sphinx website for the documentation

.github/workflows/docs.yml

@@ -0,0 +1,37 @@
+name: GCBM Belize Docs
+
+on:
+  push:
+    branches: [ sphinx-website ]
+  pull_request:
+    branches: [ sphinx-website ]
+
+jobs:
+  build-deploy-belize-docs:
+    runs-on: ubuntu-latest  
+    name: Build & Deploy Belize docs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: |
+          pip install -U sphinx
+          cd docs
+          pip install -r requirements.txt
+
+      - name: Build Belize docs
+        uses: ammaraskar/sphinx-action@master
+        with:
+          docs-folder: "docs/"
+
+      - name: Set-up Node
+        uses: actions/setup-node@v1
+        with:
+          node-version: "10.x"
+
+      - name: Deploy Belize docs
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html

.gitignore

@@ -3,3 +3,4 @@ Postprocessing/.Rhistory
 Postprocessing/.RData
 Postprocessing/.Ruserdata
 Postprocessing/renv/library
+docs/_build

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     = .
+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/about_belize/index.rst

@@ -0,0 +1,22 @@
+About Belize 
+============
+
+Belize is the only English-speaking country in Central America and as a feature of its geographical location
+and historical background, is a part of both Central America and the Caribbean. Bordered on the east by
+the Caribbean Sea, on the north and north-west by Mexico, and on the west and south by Guatemala, Belize
+lies between 15°45’ and 18°30’ north latitude, and 87°30’ and 89°15’ west longitude. The
+country’s national territory comprises 46,620 sq. km (18,000 sq. miles).
+
+Belize is highly forested, with more than 50% of the mainland covered with forests and the remaining land consisting mainly of agriculture, arable
+land, and human settlements.
+
+.. figure:: ../assets/belize.gif
+   :alt: Map of Belize
+   :align: center
+   :width: 600px
+
+   Image source https://geology.com/world/belize-satellite-image.shtml
+
+Two main ecosystems encompass Belize’s territory, the marine and the terrestrial ecosystem.
+The marine ecosystem consists of open ocean, coral reefs and seagrass beds. In contrast, the terrestrial ecosystem is made up of both broadleaf and pine forests, along with several lakes and rivers in the country.
+ecosystem is made up of both broadleaf and pine forests along with several lakes and rivers in country.

docs/conf.py

@@ -0,0 +1,52 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'GCBM Belize'
+copyright = '2022, moja global'
+author = 'moja global'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,19 @@
+.. GCBM Belize documentation master file, created by
+   sphinx-quickstart on Sun Jul 10 16:37:19 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+GCBM Belize
+===========
+
+This is the official documentation of the GCBM Belize project. 
+This project is based on the `Standalone Template for the GCBM <https://carbon.nfis.org/cbm>`_ 
+
+**Disclaimer : The calculations performed in this repository are not official and do not represent the Government of Belize in any way.**
+
+.. toctree::
+   :hidden:
+
+   about_belize/index.rst
+   run_simulation/index.rst
+   postprocessing/index.rst

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=.
+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/moja_global_docs/.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,42 @@
+name: Bug Report🐛
+description: Create a report to help us improve
+title: "Bug🐛: "
+labels: [bug]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a Bug report.
+  - type: textarea
+    attributes:
+      label: Describe the bug.
+      description: "A clear and concise description of what the bug is."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe the steps to reproduce the behavior.
+      description: "Be clear and concise while describing the steps to ensure that it can be reproduced and potentially fixed"
+      placeholder: |
+        1. Go to '...'
+        2. Click on '....'
+        3. Scroll down to '....'
+        4. See error
+  - type: textarea
+    attributes:
+      label: Expected behavior.
+      description: "A clear and concise description of what you expected to happen."
+  - type: textarea
+    attributes:
+      label: Screenshots.
+      description: "If applicable, add screenshots to help explain your problem."
+  - type: input
+    attributes:
+      label: Operating Environment
+      description: "What operating system and version are you using? If you are running it on Cloud/Cluster do mention about that."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or screenshots to clarify your suggestion here."

docs/moja_global_docs/.github/ISSUE_TEMPLATE/communication-suggestion.yml

@@ -0,0 +1,25 @@
+name: Communication Suggestion
+description: Propose a way to better communicate a feature
+title: "Communication Suggestion: "
+labels: [communication]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a Communication Suggestion report.
+  - type: textarea
+    attributes:
+      label: Describe how we are communicating and why it is not optimal.
+      description: "A clear and concise description of what the problem is. Ex. When I reach this point, I cannot [...]."
+  - type: textarea
+    attributes:
+      label: Describe the solution you'd like.
+      description: "A clear and concise description of what you want to happen."
+  - type: textarea
+    attributes:
+      label: Describe alternatives you've considered.
+      description: "A clear and concise description of any alternative solutions or features you have considered."
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or screenshots to clarify your suggestion here."

docs/moja_global_docs/.github/ISSUE_TEMPLATE/documentation-update.yml

@@ -0,0 +1,29 @@
+name: Documentation Update📄
+description: Suggest how we can improve our documentation
+title: "Documentation📄: "
+labels: [documentation]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a Documentation update report.
+  - type: textarea
+    attributes:
+      label: What is the current documentation state?
+      description: "Copy and paste the text currently in the documentation. If you want to improve graphs or photos, please provide a screenshot of the original."
+  - type: textarea
+    attributes:
+      label: Where is this stated?
+      description: "Provide additional information about the location where you have copied the above statement from."
+  - type: textarea
+    attributes:
+      label: Why do you want to improve the statement?
+      description: "Please explain why the statement needs to be updated. This can be because it is confusing, incorrect, spelling/grammatical errors, etc."
+  - type: textarea
+    attributes:
+      label: Proposed Statement
+      description: "Please propose how you would rewrite the statement. If you have a precise proposal, please make the changes and open a pull request."
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or useful information about the documentation update here."

docs/moja_global_docs/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,27 @@
+name: Feature Request
+description: Suggest an idea for this project
+title: "Feature Request: "
+labels: [enhancement]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a Feature Request report.
+  - type: textarea
+    attributes:
+      label: Is your feature request related to a problem? Please describe.
+      description: "A clear and concise description of what the problem is. Ex. I am always frustrated when [...]"
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe the solution you'd like.
+      description: "A clear and concise description of what you want to happen."
+  - type: textarea
+    attributes:
+      label: Describe alternatives you've considered
+      description: "A clear and concise description of any alternative solutions or features you have considered."
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or screenshots about the feature request here."

docs/moja_global_docs/.github/ISSUE_TEMPLATE/science-contribution-and-review-.yml

@@ -0,0 +1,27 @@
+name: Science Contribution and Review
+description: Suggest how the science behind the code can be improved
+title: "Science Contribution and Review: "
+labels: [science-review]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a Science Contribution and Review report.
+  - type: textarea
+    attributes:
+      label: Please describe the problem.
+      description: "A clear and concise description of what the problem is."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe the correct or improved scientific approach.
+      description: "A clear and concise description of what you want to happen."
+  - type: textarea
+    attributes:
+      label: Describe alternatives that could be considered
+      description: "A clear and concise description of any alternative solutions that would be scientifically correct."
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or screenshots about the feature request here."

docs/moja_global_docs/.github/ISSUE_TEMPLATE/user-feedback.yml

@@ -0,0 +1,27 @@
+name: User Feedback
+description: Describe how we can improve your experience
+title: "User Feedback: "
+labels: [user-feedback]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for taking the time to file a User Feedback report.
+  - type: textarea
+    attributes:
+      label: Describe what you are trying to do and why it is not optimal.
+      description: "A clear and concise description of what the problem is. Ex. When I reach this point, I cannot [...]"
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe the solution you'd like.
+      description: "A clear and concise description of what you want to happen."
+  - type: textarea
+    attributes:
+      label: Describe alternatives you've considered.
+      description: "A clear and concise description of any alternative solutions or features you have considered."
+  - type: textarea
+    attributes:
+      label: Additional context.
+      description: "Add any other context or screenshots about the feature request here."

docs/moja_global_docs/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,14 @@
+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+- [ ] Issue reference: <!-- Refer the issue that you have picked up link it to the Pull Request -->
+- [ ] Subject Matter Expert (SME) reviewer: <!-- Refer the SME who can provide the technical feedback. Add NA if not known -->
+- [ ] Peer reviewer: <!-- Refer the Peer reviewer who can provide the docs feedback. Add NA if not known -->
+- [ ] Preview Links: <!-- Once the ReadTheDocs CI passes, navigate to the built docs and find where your documentation is being referenced. Add the link over here for easy reviews -->
+- [ ] Explain the changes: <!-- Briefly explain the changes and purpose of your PR -->
+- [ ] Dependency changes: <!-- Y/N; Explain if there are any dependency changes -->
+
+Thanks for opening the Pull Request for moja global. Happy contributing ✨
+
+<!--- Thanks for opening this pull request! If the tests fail, please feel free to reach out to us by leaving a comment down below and we will be happy to take a look --->