Changelog

Changelog

0.4.7 (2026-09-23)

• Fixed: dendrogram-from-matrix failed on matrices whose sample names look like numbers (001, 1e3): they were parsed as numbers and no longer matched between rows and columns. Names are now kept as written.
• Fixed: Ctrl-C during sketching still ran every queued sample before stopping.
• Fixed: a sample listed twice in the metadata file was plotted twice in the PCoA; it is now an error.
• Fixed: a metadata category named "Other" was shown in grey and listed twice in the legend.
• Infinite values in a distance matrix are rejected like missing values.
• The command is logged with quotes so it can be copied and run again as is.

0.4.6 (2026-09-23)

• Available on PyPI: pip install genome-comparator (Mash must be installed separately). Releases are published to PyPI automatically.
• Bioconda recipe in recipe/meta.yaml.
• Package metadata: keywords, classifiers, and links to the documentation, changelog, issues and DOI.
• Releases are archived on Zenodo: https://doi.org/10.5281/zenodo.22920856 (all versions). DOI badge and citation added to the README and CITATION.cff.

0.4.5 (2026-09-23)

• Fixed: --me and --bootstrap crashed with exactly 3 genomes.
• Fixed: tree-renamer and tree-collapser wrote bootstrap support values as quoted labels ('95'), which tree viewers do not read as support values. They are now kept as support values.
• Fixed: reading an .xls matrix without the xlrd package gave a traceback; the error now explains how to fix it.
• Fixed: the PCoA axes showed "nan%" when all genomes were identical.
• tree-renamer warns when several tips end up with the same name.
• Packaging: SPDX license metadata (no more setuptools deprecation warning); README images use absolute links.

0.4.4 (2026-09-23)

• The main command is now genome-comparator, the same name as the tool, with the same options. mash-phylo still works but prints a deprecation warning. python -m genome_comparator also works.
• Description added to CITATION.cff (used by Zenodo).

0.4.3 (2026-09-23)

• PCoA plots use a colourblind-friendly palette (Okabe-Ito) and one marker shape per category, instead of Plotly's default colours. Missing metadata is shown as "Unknown"; past 42 categories, the least frequent ones are grouped into "Other".
• Fixed: sample_stats.tsv left the number of sequences empty for single-sequence assemblies (e.g. complete genomes).
• New example dataset (examples/listeria/, 22 public genomes) and wiki pages: Tutorial, How it works, Performance, Related tools and FAQ.
• README with example figures, features, citation information; CITATION.cff, CONTRIBUTING.md, code of conduct, security policy, and issue and pull request templates.

0.4.2 (2026-09-23)

• mash-phylo now finds Mash in its own conda environment when mash is not in the PATH, so /path/to/envs/genome_comparator/bin/mash-phylo works without activating the environment. The log shows which mash was used.

0.4.1 (2026-09-23)

• Fixed: --bootstrap could hang on Python < 3.14. Worker processes were started with fork (the Linux default before Python 3.14), which can deadlock when the parent process runs threads. They now use forkserver (or spawn where forkserver is not available).
• CI: 20-minute timeout on the test jobs, and no duplicate test runs on tag pushes.

0.4.0 (2026-09-23)

• New --bootstrap N option: support values on all the trees (UPGMA, NJ, ME), from replicates sketched with different hash seeds. Replicate trees are built in parallel worker processes. See Bootstrap support.
• Documentation moved to this wiki, maintained in the wiki/ folder of the repository.

0.3.0 (2026-09-23)

• Package layout with installable commands and a pyproject.toml; conda env create -f environment.yml works.
• Pairwise distances are computed with a single mash triangle call instead of one mash dist per sample.
• Sketches are named after the sample, so the slow file-path-to-name substitution is gone.
• Fixed: fasta files whose name contains _R1/_R2 (e.g. Iso_R10.fasta and Iso_R11.fasta) were merged into a single sample.
• Fixed: branch lengths of the hierarchical clustering tree were rounded to 2 decimals (most Mash distances became 0).
• Fixed: re-running in the same output folder kept the old all.msh because mash paste refuses to overwrite it.
• Fixed: failures of Mash were ignored; they are now reported.
• Fixed: relative input paths starting with ../ pointed to the wrong folder.
• Fixed: --clean recursively deleted every *.list file under the output folder; it now only removes files it created.
• Fixed: tree-renamer used partial matches (S1 also renamed S10); tree-collapser wrote invalid Newick when names contained commas.
• The default hierarchical clustering method is now average (UPGMA) rather than ward, which assumes Euclidean distances. Use --linkage ward for the previous behaviour.
• The PCA was replaced by a PCoA (the proper ordination for a distance matrix), with optional metadata colouring.
• New --me tree, --phylip output, --metadata/--color-by, --min-copies, --force and --version options.
• sample_stats.txt is now a tab-separated table: sample_stats.tsv.
• tree-collapser no longer needs ete3.