From db8e598ed6bdd20bc1f34a21c0c861eed9bb3b99 Mon Sep 17 00:00:00 2001 From: Julian Flesch Date: Wed, 15 Oct 2025 23:32:10 +0200 Subject: [PATCH 1/5] Adds installing nf-core at state from local workspace --- .devcontainer/setup.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh index e87d26c4c8..e10dc21d08 100755 --- a/.devcontainer/setup.sh +++ b/.devcontainer/setup.sh @@ -9,5 +9,8 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' # Update Nextflow nextflow self-update +# Install specifically the version of tools from the workspace +pip install --upgrade -r requirements-dev.txt -e . + # Update welcome message echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt From 89a028de1bfb508244d92b74fe5d0d908c44ba2f Mon Sep 17 00:00:00 2001 From: Julian Flesch Date: Fri, 17 Oct 2025 11:27:34 +0200 Subject: [PATCH 2/5] Remove building nfcore/devcontainer:dev --- .github/workflows/push_dockerhub_dev.yml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index 6f44f450bf..8144f86c41 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -49,13 +49,3 @@ jobs: --platform ${{ env.TARGET_PLATFORM }} \ -t nfcore/tools:dev \ --push --no-cache . - - - name: Build and push nfcore/devcontainer:dev image (dev) - uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3 - with: - configFile: .devcontainer/build-devcontainer/devcontainer.json - imageName: nfcore/devcontainer - imageTag: dev - platform: ${{ env.TARGET_PLATFORM }} - push: always - noCache: true From f3b23e8b4ef2e4e3406c6a58f0ec7d546848ef35 Mon Sep 17 00:00:00 2001 From: JulianFlesch Date: Sun, 19 Oct 2025 17:14:37 +0200 Subject: [PATCH 3/5] Update .devcontainer/setup.sh MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .devcontainer/setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh index e10dc21d08..f350e4204e 100755 --- a/.devcontainer/setup.sh +++ b/.devcontainer/setup.sh @@ -10,7 +10,7 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' nextflow self-update # Install specifically the version of tools from the workspace -pip install --upgrade -r requirements-dev.txt -e . +pip install --upgrade -r requirements.txt -r requirements-dev.txt -e . # Update welcome message echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt From aae7f41bc31b8325fd26b550b995ce1d93678a47 Mon Sep 17 00:00:00 2001 From: Julian Flesch Date: Sun, 19 Oct 2025 17:20:32 +0200 Subject: [PATCH 4/5] Revert "Remove building nfcore/devcontainer:dev" This reverts commit 89a028de1bfb508244d92b74fe5d0d908c44ba2f. --- .github/workflows/push_dockerhub_dev.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index 8144f86c41..6f44f450bf 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -49,3 +49,13 @@ jobs: --platform ${{ env.TARGET_PLATFORM }} \ -t nfcore/tools:dev \ --push --no-cache . + + - name: Build and push nfcore/devcontainer:dev image (dev) + uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3 + with: + configFile: .devcontainer/build-devcontainer/devcontainer.json + imageName: nfcore/devcontainer + imageTag: dev + platform: ${{ env.TARGET_PLATFORM }} + push: always + noCache: true From 06fc1a46a03b0df5af5dc569efc34ecfc9744751 Mon Sep 17 00:00:00 2001 From: Julian Flesch Date: Mon, 27 Oct 2025 09:56:00 +0100 Subject: [PATCH 5/5] Remove manually changing devcontainer tags from Checklist --- .github/RELEASE_CHECKLIST.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md index b9f4f0de76..907a119035 100644 --- a/.github/RELEASE_CHECKLIST.md +++ b/.github/RELEASE_CHECKLIST.md @@ -4,7 +4,7 @@ 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_. 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc) 4. Check that modules/subworkflows in template are up to date with the latest releases -5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:latest`. +5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`. 6. Make sure all CI tests are passing! 7. Create a PR from `dev` to `main` 8. Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR: use the `Sync template` GitHub Action from the tools repository specifying the pipeline name and running from the `dev` branch. @@ -22,4 +22,4 @@ 3. Manually trigger the `Sync template` GitHub Action for all pipelines. 4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/) 5. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065) -6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:dev`. +6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`.