- documentation skeleton

README.md

@@ -1,5 +1,5 @@
 # COPASI.js
-This project hosts a simplification of the COPASI API used
+This project hosts a wrapper for the COPASI API used
 primarily for running simulations and steady state analysis 
 of SBML/COPASI models. 
 

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/api.rst

@@ -0,0 +1,8 @@
+
+API Documentation
+=================
+
+Here the full API documentation
+
+.. doxygenindex::
+   :project: cpsapi

docs/conf.py

@@ -0,0 +1,84 @@
+# 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('.'))
+
+
+# RTD setup
+import subprocess, os
+
+def configureDoxyfile(input_dir, output_dir):
+    with open('Doxyfile.in', 'r') as file :
+        filedata = file.read()
+
+    with open('../VERSION.txt', 'r') as file :
+        version = file.read()
+
+    filedata = filedata.replace('@DOXYGEN_INPUT_DIR@', input_dir)
+    filedata = filedata.replace('@JS_VERISON_NUMBER@', version)
+    filedata = filedata.replace('@DOXYGEN_OUTPUT_DIR@', output_dir)
+
+    with open('Doxyfile', 'w') as file:
+        file.write(filedata)
+
+# Check if we're running on Read the Docs' servers
+read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
+
+breathe_projects = {}
+
+if read_the_docs_build:
+    input_dir = '../src'
+    output_dir = 'build'
+    configureDoxyfile(input_dir, output_dir)
+    subprocess.call('doxygen', shell=True)
+    breathe_projects['copasijs'] = output_dir + '/xml'
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'COPASI.js API'
+copyright = '2024, COPASI Team'
+author = 'Frank T. Bergmann'
+
+
+# -- 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 = [ "breathe" ]
+
+# Breathe Configuration
+breathe_default_project = "copasijs"
+
+# 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 = 'sphinx_rtd_theme'
+
+# 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/examples/examples.rst

@@ -0,0 +1,3 @@
+Examples
+========
+

docs/index.rst

@@ -0,0 +1,26 @@
+.. COPASI.js API documentation master file, created by
+   sphinx-quickstart on Wed Apr 14 10:45:25 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to COPASI.js API's documentation!
+======================================
+
+.. image:: ./_static/COPASI_Conly_176x176.png
+   :alt: COPASI logo
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   quickstart/get-started
+   examples/examples
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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
+
+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/quickstart/get-started.rst

@@ -0,0 +1,9 @@
+Quickstart
+==========
+
+.. _building_library:
+
+Building the library
+--------------------
+
+

docs/requirements.txt

@@ -0,0 +1 @@
+breathe