From 289e2d9149c30a6df217620b763290ee912b8902 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 19 Apr 2024 12:16:31 +0200 Subject: [PATCH 1/2] Prepare release 2.1.0 --- CHANGELOG.md | 28 +++++++++++++++------------- setup.py | 2 +- 2 files changed, 16 insertions(+), 14 deletions(-) mode change 100644 => 100755 setup.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 9af72ca4..d3d46cdb 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,17 +4,28 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [2.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.X +## [2.1.0dev] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0 ### Credits -Code contributions to the hotfix: +Code contributions to the new version: +- [Sarai Varona](https://github.com/svarona) +- [Pablo Mata](https://github.com/Shettland) +- [Daniel Valle](https://github.com/Daniel-VM) ### Template fixes and updates -- Added blast_nt template to services.json +- Added blast_nt template to services.json [#208](https://github.com/BU-ISCIII/buisciii-tools/pull/208) - Included new user to sftp_user.json -- Fixed characterization template +- Included a missing sed inside IRMA's 04-irma/lablog [#213](https://github.com/BU-ISCIII/buisciii-tools/pull/213) +- Changed singularity mount options in Viralrecon template to fix errors with Nextflow v23.10.0 +- excel_generator.py reverted to last state, now lineage tables are merged when argument -l is given +- Adapted viralrecon_results lablog to new excel_generator.py argument +- IRMA/RESULTS now creates a summary of the different types of flu found in irma_stats.txt +- Updated IRMA to v1.1.4 date 02-2024 and reduced threads to 16 +- IRMA 04-irma/lablog now creates B and C dirs only if those flu-types are present +- Fixed characterization template [#220](https://github.com/BU-ISCIII/buisciii-tools/pull/220) +- Created Chewbbaca template [#230](https://github.com/BU-ISCIII/buisciii-tools/pull/230) ### Modules @@ -28,18 +39,9 @@ Code contributions to the hotfix: - Autoclean-sftp refined folder name parsing with regex label adjustment - Autoclean_sftp does not crash anymore. New argument from 'utils.prompt_yn_question()' in v2.0.0 was missing: 'dflt' - Bioinfo-doc now sends email correctly to multiple CCs -- Included a missing sed inside IRMA's 04-irma/lablog -- Changed singularity mount options in Viralrecon template to fix errors with Nextflow v23.10.0 - #### Changed -- excel_generator.py reverted to last state, now lineage tables are merged when argument -l is given -- Adapted viralrecon_results lablog to new excel_generator.py argument -- IRMA/RESULTS now creates a summary of the different types of flu found in irma_stats.txt -- Updated IRMA to v1.1.4 date 02-2024 and reduced threads to 16 -- IRMA 04-irma/lablog now creates B and C dirs only if those flu-types are present - #### Removed - Removed empty strings from services.json diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 index ba13fa2f..dcda6436 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages -version = "2.0.0" +version = "2.1.0" with open("README.md") as f: readme = f.read() From a6019ef2509debccb02fa8f23e2a2352e70f4178 Mon Sep 17 00:00:00 2001 From: Shettland Date: Fri, 19 Apr 2024 12:33:02 +0200 Subject: [PATCH 2/2] Prepare Release 2.1.0. Included reviewer changes --- CHANGELOG.md | 62 ++++++++++++++++++++++++++++++++++------------------ 1 file changed, 41 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3d46cdb..2fd6cb6e 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,47 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [2.1.0dev] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0 +## [2.2.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.X + +### Credits + +Code contributions to the new version: + +### Template fixes and updates + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + +## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1 + +### Credits + +Code contributions to the hotfix: + +### Template fixes and updates + +### Modules + +#### Added enhancements + +#### Fixes + +#### Changed + +#### Removed + +### Requirements + +## [2.1.0] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0 ### Credits @@ -48,26 +88,6 @@ Code contributions to the new version: ### Requirements -## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1 - -### Credits - -Code contributions to the hotfix: - -### Template fixes and updates - -### Modules - -#### Added enhancements - -#### Fixes - -#### Changed - -#### Removed - -### Requirements - ## [2.0.0] - 2024-03-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0 ### Credits