Metadata-Version: 1.2
Name: scipion-em-cryoassess
Version: 3.1
Summary: Plugin to use cryoassess within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-cryoassess
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-cryoassess/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-cryoassess/
Description: =================
        Cryoassess plugin
        =================
        
        This plugin provide a wrapper around `Cryoassess <https://github.com/cianfrocco-lab/Automatic-cryoEM-preprocessing>`_ software tools for automatic micrograph and 2D classes assessment.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-cryoassess.svg
                :target: https://pypi.python.org/pypi/scipion-em-cryoassess
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-cryoassess.svg
                :target: https://pypi.python.org/pypi/scipion-em-cryoassess
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-cryoassess.svg
                :target: https://pypi.python.org/pypi/scipion-em-cryoassess
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-cryoassess?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-cryoassess
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-cryoassess
                :target: https://pypi.python.org/pypi/scipion-em-cryoassess
                :alt: Downloads
        
        
        +--------------+----------------+
        | prod: |prod| | devel: |devel| |
        +--------------+----------------+
        
        .. |prod| image:: http://scipion-test.cnb.csic.es:9980/badges/cryoassess_prod.svg
        .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/cryoassess_devel.svg
        
        
        Installation
        -------------
        
        You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
        
        a) Stable version
        
        .. code-block::
        
           scipion installp -p scipion-em-cryoassess
        
        b) Developer's version
        
           * download repository
        
            .. code-block::
        
                git clone https://github.com/scipion-em/scipion-em-cryoassess.git
        
           * install
        
            .. code-block::
        
               scipion installp -p path_to_scipion-em-cryoassess --devel
        
        Cryoassess software will be installed automatically with the plugin but you can also use an existing installation by providing *CRYOASSESS_ENV_ACTIVATION* (see below).
        You also have to download training models separately (see below).
        
        **Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
        
        Configuration variables
        -----------------------
        
        *CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the
        PATH (not recommended), which can lead to execution problems mixing scipion
        python with conda ones. One example of this could can be seen below but
        depending on your conda version and shell you will need something different:
        CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
        
        *CRYOASSESS_ENV_ACTIVATION* (default = conda activate cryoassess-1.0.0):
        Command to activate the cryoassess environment.
        
        The deep-learning models can be downloaded from
        `authors' website <https://cosmic-cryoem.org/software/cryo-assess/>`_ and the folder with models is set with:
        
        *CRYOASSESS_MODELS* (default = software/em/cryoassess-models)
        
        Verifying
        ---------
        
        To check the installation, simply run the following Scipion test:
        
        ``scipion test cryoassess.tests.test_protocols_cryoassess.TestCryoassess``
        
        Supported versions
        ------------------
        
        1.0.0
        
        Protocols
        ----------
        
        * assess micrographs
        * assess 2D classes
        
        References
        -----------
        
        1. High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines. Yilai Li, Jennifer N.Cash, John J.G. Tesmer, Michael A.Cianfrocco. Structure 2020, Volume 28 (7), Pages 858-869.e3
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
