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feat: add devcontainer #19

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feat: add devcontainer #19

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dd3d919
feat: add devcontainer
johanneskoester Jul 8, 2025
cb7fde9
fix activation
johanneskoester Jul 8, 2025
3049d69
use script
johanneskoester Jul 8, 2025
ebcfcb2
Update .devcontainer/setup.bash
johanneskoester Jul 8, 2025
8f1b13e
Update .devcontainer/setup.bash
johanneskoester Jul 8, 2025
ae2391e
fix
johanneskoester Jul 9, 2025
d6f7fb0
Merge branch 'feat/devcontainer' of github.com:snakemake/snakemake-tu…
johanneskoester Jul 9, 2025
aabac05
fix
johanneskoester Jul 9, 2025
bf5e6d5
fix
johanneskoester Jul 9, 2025
11fd8c8
Update devcontainer.json
johanneskoester Jul 9, 2025
e9928f6
Update setup.bash
johanneskoester Jul 9, 2025
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9 changes: 9 additions & 0 deletions .devcontainer/devcontainer.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
// For format details, see https://aka.ms/devcontainer.json.
{
"name": "Snakemake-Tutorial",
"build": {
"context": "..",
"dockerfile": "../Dockerfile"
},
"postCreateCommand": "bash .devcontainer/setup.bash"
}
14 changes: 14 additions & 0 deletions .devcontainer/setup.bash
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/usr/bin/env bash
# abort on error, undefined vars, and failed pipelines
set -euo pipefail

rm -f Dockerfile .gitpod.yml && rm -rf .github .devcontainer
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⚠️ Potential issue

Don’t rm -rf the directory you are executing from

rm -rf .devcontainer deletes the folder that contains this very script while it is still running.
Although the inode stays open, this is brittle and may break future re-runs or tooling that expects .devcontainer to exist after setup. Remove only the obsolete sub-artifacts instead.

-rm -f Dockerfile .gitpod.yml && rm -rf .github .devcontainer
+rm -f Dockerfile .gitpod.yml && rm -rf .github
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
rm -f Dockerfile .gitpod.yml && rm -rf .github .devcontainer
rm -f Dockerfile .gitpod.yml && rm -rf .github
🤖 Prompt for AI Agents 
In .devcontainer/setup.bash at line 5, avoid removing the entire .devcontainer
directory since it contains the running script. Instead of `rm -rf
.devcontainer`, modify the command to only delete obsolete sub-artifacts inside
.devcontainer, preserving the directory itself to prevent breaking future runs
or tooling that relies on its existence.

echo -e "# Snakemake-Tutorial\n\nYour gitpod workspace for the snakemake-tutorial has been initialized. Now you can start with the [basic tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/basics.html)." > README.md
echo "*" > .gitignore
Comment on lines +6 to +7
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⚠️ Potential issue

Overwrites & then hides almost everything
README.md is overwritten unconditionally and the subsequent
echo "*" ignores all new files—including the freshly written README.md—so the user ends up with a repository that only tracks .gitignore itself.

Consider either:

  1. Guarding creation ([ -e README.md ] || …) and using a narrower ignore pattern, or
  2. Adding explicit negations for the few files you do want under version control.

Example:

-echo "*" > .gitignore
+cat > .gitignore <<'EOF'
+*
+!*.md
+!.devcontainer/**
+EOF
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
echo -e "# Snakemake-Tutorial\n\nYour gitpod workspace for the snakemake-tutorial has been initialized. Now you can start with the [basic tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/basics.html)." > README.md
echo "*" > .gitignore
echo -e "# Snakemake-Tutorial\n\nYour gitpod workspace for the snakemake-tutorial has been initialized. Now you can start with the [basic tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/basics.html)." > README.md
cat > .gitignore <<'EOF'
*
!*.md
!.devcontainer/**
EOF
🤖 Prompt for AI Agents 
In .devcontainer/setup.bash at lines 6-7, the script overwrites README.md
unconditionally and then writes "*" to .gitignore, which causes all files
including README.md to be ignored. To fix this, modify the script to check if
README.md exists before creating it, and update .gitignore to use a narrower
pattern or add explicit negations to ensure README.md and other important files
are not ignored.

conda init
set +u
source ~/.bashrc
set -u

echo 'conda activate snakemake-tutorial' >> ~/.bashrc
echo "Setup done"