refactor the add nodes methods (#251)

- Move the add_nodes method into a separate file and split the different node types into separate functions.
- Create separate functions for tasks that are shared across nodes.
- Remove the generic-input type. This will be replaced by custom nodes in a forthcoming PR.

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     hooks:
     - id: isort
 -   repo: https://github.com/ambv/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
     - id: black
       language_version: python3
@@ -24,7 +24,7 @@ repos:
         args: ['--ignore', 'D213,D100,D203,D104']
         files: ^src/
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.11.2'
+    rev: 'v1.13.0'
     hooks:
     - id: mypy 
       files: ^src/

docs/source/api.rst

@@ -179,6 +179,14 @@ and creates a standard node structure for these models.
 
    HGF
    Network
+   add_continuous_state
+   add_binary_state
+   add_ef_state
+   add_categorical_state
+   add_dp_state
+   get_couplings
+   update_parameters
+   insert_nodes
 
 Plots
 *****

docs/source/conf.py

@@ -17,15 +17,15 @@
 # -- Project information -----------------------------------------------------
 
 project = "pyhgf"
-copyright = u"2022-{}, Nicolas Legrand".format(time.strftime("%Y"))
+copyright = "2022-{}, Nicolas Legrand".format(time.strftime("%Y"))
 author = "Nicolas Legrand"
 release = pyhgf.__version__
 
 nb_execution_timeout = 300
 
 image_scrapers = ("matplotlib",)
 
-bibtex_bibfiles = ['refs.bib']
+bibtex_bibfiles = ["refs.bib"]
 bibtex_reference_style = "author_year"
 bibtex_default_style = "unsrt"
 
@@ -73,10 +73,10 @@
 plot_html_show_source_link = False
 
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.md': 'myst-nb',
-    '.ipynb': 'myst-nb',
-    '.myst': 'myst-nb',
+    ".rst": "restructuredtext",
+    ".md": "myst-nb",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
 }
 
 # The master toctree document.
@@ -112,13 +112,13 @@
     "logo": {
         "text": "pyhgf",
     },
-    "show_nav_level": 2
+    "show_nav_level": 2,
 }
 
 myst_enable_extensions = ["dollarmath", "colon_fence"]
 
 html_sidebars = {
-  "api": [],
-  "cite": [],
-  "references": [],
+    "api": [],
+    "cite": [],
+    "references": [],
 }

pyhgf/model/__init__.py

@@ -1,5 +1,27 @@
+from .add_nodes import (
+    add_binary_state,
+    add_categorical_state,
+    add_continuous_state,
+    add_dp_state,
+    add_ef_state,
+    get_couplings,
+    insert_nodes,
+    update_parameters,
+)
 from .network import Network
 
 from .hgf import HGF  # isort: skip
 
-__all__ = ["HGF", "Network"]
+__all__ = [
+    "HGF",
+    "Network",
+    "add_nodes",
+    "add_continuous_state",
+    "add_binary_state",
+    "add_ef_state",
+    "add_categorical_state",
+    "add_dp_state",
+    "get_couplings",
+    "update_parameters",
+    "insert_nodes",
+]