What's Changed

• Drop Python 3.8, add 3.11/3.12 support
• Fix incorrect conda environment creation command in README by @Copilot in #352
• Fix maf2sam crash on MAF files containing comment lines (#) by @Copilot in #351
• Add GENBANK2FAA converter by @Copilot in #353
• Add .gbff as a recognized genbank extension
• Migrate CLI from argparse to click/rich_click
• Fix CRAM2FASTQ and CRAM2FASTA
• Add network graph format converters: GML, Pajek, GraphML by @Copilot in #357
• Add small molecule converters: MOL2/SDF/PDB → SMILES by @Copilot in #359
• Add TRANSFAC ↔ JASPAR motif format converters by @Copilot in #358
• Fix test_converter_benchmark: logger.info() incompatible with easydev Logging API by @Copilot in #363
• Fix all-versions test failures by making Benchmark import lazy by @Copilot in #365
• Fix goalign nexus format mismatch and missing RTD sphinx dependencies
• Fix xlsx2csv: replace xlrd with openpyxl engine
• sra2fastq: add fasterq-dump method as default, keep fastq-dump as fallback
• Fix xlsx2csv CI: replace xlrd with openpyxl and pyexcel-xls with pyexcel-xlsx

New Contributors

• @just-simon-5 made their first contribution in #340
• @Copilot made their first contribution in #348

Full Changelog: v1.1.1...v1.12.0

What's Changed

• update requirements in methods by @cokelaer in #337
• add fast52pod5

Full Changelog: v1.1.0...v1.1.1

What's Changed

• benchmark incorporates CPU/memory usage by @cokelaer in #336

New Contributors

• @ambuvjyn made their first contribution in #331

Full Changelog: v1.0.0...v1.1.0

What's Changed

• Fixing bam2fastq issue and update material for paper by @cokelaer in #326
• add log, update docs by @cokelaer in #328
• remove deprecated warnings linked to excel formats / pandas

Full Changelog: v0.6.3...v1.0.0

What's Changed

General cleanup and 0.6.3 before a main major release

• update CI by @cokelaer in #321
• Fixing CI for pdb2faa and gff32gtf by @cokelaer in #322
• General cleanup by @cokelaer in #323

Full Changelog: v0.6.2...v0.6.3

What's Changed

• add new conversion gff3 to gtf2 by @cokelaer in #313
• add pdb2faa and fix cram2sam by @cokelaer in #315

Full Changelog: v0.6.1...v0.6.2

What's Changed

• Correct license classifier. by @cbrueffer in #310
• Switch master branch to 'main' by @cokelaer in #311
• Create directories if included in output file by @cokelaer in #312

New Contributors

• @cbrueffer made their first contribution in #310

Full Changelog: v0.6.0...v0.6.1

fixing requirements file

remove biocode dependencies for the genbank2gff3 converter before final bioconda release