MirMachine/CHANGELOG at master · sinanugur/MirMachine · GitHub

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## [0.3.0.3] - 2026-03-04
### Changed
  - Documentation refresh under `docs/` to match current `MirMachine.py` and workflow behavior.
  - Rewrote installation, quick start, CLI options, output, and troubleshooting pages with current flags and outputs.
  - Updated docs metadata in `docs/conf.py` to `release = 0.3.0.3`.
### Added
  - New `docs/concepts.rst` page covering node/family/model scope, search behavior, and scoring concepts.

## [0.3.0] - 2025-05-14
### Changed
  - MirGeneDB v3.0
  - Proto: 449
  - Deutero: 837
  - Combined: 1293
  - Python, Bedtools, Infernal, Snakemake and dependency updates
  - Seed match bug fixes.
  - Seed file updates.
  - Requirements.txt and environment.yml update.
  - Losses bug fixes.
  - Clean .snakemake directory after each run.
### Added
  - Now incE is a cli parameter.
  - Print basic results.

## [0.2.13] - 2024-02-02
### Changed
  - cmsearch --incE 0.2 argument is added to the cmsearch command.
  - fewer than 50 nucleotides are not considered as a hit anymore.
  - GFF files have "MirMachine" and "microRNA" fields that replaced the previous fields.
  - Some bug fixes and improvements.
### Added
  - microRNA score reported in GFF files.
  - microRNA losses reported in GFF files
  - Seed match reported in FASTA headers with seeds.

## [0.2.12] - 2023-02-17
### Changed
  - Minor change, heatmap file node, query_node update

## [0.2.11.2022] - 2022-02-28
### Changed
  - MirGeneDB v2.1(2022)
  - Proto: 143 but 326 models available
  - Deutero: 388 but 825 models available
  - Combined: 509 but 1157 models available
### Added
  - Some minor additions.

## [0.2.11.2] - 2021-12-29
### Added
  - Family and node printing.
  - Exception handling for wrong model selection.
  - Exception handling for single family mode.
### Changed
  - New header for GFFs.
  - Snakemake workflow update to better handle output files.

## [0.2.11.1] - 2021-09-29
### Changed
  - Bioconda installation problem is fixed by updating requirements.txt.

## [0.2.11] - 2021-05-17
### Added
  - Some features were added to main executable such as printing ascii tree, nodes etc.
### Changed
  - Tree parser now using re.search function. This can potentially cause a different behaviour.

## [0.2.10] - 2021-05-12
### Changed
  - Versioning

## [0.2.1a] - 2021-05-12
### Changed
  - MirGeneDB v2.1
  - Proto: 315
  - Deutero: 825
  - Combined: 1146

## [0.1.31] - 2021-03-09
### Added
  - Headers for GFFs files.
  - Single family and single node run options.

## [0.1.2] - 2020-12-05
### Added
  - MirGeneDB v2.0
  - Proto: 304
  - Deutero: 782
  - Combined: 1054