fix: bump cadd script version to 1.6.1 (#16) #17
Conversation
WalkthroughThe changes in this pull request involve updates to the CI workflow and the Dockerfile related to the Changes
Sequence Diagram(s)sequenceDiagram
participant CI
participant Docker
CI->>Docker: Install cadd-scripts==1.6.1
Docker->>Docker: Set up environment
Docker->>Docker: Run application
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
utils/docker/Dockerfile (1)
61-61: LGTM! Version update is correctly implemented.The version update to 1.6.1 is consistent with the CI workflow and follows conda best practices.
Consider adding channel priority to ensure consistent package resolution:
- cadd-scripts==1.6.1 && \ + cadd-scripts==1.6.1 && \ + conda config --set channel_priority strict && \
stolpeo
force-pushed
the
16-bump-cadd-script-version-to-161
branch
from
81ddcc8 to
7f66f9c
Compare
stolpeo
force-pushed
the
16-bump-cadd-script-version-to-161
branch
from
7f66f9c to
f481982
Compare
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
utils/docker/Dockerfile (2)
56-61: Consider conda environment best practicesWhile the current setup works, consider these improvements for better maintainability:
- Use a conda environment file to lock dependencies
- Add conda environment name for better isolation
- Consider using environment activation in the ENTRYPOINT
RUN ["/bin/bash","-c", "cd /tmp && \ wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \ bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge3 && \ source /opt/miniforge3/bin/activate && \ + conda create -n cadd-env && \ + conda activate cadd-env && \ conda install -c conda-forge -c bioconda -y \ cadd-scripts==1.6.1 && \ rm -f Miniforge3-Linux-x86_64.sh"]Also, consider creating a
conda-env.ymlfile:name: cadd-env channels: - conda-forge - bioconda dependencies: - cadd-scripts=1.6.1
56-61: Consider layer optimization for reduced image sizeThe current RUN instruction creates a single layer but could be optimized:
- Download the installer to a specific version instead of latest
- Clean conda caches after installation
RUN ["/bin/bash","-c", "cd /tmp && \ - wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \ + wget https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Miniforge3-Linux-x86_64.sh && \ bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge3 && \ source /opt/miniforge3/bin/activate && \ conda install -c conda-forge -c bioconda -y \ cadd-scripts==1.6.1 && \ + conda clean -afy && \ rm -f Miniforge3-Linux-x86_64.sh"]
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
.github/workflows/ci.yml(1 hunks)utils/docker/Dockerfile(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- .github/workflows/ci.yml
🔇 Additional comments (2)
utils/docker/Dockerfile (2)
56-57: Verify Miniforge3 compatibility with the application stack
The switch from Mambaforge to Miniforge3 represents a change in the base conda distribution. While both are maintained by conda-forge, they have different default configurations.
✅ Verification successful
Miniforge3 switch is compatible with the application stack
The switch from Mambaforge to Miniforge3 is safe because:
- The codebase only uses basic conda commands (
conda install) without any mamba-specific features - The application's conda integration is minimal and version-agnostic, only using conda for:
- Basic package installation in Dockerfile
- CADD script execution through a configurable conda environment path (
CADD_CONDA)
- Both Mambaforge and Miniforge3 are conda-forge distributions that support the required channels (conda-forge, bioconda)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if there are any specific Mamba dependencies or configurations in the codebase
# that might be affected by the switch to Miniforge3
# Search for mamba-specific configurations or dependencies
rg -i 'mamba'
# Check if there are any conda environment files that might need updates
fd -e yml -e yaml | xargs grep -l 'conda'
Length of output: 55
Script:
#!/bin/bash
# Let's verify the conda/mamba setup more thoroughly
# Check Dockerfile history for conda/mamba related configurations
rg -i "conda|mamba|forge" utils/docker/Dockerfile
# Look for any environment setup files
fd "environment|requirements" -e yml -e yaml -e txt
# Check for any conda/mamba specific instructions in documentation
fd "README|INSTALL|SETUP" -e md | xargs rg -i "conda|mamba"
Length of output: 1297
59-60: Verify CADD version compatibility and changelog
The version change from 1.6.post1 to 1.6.1 appears to be a downgrade from a post-release version to a stable version. This could have potential implications on functionality.
✅ Verification successful
Version change from 1.6.post1 to 1.6.1 is safe to proceed
The version change appears to be a minor version format adjustment rather than a downgrade. In semantic versioning, both formats represent the same version, where:
- 1.6.1 is the standard format
- 1.6.post1 is a PEP 440 post-release format
The codebase shows no version-specific dependencies or configurations that would be impacted by this change. The CADD integration is primarily through shell script execution and the version is only used during package installation.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for any version-specific dependencies or configurations
# Search for CADD version references in the codebase
rg -i 'cadd.*1\.6\.'
# Look for any configuration files that might reference CADD versions
fd -e json -e yaml -e yml -e config | xargs grep -l 'cadd'
Length of output: 142
Script:
#!/bin/bash
# Let's check for any CADD-related configurations or dependencies more broadly
rg -i 'cadd' -A 3 -B 3
# Also check for any documentation or README files that might mention CADD version requirements
fd -e md | xargs rg -i 'cadd'
Length of output: 27450
Script:
#!/bin/bash
# Let's check the changelog or release notes of CADD-scripts package
rg -i "changelog|release.*notes|version.*history" -g "!node_modules"
# Check for any version-specific configurations or requirements
rg -i "cadd.*version|version.*requirement" -g "!node_modules"
# Look for any version constraints in package requirements
fd -e txt -e ini -e cfg -e yaml -e yml | xargs rg "cadd-scripts"
Length of output: 714
Summary by CodeRabbit
cadd-scriptspackage version to1.6.1in the CI workflow and Dockerfile to ensure consistent dependency resolution.