ENCORE Version 4.1.1 (Nat. Comm Supplement)

ENCORE VERSION 4.1.1 (Nat. Comm Supplement) (26 July 2024)
This release includes the ENCORE V4.1.1 Template and compiled binaries of the sFSS Navigator:

Navigate_W.exe. Windows executable if you don't have Python installed (Navigate.exe -h).
Navigate_M. MacOS executable (macOS 13.3.1 (Ventura), Apple M1)
Navigate_MacIntel. MacOS executable (macOS 10.13.6 (High Sierra), Intel Core i5 )

sFSS Navigator Version 1.5 (23 May 2023) - Compatible with ENCORE Template Version 3.x and 4.x

Changes

Various changes, extensions, and changes to the README files
Update of the Step-By-Step User Guide (Version 13.2)
Update of 2_CITATION.md

ENCORE Version 4.1.1

ENCORE VERSION 4.1.1 (19 June 2024)
This release includes the ENCORE V4.1.1 Template and compiled binaries of the sFSS Navigator:

Navigate_W.exe. Windows executable if you don't have Python installed (Navigate.exe -h).
Navigate_M. MacOS executable (macOS 13.3.1 (Ventura), Apple M1)
Navigate_MacIntel. MacOS executable (macOS 10.13.6 (High Sierra), Intel Core i5 )

sFSS Navigator Version 1.5 (23 May 2023) - Compatible with ENCORE Template Version 3.x and 4.x

Changes

• Various changes, extentions, and changes to the README files
• Update of the Step-By-Step User Guide (Version 13.2)
• Update of 2_CITATION.md

ENCORE Version 4.1

ENCORE VERSION 4.1 (22 May 2024)
This release includes the ENCORE V4.1 Template and compiled binaries of the sFSS Navigator:

Navigate_W.exe. Windows executable if you don't have Python installed (Navigate.exe -h).
Navigate_M. MacOS executable (macOS 13.3.1 (Ventura), Apple M1)
Navigate_MacIntel. MacOS executable (macOS 10.13.6 (High Sierra), Intel Core i5 )

sFSS Navigator Version 1.5 (23 May 2023) - Compatible with ENCORE Template Version 3.x and 4.x

Changes
(1) Template

• Rename 00-README-FIRST.md to README.md such that it occurs on the landing page of the GitHub Template Repository (https://github.com/EDS-Bioinformatics-Laboratory/ENCORE).
• Updated README.md to make a distinction between information for the ‘Project Team’ running a project, and the 'Compendium Recipient' to who a project is shared.
• To avoid confusion about the various formats of some of the files we removed 00_README-FIRST.txt, 2_CITATION.txt and 3_LICENSE.txt. The Markdown files were left in the template for the 'Compendium Recipient' who doesn’t need multiple formats. The multiple formats are only for the Project Team.
• Update of 0_README.md in \Code. Now refers to 0_README.md in 0_SoftwareEnvironment to stress the importance of preserving the software environment/dependencies.
• Update of 0_README.md in 0_SoftwareEnvironment. Now contains more detailed information and links to conda, renv, etc
• Updated gitignore-FSS-template.txt in \Processing to exclude all Data directories.
• Release 4.1 has been added to the repository

(2) 'Discussions' and 'Wiki' has been activated for the ENCORE template GitHub repository.

• The ‘Discussions’ (https://github.com/EDS-Bioinformatics-Laboratory/ENCORE/discussions) will provide a channel to communicate with the scientific community about ENCORE.
• The WIKI (https://github.com/EDS-Bioinformatics-Laboratory/ENCORE/wiki) contains general information about ENCORE and the ENCORE version History has been moved from 'Issues' to the Wiki.
• The WIKI provides information about the compatibility of specific versions of the sFSS Navigator with versions of the ENCORE template (https://github.com/EDS-Bioinformatics-Laboratory/ENCORE/wiki/sFSS-Navigator). This version information is also added to the FSS Navigator repository (https://github.com/EDS-Bioinformatics-Laboratory/FSS-Navigator/releases). This is now also referred to from the README.md file in the sFSS root.

(3) ENCORE-AUTOMATION
We created a separate GitHub repository (ENCORE AUTOMATION; https://github.com/EDS-Bioinformatics-Laboratory/ENCORE_AUTOMATION), which currently contains scripts to automatically setup an ENCORE project (including new GitHub repository). We will expand this repository in the future with additional scripts to automate tasks.

(4) Update of the Step-by-Step-ENCORE guide

• Several small changes
• Now refers to repository Discussion and Wiki, and to ENCORE AUTOMATION
• In the instructions for setting up an ENCORE project and GitHub repository, it now explains which steps are taken care of by the scripts in ENCORE-AUTOMATION.
• We explained the compatibility between sFSS Navigator and ENCORE template versions and refer to the WIKI.
• We clarified that files that are not relevant for the Compendium Recipient can/should be removed.

ENCORE Version 4.0

ENCORE VERSION 4.0

This release includes the ENCORE V4.0 Template and compiled binaries of the sFSS Navigator:

• Navigate_W.exe. Windows executable if you don't have Python installed (Navigate.exe -h).
• Navigate_M. MacOS executable (macOS 13.3.1 (Ventura), Apple M1)
• Navigate_MacIntel. MacOS executable (macOS 10.13.6 (High Sierra), Intel Core i5 )

ENCORE (pre-release)

ENCORE pre-release. The future version V4.0.0 will accompany the ENCORE publication.
This pre-release does not contain the executables of the FSS navigator