v3.1.1

[3.1.1] - 2026-09-10

Inconveniences fixed. No known incompatibilities. Nothing you set changes, nothing you have installed needs touching, and no result computed under 3.1.0 is affected. This tidies two things that were merely noisy and one page that was actively misleading.

Fixed

• analysis modules available listed every published version of every module. The catalogue holds one row per version — that is what install resolves against — so a listing of rows was each module's history rather than something to act on, and it grew with every publish. It now shows one line per module: the newest version your release can run, which is exactly what install <name> would take. Both commands ask the same question through the same code, so they cannot tell you different things. Older versions stay published and stay installable by naming one.
• Installing a module asked conda to install packages that were already there. A module declares everything it needs whether or not the release's own environment already carries it, and most of what a manifest names normally is already there — so installing one meant a network round trip and a solve to be told nothing had to happen. Only what is actually missing is installed now, and a module needing nothing new says so instead of listing seven packages it is not going to touch. What a manifest declares is unchanged, and uninstalling still reasons over the whole list.
• The published modules page offered libraries as though you could install them. Published modules rendered every catalogue row, so the five libraries appeared beside the modules — and a library is never installed by name. It now lists modules only, newest version each, matching what available shows, and names the libraries as reference. The page corrects itself on the next site deploy rather than on upgrade.

Changed

• The CHANGELOG says what the public API is. Semantic Versioning requires a project to declare one and this had not, which left every release number a judgment call. It is what a result depends on — the published table formats, parameters.config, metadata.csv, and what an analysis folder contains. The command line is documented, not frozen.

Commits

• (a7d68a5) Published basicstats, association, and mds modules
• (8270a4e) module list was showing every version, fixed to latest version
• (028b391) for analysis install redundant conda install is removed
• (61c34f8) Documentation update
• (b31e291) Clarification on versioning on CHANGELOG

Download and install

curl -LO https://github.com/ozankiratli/PoolSeqFlow/releases/download/v3.1.1/PoolSeqFlow-3.1.1.tar.gz
tar -xzf PoolSeqFlow-3.1.1.tar.gz
cd PoolSeqFlow-3.1.1

cp parameters.config.template parameters.config
./PoolSeqFlow install

Then edit parameters.config and metadata.csv for your data and run
./PoolSeqFlow run.

Verify the download with sha256sum -c SHA256SUMS.

PoolSeqFlow.tar.gz is the same archive under a stable name, for
scripted installs:
https://github.com/ozankiratli/PoolSeqFlow/releases/latest/download/PoolSeqFlow.tar.gz

Upgrading an existing project? Your parameters.config is not
touched by a new version and can be missing parameters this release
expects. Run ./PoolSeqFlow migrate_config and read what it reports —
see Upgrading.

Full documentation: https://ozankiratli.github.io/PoolSeqFlow/
The full changelog, including every commit, is in CHANGELOG.md in the download and in the repository.