📝 Document "♻️ Split ResourcePool into three classes"

docs/_sources/_templates/layout.html

@@ -1,5 +1,9 @@
 {% extends "!layout.html" %}
-
+{%- block scripts %}
+    {{ super() }}
+    <script src="{{ pathto('assets/js/jquery.min.js', 1) }}"></script>
+    <script src="{{ pathto('_static/underscore.js', 1) }}"></script>
+{%- endblock %}
 {% block footer %}
 {{ super() }}
     <script async src="https://www.googletagmanager.com/gtag/js?id=UA-19224662-10"></script>

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
 

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']

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:
 

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:
 

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:

docs/_sources/developer/schema.rst

@@ -1,8 +1,7 @@
 .. _validation_schema:
 
-*****************
 Validation Schema
-*****************
+^^^^^^^^^^^^^^^^^
 
 C-PAC uses `voluptuous <alecthomas.github.io/voluptuous/docs/_build/html>`_ to validate pipeline configurations against defined types and value restrictions. Default values should be set in :doc:`the default pipeline </user/pipelines/default>` along with comments explaining each option.
 

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:

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