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Update user_documentation.rst - installation
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doc/source/user_documentation.rst

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@@ -2803,29 +2803,26 @@ Below is a diagram of the interactions between the wrapper commands in the four
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1. Setting up batchtools
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^^^^^^^^^^^^^^^^^^^^^^^^
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Beyond the necessary dependency installations for NetPyNE and NEURON, the following `pip` installations are preferred.
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The NetPyNE installation should be handled as a development installation to allow for up to date fixes
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Beyond the necessary installation of NetPyNE and NEURON, the following `pip` installations are required:
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.. code-block::
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git clone https://github.com/Neurosim-lab/netpyne.git
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cd netpyne
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pip install -e .
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pip install -U ray
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pip install -U batchtk
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A development install of the batchtools subpackage
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``batchtk`` is the NetPyNE ``batchtools`` subpackage, and ``ray`` is the Ray Tune package, a dependency for batchtools.
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To allow for up to date fixes of these packages, NetPyNE and batchtk should be set up as development installations:
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.. code-block::
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git clone https://github.com/jchen6727/batchtk.git
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cd batchtk
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git clone https://github.com/suny-downstate-medical-center/netpyne.git
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cd netpyne
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pip install -e .
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Ray is a dependency for batchtools, and should be installed with the following command
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.. code-block::
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pip install -U ray[default]
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git clone https://github.com/suny-downstate-medical-center/batchtk.git
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cd batchtk
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pip install -e .
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You can validate that the correct packages are installed by checking the ``sim.send`` and ``cfg.update`` methods in an interactive python instance
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Help on method update in module netpyne.batchtools.runners:
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...
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If there is an issue with installation, the following message will be presented instead when calling help on either function
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If there is an issue with the installation, the following message will be presented instead when calling help on either function
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.. code-block::
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