v0.4.1

This release provides updates to the v0.4.0 release that could not be made
available on pypi because of outdated package metadata and formats

• Fixes and modernizes metadat and package structure

• Add new options to OMArk (via 0.4.0):

  • Option -n/--min_n_species: allow users to chose the minimal number of representative species needed in the OMA database for selecting an ancestral clade (default:5)
  • Option -s/--summarize_db : standalone option to create a summary of the available lineage in the OMAmer database
  • Change in memory access that result in computational efficiency gains, at the cost of increased RAM usage.

Full Changelog: v0.4.0...v0.4.1

v0.4.0

Add new options to OMArk:

• Option -n/--min_n_species : allow users to chose the minimal number of representative species needed in the OMA database for selecting an ancestral clade (default:5)
• Option -s/--summarize_db : standalone option to create a summary of the available lineage in the OMAmer database
• Change in memory access that result in computational efficiency gains, at the cost of increased RAM usage.

v0.3.1

• Added an option to use a local ete3 database for access to the NCBI taxonomy
• Added better handling of taxonomic rank selection, which can now chose the closest rank when the one selected is not available in the OMAmer database
• Added new file checks to make sure the files provided by an user are compatible, and exit cleanly if not

v0.3.0

New OMArk version compatible with OMAmer v 2.0.0.

Changes are:

• Due to changes in OMAmer, dubious proteins or proteins with no homologs now will tend to be placed as Unknown rather than Inconsistent.
• Slight changes to contamination detection module that account only for most significant hits and handle better close contaminants.
• Adding -r option that allows to gives a taxonomic rank as parameter (order, class, phylum) for ancestra lineage selection.
• Adding a warning when the clade chosen is subgenus or phylum and higher.
• Adding the -c options that only outputs a list of conserved HOGs for a given clade.
• Adding a new companion Notebook to contextualize OMArk results with OMA data (sequences, synteny).
• Adding new simulation for benchmarking (genome_simulation.py)
• Minor fix to setup.cfg and import of the Bio library

v0.2.5

• Fixed an issue (Reported in #13) where OMArk was assuming the OMAmer database was issued from a complete main OMA release and was throwing errors when using other databases (Example: Metazoa.h5 ).
• Updated and fixed typos in the README
• Fixed a minor typo in the graphical output

v0.2.4

-Fixes a compatibilty issue with matplotlib on newer versions and newer python, that enforces linewidth argument to be numeric.

v0.2.3

• Added a companion script and a Jupyter Notebook to allow for vizualisation of multiple results on a single figure
• Fixed typos in Readme
• handle filenames that contain '.sum' in the middle of their filename
• update github action versions

v0.2.2

Full Changelog:

• fixes an issue with that matplotlib on newer versions and newer python enforces linewidth argument to be numeric

v0.2.1

-Changed color schemes of figures
-Minor fix to contamination detection module

v0.2.0

v0.2.0