Update Commec #52177
Update Commec #52177
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces modifications to the Possibly related PRs
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🔇 Additional comments (7)recipes/commec/meta.yaml (7)
The change to
As noted in the previous review, consider using a more flexible Python version constraint unless specific Python 3.12 features are required. Line range hint Since this is a version update (0.1.2 → 0.2.0), please verify if there are any new features or commands that should be included in the test section. #!/bin/bash
# Description: Check for new commands in the help output
# Download and extract the new version
curl -sL https://github.com/ibbis-screening/common-mechanism/archive/refs/tags/v0.2.0.tar.gz | tar xz
# Search for potential new commands in the source
cd common-mechanism-0.2.0
rg -i "def.*command|@click\.command"
The diamond requirement has been updated to >=2.1. Let's verify this version is available. #!/bin/bash
# Description: Check if diamond >=2.1 is available in conda-forge/bioconda
echo "=== Available versions for diamond ==="
conda search -c conda-forge -c bioconda diamond
The version constraints have been removed from biopython, numpy, pandas, and pytaxonkit. Please ensure this doesn't lead to compatibility issues. #!/bin/bash
# Description: Check for potential compatibility issues with the dependencies
# Check available versions in conda-forge/bioconda
for pkg in biopython numpy pandas pytaxonkit; do
echo "=== Available versions for $pkg ==="
conda search -c conda-forge -c bioconda $pkg
done
A new wget dependency has been added. Please confirm if this is required for the new version's functionality.
The version bump from 0.1.2 to 0.2.0 indicates potential breaking changes. Let's verify the checksum matches the source. 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:
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/commec/meta.yaml (1)
10-12: Remove commented local pathConsider removing the commented local path as it's not needed in the production recipe.
- #path: /root/TestingCommec/common-mechanism-0.2.0/common-mechanism-0.2.0 url: https://github.com/ibbis-screening/common-mechanism/archive/refs/tags/v{{version}}.tar.gz sha256: {{ sha256 }}
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🔇 Additional comments (4)
recipes/commec/meta.yaml (4)
2-3: LGTM: Version and checksum updates are consistent
The version bump to 0.2.0 and corresponding SHA256 checksum update are properly configured.
18-18: LGTM: Stricter version pinning improves stability
The change to max_pin="x.x.x" provides tighter version control, which helps prevent API/ABI breakage in downstream dependencies.
34-34: LGTM: Diamond version requirement is appropriate
The increased minimum version requirement for Diamond (>=2.1) is well-specified and maintains compatibility while ensuring access to newer features.
26-29: Verify dependency compatibility with removed version constraints
Several dependencies have had their version constraints removed. This could potentially lead to compatibility issues if older versions are installed. Please verify:
- The minimum working versions for critical dependencies
- Any known incompatibilities with older versions
Also applies to: 31-40
recipes/commec/meta.yaml
Outdated
| - python=3.12 | ||
| - pip |
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Consider using a more flexible Python version constraint
The strict Python 3.12 requirement might be unnecessarily restrictive. Consider using a range (e.g., python >=3.8) unless there are specific 3.12 features needed.
- - python=3.12
+ - python >=3.8📝 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.
| - python=3.12 | |
| - pip | |
| - python >=3.8 | |
| - pip |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/commec/meta.yaml (2)
10-10: Remove development artifactThe commented path appears to be a local development path that should be removed to maintain clean recipe code.
- #path: /root/TestingCommec/common-mechanism-0.2.0/common-mechanism-0.2.0
Line range hint
43-47: Consider expanding test coverageWith the update to version 0.2.0 and significant dependency changes, consider adding more comprehensive tests to verify the functionality with the new dependency versions. The current test commands only verify the CLI help messages.
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🔇 Additional comments (3)
recipes/commec/meta.yaml (3)
23-24: Python version constraint is too restrictive
27-41: Verify dependency version constraints removal
Several dependencies have had their version constraints removed, which could potentially lead to compatibility issues. Please verify:
- Why were the version constraints removed from biopython, numpy, pandas, etc.?
- Is there a specific reason for keeping version constraints only on blast (>=2.16) and diamond (>=2.1)?
- What is the rationale for adding wget as a new dependency?
19-19: Consider if strict version pinning is necessary
The change from x.x to x.x.x implements stricter version pinning. While this can prevent compatibility issues, it might be overly restrictive for a Python package. Consider if this level of strictness is required based on the package's API stability.
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@BiocondaBot please add label |
Update for Commec, The Common Mechanism, recipe 0.2.0.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
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