From 8da32f02f28326872193a2e43ecd8cea6ad75ffd Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Wed, 21 Aug 2024 13:30:27 +0200 Subject: [PATCH] RLS Version 0.6.0 Big change is adding GROOT support Full Changelog: - argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot - GROOT support is via the `GrootNormalizer` (for use in python scripts) and the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters in the CLI. Other ----- - `__version__` attribute added to the package (accessible as `argnorm.__version__` or `argnorm.lib.__version__`) - Use atomic writing for outputs (https://github.com/untitaker/python-atomicwrites/tree/master) funcscan integration -------------------- - argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/ - argNorm will also be available on the funcscan pipeline: https://github.com/nf-core/funcscan/pull/410 DB harmonisation ---------------- - SARG db link was changed in `crude_db_harmonisation` to https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta as old link (Galaxy instance, http://smile.hku.hk/SARGs) is down - RGI outputs in `crude_db_harmonisation` are concatenated so frequencies of `perfect`, `strict`, and `loose` hits can be calculated from concatenated file --- CHANGELOG.md | 2 +- argnorm/argnorm_version.py | 2 +- docs/whatsnew.md | 11 ++++------- 3 files changed, 6 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ab735b..b3e481e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,7 @@ ## Unreleased -### New Features +## 0.6.0 - 21 August 2024 #### GROOT support - argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot diff --git a/argnorm/argnorm_version.py b/argnorm/argnorm_version.py index 31d8e4c..ef7eb44 100644 --- a/argnorm/argnorm_version.py +++ b/argnorm/argnorm_version.py @@ -1 +1 @@ -__version__ = '0.6.0.dev0' +__version__ = '0.6.0' diff --git a/docs/whatsnew.md b/docs/whatsnew.md index 017d7f4..7dfe0ef 100644 --- a/docs/whatsnew.md +++ b/docs/whatsnew.md @@ -2,24 +2,21 @@ argNorm is under active development and outputs may change between versions. Particular versions of argNorm should, however, be reproducible as the databases are bundled with the tool. -## 0.6.0 (Coming Soon!) +## 0.6.0 - 21 August 2024 ### User-facing changes #### GROOT support -- argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot -- GROOT support is via the `GrootNormalizer` (for use in python scripts) and the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters in the CLI. - -#### Other +- argNorm supports [GROOT v1.1.2](https://github.com/will-rowe/groot). Use the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters on the command line. The `GrootNormalizer` is available for use in Python scripts. - `__version__` attribute added to the package (accessible as `argnorm.__version__` or `argnorm.lib.__version__`) -- Use atomic writing for outputs (https://github.com/untitaker/python-atomicwrites/tree/master) +- atomic writing is used for outputs (https://github.com/untitaker/python-atomicwrites/tree/master). When everything is alright, this should not make a difference, but it avoids certain categories of failures. ### funcscan integration - argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/ - argNorm will also be available on the funcscan pipeline: https://github.com/nf-core/funcscan/pull/410 ### Internal changes -- SARG db link was changed in `crude_db_harmonisation` to https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta as old link (Galaxy instance, http://smile.hku.hk/SARGs) is down +- SARG db link was updated as old link is down - RGI outputs in `crude_db_harmonisation` are concatenated so frequencies of `perfect`, `strict`, and `loose` hits can be calculated from concatenated file ## 0.5.0 - 25 June 2024