Merge pull request bigbio#714 from bigbio/dev

Changelog included, and folder repeated with docs removed.
ypriverol · Aug 26, 2024 · 1cd2e2f · 1cd2e2f
2 parents 4d9af25 + bb33282
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,44 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- Validation of 256 annotated projects. 
+- Introduction of the ChangeLog file to the project.
+
+### Changed
+
+- Small changes in typos and grammar in the SDRF specification document (sdrf-proteomics/README.adoc).
+- Update of the enzyme.tsv file in the SDRF specification document (sdrf-proteomics/enzymes.tsv).
+- Remove enzyme regular expression as recommended in the SDRF specification document (sdrf-proteomics/README.adoc).
+
+### Removed
+
+- Outdated readthedocs link, main documentation is the SDRF specification document (sdrf-proteomics/README.adoc).
+
+## [1.0.0] - 2023-05-24
+
+### Added
+
+- First release of the project.
+- First version of the SDRF specification document (psi-document/SDRF_Proteomics_Specification_v1.0.0.docx).
+- First projects annotated in the SDRF format.
+
+### Fixed
+
+- Nothing fixed.
+
+### Changed
+
+- Nothing changed. 
+
+### Removed
+
+- Nothing removed.
+
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # Proteomics Sample Metadata Format
 
+[![Version](https://flat.badgen.net/static/sdrf-proteomics/1.0.0/orange)](CHANGELOG.md)
 [![License](https://flat.badgen.net/github/license/bigbio/proteomics-metadata-standard)](https://github.com/bigbio/proteomics-metadata-standard/blob/master/LICENSE)
 [![Open Issues](https://flat.badgen.net/github/open-issues/HUPO-PSI/mzSpecLib)](https://github.com/bigbio/proteomics-metadata-standard/issues)
 [![Open PRs](https://flat.badgen.net/github/open-prs/bigbio/proteomics-metadata-standard)](https://github.com/bigbio/proteomics-metadata-standard/pulls)
@@ -32,7 +33,7 @@ While the experiment general description is captured for all the PX submissions
 
 ## Final PSI specification
 
-The final HUPO-PSI specification is: [SDRF HUPO-PSI](psi-document/SDRF_Proteomics_Specification_20230524_Final.pdf)
+The final HUPO-PSI specification is: [SDRF HUPO-PSI](psi-document/SDRF_Proteomics_Specification_v1.0.0.pdf)
 
 ## How to contribute
 
@@ -67,12 +68,10 @@ You can read more about the validator [here](https://github.com/bigbio/sdrf-pipe
 
 ## 30 Minutes Guide to MAGE-TAB for Proteomics 
 
-Documentation page (https://proteomics-sample-metadata.readthedocs.io/en/latest/)
-
 We have created a 30-minute Guide to the file format in [the github repository](https://github.com/bigbio/proteomics-metadata-standard/wiki). Additionally, the following materials are relevant for new users: 
 
 - [Introduction to MAGE-TAB proteomics - Slides](https://github.com/bigbio/proteomics-metadata-standard/raw/master/additional-documentation/presentation-20200313.pptx)
-- [Introduction to MAGE-TAB proteomics - Youtube Video](https://www.youtube.com/watch?v=TMDu_yTzYQM)
+- [Introduction to MAGE-TAB proteomics - YouTube Video](https://www.youtube.com/watch?v=TMDu_yTzYQM)
 
 
 ## Core contributors and collaborators

diff --git a/docs/README.adoc b/docs/README.adoc
diff --git a/docs/additional.rst b/docs/additional.rst
diff --git a/docs/conf.py b/docs/conf.py
diff --git a/docs/documentation.rst b/docs/documentation.rst
diff --git a/docs/images/contact.png b/docs/images/contact.png
diff --git a/docs/images/sample-metadata.png b/docs/images/sample-metadata.png
diff --git a/docs/images/sdrf-nutshell.png b/docs/images/sdrf-nutshell.png
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/docs/introduction.rst b/docs/introduction.rst
diff --git a/docs/requirements.txt b/docs/requirements.txt