chore: use composite snakemake action [test] #345
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WalkthroughThe changes in this pull request involve updating the GitHub Actions workflow in Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant GitHub Actions
participant Snakemake
User->>GitHub Actions: Trigger workflow
GitHub Actions->>Snakemake: Execute tests with Conda
Snakemake-->>GitHub Actions: Return test results
GitHub Actions-->>User: Notify completion
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
.github/workflows/main.yml (2)
Line range hint
29-35: Consider updating Snakemake action version in Linting jobThe Linting job still uses
@v1while all other jobs have been updated to@use-conda-instead-of-docker. Consider updating this job for version consistency across the workflow.- uses: snakemake/snakemake-github-action@v1 + uses: snakemake/snakemake-github-action@use-conda-instead-of-docker🧰 Tools
🪛 actionlint (1.7.4)
48-48: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
🪛 yamllint (1.35.1)
[warning] 48-48: wrong indentation: expected 6 but found 4
(indentation)
Line range hint
132-193: Consider monitoring disk usage with Conda-based executionThe workflow includes disk space management steps, suggesting resource constraints. With the switch to Conda-based execution:
- The
--conda-cleanup-pkgs cacheflag is properly set to manage package cache- The
stageincleanup commands help manage disk space between stepsHowever, consider monitoring disk usage patterns with this new execution method to ensure it doesn't exceed GitHub Actions' limits.
🧰 Tools
🪛 actionlint (1.7.4)
129-129: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
.github/workflows/main.yml(6 hunks)
🔇 Additional comments (3)
.github/workflows/main.yml (3)
Line range hint 1-226: Overall changes look good with some verification points
The update to use the composite Snakemake action with Conda-based execution is consistently applied across the workflow. The changes maintain the existing functionality while potentially improving resource usage. The key points to verify have been highlighted in the previous comments.
🧰 Tools
🪛 actionlint (1.7.4)
48-48: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
🪛 yamllint (1.35.1)
[warning] 48-48: wrong indentation: expected 6 but found 4
(indentation)
Line range hint 221-226: Verify performance with Conda-based parallel execution
The Long_Tests job maintains parallel execution settings (--set-scatter calling=4). Please verify that the switch to Conda-based execution:
- Maintains similar performance characteristics for parallel execution
- Doesn't introduce additional overhead in the CI environment
🧰 Tools
🪛 actionlint (1.7.4)
218-218: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
51-102: Verify implications of switching from Docker to Conda-based execution
The change from @v1 to @use-conda-instead-of-docker shifts the execution environment from Docker to Conda. While this might improve performance and reduce overhead, please verify:
- If this aligns with the project's containerization strategy
- If reproducibility is maintained across different CI environments
- If all required dependencies are properly specified in the Conda environment files
✅ Verification successful
Let me gather more information about the project's dependency management and build configuration.
Let me check one more thing to understand the Snakemake workflow's dependency management.
Based on the analysis of the codebase, I can now provide a final response:
Switching from Docker to Conda is well-supported and safe
The change from Docker to Conda-based execution is well-aligned with the project's architecture:
- The workflow already supports both containerization methods, as evidenced by the Snakefile's container configuration:
container: "docker://continuumio/miniconda3" - The workflow uses Snakemake's built-in conda integration (
--use-condaflag) which ensures reproducibility through environment specifications - The change is consistent with the project's dependency management approach, as it maintains the same execution environment through Conda, which is the underlying technology even in the Docker setup
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for Conda environment files in the repository
echo "Checking for environment.yaml files:"
fd -e yaml -e yml . | grep -i "environment"
# Check if there are any Docker-related files that might need updates
echo -e "\nChecking for Docker-related files:"
fd "Dockerfile|docker-compose.yml"
Length of output: 248
Script:
#!/bin/bash
# Check for conda/mamba environment files in workflow directory
echo "=== Checking for environment files in workflow directory ==="
fd -t f . workflow/ -x cat {} | grep -B2 -A2 "conda\|mamba\|dependencies:"
# Check for any migration or update related discussions in recent commits
echo -e "\n=== Checking recent commit messages for context ==="
git log --grep="conda\|docker" --pretty=format:"%h %s" -n 5
# Look for snakemake configuration files
echo -e "\n=== Checking Snakemake configuration files ==="
fd "Snakefile|config.yaml" -x head -n 20 {}
Length of output: 781
Script:
#!/bin/bash
# Check for environment files in workflow/envs directory (common Snakemake pattern)
echo "=== Checking for environment files in workflow/envs ==="
fd . "workflow/envs" -x cat {}
# Check rules files for conda environment specifications
echo -e "\n=== Checking rules for conda environment specifications ==="
fd . "workflow/rules" -x grep -l "conda:" {} | xargs cat
# Check common.smk specifically
echo -e "\n=== Checking common.smk for container/conda configurations ==="
cat workflow/rules/common.smk
Length of output: 49718
Summary by CodeRabbit