synchronize recent changes from other CWL repos (#454)

common-workflow-language · Oct 18, 2021 · 19cebce · 19cebce
1 parent cf52293
commit 19cebce
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Showing 39 changed files with 53 additions and 288 deletions.
diff --git a/Makefile b/Makefile
@@ -49,7 +49,7 @@ install-dep: install-dependencies
 
 install-dependencies: FORCE
 	pip install --upgrade $(DEVPKGS)
-	pip install -r requirements.txt
+	pip install -r requirements.txt -r mypy-requirements.txt -r docs/requirements.txt
 
 ## install     : install the ${MODULE} module and schema-salad-tool
 install: FORCE

diff --git a/README.rst b/README.rst
@@ -1,9 +1,12 @@
-|Linux Build Status| |Code coverage| |CII Best Practices|
+|Linux Build Status| |Code coverage| |Documentation Status| |CII Best Practices|
 
 .. |Linux Build Status| image:: https://github.com/common-workflow-language/schema-salad/actions/workflows/ci-tests.yml/badge.svg?branch=main
    :target: https://github.com/common-workflow-language/schema-salad/actions/workflows/ci-tests.yml
 .. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/schema_salad/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/common-workflow-language/schema_salad
+.. |Documentation Status| image:: https://readthedocs.org/projects/schema-salad/badge/?version=latest
+   :target: https://schema-salad.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
 .. |CII Best Practices| image:: https://bestpractices.coreinfrastructure.org/projects/1867/badge
    :target: https://bestpractices.coreinfrastructure.org/projects/1867
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -33,7 +33,11 @@
 extensions = [
         "sphinx.ext.autodoc",
         "sphinx.ext.autosummary",
+        "sphinx.ext.inheritance_diagram",
+        "autoapi.extension",
+        "sphinx_autodoc_typehints",
         "sphinx_rtd_theme",
+        "sphinxcontrib.autoprogram"
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -60,3 +64,14 @@
 
 release = get_distribution('schema-salad').version
 version = '.'.join(release.split('.')[:2])
+
+autoapi_dirs = ['../schema_salad']
+autodoc_typehints = 'description'
+autoapi_keep_files = True
+autoapi_ignore = ['*migrations*', '*.pyi']
+autoapi_options = [ 'members', 'undoc-members', 'show-inheritance', 'show-inheritance-diagram', 'show-module-summary', 'imported-members', 'special-members' ]
+#sphinx-autodoc-typehints
+always_document_param_types = True
+# If False, do not add type info for undocumented parameters.
+# If True, add stub documentation for undocumented parameters to be able to add type info.
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -12,16 +12,20 @@ generation, and transformation to RDF_. Salad provides a bridge
 between document and record oriented data modeling and the Semantic
 Web.
 
-
 Modules
 =======
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
-   modules
-   typeshed
+Command Line Options
+====================
+
+.. autoprogram:: schema_salad.main:arg_parser()
+   :prog: schema-salad-tool
+
+.. autoprogram:: schema_salad.makedoc:arg_parser()
+   :prog: schema-salad-doc
 
 Indices and tables
 ==================

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,6 @@
+sphinx >= 2.2
+sphinx-rtd-theme
+sphinx-autoapi
+sphinx-autodoc-typehints
+typed_ast;python_version<'3.8'
+sphinxcontrib-autoprogram
diff --git a/docs/schema_salad.avro.rst b/docs/schema_salad.avro.rst
diff --git a/docs/schema_salad.avro.schema.rst b/docs/schema_salad.avro.schema.rst
diff --git a/docs/schema_salad.codegen.rst b/docs/schema_salad.codegen.rst
diff --git a/docs/schema_salad.codegen_base.rst b/docs/schema_salad.codegen_base.rst
diff --git a/docs/schema_salad.exceptions.rst b/docs/schema_salad.exceptions.rst
diff --git a/docs/schema_salad.java_codegen.rst b/docs/schema_salad.java_codegen.rst
diff --git a/docs/schema_salad.jsonld_context.rst b/docs/schema_salad.jsonld_context.rst
diff --git a/docs/schema_salad.main.rst b/docs/schema_salad.main.rst
diff --git a/docs/schema_salad.makedoc.rst b/docs/schema_salad.makedoc.rst
diff --git a/docs/schema_salad.metaschema.rst b/docs/schema_salad.metaschema.rst
diff --git a/docs/schema_salad.python_codegen.rst b/docs/schema_salad.python_codegen.rst
diff --git a/docs/schema_salad.python_codegen_support.rst b/docs/schema_salad.python_codegen_support.rst
diff --git a/docs/schema_salad.ref_resolver.rst b/docs/schema_salad.ref_resolver.rst
diff --git a/docs/schema_salad.rst b/docs/schema_salad.rst
diff --git a/docs/schema_salad.schema.rst b/docs/schema_salad.schema.rst
diff --git a/docs/schema_salad.sourceline.rst b/docs/schema_salad.sourceline.rst
diff --git a/docs/schema_salad.tests.matcher.rst b/docs/schema_salad.tests.matcher.rst
diff --git a/docs/schema_salad.tests.rst b/docs/schema_salad.tests.rst
diff --git a/docs/schema_salad.tests.test_cg.rst b/docs/schema_salad.tests.test_cg.rst
diff --git a/docs/schema_salad.tests.test_cli_args.rst b/docs/schema_salad.tests.test_cli_args.rst
diff --git a/docs/schema_salad.tests.test_errors.rst b/docs/schema_salad.tests.test_errors.rst
diff --git a/docs/schema_salad.tests.test_examples.rst b/docs/schema_salad.tests.test_examples.rst
diff --git a/docs/schema_salad.tests.test_fetch.rst b/docs/schema_salad.tests.test_fetch.rst
diff --git a/docs/schema_salad.tests.test_fp.rst b/docs/schema_salad.tests.test_fp.rst
diff --git a/docs/schema_salad.tests.test_print_oneline.rst b/docs/schema_salad.tests.test_print_oneline.rst
diff --git a/docs/schema_salad.tests.test_real_cwl.rst b/docs/schema_salad.tests.test_real_cwl.rst
diff --git a/docs/schema_salad.tests.test_ref_resolver.rst b/docs/schema_salad.tests.test_ref_resolver.rst
diff --git a/docs/schema_salad.tests.util.rst b/docs/schema_salad.tests.util.rst
diff --git a/docs/schema_salad.utils.rst b/docs/schema_salad.utils.rst
diff --git a/docs/schema_salad.validate.rst b/docs/schema_salad.validate.rst