Metadata-Version: 2.1
Name: morphology-workflows
Version: 0.1.2
Summary: Workflows used for morphology processing.
Home-page: https://github.com/BlueBrain/morphology-workflows
Author: Blue Brain Project, EPFL
License: Apache-2.0
Project-URL: Tracker, https://github.com/BlueBrain/morphology-workflows/issues
Project-URL: Source, https://github.com/BlueBrain/morphology-workflows
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        # Morphology Workflows
        
        This project contains several workflows for processing morphologies:
        - **Curate:** from raw morphologies, ensures that morphologies can be used with the rest of
          BBP codes
          [![](autoapi/tasks/workflows/Curate.png)](autoapi/tasks/workflows/index.html#tasks.workflows.Curate)
        - **Annotate:** create various annotations on morphologies needed by specific BBP codes
          [![](autoapi/tasks/workflows/Annotate.png)](autoapi/tasks/workflows/index.html#tasks.workflows.Annotate)
        - **Repair:** process morphologies to correct for artifacts of in-vitro reconstruction
          [![](autoapi/tasks/workflows/Repair.png)](autoapi/tasks/workflows/index.html#tasks.workflows.Repair)
        
        
        In a nutshell, the user provides a list of morphologies in a ``.csv`` file, with their names and
        paths and a ``luigi.cfg`` configuration file. Each workflow is run independently and creates an
        output folder, with one subfolder per task. In each, there will be a ``report.csv`` and a ``data``
        folder containing the output files of the task if any. In the ``report.csv`` file, columns contain
        paths to these files, additional information, error messages if the task failed on that
        morphologies, as well as a flag ``is_valid``, used in subsequent tasks to filter valid morphologies.
        At the end of each workflow, another ``report.csv`` file is created, with the main output columns of
        each tasks, and a ``report.pdf`` containing a human readable summary of the result of the workflow.
        
        
        ## Installation
        
        This should be installed using pip:
        
        ```bash
        pip install morphology-workflows
        ```
        
        
        ## Usage
        
        This workflow is based on the ``luigi`` library but can be run via the command line interface:
        
        ```bash
        morphology_workflows --local-scheduler Curate
        ```
        
        > **NOTE** This command must be executed from a directory containing a ``luigi.cfg`` file.
        > An example of such file is given in the ``examples`` directory.
        
        More details can be found in the command line interface section of the documentation.
        
        
        ## Examples
        
        The `examples` folder contains a simple example that will process a set of morphologies.
        A ``dataset.csv`` file is provided which is taken as input for the workflows. A ``luigi.cfg`` file
        is also provided to give a default configuration for the workflows.
        This example can simply be run using the following command:
        
        ```bash
        ./run_curation.sh
        ```
        
        This script will create a new directory ``out_curated`` which will contain the report and all the
        results.
        
        
        ## 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.
        
        For license and authors, see `LICENSE.txt` and `AUTHORS.md` respectively.
        
        Copyright © 2021 Blue Brain Project/EPFL
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: docs
Provides-Extra: test
