Antibiotic Sensitivity Testing (AST) for SENAITE
================================================
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About
-----
This add-on enables Antibiotic Sensitivity Testing (AST) for `SENAITE LIMS`_ by
allowing the user to add analyses to a sample that are specifically designed for
the measurement of the susceptibility of microorganisms to antibiotics. These
analyses can be added either by means of pre-defined AST Panels or by direct
assignment of Antibiotics and Microorganisms through a matrix.
`senaite.ast`_ also incorporates a default analysis for the identification of
microorganisms present in a given sample. Once microorganisms are identified by
means of this identification analysis, the system automatically populates the
list of available AST Panels for selection with those that fit better with the
identified microorganism(s).
Resistance analyses are qualitative and the supported results are in accordance
with the `new definitions of susceptibility testing categories by EUCAST 2019`_:
- S: Susceptible, standard dosing regimen
- I: Susceptible, increased exposure
- R: Resistant
Although user can configure AST Panels for the automatic addition of analyses
for the capture of diameter of the zone of inhibition, the system does not
automatically calculate the qualitative results based on the diameter of zone
and the minimum inhibitory concentrations (MICs). However, system can infere
the susceptibility testing category automatically based on pre-defined
Breakpoints Tables, along with the diameter of the inhibitory zone or the MIC
value.
Once installed, this add-on allows the laboratory to:
* Maintain microorganisms (via `senaite.microorganism`_)
* Maintain antibiotics and antibiotic classes (via `senaite.abx`_)
* Maintain pre-defined AST Panels
* Maintain pre-defined Breakpoints Tables
* Analysis for the identification of microorganisms
* Assignment of pre-defined AST Panels to a sample
* Sample-level customization of AST Panel
* Selective reporting of resistance results
* Support for and selective reporting of extrapolated antibiotics
Documentation
-------------
* https://senaiteast.readthedocs.io
Contribute
----------
We want contributing to SENAITE.AST to be fun, enjoyable, and educational
for anyone, and everyone. This project adheres to the `Contributor Covenant`_.
By participating, you are expected to uphold this code. Please report
unacceptable behavior.
Contributions go far beyond pull requests and commits. Although we love giving
you the opportunity to put your stamp on SENAITE.AST, we also are thrilled
to receive a variety of other contributions.
Please, read `Contributing to senaite.ast document`_.
If you wish to contribute with translations, check the project site on `Transifex`_.
License
-------
**SENAITE.AST** Copyright (C) 2020-2024 RIDING BYTES & NARALABS
This program is free software; you can redistribute it and/or modify it under
the terms of the `GNU General Public License version 2`_ as published
by the Free Software Foundation.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.. Links
.. _SENAITE LIMS: https://www.senaite.com
.. _senaite.ast: https://pypi.org/project/senaite.ast
.. _new definitions of susceptibility testing categories by EUCAST 2019: https://www.eucast.org/newsiandr/
.. _senaite.microorganism: https://pypi.org/project/senaite.microorganism
.. _senaite.abx: https://pypi.org/project/senaite.abx
.. _Contributor Covenant: https://github.com/senaite/senaite.ast/blob/master/CODE_OF_CONDUCT.md
.. _Contributing to senaite.ast document: https://github.com/senaite/senaite.ast/blob/master/CONTRIBUTING.md
.. _Transifex: https://www.transifex.com/senaite/senaite-ast
.. _Community site: https://community.senaite.org/
.. _Gitter channel: https://gitter.im/senaite/Lobby
.. _Users list: https://sourceforge.net/projects/senaite/lists/senaite-users
.. _GNU General Public License version 2: https://www.gnu.org/licenses/old-licenses/gpl-2.0.txt
Changelog
=========
1.1.0 (2024-01-04)
------------------
- #31 Support lower than, greater than and fractions for MIC values
- #30 Fix sizes for numeric fields are too small
- #26 Fix Sensitivity result is not updated when selective reporting is missing
- #25 Do not allow to "submit" AST analyses with no result save
- #23 Fix AST calculation does not work when extrapolated antibiotics
- #22 Hide Unit and display Submitter before Captured in AST entry
- #21 Fix AST entry is empty when analyses categorization for sample is checked
- #20 Compatibility with senaite.app.listing#87
1.0.0 (2022-06-18)
------------------
- #17 Selective reporting for extrapolated antibiotics
- #15 Support for extrapolated antibiotics
- #13 Allow addition of new antibiotics to submitted/verified AST analyses
- #12 Negative values for diameter and zone size tests not permitted
- #12 Do not allow to submit AST analyses with empties
- #11 Better styling of AST Panel selector in Sample view
- #10 Allow to remove retracted AST analyses retests
- Initial Release
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"description": "Antibiotic Sensitivity Testing (AST) for SENAITE\n================================================\n\n.. image:: https://img.shields.io/pypi/v/senaite.ast.svg?style=flat-square\n :target: https://pypi.python.org/pypi/senaite.ast\n\n.. image:: https://img.shields.io/travis/com/senaite/senaite.ast/master.svg?style=flat-square\n :target: https://app.travis-ci.com/github/senaite/senaite.ast\n\n.. image:: https://readthedocs.org/projects/pip/badge/\n :target: https://senaiteast.readthedocs.org\n\n.. image:: https://img.shields.io/github/issues-pr/senaite/senaite.ast.svg?style=flat-square\n :target: https://github.com/senaite/senaite.ast/pulls\n\n.. image:: https://img.shields.io/github/issues/senaite/senaite.ast.svg?style=flat-square\n :target: https://github.com/senaite/senaite.ast/issues\n\n.. image:: https://img.shields.io/badge/Made%20for%20SENAITE-%E2%AC%A1-lightgrey.svg\n :target: https://www.senaite.com\n\n\nAbout\n-----\n\nThis add-on enables Antibiotic Sensitivity Testing (AST) for `SENAITE LIMS`_ by\nallowing the user to add analyses to a sample that are specifically designed for\nthe measurement of the susceptibility of microorganisms to antibiotics. 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