ANN : Macrel 1.6.1 released

[Luis Pedro Coelho]

Dear List,

We released Macrel 1.6.1!

This is primarily a stability and polish release on top of 1.6.0. This is a large round of bug fixes and documentation corrections, including:

• More robust input handling: empty sequences and sequences with non-standard amino acids are now skipped with a warning instead of crashing, and AMP-density no longer errors on empty input.
• AMPSphere querying fixes: sequences are URL-encoded in remote queries, HTTP status is checked on all API requests and downloads, --file-output is now supported for query-ampsphere, and a wrong-accession bug in local M-stripped exact matches was fixed.
• Better CLI behavior: unknown subcommands now list the available commands, --outtag is accepted as an alias for --tag, and a bug where parse_args ignored its argument (breaking programmatic use) was fixed.
• Fixes to the output-directory README files (correct filenames and table descriptions) and a fix for a crash in get-smorfs --file-output.
• Extensive documentation corrections across usage.md, install.md, faq.md, and the tutorials — flag names, Python-version claims, AMPSphere query modes (--query-mode=hmmer), and example paths.
• Dropped the unused tzlocal dependency and added the missing pyrodigal dependency to the package metadata.

The recommended way to install is with pixi:

pixi global install -c conda-forge -c bioconda macrel 

Or, if you just want to run it once without installing anything, pixi can do that too:

pixi exec -c conda-forge -c bioconda macrel

This downloads Macrel and its dependencies into a temporary environment and runs it — convenient for one-off usage. You can of course still install/update via conda (conda install -c bioconda macrel).Bug reports and comments are appreciated!

Best, Luis

--

Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885

Recent preprints: https://doi.org/10.64898/2026.05.11.724158 / https://doi.org/10.1101/2025.09.17.676595