docs: add sphinx and readthedocs (#187)

.readthedocs.yml

@@ -0,0 +1,17 @@
+---
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: '3.12'
+  jobs:
+    post_create_environment:
+      - pip install poetry
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install --only docs
+
+sphinx:
+  configuration: docs/source/conf.py
+...

README.md

@@ -1,4 +1,5 @@
 [![codecov](https://codecov.io/gh/elixir-cloud-aai/TESK/branch/main/graph/badge.svg)](https://codecov.io/gh/elixir-cloud-aai/TESK)
+[![Documentation Status](https://readthedocs.org/projects/tesk/badge/?version=latest)](https://tesk.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](./LICENSE)
 [![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/downloads/release/python-311/)
 [![Development Status](https://img.shields.io/badge/status-beta-yellow.svg)](https://github.com/elixir-cloud-aai/TESK)
@@ -7,7 +8,7 @@
 [![Safety](https://img.shields.io/badge/security-safety-orange.svg)](https://safetycli.com/product/safety-cli)
 [![Ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://docs.astral.sh/ruff/)
 
-<img src="images/TESKlogowfont.png" height="200">
+<img src="/images/TESKlogowfont.png" height="200">
 
 An implementation of a task execution engine based on the
 [TES standard](https://github.com/ga4gh/task-execution-schemas) running on

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/conf.py

@@ -0,0 +1,100 @@
+"""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 datetime
+import os
+import sys
+from pathlib import Path
+
+import tomli
+
+sys.path.insert(0, os.path.abspath('../..'))
+
+
+# -- Project information -----------------------------------------------------
+def _get_project_meta():
+	_pyproject_path = Path(__file__).parents[2] / 'pyproject.toml'
+	with open(_pyproject_path, mode='rb') as pyproject:
+		return tomli.load(pyproject)['tool']['poetry']
+
+
+pkg_meta = _get_project_meta()
+current_year = datetime.datetime.now().year
+project = str(pkg_meta['name'])
+project_copyright = f"{current_year}, {str(pkg_meta['authors'][0])}"
+author = str(pkg_meta['authors'][0])
+
+version = str(pkg_meta['version'])
+release = version
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+	'sphinx.ext.autodoc',
+	'sphinx.ext.doctest',
+	'sphinx.ext.todo',
+	'sphinx.ext.coverage',
+	'sphinx.ext.viewcode',
+	'sphinx.ext.autosummary',
+	# Used to write beautiful docstrings:
+	'sphinx.ext.napoleon',
+	# Used to include .md files:
+	'm2r2',
+	# Used to insert typehints into the final docs:
+	'sphinx_autodoc_typehints',
+	# Used to embed values from the source code into the docs:
+	'added_value',
+]
+
+# Set `typing.TYPE_CHECKING` to `True`:
+# https://pypi.org/project/sphinx-autodoc-typehints/
+set_type_checking_flag = False
+always_document_param_types = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+
+source_suffix = ['.rst', '.md']
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# 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 -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#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']
+
+# -- Extension configuration -------------------------------------------------
+napoleon_numpy_docstring = False
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True

docs/source/index.rst

@@ -0,0 +1,31 @@
+TESK
+=================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: TESK
+
+.. mdinclude:: ../../README.md
+.. mdinclude:: ../tesintro.md
+
+.. Not adding a heading to separate deployment docs because 
+.. these md files already have heading.
+.. mdinclude:: ../../deployment/documentation/deployment.md
+.. mdinclude:: ../../deployment/documentation/integrated_wes_tes.md
+.. mdinclude:: ../../deployment/documentation/local_ftp.md
+
+Package contents
+==================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: package
+
+   pages/tesk/modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/pages/tesk/modules.rst

@@ -0,0 +1,7 @@
+tesk
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk

docs/source/pages/tesk/tesk.rst

@@ -0,0 +1,18 @@
+tesk package
+============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tesk.services
+
+Module contents
+---------------
+
+.. automodule:: tesk
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tesk/tesk.services.rst

@@ -0,0 +1,101 @@
+tesk.services package
+=====================
+
+Submodules
+----------
+
+tesk.services.constants module
+------------------------------
+
+.. automodule:: tesk.services.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.exceptions module
+-------------------------------
+
+.. automodule:: tesk.services.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.filer module
+--------------------------
+
+.. automodule:: tesk.services.filer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.filer\_class module
+---------------------------------
+
+.. automodule:: tesk.services.filer_class
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.filer\_s3 module
+------------------------------
+
+.. automodule:: tesk.services.filer_s3
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.job module
+------------------------
+
+.. automodule:: tesk.services.job
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.path module
+-------------------------
+
+.. automodule:: tesk.services.path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.pvc module
+------------------------
+
+.. automodule:: tesk.services.pvc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.taskmaster module
+-------------------------------
+
+.. automodule:: tesk.services.taskmaster
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.transput module
+-----------------------------
+
+.. automodule:: tesk.services.transput
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tesk.services.utils module
+--------------------------
+
+.. automodule:: tesk.services.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tesk.services
+   :members:
+   :undoc-members:
+   :show-inheritance: