Farms core integration

.github/workflows/github-page-builder.yml

@@ -5,14 +5,17 @@ on:
   push:
     branches:
       - main
+      # - farms-core-integration
 
 jobs:
   build:
     name: Build Documentation
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
+        with:
+          ref: farms-core-integration
 
       - name: Set up Python
         uses: actions/setup-python@v2
@@ -23,14 +26,29 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y make automake gcc g++ subversion python3-dev
-          pip install sphinx sphinx-rtd-theme cython numpy
+          python3 -m pip install setuptools wheel
+          python3 -m pip install --no-use-pep517 pip==23.2.1
+          python3 -m pip install --no-use-pep517 distlib==0.3.8
+          python3 -m pip install --no-use-pep517 setuptools==65.5.0
+          python3 -m pip install --no-use-pep517 cython
+          python3 -m pip install --no-use-pep517 numpy
+          python3 -m pip install --no-use-pep517 networkx
+          python3 -m pip install --no-use-pep517 -r ducks/source/requirements.txt
+          cd ../
+          git clone https://github.com/farmsim/farms_core.git
+          cd farms_core
+          python3 -m pip install --no-use-pep517 .
+          python3 -m pip --version
+          python3 -m pip list
+          cd ../farms_network
+          python setup.py build_ext --inplace
 
       - name: Build HTML
         run: |
-          cd docs
+          cd ducks
           make html
           cd ..
-          mv docs/build/html/ public/
+          mv ducks/build/html/ public/
 
       - name: Cache documentation artifacts
         uses: actions/upload-artifact@v4
@@ -40,7 +58,7 @@ jobs:
 
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v4
-        if: github.ref == 'refs/heads/main'
+        # if: github.ref == 'refs/heads/main'
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./public

.github/workflows/python-cross-platform-installer.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main",]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.11", "3.13"]
+        exclude:
+          - os: macos-latest
+            python-version: "3.13"
+          - os: windows-latest
+            python-version: "3.13"
+          - os: ubuntu-latest
+            python-version: "3.13"
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    # You can test your matrix by printing the current Python version
+    - name: Display Python version
+      run: python -c "import sys; print(sys.version)"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run installation
+      run: python -m pip install . --verbose

.gitignore

@@ -36,8 +36,9 @@ build/
 *.so
 *.dylib
 
-# Generated cython c-files
+# Generated cython c/cpp-files
 *.c
+*.cpp
 
 # Generated cython perf html files
 *.html

CNAME

@@ -0,0 +1 @@
+network.farmsim.dev

docs/source/conf.py → ducks/source/conf.py

@@ -17,33 +17,53 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'FARMS_NETWORK'
-copyright = '2019, BioRob'
+project = 'FARMS-NETWORK'
+copyright = '2025, Jonathan Arreguit & Shravan Tata Ramalingasetty'
 author = 'FARMSIM'
 master_doc = 'index'
 
+# Github
+github_username = "farmsim"
+github_repository = "farms_network"
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["sphinx.ext.autodoc",]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinxcontrib.bibtex",
+    "sphinxcontrib.youtube",
+    "sphinx_copybutton",
+    "sphinx_favicon",
+    "sphinx_reredirects",
+    "sphinx_toolbox.collapse",
+    "sphinx_toolbox.sidebar_links",
+    "sphinx_toolbox.github",
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = [
+    '_build',
+    'Thumbs.db',
+    '.DS_Store'
+]
 
+# Bibtex references for sphinxcontrib.bibtex
+bibtex_bibfiles = ["references.bib"]
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
+# sphinx_rtd_theme
+html_theme = "furo"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

ducks/source/core/data.rst

@@ -0,0 +1,8 @@
+.. automodule:: farms_network.core.data
+   :platform: Unix, Windows
+   :synopsis: Provides Node C-Structure and Python interface for nodes in a dynamical system.
+   :members:
+   :show-inheritance:
+   :private-members:
+   :special-members:
+   :noindex:

ducks/source/core/index.rst

@@ -0,0 +1,8 @@
+Core
+====
+
+.. toctree::
+   :hidden:
+
+   options
+   node

ducks/source/core/node.rst

@@ -0,0 +1,85 @@
+Node
+====
+
+This documentation describes the Node structure and Python interface provided in the `node_cy.pyx` and `node_cy.pxd` files.
+
+Contents
+--------
+
+- Node C Structure
+- Node Python Class
+- Functions (ODE and Output)
+
+Node C Structure
+----------------
+
+The Node C structure defines the internal state and behavior of a node in a dynamical system.
+It contains generic attributes like state variables, inputs, and parameters.
+All nodes are many-inputs-single-output (MISO).
+The simplest case would be a node with one input and one input.
+A node can have N-states that will be integrated by a numerical integrator over time.
+A stateless node will have zero states and is useful in using the node as a transfer function.
+
+
+Node
+====
+
+.. autoclass:: farms_network.core.node.Node
+   :members:
+
+The Node class provides a high-level interface for neural network nodes.
+
+Constructor
+----------
+
+.. code-block:: python
+
+    Node(name: str, **kwargs)
+
+**Parameters:**
+
+- ``name`` (str): Unique identifier for the node
+- ``**kwargs``: Additional configuration parameters passed to NodeCy
+
+Class Methods
+------------
+
+from_options
+^^^^^^^^^^^
+
+Create a node from configuration options.
+
+.. code-block:: python
+
+    @classmethod
+    def from_options(cls, node_options: NodeOptions) -> Node
+
+**Parameters:**
+
+- ``node_options`` (NodeOptions): Configuration options
+
+**Returns:**
+
+- Node: Configured node instance
+
+Examples
+--------
+
+Creating a node:
+
+.. code-block:: python
+
+    # Direct instantiation
+    node = Node("neuron1")
+
+    # From options
+    options = NodeOptions(name="neuron1")
+    node = Node.from_options(options)
+
+
+.. automodule:: farms_network.core.node_cy
+   :platform: Unix, Windows
+   :synopsis: Provides Node C-Structure for nodes in a dynamical system.
+   :members:
+   :show-inheritance:
+   :noindex: