fix: remove paramiko dependency as issue has been fixed#3110
fix: remove paramiko dependency as issue has been fixed#3110johanneskoester merged 4 commits intosnakemake:mainfrom
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WalkthroughThe Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant System
User->>System: Request to update dependencies
System->>System: Comment out paramiko dependency
System->>System: Correct indentation for nodejs
System->>System: Add snakemake plugins to pip section
System-->>User: Dependencies updated successfully
User->>System: Request to run workflow
System->>System: Execute testing job
System->>System: Build Docker container image
System-->>User: Workflow completed successfully
Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
.github/workflows/main.yml (3)
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144-151: LGTM! Consider enhancing the container build process.The addition of the
build-container-imagejob is a good step towards ensuring the Docker image builds successfully after changes. This aligns well with the PR objectives.Consider enhancing this job to push the built image to a container registry if that's part of your CI/CD pipeline. If not needed, you might want to add a comment explaining why only building is necessary.
Example enhancement:
- name: Build and push container image env: REGISTRY: your-registry-here IMAGE_NAME: ${{ github.repository }} run: | docker build -t $REGISTRY/$IMAGE_NAME:${{ github.sha }} . echo ${{ secrets.REGISTRY_PASSWORD }} | docker login $REGISTRY -u ${{ secrets.REGISTRY_USERNAME }} --password-stdin docker push $REGISTRY/$IMAGE_NAME:${{ github.sha }}
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154-159: LGTM! Consider pinning the miniforge version.The correction of the typo in the step name from "snakemke" to "snakemake" improves readability and consistency. Good catch!
Consider pinning the
miniforge-versionto a specific version instead of usinglatest. This can help ensure reproducibility and prevent unexpected issues from future updates. For example:- name: Setup snakemake environment uses: conda-incubator/setup-miniconda@v3 with: miniforge-version: 4.12.0-2 environment-file: test-environment.yml environment-name: snakemakeYou can periodically update this version as part of your maintenance process.
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161-164: LGTM! Consider usingpip install -e .for consistency.The simplification of the installation step improves cross-platform compatibility, especially for Windows. Good job on removing the bash-specific shell directive.
For consistency with the installation step in the
testingjob, consider usingpip install -e .instead ofpip install .. The-eflag installs the package in editable mode, which can be beneficial for testing. For example:- name: Install snakemake from source run: | pip install -e .This ensures that both Windows and non-Windows environments use the same installation method.
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🔇 Additional comments (1)
.github/workflows/main.yml (1)
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1-164: Overall, the changes align well with the PR objectives.The modifications to the GitHub Actions workflow file contribute to removing the Paramiko dependency and improving cross-platform compatibility. Key improvements include:
- Adding a new job to build the container image.
- Enhancing the Windows testing job for better cross-platform support.
- Simplifying the Snakemake installation process.
These changes should help in achieving the goal of removing the Paramiko dependency while ensuring the CI/CD pipeline remains robust across different platforms.
To ensure that the Paramiko dependency has been completely removed, you can run the following script:
This script will help verify that the Paramiko dependency has been completely removed from the project.
🤖 I have created a release *beep* *boop* --- ## [8.22.0](v8.21.0...v8.22.0) (2024-10-13) ### Features * switch from toposort to graphlib ([#3109](#3109)) ([91e875d](91e875d)) ### Bug Fixes * configfile `group` and `group-components` were not being registered ([#3135](#3135)) ([4397c7d](4397c7d)) * remove paramiko dependency as issue has been fixed ([#3110](#3110)) ([1b43250](1b43250)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).Summary by CodeRabbit
paramikodependency as a temporary workaround.nodejsdependency.pipsection to include new plugins forsnakemakewith specific version requirements.peppydependency.