MacSyFinder 2.1.4

MacSyFinder support Python 3.10 and higher

Installation

The release will be available via Pypi

for user

python3 -m pip install --upgrade macsyfinder

for modeler

python3 -m pip install --upgrade macsyfinder[model]

Or on bioconda channel

For user and modeler

conda config --add channels bioconda
conda config --add channels conda-forge
conda install macsyfinder

Or via Docker

see https://hub.docker.com/r/gempasteur/macsyfinder

For developpers

See documentation,
and read contrubuting guide.

What's new

This release includes some new features, bug fixes. We recommend that all users upgrade to this version.
(see full version)

For users

Fix minor bugs

• when profile name ends with hmm, then the profile was not retrieved by msf (#69).
• fix omitted parameter timeout in macsyfinder step in parallel_macsyfinder

For modelers

new features

• The vers is now deprecated in model/metadata file.
  macsydata rely only on the tag version to get the version of the model.
• macsydata now create a git repository for you and add files to it.
• a pre-push git hook is installed by macsydata init to prevent to push a tag (publish)
  a buggy nodel.

For developers

• all the msf code (macsypy and tests) pass the ruff linter
• all the code use type hints (required python >3.10) see (https://github.com/gem-pasteur/macsyfinder/blob/master/CONTRIBUTING.md)

Update references

Update references
Add some new features
Fix minor bugs

for details visit https://macsyfinder.readthedocs.io/en/latest/user_guide/new_v2.html

MacSyFinder v2.1

Creation of a Release based on 2.1 tag in order to obtain doi to comply with Peer Com J policies.

Release mentioned in the corresponding article:

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes.
Néron et al., Peer Community Journal, 2023

Obtained doi: 10.5281/zenodo.7704885