Merge 22f1f95 into c5314b0

.gitignore

@@ -55,6 +55,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/source/_autosummary/
 
 # PyBuilder
 target/
@@ -64,3 +65,6 @@ target/
 
 # SublimeText docs
 *.sublime-*
+
+# temp folder
+temp/

.travis.yml

@@ -20,3 +20,19 @@ jobs:
       script: pytest --cov=pyDeltaRCM/
       after_success: 
         - coveralls
+    - stage: docs
+      python: "3.8"
+      install: 
+        - pip install -r requirements.txt 
+        - pip install sphinx sphinx-automodapi
+        - sudo apt update -y && sudo apt install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng
+      script: (cd docs && make html)
+      deploy:
+        provider: pages:git
+        github_token: $GITHUB_TOKEN
+        committer_from_gh: true
+        verbose: true
+        edge: true
+        local-dir: docs/build/html
+        on:
+          branch: develop

CODE_OF_CONDUCT.rst

@@ -0,0 +1,79 @@
+***************
+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.
+
+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 the issue tracker. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and 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 <http://contributor-covenant.org>`_, `version 1.4 <http://contributor-covenant.org/version/1/4>`_,
+available at http://contributor-covenant.org/version/1/4.

LICENSE

@@ -1,6 +1,7 @@
 MIT License
 
 Copyright (c) 2016 Mariela Perignon
+Copyright (c) 2020 The DeltaRCM Team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,10 +1,11 @@
 # pyDeltaRCM_WMT
 
-[![Build Status](https://travis-ci.org/elbeejay/pyDeltaRCM_WMT.svg?branch=develop)](https://travis-ci.org/elbeejay/pyDeltaRCM_WMT)
+[![Build Status](https://travis-ci.com/DeltaRCM/pyDeltaRCM_WMT.svg?branch=develop)](https://travis-ci.org/DeltaRCM/pyDeltaRCM_WMT)
 
-[![Coverage Status](https://coveralls.io/repos/github/elbeejay/pyDeltaRCM_WMT/badge.svg?branch=develop)](https://coveralls.io/github/elbeejay/pyDeltaRCM_WMT?branch=develop)
+[![Coverage Status](https://coveralls.io/repos/github/DeltaRCM/pyDeltaRCM_WMT/badge.svg?branch=develop)](https://coveralls.io/github/DeltaRCM/pyDeltaRCM_WMT?branch=develop)
 
-pyDeltaRCM is the Python version of the [Matlab deltaRCM](http://csdms.colorado.edu/wiki/Model:DeltaRCM) model by Man Liang. This model has been turned into a component for WMT, the [Community Surface Dynamics Modeling System (CSDMS)](http://csdms.colorado.edu/wiki/Main_Page) Web Modeling Interface.
+pyDeltaRCM is the Python version of the [Matlab deltaRCM](http://csdms.colorado.edu/wiki/Model:DeltaRCM) model by Man Liang. 
+This model has been turned into a component for WMT, the [Community Surface Dynamics Modeling System (CSDMS)](http://csdms.colorado.edu/wiki/Main_Page) Web Modeling Interface.
 
 The pyDeltaRCM scripts in this repository can be run as a stand-alone model following the instructions below.
 

docs/Makefile

@@ -0,0 +1,23 @@
+# 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 $(SPHINXOPTS).
+%: Makefile
+	rm -rf source/api/
+	rm -rf source/_autosummary/
+	rm -rf ../build/
+	@$(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
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_static/style.css

@@ -0,0 +1,112 @@
+@import url("default.css"); /* make sure to sync this with the base theme's css filename */
+
+/*:root {
+  --main-bg-color: DarkGreen;
+  --url-color: Brown;
+  --url-color-hover: Coral;
+  --sidebar-box-bg-color: DarkOrange;
+  --sidebar-border-color: Black;
+}*/
+
+:root {
+  --main-bg-color: #f2f2f2;
+  --h1-color: #93776C;
+  --hplus-color: black;
+  --url-color: #D8925D;
+  --url-color-hover: #9BAF9B;
+  --sidebar-box-bg-color: #B3CF89;
+  --sidebar-border-color: Black;
+  --footer-bg-color: #B3CF89;
+}
+
+
+body {
+    background-color: var(--main-bg-color);
+}
+
+h1 {
+    margin: 0;
+    padding: 0.7em 0 0.3em 0;
+    font-size: 1.5em;
+    color: var(--h1-color);
+}
+
+div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a {
+    color: var(--hplus-color)!important;
+}
+
+a {
+    color: var(--url-color);
+    text-decoration: none;
+}
+
+a:hover {
+    color: var(--url-color-hover);
+}
+
+a code {
+    border: 0;
+    color: var(--url-color);
+}
+
+a code:hover {
+    color: var(--url-color-hover);
+}
+
+a.headerlink {
+    color: PeachPuff!important;
+    font-size: 1em;
+    margin-left: 6px;
+    padding: 0 4px 0 4px;
+    text-decoration: none!important;
+}
+
+div.related ul li a {
+    margin: 0;
+    padding: 0 5px 0 5px;
+    line-height: 1.75em;
+    color: var(--url-color);
+}
+
+div.related ul li a:hover {
+    color: var(--url-color-hover);
+}
+
+div.sphinxsidebar h3, div.sphinxsidebar h4 {
+    color: white;
+    border: 1px solid var(--sidebar-border-color);
+    background-color: var(--sidebar-box-bg-color);
+}
+
+div.sphinxsidebar input {
+    border: 1px solid var(--sidebar-border-color);
+}
+
+pre {
+    font-family: 'Consolas', 'Deja Vu Sans Mono',
+                 'Bitstream Vera Sans Mono', monospace;
+    font-size: 0.95em;
+    letter-spacing: 0.015em;
+    line-height: 120%;
+    padding: 0.5em;
+    border: 1px solid #ccc;
+    background-color: #eaece5;
+}
+
+pre span gp { 
+    color: red;
+ }
+
+div.footer {
+    background-color: var(--footer-bg-color);
+    color: #969696;
+    padding: 3px 8px 3px 0;
+    clear: both;
+    font-size: 0.8em;
+    text-align: right;
+}
+
+div.footer a {
+    color: #969696;
+    text-decoration: underline;
+}

docs/source/_templates/page.html

@@ -0,0 +1,4 @@
+{% extends "!page.html" %}
+
+{% set css_files = css_files + ["_static/style.css"] %}
+