Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

‘M’, ‘m’ and ‘p’ are respectively corresponding to major, minor and patch

[0.9.0] - 2023-05-26#

Added#

  • [p] Data to test

Changed#

  • [m] to_networkx.add_vertices_of_regions_in_nxdigraph becomes to_networkx.add_result_in_nxdigraph_from_debug and uses a khloraascaf.MetadataDebug object

  • [p] Simpler multiplicity computation

Fixed#

  • [p] Documentation of the multiplicity computation

[0.8.2] - 2023-05-21#

Fixed#

  • [p] Assembly graph to FASTA: be more permissive for link sequence in the FASTA file but from which the identifier is not in the contig link file

[0.8.1] - 2023-05-17#

Fixed#

  • [p] Use decimal calculus for multiplicity attribute

  • [p] Add presence score attribute in NetworkX graph

  • [p] Prevent artificial data from generating multi-graph

[0.8.0] - 2023-05-09#

Changed#

  • [m] upgrade khloraascaf

Fixed#

  • [p] tests for NetworkX

[0.7.0] - 2023-05-08#

Changed#

  • [m] upgrade khloraascaf

[0.6.2] - 2023-05-07#

Changed#

  • [p] Update sphinx

  • [p] Update khloraascaf

[0.6.1] - 2023-05-03#

Fixed#

  • [p] ArtificialData forces the multiplicity of the starter to be equal to one

[0.6.0] - 2023-05-03#

Added#

  • [m] ArtificialData.region_contigs method

  • [m] ArtificialData.extra_links method

[0.5.3] - 2023-04-18#

Changed#

  • [p] khloraascaf version

Fixed#

  • [p] CI/CD GitLab

[0.5.2] - 2023-04-12#

Changed#

  • [p] upgrade khloraascaf

[0.5.1] - 2023-03-30#

Fixed#

  • [p] tests failed

[0.5.0] - 2023-03-30#

Changed#

  • [m] upgrade khloraascaf

[0.4.0] - 2023-03-20#

Added#

  • [m] ArtificialData class to generate artificial contigs and links according a given genome structure.

Changed#

  • [p] Upgrade khloraascaf

[0.3.0] - 2023-03-15#

Added#

  • [m] Region paths to FASTA sequences

Changed#

  • [p] Upgrade khloraascaf

[0.2.2] - 2023-03-12#

Changed#

  • [p] NetworkX vertex identifier formatting <CID>_<COR>_<COCC> becomes <CID>_<COR>_<COCC>

[0.2.1] - 2023-03-11#

Fixed#

  • [p] khloraascaf hotfix

[0.2.0] - 2023-03-10#

Changed#

  • [m] Upgrade khloraascaf version

Fixed#

  • [p] Documentation links

[0.1.0] - 2023-03-08#

Added#

  • [m] to_networkx.add_vertices_of_regions_in_nxdigraph quasi-complete function and other sub-functions

Changed#

  • [m] to_networkx functions, more user-friendly

Removed#

  • [m] to_networkx.add_solutions_pos_in_nxdigraph function

Fixed#

  • [m] Fix upgrade of khloraascaf

[0.0.0] - 2023-03-07#

Added#

  • [p] NetworkX dependency

  • [p] khloraascaf version range

Fixed#

  • [m] Upgrade khloraascaf package