Merge pull request #48 from sybila/38-add-docs

Add docs sources for ReadTheDocs

.readthedocs.yaml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+
+python:
+  version: "3.8"
+  install:
+    - requirements: docs/requirements.txt

docs/requirements.txt

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+numpy
+pandas
+pyparsing
+regex
+requests
+scipy
+setuptools
+sortedcontainers
+sympy
+python-libsbml
+lark
+lark-parser
+pip
+pytest
+pymodelchecking
+sphinx
+sphinx_rtd_theme
+myst-parser

docs/source/conf.py

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+# 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('../../'))
+from shutil import copyfile
+copyfile('../../README.md', 'readme.md')
+
+import eBCSgen
+
+# -- Project information -----------------------------------------------------
+
+project = 'eBCSgen'
+copyright = '2022, Matej Trojak'
+author = 'Matej Trojak'
+
+
+# -- 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 = ['sphinx.ext.autodoc', 'myst_parser']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# 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 = []
+
+
+# -- 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/source/eBCSgen.Analysis.rst

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+eBCSgen.Analysis package
+========================
+
+eBCSgen.Analysis.CTL module
+---------------------------
+
+.. automodule:: eBCSgen.Analysis.CTL
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Analysis.PCTL module
+----------------------------
+
+.. automodule:: eBCSgen.Analysis.PCTL
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Analysis.Static module
+------------------------------
+
+.. automodule:: eBCSgen.Analysis.Static
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/eBCSgen.Core.rst

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+eBCSgen.Core package
+====================
+
+eBCSgen.Core.Atomic module
+--------------------------
+
+.. automodule:: eBCSgen.Core.Atomic
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Complex module
+---------------------------
+
+.. automodule:: eBCSgen.Core.Complex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Formula module
+---------------------------
+
+.. automodule:: eBCSgen.Core.Formula
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Model module
+-------------------------
+
+.. automodule:: eBCSgen.Core.Model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Rate module
+------------------------
+
+.. automodule:: eBCSgen.Core.Rate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Reaction module
+----------------------------
+
+.. automodule:: eBCSgen.Core.Reaction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Rule module
+------------------------
+
+.. automodule:: eBCSgen.Core.Rule
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Side module
+------------------------
+
+.. automodule:: eBCSgen.Core.Side
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Core.Structure module
+-----------------------------
+
+.. automodule:: eBCSgen.Core.Structure
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/eBCSgen.Errors.rst

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+eBCSgen.Errors package
+======================
+
+eBCSgen.Errors.ComplexOutOfScope module
+---------------------------------------
+
+.. automodule:: eBCSgen.Errors.ComplexOutOfScope
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.ComplexParsingError module
+-----------------------------------------
+
+.. automodule:: eBCSgen.Errors.ComplexParsingError
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.FormulaParsingError module
+-----------------------------------------
+
+.. automodule:: eBCSgen.Errors.FormulaParsingError
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.InvalidInputError module
+---------------------------------------
+
+.. automodule:: eBCSgen.Errors.InvalidInputError
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.ModelParsingError module
+---------------------------------------
+
+.. automodule:: eBCSgen.Errors.ModelParsingError
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.RatesNotSpecifiedError module
+--------------------------------------------
+
+.. automodule:: eBCSgen.Errors.RatesNotSpecifiedError
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.StormNotAvailable module
+---------------------------------------
+
+.. automodule:: eBCSgen.Errors.StormNotAvailable
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Errors.UnspecifiedParsingError module
+---------------------------------------------
+
+.. automodule:: eBCSgen.Errors.UnspecifiedParsingError
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/eBCSgen.Export.rst

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+eBCSgen.Export package
+======================
+
+eBCSgen.Export.ModelSBML module
+-------------------------------
+
+.. automodule:: eBCSgen.Export.ModelSBML
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/eBCSgen.Parsing.rst

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+eBCSgen.Parsing package
+=======================
+
+eBCSgen.Parsing.ParseBCSL module
+--------------------------------
+
+.. automodule:: eBCSgen.Parsing.ParseBCSL
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Parsing.ParseCTLformula module
+--------------------------------------
+
+.. automodule:: eBCSgen.Parsing.ParseCTLformula
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Parsing.ParsePCTLformula module
+---------------------------------------
+
+.. automodule:: eBCSgen.Parsing.ParsePCTLformula
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/eBCSgen.Regulations.rst

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+eBCSgen.Regulations package
+===========================
+
+eBCSgen.Regulations.Base module
+-------------------------------
+
+.. automodule:: eBCSgen.Regulations.Base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Regulations.ConcurrentFree module
+-----------------------------------------
+
+.. automodule:: eBCSgen.Regulations.ConcurrentFree
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Regulations.Conditional module
+--------------------------------------
+
+.. automodule:: eBCSgen.Regulations.Conditional
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Regulations.Ordered module
+----------------------------------
+
+.. automodule:: eBCSgen.Regulations.Ordered
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Regulations.Programmed module
+-------------------------------------
+
+.. automodule:: eBCSgen.Regulations.Programmed
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+eBCSgen.Regulations.Regular module
+----------------------------------
+
+.. automodule:: eBCSgen.Regulations.Regular
+   :members:
+   :undoc-members:
+   :show-inheritance: