Synthesis Workflow
==================
This project contains several workflows used for neuron synthesis and the validation of this process.
It is divided into two packages:
* **synthesis-workflow**, which contains the workflow tasks and tools.
* **MorphVal**, which is a library used for morphology validation and can be used as a standalone.
Installation
------------
To install:
.. code::
pip install synthesis-workflow
Usage
-----
Synthesis workflow
~~~~~~~~~~~~~~~~~~
The usual command is the following:
.. code::
synthesis_workflow <workflow>
You can get help and complete parameter description with the following commands:
.. code::
synthesis_workflow --help
synthesis_workflow <workflow> --help
You can also run a complete ``luigi`` command in order to fine-control task parameters:
.. code::
luigi --module synthesis_workflow.tasks.workflows --help
luigi --module synthesis_workflow.tasks.workflows <workflow> --help
luigi --module synthesis_workflow.tasks.workflows <workflow> [specific arguments]
.. note::
The ``synthesis_workflow`` command (or the complete ``luigi`` command) must be
executed from a directory containing a ``luigi.cfg`` file.
A simple example of such file is given in the ``examples`` directory.
Morphology validation
~~~~~~~~~~~~~~~~~~~~~
The usual command is the following:
.. code::
morph_validation -t <path to reference data> -r <path to test data> -o <output path> -c <YAML config file> --bio-compare
You can get help and complete parameter description with the following command:
.. code::
morph_validation --help
Funding & Acknowledgment
~~~~~~~~~~~~~~~~~~~~~~~~
The development of this software was supported by funding to the Blue Brain Project,
a research center of the École polytechnique fédérale de Lausanne (EPFL),
from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
Copyright (c) 2022-2024 Blue Brain Project/EPFL
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"description": "Synthesis Workflow\n==================\n\nThis project contains several workflows used for neuron synthesis and the validation of this process.\nIt is divided into two packages:\n\n* **synthesis-workflow**, which contains the workflow tasks and tools.\n* **MorphVal**, which is a library used for morphology validation and can be used as a standalone.\n\n\nInstallation\n------------\nTo install:\n\n.. code::\n\n pip install synthesis-workflow\n\n\nUsage\n-----\n\nSynthesis workflow\n~~~~~~~~~~~~~~~~~~\n\nThe usual command is the following:\n\n.. code::\n\n synthesis_workflow <workflow>\n\nYou can get help and complete parameter description with the following commands:\n\n.. code::\n\n synthesis_workflow --help\n synthesis_workflow <workflow> --help\n\nYou can also run a complete ``luigi`` command in order to fine-control task parameters:\n\n.. code::\n\n luigi --module synthesis_workflow.tasks.workflows --help\n luigi --module synthesis_workflow.tasks.workflows <workflow> --help\n luigi --module synthesis_workflow.tasks.workflows <workflow> [specific arguments]\n\n.. note::\n\n\tThe ``synthesis_workflow`` command (or the complete ``luigi`` command) must be\n\texecuted from a directory containing a ``luigi.cfg`` file.\n\tA simple example of such file is given in the ``examples`` directory.\n\nMorphology validation\n~~~~~~~~~~~~~~~~~~~~~\n\nThe usual command is the following:\n\n.. code::\n\n morph_validation -t <path to reference data> -r <path to test data> -o <output path> -c <YAML config file> --bio-compare\n\nYou can get help and complete parameter description with the following command:\n\n.. code::\n\n morph_validation --help\n\nFunding & Acknowledgment\n~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe development of this software was supported by funding to the Blue Brain Project,\na research center of the \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL),\nfrom the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright (c) 2022-2024 Blue Brain Project/EPFL\n",
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