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Local devcontainers enablement #539

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Local devcontainers enablement #539

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aa6dbdd
Local devcontainers enablement
pinin4fjords Mar 5, 2025
db07194
Don't symlink
pinin4fjords Mar 5, 2025
dcc3367
Fix postcreate
pinin4fjords Mar 5, 2025
d4fe3e3
Add missing comma
pinin4fjords Mar 5, 2025
21d5d6f
Remove unnecessary line
pinin4fjords Mar 5, 2025
7ce3608
Remove unnecessary line
pinin4fjords Mar 5, 2025
267622a
Remove unnecessary line
pinin4fjords Mar 5, 2025
595168b
Remove superfluous comments
ewels Mar 5, 2025
a29a5e4
Remove defunct svg viewer extension
ewels Mar 5, 2025
56e300c
Cross-arch fixes for local devcontainer (e.g. Mac)
pinin4fjords Mar 6, 2025
1f79ad7
Docs updates
pinin4fjords Mar 6, 2025
5a07633
Prettier
pinin4fjords Mar 6, 2025
7ff6464
Prettier
pinin4fjords Mar 6, 2025
3488dc4
Add to mkdocs
pinin4fjords Mar 6, 2025
cb6169f
Prettier
pinin4fjords Mar 6, 2025
957ab43
Fix img link
pinin4fjords Mar 6, 2025
460de86
Formatting fixes
pinin4fjords Mar 6, 2025
f3e3bd4
Prettier
pinin4fjords Mar 6, 2025
8d69d56
Change title
pinin4fjords Mar 6, 2025
30fcf73
Merge branch 'master' into local_devcontainer
pinin4fjords Mar 7, 2025
e33405d
Remove VSCode extensions that are part of the nf-core extension pack
ewels Mar 8, 2025
80f656a
Fix pre commit
ewels Mar 8, 2025
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35 changes: 35 additions & 0 deletions .devcontainer/codespaces/devcontainer.json
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Original file line number Diff line number Diff line change
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{
"name": "nextflow-training (codespaces)",

// Update this to pin the release tag before release
"image": "ghcr.io/nextflow-io/training:latest",
// Uncomment this and comment "image" when testing Dockerfile changes
// "build": { "dockerfile": "../Dockerfile", "context": ".." },

"features": {
"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {
"version": "latest"
}
},
"workspaceFolder": "/workspaces/training",
"remoteEnv": {
"NXF_HOME": "/workspaces/.nextflow",
"HOST_PROJECT_PATH": "/workspaces/training"
},
"customizations": {
"vscode": {
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},
"extensions": [
"ms-python.python",
"ms-python.vscode-pylance",
"nf-core.nf-core-extensionpack", // nf-core recommended extensions
"nextflow.nextflow", // Nextflow VS Code extension
"codezombiech.gitignore", // Language support for .gitignore files
"cssho.vscode-svgviewer" // SVG viewer
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I think we can simplify these - nextflow.nextflow shouldn't be needed as it's already part of the nf-core extension pack, and the other two could be added to that. Then we just have the nf-core extension pack and be done with it.

I'd also like to remove a couple of the more subjective packages from the nf-core extension pack (rainbow indentation, TODO tree, code spell checker). I find myself disabling these each time in devcontainers, which is annoying.

We can do this in a separate PR, as needs upstream changes to the nf-core extension pack first.

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nf-core/vscode-extensionpack#25

]
}
},
"remoteUser": "root"
}
41 changes: 0 additions & 41 deletions .devcontainer/devcontainer.json
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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Original file line number Diff line number Diff line change
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./codespaces/devcontainer.json
39 changes: 39 additions & 0 deletions .devcontainer/local/devcontainer.json
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Original file line number Diff line number Diff line change
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{
"name": "nextflow-training (local)",

// Update this to pin the release tag before release
"image": "ghcr.io/nextflow-io/training:latest",
// Uncomment this and comment "image" when testing Dockerfile changes
// "build": { "dockerfile": "../Dockerfile", "context": ".." },

"features": {
"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {
"version": "latest"
}
},
"workspaceFolder": "${localWorkspaceFolder}",
"workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
"remoteEnv": {
"NXF_HOME": "/workspaces/training/.nextflow",
"HOST_PROJECT_PATH": "/workspaces/training"
},
"postCreateCommand": "sudo mkdir -p /workspaces && sudo rm -rf /workspaces/training && sudo ln -s ${localWorkspaceFolder} /workspaces/training",
"customizations": {
"vscode": {
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"terminal.integrated.cwd": "/workspaces/training",
"terminal.integrated.defaultLocation": "workspace"
},
"extensions": [
"ms-python.python",
"ms-python.vscode-pylance",
"nf-core.nf-core-extensionpack", // nf-core recommended extensions
"nextflow.nextflow", // Nextflow VS Code extension
"codezombiech.gitignore", // Language support for .gitignore files
"cssho.vscode-svgviewer" // SVG viewer
]
}
},
"remoteUser": "root"
}