added changelog

CHANGELOG.md

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+# Taranys Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [3.0.1dev] - 202X-XX-XX : https://github.com/BU-ISCIII/relecov-tools/releases/tag/
+
+### Credits
+
+Code contributions to the release:
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+## [3.0.0] - 2025-01-02 : https://github.com/BU-ISCIII/taranys/releases/tag/3.0.0
+
+- Code refactor to create a proper python package
+- Implementation of parallel computation for execution speed.
+- New implementation of reference-alleles module using leiden algorithm for allele clustering.
+- New param defaults based on empirical testing.
+- Distance matrix is rewritten with more params available.
+
+## [2.0.1beta] - 2021-07-14 : https://github.com/BU-ISCIII/taranys/releases/tag/2.0.1
+
+### New features
+
+- New default missing values threshold imposed for samples in distance matrix creation
+- New default perc_identity_ref value for loci search in allele calling analysis
+- Github actions for testing and docker generation.
+
+### Bug fixes
+
+- multiple statistic modes bug fixed
+- BLAST database creation bug due to punctuation signs in file name fixed
+- ST profile identification bug fixed
+- Python modules installed from conda-forge in environment.yml
+
+### Documentation
+
+- Channel order in conda installation command
+
+## [2.0.0beta] - 2021-06-24 : https://github.com/BU-ISCIII/taranys/releases/tag/2.0.0edge
+
+Pre-release
+
+## [0.3.3beta] - 2018-11-05 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.3
+
+**BUG FIX:**
+
+- Fix num_threads in blast commands
+
+## [0.3.2beta] - 2018-11-02 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.2
+
+**BUG FIX:**
+
+- Added ERROR posibility to allele classification, when the allele is not PLOT but is too near to contig end, and protein codification finishes without finding a stop codon.
+
+## [0.3.1beta] - 2018-10-27 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.1
+
+- Added cpus as parameter.
+
+## [0.3.0beta] - 2018-10-25 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.0
+
+**Bug fixes:**
+
+- Allow dependency check for versions greater than needed.
+
+**Features:**
+
+- Added graphics for schema evaluation(beta)
+- Added SNP calling (beta)
+
+## [0.0.1beta] - 2018-10-22 : https://github.com/BU-ISCIII/taranys/releases/tag/0.1
+
+- cg/wgMLST analysis using assembled contigs as input using a defined schema. Comparison matrix is generated for phyloviz visualization. Blast hit are classified as Exact match , new allele, etc.
+- cg/wgMLST statistics.
+- beta: SNP analysis.
+- Insertions, deletions and paralogues detection.