Merge pull request #1216 from common-workflow-language/rtd

mr-c · web-flow · commit 0b3846fbf866 · 2019-10-25T15:07:57.000+02:00
enable basic docs
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,21 @@
+# .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:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+   - method: pip
+     path: .
+     extra_requirements: [ docs ]
diff --git a/docs/Makefile b/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)
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,60 @@
+# 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 = 'Common Workflow Language reference implementation'
+copyright = '2019, Peter Amstutz and contributors'
+author = 'Peter Amstutz and contributors'
+
+
+# -- 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",
+        "sphinx.ext.autosummary",
+        "sphinx_rtd_theme",
+]
+
+# 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']
+
+
+from pkg_resources import get_distribution
+release = get_distribution('cwltool').version
+version = '.'.join(release.split('.')[:2])
diff --git a/docs/cwltool.argparser.rst b/docs/cwltool.argparser.rst
@@ -0,0 +1,7 @@
+cwltool.argparser module
+========================
+
+.. automodule:: cwltool.argparser
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.builder.rst b/docs/cwltool.builder.rst
@@ -0,0 +1,7 @@
+cwltool.builder module
+======================
+
+.. automodule:: cwltool.builder
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.checker.rst b/docs/cwltool.checker.rst
@@ -0,0 +1,7 @@
+cwltool.checker module
+======================
+
+.. automodule:: cwltool.checker
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.command_line_tool.rst b/docs/cwltool.command_line_tool.rst
@@ -0,0 +1,7 @@
+cwltool.command\_line\_tool module
+==================================
+
+.. automodule:: cwltool.command_line_tool
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.context.rst b/docs/cwltool.context.rst
@@ -0,0 +1,7 @@
+cwltool.context module
+======================
+
+.. automodule:: cwltool.context
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.cwlrdf.rst b/docs/cwltool.cwlrdf.rst
@@ -0,0 +1,7 @@
+cwltool.cwlrdf module
+=====================
+
+.. automodule:: cwltool.cwlrdf
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.docker.rst b/docs/cwltool.docker.rst
@@ -0,0 +1,7 @@
+cwltool.docker module
+=====================
+
+.. automodule:: cwltool.docker
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.docker_id.rst b/docs/cwltool.docker_id.rst
@@ -0,0 +1,7 @@
+cwltool.docker\_id module
+=========================
+
+.. automodule:: cwltool.docker_id
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.errors.rst b/docs/cwltool.errors.rst
@@ -0,0 +1,7 @@
+cwltool.errors module
+=====================
+
+.. automodule:: cwltool.errors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.executors.rst b/docs/cwltool.executors.rst
@@ -0,0 +1,7 @@
+cwltool.executors module
+========================
+
+.. automodule:: cwltool.executors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.expression.rst b/docs/cwltool.expression.rst
@@ -0,0 +1,7 @@
+cwltool.expression module
+=========================
+
+.. automodule:: cwltool.expression
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.factory.rst b/docs/cwltool.factory.rst
@@ -0,0 +1,7 @@
+cwltool.factory module
+======================
+
+.. automodule:: cwltool.factory
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.flatten.rst b/docs/cwltool.flatten.rst
@@ -0,0 +1,7 @@
+cwltool.flatten module
+======================
+
+.. automodule:: cwltool.flatten
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.job.rst b/docs/cwltool.job.rst
@@ -0,0 +1,7 @@
+cwltool.job module
+==================
+
+.. automodule:: cwltool.job
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.load_tool.rst b/docs/cwltool.load_tool.rst
@@ -0,0 +1,7 @@
+cwltool.load\_tool module
+=========================
+
+.. automodule:: cwltool.load_tool
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.loghandler.rst b/docs/cwltool.loghandler.rst
@@ -0,0 +1,7 @@
+cwltool.loghandler module
+=========================
+
+.. automodule:: cwltool.loghandler
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.main.rst b/docs/cwltool.main.rst
@@ -0,0 +1,7 @@
+cwltool.main module
+===================
+
+.. automodule:: cwltool.main
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.mutation.rst b/docs/cwltool.mutation.rst
@@ -0,0 +1,7 @@
+cwltool.mutation module
+=======================
+
+.. automodule:: cwltool.mutation
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.pack.rst b/docs/cwltool.pack.rst
@@ -0,0 +1,7 @@
+cwltool.pack module
+===================
+
+.. automodule:: cwltool.pack
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.pathmapper.rst b/docs/cwltool.pathmapper.rst
@@ -0,0 +1,7 @@
+cwltool.pathmapper module
+=========================
+
+.. automodule:: cwltool.pathmapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.process.rst b/docs/cwltool.process.rst
@@ -0,0 +1,7 @@
+cwltool.process module
+======================
+
+.. automodule:: cwltool.process
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.procgenerator.rst b/docs/cwltool.procgenerator.rst
@@ -0,0 +1,7 @@
+cwltool.procgenerator module
+============================
+
+.. automodule:: cwltool.procgenerator
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.provenance.rst b/docs/cwltool.provenance.rst
@@ -0,0 +1,7 @@
+cwltool.provenance module
+=========================
+
+.. automodule:: cwltool.provenance
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.resolver.rst b/docs/cwltool.resolver.rst
@@ -0,0 +1,7 @@
+cwltool.resolver module
+=======================
+
+.. automodule:: cwltool.resolver
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.rst b/docs/cwltool.rst
@@ -0,0 +1,50 @@
+cwltool package
+===============
+
+Submodules
+----------
+
+.. toctree::
+
+   cwltool.argparser
+   cwltool.builder
+   cwltool.checker
+   cwltool.command_line_tool
+   cwltool.context
+   cwltool.cwlrdf
+   cwltool.docker
+   cwltool.docker_id
+   cwltool.errors
+   cwltool.executors
+   cwltool.expression
+   cwltool.factory
+   cwltool.flatten
+   cwltool.job
+   cwltool.load_tool
+   cwltool.loghandler
+   cwltool.main
+   cwltool.mutation
+   cwltool.pack
+   cwltool.pathmapper
+   cwltool.process
+   cwltool.procgenerator
+   cwltool.provenance
+   cwltool.resolver
+   cwltool.sandboxjs
+   cwltool.secrets
+   cwltool.singularity
+   cwltool.software_requirements
+   cwltool.stdfsaccess
+   cwltool.subgraph
+   cwltool.update
+   cwltool.utils
+   cwltool.validate_js
+   cwltool.workflow
+
+Module contents
+---------------
+
+.. automodule:: cwltool
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.sandboxjs.rst b/docs/cwltool.sandboxjs.rst
@@ -0,0 +1,7 @@
+cwltool.sandboxjs module
+========================
+
+.. automodule:: cwltool.sandboxjs
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.secrets.rst b/docs/cwltool.secrets.rst
@@ -0,0 +1,7 @@
+cwltool.secrets module
+======================
+
+.. automodule:: cwltool.secrets
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.singularity.rst b/docs/cwltool.singularity.rst
@@ -0,0 +1,7 @@
+cwltool.singularity module
+==========================
+
+.. automodule:: cwltool.singularity
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.software_requirements.rst b/docs/cwltool.software_requirements.rst
@@ -0,0 +1,7 @@
+cwltool.software\_requirements module
+=====================================
+
+.. automodule:: cwltool.software_requirements
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.stdfsaccess.rst b/docs/cwltool.stdfsaccess.rst
@@ -0,0 +1,7 @@
+cwltool.stdfsaccess module
+==========================
+
+.. automodule:: cwltool.stdfsaccess
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.subgraph.rst b/docs/cwltool.subgraph.rst
@@ -0,0 +1,7 @@
+cwltool.subgraph module
+=======================
+
+.. automodule:: cwltool.subgraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/cwltool.update.rst b/docs/cwltool.update.rst
diff --git a/docs/cwltool.utils.rst b/docs/cwltool.utils.rst
diff --git a/docs/cwltool.validate_js.rst b/docs/cwltool.validate_js.rst
diff --git a/docs/cwltool.workflow.rst b/docs/cwltool.workflow.rst
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/modules.rst b/docs/modules.rst
diff --git a/setup.py b/setup.py
