Update decom recipe to version 0.0.32 and align dependencies #51723
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/decom/meta.yaml (1)
10-11: Remove redundant SHA256 commentThe comment "Update this if necessary" is redundant since SHA256 checksums must always match the source package exactly. Consider removing this comment to avoid confusion.
- sha256: c9efaa97b7abfe6f19f01a199ca6c7a7b32ec699f886d226667b8b5fe562dd88 # Update this if necessary + sha256: c9efaa97b7abfe6f19f01a199ca6c7a7b32ec699f886d226667b8b5fe562dd88
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- recipes/decom/meta.yaml (3 hunks)
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🪛 yamllint
recipes/decom/meta.yaml
[error] 63-63: trailing spaces
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[error] 64-64: trailing spaces
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🔇 Additional comments (5)
recipes/decom/meta.yaml (5)
5-6: LGTM: Package naming follows best practicesThe change to lowercase package naming using Jinja templating aligns with Python packaging conventions.
Line range hint
13-22: LGTM: Build configuration is correctThe build number increment is appropriate for the dependency updates, and entry points are properly configured.
40-48: LGTM: Comprehensive test configurationThe test configuration is thorough, covering all major modules and command-line interfaces.
61-64:⚠️ Potential issueAdd missing metadata fields
Several important metadata fields are empty:
license_fileshould point to the LICENSE file in the packagedoc_urlanddev_urlshould be populated to improve package discoverabilityThe previous values were:
- doc_url: "https://github.com/CamilaDuitama/decOM"
- dev_url: "https://camiladuitama.github.io/gradfolio/"
Please verify if these URLs are still valid and restore them if appropriate.
✅ Verification successful
Add LICENSE file path and restore documentation URLs
The verification shows:
- A LICENSE file exists at the repository root that can be referenced
- Both documentation URLs are still valid and accessible:
Please update the metadata fields:
license_file: LICENSE doc_url: https://github.com/CamilaDuitama/decOM dev_url: https://camiladuitama.github.io/gradfolio/🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if LICENSE file exists in the package fd -t f -i "license" # Verify if the documentation URLs are still valid curl -I https://github.com/CamilaDuitama/decOM curl -I https://camiladuitama.github.io/gradfolio/Length of output: 14238
🧰 Tools
🪛 yamllint
[error] 63-63: trailing spaces
(trailing-spaces)
[error] 64-64: trailing spaces
(trailing-spaces)
27-36: Consider more flexible version constraintsThe current version constraints might be overly restrictive:
- Limiting Python to 3.12 only might unnecessarily exclude compatible Python versions
- Very tight version constraints (e.g., pandas >=2.2.3,<2.3) could cause dependency resolution issues
Consider:
- Supporting a broader Python range (e.g., >=3.9)
- Using more flexible version constraints unless there are known compatibility issues
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/decom/meta.yaml (2)
68-69: Consider adding documentation and development URLs.The
doc_urlanddev_urlfields are empty. Consider adding:
doc_urlpointing to the GitHub repository (since it contains documentation)dev_urlpointing to the GitHub repository for development references- doc_url: - dev_url: + doc_url: https://github.com/CamilaDuitama/decOM + dev_url: https://github.com/CamilaDuitama/decOM🧰 Tools
🪛 yamllint
[error] 68-68: trailing spaces
(trailing-spaces)
[error] 69-69: trailing spaces
(trailing-spaces)
65-67: Fix trailing spaces in description.Remove trailing spaces from the description field to resolve yamllint warnings.
- decOM is a similarity-based microbial source tracking tool for - contamination assessment of ancient oral samples using k-mer-based methods. + decOM is a similarity-based microbial source tracking tool for + contamination assessment of ancient oral samples using k-mer-based methods.🧰 Tools
🪛 yamllint
[error] 66-66: trailing spaces
(trailing-spaces)
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- recipes/decom/meta.yaml (3 hunks)
🧰 Additional context used
🪛 yamllint
recipes/decom/meta.yaml
[error] 66-66: trailing spaces
(trailing-spaces)
[error] 68-68: trailing spaces
(trailing-spaces)
[error] 69-69: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/decom/meta.yaml (4)
5-5: LGTM: Package naming follows Conda best practices.The change to lowercase package name using Jinja template is correct and follows Conda packaging conventions.
42-50: LGTM: Comprehensive test imports.The test imports cover all major submodules, providing good coverage for package integrity verification.
29-38:⚠️ Potential issueEnsure consistent dependency version constraints.
A few observations about the dependency specifications:
- The Python requirement (>=3.12,<3.13) is very restrictive. Consider if this is intentional as it limits the package to only Python 3.12.
- Some dependencies have upper bounds (numpy, pandas, plotly) while others (dask, importlib_resources) don't. Consider adding upper bounds for consistency.
Let's verify if other packages support this Python version:
#!/bin/bash # Check Python version constraints in dependencies echo "Checking dask Python requirements:" rg -A 2 'name: "dask"' . | rg 'python' echo "Checking pandas Python requirements:" rg -A 2 'name: "pandas"' . | rg 'python'
23-24: 🛠️ Refactor suggestionConsider relaxing the version pinning strategy.
The current
max_pin='x.x.x'is very restrictive, requiring an exact version match. For a package at version 0.0.32 (pre-1.0), consider using a more relaxed pinning strategy likemax_pin='x.x'to allow patch-level updates, unless there are specific ABI compatibility concerns.
recipes/decom/meta.yaml
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| summary: "decOM: Similarity-based microbial source tracking for contamination assessment of ancient oral samples using k-mer-based methods" | ||
| doc_url: "https://github.com/CamilaDuitama/decOM" | ||
| dev_url: "https://camiladuitama.github.io/gradfolio/" | ||
| license_file: |
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Add the license file specification.
The license_file field is empty but the package is MIT licensed. This field should point to the LICENSE file in the source distribution.
Please add:
- license_file:
+ license_file: LICENSE📝 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.
| license_file: | |
| license_file: LICENSE |
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@bgruening, thank you for pointing that out. Please ensure that the LICENSE file is included in the source distribution and update the license_file field in meta.yaml accordingly.
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The PyPI distribution includes the LICENSE file. I added a pointer to the meta.yaml file; I hope this fixes the issue.
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Seems like the humans are having a chat. I'll hop back into my burrow for now. If you need me again, just tag @coderabbitai in a new comment, and I'll come hopping out!
recipes/decom/meta.yaml
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| - pandas | ||
| - plotly >=5.5.0 | ||
| - python | ||
| - python >=3.12,<3.13 |
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Why are so strict pinning needed?
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I removed the strict pinning
CamilaDuitama
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CamilaDuitama
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/decom/meta.yaml (1)
69-70: Consider separating documentation and development URLs
Both doc_url and dev_url point to the same GitHub repository. Consider:
- Creating dedicated documentation (e.g., using GitHub Pages, ReadTheDocs)
- Using the documentation URL for
doc_urland keeping the GitHub repository fordev_url
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🔇 Additional comments (4)
recipes/decom/meta.yaml (4)
Line range hint 13-24: LGTM: Build configuration follows best practices
The build configuration is well structured with:
- Appropriate build number increment
- Correct entry points configuration
- Good pinning strategy in run_exports
44-52: LGTM: Comprehensive test coverage
The test section provides good coverage by:
- Testing imports of all main modules
- Including command-line interface tests
29-40: Consider relaxing version constraints
The current version constraints might be overly restrictive:
- Python 3.12-3.14 is a very narrow range and 3.12 is quite recent
- Dependencies like numpy, pandas, and dask are pinned to very recent versions
This could limit the package's compatibility with other tools in the bioconda ecosystem. Consider:
- Supporting Python 3.8+ unless there's a specific need for 3.12 features
- Relaxing dependency version upper bounds unless there are known compatibility issues
#!/bin/bash
# Check other bioconda packages' Python compatibility
rg "python.*3\.12" | grep "run:"9-11: Verify the SHA256 checksum for version 0.0.32
Please verify that the SHA256 checksum matches the source tarball for version 0.0.32.
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...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
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