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