diff --git a/docs/_sources/_templates/layout.html b/docs/_sources/_templates/layout.html index d3feb2edc..da38154dc 100644 --- a/docs/_sources/_templates/layout.html +++ b/docs/_sources/_templates/layout.html @@ -1,5 +1,9 @@ {% extends "!layout.html" %} - +{%- block scripts %} + {{ super() }} + + +{%- endblock %} {% block footer %} {{ super() }} diff --git a/docs/_sources/autodoc_nodeblock.py b/docs/_sources/autodoc_nodeblock.py index cc91d5098..adf20d1b3 100644 --- a/docs/_sources/autodoc_nodeblock.py +++ b/docs/_sources/autodoc_nodeblock.py @@ -1,5 +1,5 @@ from typing import TYPE_CHECKING, Any -from CPAC.pipeline.nodeblock import NodeBlockFunction +from CPAC.pipeline.engine.nodeblock import NodeBlockFunction from docutils.statemachine import StringList from sphinx.ext.autodoc import Documenter, FunctionDocumenter, bool_option diff --git a/docs/_sources/conf.py b/docs/_sources/conf.py index ba3e2d7b4..6b8e99e36 100644 --- a/docs/_sources/conf.py +++ b/docs/_sources/conf.py @@ -19,7 +19,7 @@ from dateutil import parser as dparser from CPAC import __version__ -from CPAC.pipeline.nodeblock import NodeBlockFunction +from CPAC.pipeline.engine.nodeblock import NodeBlockFunction from CPAC.utils.monitoring import custom_logging from github import Github from github.GithubException import RateLimitExceededException, \ @@ -169,6 +169,13 @@ def yaml_to_rst(path): 'exec', 'nbsphinx'] +add_module_names = False +maximum_signature_line_length = 90 + +autoclass_content = "both" +autodoc_typehints = "both" +autodoc_typehints_format = "short" + bibtex_bibfiles = [f'references/{bib}' for bib in os.listdir('references') if bib.endswith('.bib')] bibtex_default_style = 'cpac_docs_style' @@ -179,7 +186,11 @@ def yaml_to_rst(path): issues_github_path = 'FCP-INDI/C-PAC' +napoleon_attr_annotations = True +napoleon_include_private_with_doc = True napoleon_preprocess_types = True +napoleon_use_admonition_for_notes = True + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/docs/_sources/developer/logging.rst b/docs/_sources/developer/logging.rst index acea66843..fca5feb7d 100644 --- a/docs/_sources/developer/logging.rst +++ b/docs/_sources/developer/logging.rst @@ -26,7 +26,6 @@ A ``CPAC.utils.monitoring.custom_logging.MockLogger`` can be used in place of a .. autofunction:: CPAC.utils.monitoring.custom_logging.getLogger .. autoclass:: CPAC.utils.monitoring.custom_logging.MockLogger - :special-members: __init__ :members: :inherited-members: diff --git a/docs/_sources/developer/nodes.rst b/docs/_sources/developer/nodes.rst index 3744ec920..e11e5a4fd 100644 --- a/docs/_sources/developer/nodes.rst +++ b/docs/_sources/developer/nodes.rst @@ -30,17 +30,14 @@ For nodes that will use a varying amount of memory depending on the node's input .. autoclass:: CPAC.pipeline.nipype_pipeline_engine.Node - :special-members: __init__ :members: :inherited-members: .. autoclass:: CPAC.pipeline.nipype_pipeline_engine.MapNode - :special-members: __init__ :members: :inherited-members: .. autoclass:: nipype.interfaces.base.core.Interface - :special-members: __init__ :members: :inherited-members: @@ -50,12 +47,10 @@ For nodes that will use a varying amount of memory depending on the node's input .. autoclass:: CPAC.utils.interfaces.function.Function - :special-members: __init__ :members: :inherited-members: .. autoclass:: CPAC.pipeline.nipype_pipeline_engine.Workflow - :special-members: __init__ :members: :inherited-members: diff --git a/docs/_sources/developer/pipeline.rst b/docs/_sources/developer/pipeline.rst index 850d26aa9..077eca26f 100644 --- a/docs/_sources/developer/pipeline.rst +++ b/docs/_sources/developer/pipeline.rst @@ -3,9 +3,40 @@ Pipeline Development .. include:: /developer/schema.rst +Engine +^^^^^^ + +NodeBlock +--------- + +.. automodule:: CPAC.pipeline.engine.nodeblock + :members: + :inherited-members: + :private-members: + :undoc-members: + +Resource +-------- + +.. automodule:: CPAC.pipeline.engine.resource + :members: + :inherited-members: + :private-members: + :undoc-members: + +Tests +----- + +.. automodule:: CPAC.pipeline.test.test_engine + :members: + :inherited-members: + :private-members: + :undoc-members: + Pipeline Utilities ^^^^^^^^^^^^^^^^^^ .. automodule:: CPAC.pipeline.utils :members: + :inherited-members: :undoc-members: diff --git a/docs/_sources/developer/schema.rst b/docs/_sources/developer/schema.rst index 1c0557977..1faad9334 100644 --- a/docs/_sources/developer/schema.rst +++ b/docs/_sources/developer/schema.rst @@ -1,8 +1,7 @@ .. _validation_schema: -***************** Validation Schema -***************** +^^^^^^^^^^^^^^^^^ C-PAC uses `voluptuous `_ to validate pipeline configurations against defined types and value restrictions. Default values should be set in :doc:`the default pipeline ` along with comments explaining each option. diff --git a/docs/_sources/developer/workflows/network_centrality.rst b/docs/_sources/developer/workflows/network_centrality.rst index e4edd5fad..80620ce8a 100644 --- a/docs/_sources/developer/workflows/network_centrality.rst +++ b/docs/_sources/developer/workflows/network_centrality.rst @@ -2,19 +2,16 @@ Network Centrality ================== .. automodule:: CPAC.network_centrality.network_centrality - :special-members: __init__ :members: :private-members: :undoc-members: .. automodule:: CPAC.network_centrality.pipeline - :special-members: __init__ :members: :private-members: :undoc-members: .. automodule:: CPAC.network_centrality.utils - :special-members: __init__ :members: :private-members: :undoc-members: diff --git a/requirements.txt b/requirements.txt index 77b5010eb..d892e303e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,6 +8,7 @@ m2r mistune==0.8.4 nbsphinx PyGithub +pytest sphinx==7.3.2 sphinx-basic-ng>=1.0.0.beta2 sphinxcontrib-bibtex==2.5.0