fix docker, and license

.github/workflows/docker-push.yaml

@@ -13,35 +13,38 @@ jobs:
   build-docker-and-push:
     runs-on: ubuntu-latest
     steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6
         with:
-          ref: ${{ github.event.client_payload.sha }}
+          context: .
           push: true
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: rformassspectrometry/metabonaut:latest
+          tags: |
+            rformassspectrometry/metabonaut:latest
+            rformassspectrometry/metabonaut:RELEASE_3_23
       -
         name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}
 
       - name: Trigger next workflow
         if: success()
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v3
         with:
           token: ${{ secrets.REPO_GHA_PAT }}
           repository: ${{ github.repository }}

DESCRIPTION

@@ -40,7 +40,7 @@ Authors@R:
 Description: This resource hosts tutorials and end-to-end workflows
              describing how to analyze LC-MS/MS data, from raw files
              to annotation, using Bioconductor packages.
-License: Artistic-2.0
+License: CC BY-SA 4.0
 Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)

Dockerfile

@@ -1,10 +1,10 @@
-FROM bioconductor/bioconductor_docker:RELEASE_3_22
+FROM bioconductor/bioconductor_docker:RELEASE_3_23
 
 LABEL name="rformassspectrometry/Metabonaut" \
       url="https://github.com/rformassspectrometry/Metabonaut" \
       maintainer="philippine.louail@outlook.com" \
-      description="Docker container to run the different tutorials hosted on metabonaut. Includes Sirius 6.3 and RuSirius for the advanced feature annotation vignette. This version bases on the Bioconductor devel docker image." \
-      license="Artistic-2.0"
+      description="Docker container to run the different tutorials hosted on metabonaut. Includes Sirius 6.3 and RuSirius for the advanced feature annotation vignette. This version is based on the Bioconductor release 3.23 docker image." \
+      license="CC-BY-SA-4.0"
 
 WORKDIR /home/rstudio
 
@@ -14,7 +14,7 @@ RUN rm -rf /home/rstudio/scripts /home/rstudio/vignettes/.quarto
 ## Global installation of required packages
 ## Need MsBackendMetaboLights to pre-download the dataset.
 ## Need MsIO because not on any repository
-RUN Rscript -e "BiocManager::install(c('RforMassSpectrometry/MsIO', 'MsBackendMetaboLights', 'mzR') , ask = FALSE, dependencies = c('Depends', 'Imports'), build_vignettes = FALSE)"
+RUN Rscript -e "install.packages('remotes'); BiocManager::install(c('RforMassSpectrometry/MsIO', 'MsBackendMetaboLights', 'mzR') , ask = FALSE, dependencies = c('Depends', 'Imports'), build_vignettes = FALSE)"
 
 ## Install keyring package from github using pak
 RUN Rscript -e "install.packages('pak');pak::pak('r-lib/keyring', ask = FALSE)"

LICENSE

@@ -0,0 +1,35 @@
+Metabonaut: Exploring and Analyzing LC-MS Data
+
+Copyright (c) 2024-2026 The Metabonaut authors (see DESCRIPTION / Authors@R).
+
+This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
+International License (CC BY-SA 4.0).
+
+You are free to:
+
+  * Share  — copy and redistribute the material in any medium or format.
+  * Adapt  — remix, transform, and build upon the material for any purpose,
+             even commercially.
+
+Under the following terms:
+
+  * Attribution — You must give appropriate credit, provide a link to the
+    license, and indicate if changes were made. You may do so in any
+    reasonable manner, but not in any way that suggests the licensor
+    endorses you or your use.
+
+  * ShareAlike  — If you remix, transform, or build upon the material, you
+    must distribute your contributions under the same license as the
+    original.
+
+  * No additional restrictions — You may not apply legal terms or
+    technological measures that legally restrict others from doing anything
+    the license permits.
+
+To view the full legal text of this license, visit:
+
+    https://creativecommons.org/licenses/by-sa/4.0/legalcode
+
+A human-readable summary of the license is available at:
+
+    https://creativecommons.org/licenses/by-sa/4.0/

README.md

@@ -1,6 +1,6 @@
 # Let's Explore and Learn to Analyze Untargeted Metabolomics Data
 
-[![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)
+[![License: CC BY-SA 4.0](https://img.shields.io/badge/License-CC%20BY--SA%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-sa/4.0/)
 [![DOI](https://zenodo.org/badge/849331979.svg)](https://doi.org/10.5281/zenodo.15062929)
 
 ## Welcome to **Metabonaut**! 🚀
@@ -86,7 +86,7 @@ one comprehensive **super-vignette**.
 
 -   **Major updates** will be documented here.
     -   Metabonaut now works with a stable version of Bioconductor
-        (3.22)
+        (3.23)
 -   **Minor updates** can be found in the
     [News section](https://rformassspectrometry.github.io/Metabonaut/news/index.html).