diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml index 3c47534..42cc75b 100644 --- a/.github/workflows/docker-push.yaml +++ b/.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 }} diff --git a/DESCRIPTION b/DESCRIPTION index f6d03ed..79b6f2b 100644 --- a/DESCRIPTION +++ b/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) diff --git a/Dockerfile b/Dockerfile index 9c0ca1f..f6d71b1 100644 --- a/Dockerfile +++ b/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)" diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..11c7d66 --- /dev/null +++ b/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/ diff --git a/README.md b/README.md index 52701ee..b21ca54 100644 --- a/README.md +++ b/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).