Add Python 3.13 to devcontainer to support latest nf-core tools - #683
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Adds the official Python devcontainer feature (version 3.13) to both codespaces-dev and local-dev configurations. This ensures that when uv installs nf-core tools, it uses Python 3.13 and can install the latest version of nf-core that requires this Python version. Previously, uv was falling back to Ubuntu 22.04's system Python 3.10, which meant it could only install older versions of nf-core that were compatible with Python 3.10. Also updates the uv-tools feature to declare it installs after the Python feature, ensuring proper installation order. This change aligns with the native installation philosophy introduced in PR #609, using native Python installation rather than conda for dev container tooling, while keeping conda available for pipeline execution within training materials. Related to #609 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Note: build logs now show correct version of nf-core tools, so I'm pretty sure this has worked |
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Thanks @kenibrewer ! |
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PR #683 enabled automatic installation of the latest nf-core version by adding Python 3.13 support. While this approach ensures access to new features, pinning to a specific version provides consistency for training environments where reproducible behavior is important. Related to #683 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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pinin4fjords
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* Pin nf-core to 3.4.1 for training stability PR #683 enabled automatic installation of the latest nf-core version by adding Python 3.13 support. While this approach ensures access to new features, pinning to a specific version provides consistency for training environments where reproducible behavior is important. Related to #683 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> * Fix check-headings workflow to run on all PRs The workflow was only triggered when markdown files changed, causing it to be skipped entirely for non-markdown PRs. Since check-headings is a required status check, this blocked PRs that didn't touch markdown. Now the workflow runs on all PRs but conditionally skips the actual check when no markdown files have changed. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> --------- Co-authored-by: Claude <noreply@anthropic.com>
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Problem
The devcontainer configuration was unable to install the latest version of nf-core tools. When
uv tool install nf-coreran, it was using Ubuntu 22.04's system Python 3.10 to create the isolated environment, which limited it to installing only versions of nf-core compatible with Python 3.10. If the latest nf-core requires Python 3.13, an older version would be installed instead.Solution
This PR adds the official
ghcr.io/devcontainers/features/python:1feature with version 3.13 to both thecodespaces-devandlocal-devdevcontainer configurations. By installing Python 3.13 early in the feature installation order (beforeuv), we ensure that whenuv tool install nf-coreruns, it will:Changes
Design Rationale
This approach aligns with the native installation philosophy introduced in #609:
uvautomatically gets the latest compatible nf-core versionTesting
The changes should be tested by:
python --version(should show 3.13.x)nf-core --version(should show latest version)/root/.local/share/uv/tools/nf-core/bin/python --versionRelated to #609