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Merge pull request #568 from ModECI/development
Working cyclical networks example
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‎.github/workflows/ci.yml‎

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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.10', '3.13']
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python-version: ['3.11', '3.13']
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os: [ubuntu-latest, macos-latest, windows-latest]
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test-suite: [core, actr, pytorch, neuroml, tensorflow, psyneulink]
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exclude:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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python-version: '3.11'
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@v6
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with:
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python-version: '3.10'
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python-version: '3.11'
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- name: Generate and Build Docs
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run: |
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uv sync --group docs

‎.github/workflows/ci_test_all.yml‎

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- name: Run test script
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run: |
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# pip install torch==2.8.0 # pinned to avoid issues with latest version taking up too much space...
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export NEURON_HOME=$pythonLocation
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./test_all.sh
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‎.gitignore‎

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/examples/PyTorch/simple_pytorch_to_mdf.1
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/examples/MDF/NLP/TestNLP_3
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/examples/MDF/NLP/TestNLP
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/examples/MDF/networks/Net_acyclical
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/examples/MDF/net/Net_acyclical
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/examples/MDF/net/weight.py
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/examples/MDF/conditions/composite_example
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/examples/NeuroML/arm64
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/examples/MDF/RNN/iaf.net
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/checkoutpngs.sh
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/docs/sphinx/source/api/export_format/MDF/images/newton.png
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/docs/sphinx/source/api/export_format/MDF/images/newton_plot.png
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/examples/MDF/networks/Net_acyclical

‎.readthedocs.yml‎

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/sphinx/source/conf.py
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configuration: docs/sphinx/source/conf.py
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build:
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os: ubuntu-24.04
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tools:
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python: "3.13"
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jobs:
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pre_create_environment:
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- asdf plugin add uv
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- asdf install uv latest
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- asdf global uv latest
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create_environment:
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- uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
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install:
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- UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --group docs
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# Just generate htmlzip version, as pdf failing due to inclusion of svg files (in badges)
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formats:
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- htmlzip
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python:
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install:
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- requirements: docs/sphinx/requirements.txt
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‎docs/MDF_specification.json‎

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"type": "str",
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"description": "The unique (for this Node) id of the input port,"
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},
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"default_value": {
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"type": "Union",
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"description": "Value to set at this input port if no edge connected to it."
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},
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"shape": {
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"type": "Optional",
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"description": "The shape of the input port. This uses the same syntax as numpy ndarray shapes\n(e.g., :code:`numpy.zeros(shape)` would produce an array with the correct shape"
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},
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"type": {
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"type": "Optional",
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"description": "The data type of the input received at a port."
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},
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"reduce": {
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"type": "Optional",
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"description": "Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)"
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}
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}
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},

‎docs/MDF_specification.yaml‎

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id:
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type: str
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description: The unique (for this Node) id of the input port,
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default_value:
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type: Union
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description: Value to set at this input port if no edge connected
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to it.
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shape:
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type: Optional
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description: 'The shape of the input port. This uses the same syntax
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type:
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description: The data type of the input received at a port.
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reduce:
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type: Optional
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description: 'Specifies how to deal with multiple inputs to one port
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during a single timestep: add: add up all the values; multiply:
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multiply the values, overwrite: just use the last value supplied
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(default)'
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Function:
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definition: A single value which is evaluated as a function of values on :class:`InputPort`(s)
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and other Functions

‎docs/README.md‎

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<tr>
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<td><b>default_value</b></td>
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<td>Union</td>
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<td><i>Value to set at this input port if no edge connected to it.</i></td>
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</tr>
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<tr>
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<td><b>reduce</b></td>
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<td>Optional</td>
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<td><i>Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)</i></td>
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</tr>
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## Function

‎docs/sphinx/requirements.txt‎

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‎docs/sphinx/source/api/Specification.rst‎

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**Allowed parameters**
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=============== =========== =============================================================================================
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Allowed field Data Type Description
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=============== =========== =============================================================================================
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**metadata** Optional Optional metadata field, an arbitrary dictionary of string keys and JSON serializable values.
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**id** str The unique (for this Node) id of the input port,
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**shape** Optional The shape of the input port. This uses the same syntax as numpy ndarray shapes
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=============== =========== =============================================================================================
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================= =========== =================================================================================================================================================================================================
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Allowed field Data Type Description
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================= =========== =================================================================================================================================================================================================
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**metadata** Optional Optional metadata field, an arbitrary dictionary of string keys and JSON serializable values.
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**id** str The unique (for this Node) id of the input port,
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**default_value** Union Value to set at this input port if no edge connected to it.
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**shape** Optional The shape of the input port. This uses the same syntax as numpy ndarray shapes
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(e.g., **numpy.zeros(shape)** would produce an array with the correct shape
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**type** Optional The data type of the input received at a port.
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**reduce** Optional Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)
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================= =========== =================================================================================================================================================================================================
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Function

‎docs/sphinx/source/api/export_format/MDF/images/switched_rlc_plot.png‎

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