Metadata-Version: 2.1
Name: scipion-em-facilities
Version: 3.3.1
Summary: Plugin to use Scipion in facilities
License: GNU General Public License v3 (GPLv3)
Project-URL: Homepage, https://github.com/scipion-em/scipion-em-facilities
Project-URL: Issues, https://github.com/scipion-em/scipion-em-facilities/issues
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0 Facilities Facility Streaming
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: scipion-pyworkflow>=3.0.31
Requires-Dist: scipion-em
Requires-Dist: nvidia-ml-py3
Requires-Dist: pytz
Requires-Dist: paramiko
Requires-Dist: influxdb
Requires-Dist: joblib
Requires-Dist: networkx
Requires-Dist: scipion-em-xmipp
Requires-Dist: pyyaml

======================
Scipion for facilities
======================

+------------------+------------------+
| stable: |stable| | devel: |devel|   |
+------------------+------------------+

.. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_prod.svg
.. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/facilities_sdevel.svg

'scipion-em-facilities' plugin allows to use different utils for cryo-EM facilities
(like monitors) within the Scipion framework.

Monitors are used to produce live analysis plots, generate reports or
raise alerts when some problems are detected. A monitor example is the CTF-monitor,
that checks the computed defocus values for each micrograph as they are generated.
CTF-monitor may raise an alert if the defocus values are above or below certain thresholds.
A special case of this monitors is the monitor summary which encapsulates the CTF Monitor,
the system monitor and the movie gain monitor and continuously creates a report.

This module contains protocols and utilities related with monitors.

Please, check the `facilities documentation <https://scipion-em.github.io/docs/docs/facilities/facilities.html>`_
for more details.


Installation
------------

You will need to use `Scipion 3.0 <https://scipion-em.github.io/docs/release-3.0.0/index.html>`_
to be able to run these protocols. If you want to use the summary monitor with grafana
you will need to create the file secrets.cfg in the directory defined by the variable EMFACILITIES_HOME
(see the above mention web site for details).

To install the plugin, you have two options:

a) Stable version

.. code-block::

   scipion3 installp -p scipion-em-facilities

b) Developer's version

   * 1st. Download repository

   .. code-block::

      git clone https://github.com/scipion-em/scipion-em-facilities.git /path/to/scipion-em-facilities

   * 2nd. Install the plugin

   .. code-block::

      scipion3 installp -p /path/to/scipion-em-facilities --devel

Testing
-------

To check the installation, simply run the following Scipion test:

.. code-block::

  scipion3 test --grep emfacilities --mode modules --run

If ``--run`` is not passed, it only shows the available tests to check.
