Repository <https://github.com/cmelab/hoomd-organics>`_: Source code and issue tracker.
+
+`Tutorials <https://github.com/cmelab/hoomd-organics/tree/main/tutorials>`_: Examples of how to use HOOMD-Organics.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Python API
+
+   base
+   modules
+   library
+   tutorials
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/installation.rst

@@ -0,0 +1,19 @@
+============
+Installation
+============
+
+Install from source
+---------------------------------------
+
+1. Clone this repository:
+::
+
+    $ git clone git@github.com:cmelab/hoomd-organics.git
+    $ cd hoomd-organics
+
+2. Set up and activate environment:
+::
+
+    $ conda env create -f environment-cpu.yml
+    $ conda activate hoomd-organics
+    $ python -m pip install .

docs/source/library.rst

@@ -0,0 +1,19 @@
+Library
+=======
+
+.. rubric:: Overview
+
+.. py:currentmodule:: hoomd_organics.library
+
+.. rubric:: Details
+
+.. automodule:: hoomd_organics.library
+
+.. rubric:: Library
+
+.. toctree::
+   :maxdepth: 1
+
+   polymers
+   forcefields
+   simulations

docs/source/modules.rst

@@ -0,0 +1,17 @@
+Modules
+=======
+
+.. rubric:: Overview
+
+.. py:currentmodule:: hoomd_organics.modules
+
+.. rubric:: Details
+
+.. automodule:: hoomd_organics.modules
+
+.. rubric:: Modules
+
+.. toctree::
+   :maxdepth: 1
+
+   welding