BarcodeMapper 1.2.3

Added

• Dependency check at release time: scripts/check_dependencies.py compares the pinned dependencies with the latest releases, tests/regression/ and scripts/regression_check.py verify that a small dataset still gives an identical taxonomy table, scripts/release_dependency_check.sh runs both with the newer versions on Mjolnir, and a weekly GitHub Actions workflow repeats the check. The Mjolnir check also repeats the regression through Slurm, and --record appends each run to docs/dependency-checks.md, which lists the checks and their commands.

Changed

• Update the pinned environment to the newest compatible releases, verified on Mjolnir to give a taxonomy table identical to the golden regression table: snakemake 9.27.0, snakemake-executor-plugin-slurm 2.8.0, fastp 1.4.0, samtools 1.24, Bowtie2 2.5.5, numpy 2.5.4, pandas 2.3.3, plotly 7.1.0, Biopython 1.88, pysam 0.24.1, PyYAML 6.0.3. The Bioconda recipe and the Python dependencies in pyproject.toml pin the same versions.
• --update says "No local database found" instead of reporting newer sources when there is nothing to compare with.
• When the dated database folder already exists (for example a second build on the same day), the error suggests -n/--name for a differently named database.