What's Changed

minor JOSS changes by @danielskatz in https://github.com/Wytamma/snk/pull/95
:abc: adding citation details. by @rbturnbull in https://github.com/Wytamma/snk/pull/96

New Contributors

@danielskatz made their first contribution in https://github.com/Wytamma/snk/pull/95
@rbturnbull made their first contribution in https://github.com/Wytamma/snk/pull/96

Full Changelog: https://github.com/Wytamma/snk/compare/v0.31.0...v0.31.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 1 year ago

Snk - joss-publication-release

This is a tagged release of the codebase for publication.

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 1 year ago

What's Changed

➖ remove write-the by @Wytamma in https://github.com/Wytamma/snk/pull/86
JOSS review: Fix contributing typos by @huddlej in https://github.com/Wytamma/snk/pull/84
JOSS review: Fix minor paper typos by @huddlej in https://github.com/Wytamma/snk/pull/87
Add snk edit command by @Wytamma in https://github.com/Wytamma/snk/pull/93
Add snk create command by @Wytamma in https://github.com/Wytamma/snk/pull/94
Add minsnkcli_version to version the cli.

New Contributors

@huddlej made their first contribution in https://github.com/Wytamma/snk/pull/84

Full Changelog: https://github.com/Wytamma/snk/compare/v0.30.1...v0.31.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma over 1 year ago

Snk - v0.30.1

Full Changelog: https://github.com/Wytamma/snk/compare/v0.30.0...v0.30.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma over 1 year ago

Snk - v0.30.0

Bump snk-cli version
Add install progress bar (spinner)
Minor fixes Full Changelog: https://github.com/Wytamma/snk/compare/v0.29.0...v0.30.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma over 1 year ago

Adds Choices (Enum) support. yaml cli: choice: choices: [a, b, c] default: a bash ❯ example run --choice d Error │ Invalid value for '--choice': 'd' is not one of 'a', 'b', 'c'. │ Full Changelog: https://github.com/Wytamma/snk/compare/v0.27.2...v0.29.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma over 1 year ago

Snk - Version 0.27.2

Full Changelog: https://github.com/Wytamma/snk/compare/v0.27.1...v0.27.2

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.27.1

✨ non-standard snakemake files with snk install --snakefile ...

Full Changelog: https://github.com/Wytamma/snk/compare/v0.27.0...v0.27.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.27.0

📌 update snk-cli 🐛 fix bug with missing snk file and versions

Full Changelog: https://github.com/Wytamma/snk/compare/v0.26.0...v0.27.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.26.0

What's Changed

Dependancies by @Wytamma in https://github.com/Wytamma/snk/pull/70

Full Changelog: https://github.com/Wytamma/snk/compare/v0.25.1...v0.26.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.25.1

🐛 check if the version of Snakemake installed is greater than or equal to the minimum version

Full Changelog: https://github.com/Wytamma/snk/compare/v0.25.0...v0.25.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.25.0

What's Changed

Support Snakemake v8 by @Wytamma in https://github.com/Wytamma/snk/pull/68

Full Changelog: https://github.com/Wytamma/snk/compare/v0.24.1...v0.25.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.24.1

⬆️ Update snk-cli dep to v0.1.2

Full Changelog: https://github.com/Wytamma/snk/compare/v0.24.0...v0.24.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.24.0

What's Changed

Snk cli refactor by @Wytamma in https://github.com/Wytamma/snk/pull/67

Full Changelog: https://github.com/Wytamma/snk/compare/v0.23.2...v0.24.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.23.2

Stop Snakemake v8.0.0 from being installed with python >= 3.11

Full Changelog: https://github.com/Wytamma/snk/compare/v0.23.1...v0.23.2

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.23.1

workflow will now check if it's an editable workflow package installed by pip install . -e

Full Changelog: https://github.com/Wytamma/snk/compare/v0.23.0...v0.23.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma almost 2 years ago

Snk - Version 0.23.0

I added back pipeline_dir_path to CLI so that it's back compatible.

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.5...v0.23.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.5

Preserve the order of options as they are defined in the snk.yaml file.

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.4...v0.22.5

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.4

Some minor bug fixes 🐛

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.3...v0.22.4

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.3

✨ Allow pass SnkConfig to CLI

This means that you can create a cli without a snk.yaml by passing a SnkConfig class to snk.CLI.

🎨 logging to stderr

Logging defaults to stderr.

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.2...v0.22.3

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.2

✨added additional_snakemake_args to snk config: A list of additional arguments to pass to snakemake.

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.1...v0.22.2

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.1

Improve snk list cli
Minor updates

Full Changelog: https://github.com/Wytamma/snk/compare/v0.22.0...v0.22.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.22.0

✨Create conda envs in parallel

A snakemake workflow that uses a lot of conda envs can take a long time to install as each env is created sequentially. Now running <workflow-name> env create will create all the conda envs in parallel (up to --workers at a time, defaults to number of cores). Single envs can be create with <workflow-name> env create <env-name>.

✨List commands now return tables

Running <workflow-name> env list/<workflow-name> profile list/<workflow-name> script list will now return a rich table. Screenshot 2024-01-30 at 2 24 31 pm

✅ Improved testing

Better testing of environment commands.

Full Changelog: https://github.com/Wytamma/snk/compare/v0.21.2...v0.22.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.21.2

Minor updates and fixes

Full Changelog: https://github.com/Wytamma/snk/compare/v0.21.1...v0.21.2

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.21.1

🐛 fix bug in environment subcommand ⬆️ Bump snakemake to < 8

Full Changelog: https://github.com/Wytamma/snk/compare/v0.21.0...v0.21.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.21.0

What's Changed

:truck: rename pipeline to workflow by @Wytamma in https://github.com/Wytamma/snk/pull/61
💥 remove 3.7 support
✨ add validate function

Full Changelog: https://github.com/Wytamma/snk/compare/v0.20.1...v0.21.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.20.1

🐛 fix bug in profile show

Full Changelog: https://github.com/Wytamma/snk/compare/v0.20.0...v0.20.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.20.0

🐛 check if option is passed via cli (solves #56) ✅ Add more tests

Full Changelog: https://github.com/Wytamma/snk/compare/v0.19.1...v0.20.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.19.1

🐛 fix bug in version displayed

Full Changelog: https://github.com/Wytamma/snk/compare/v0.19.0...v0.19.1

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.19.0

✨ Add --no-conda flag to snk install ➖ Renamed snk config param conda_required to conda (--use-conda flag will only be passed if conda: True and conda is available).

Full Changelog: https://github.com/Wytamma/snk/compare/v0.18.0...v0.19.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.18.0

🐛 Pin pulp to <2.8 (#57 & https://github.com/snakemake/snakemake/issues/2607)
🎨 consistent cli help

Full Changelog: https://github.com/Wytamma/snk/compare/v0.17.2...v0.18.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.17.2

What's Changed

Add profile subcommands by @Wytamma in https://github.com/Wytamma/snk/pull/52
Other small updates

Full Changelog: https://github.com/Wytamma/snk/compare/v0.17.0...v0.17.2

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago

Snk - Version 0.17.0

What's Changed

Install pipeline from commit SHA by @ktmeaton in https://github.com/Wytamma/snk/pull/50

New Contributors

@ktmeaton made their first contribution in https://github.com/Wytamma/snk/pull/50

Full Changelog: https://github.com/Wytamma/snk/compare/v0.16.0...v0.17.0

Scientific Software - Peer-reviewed - Python
Published by Wytamma about 2 years ago