Update meta.yaml, VITAP v.1.7 #51220
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🧹 Outside diff range and nitpick comments (1)
recipes/vitap/meta.yaml (1)
49-49: Remove trailing spacesThe static analysis tool (yamllint) has reported trailing spaces on this line. While this doesn't affect functionality, it's good practice to remove them for consistency and cleanliness of the code.
Please remove the trailing spaces from this line.
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🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
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- recipes/vitap/meta.yaml (3 hunks)
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🪛 yamllint
recipes/vitap/meta.yaml
[error] 49-49: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/vitap/meta.yaml (4)
2-2: LGTM: Version updateThe version has been correctly updated from "1.5" to "1.7" as per the PR objectives.
48-49: LGTM: Description updateThe description has been slightly modified to use "taxonomic assignments" instead of "classification". This change maintains the overall meaning while potentially improving clarity. The addition of a period at the end of the description is a minor improvement in punctuation.
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
34-34: Verify dependency change from prodigal-gv to prodigalThe dependency has been changed from
prodigal-gv >=2.6toprodigal >=2.6. Please confirm that this change is intentional and thatprodigalprovides the same functionality asprodigal-gvfor VITAP.To verify the impact of this change, you can run the following script to check for any references to
prodigal-gvin the VITAP source code:#!/bin/bash # Description: Check for references to prodigal-gv in the VITAP source code # Search for prodigal-gv in Python files echo "Searching for 'prodigal-gv' references:" rg --type python 'prodigal-gv' echo "Searching for 'prodigal' references:" rg --type python '\bprodigal\b' # Check if there are any configuration files that might reference prodigal-gv echo "Checking configuration files:" rg --type yaml 'prodigal-gv' rg --type json 'prodigal-gv'If there are any references to
prodigal-gvin the source code, they may need to be updated toprodigal.
10-10: Verify SHA256 checksumThe SHA256 checksum has been updated for the new version. Please ensure that this checksum is correct for the v.1.7 tarball.
To verify the SHA256 checksum, you can run the following script:
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🧹 Outside diff range and nitpick comments (1)
recipes/vitap/meta.yaml (1)
50-50: Remove trailing spaces.There are trailing spaces at the end of line 50. While this doesn't affect functionality, it's good practice to remove them for consistency and to avoid potential issues in some systems.
Please apply the following change:
- +🧰 Tools
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[error] 50-50: trailing spaces
(trailing-spaces)
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- recipes/vitap/meta.yaml (3 hunks)
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🪛 yamllint
recipes/vitap/meta.yaml
[error] 50-50: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/vitap/meta.yaml (4)
2-2: LGTM: Version update is correct.The version has been successfully updated from "1.5" to "1.7", which aligns with the PR objectives.
49-49: LGTM: Description update is appropriate.The change from "classification" to "taxonomic assignments" in the description is a suitable refinement that better reflects the tool's functionality. The overall meaning remains consistent with the previous version.
35-35: Verify the dependency change from prodigal-gv to prodigal.The dependency has been changed from
prodigal-gv >=2.6toprodigal >=2.6. Please confirm that this change is intentional and that VITAP is compatible with the main prodigal package instead of the specific prodigal-gv variant.To verify the compatibility and availability of the prodigal package, you can run the following script:
#!/bin/bash # Description: Verify the availability and version of prodigal package # Check if prodigal is available in the bioconda channel conda search prodigal --channel bioconda # Check if prodigal-gv is still available (for comparison) conda search prodigal-gv --channel bioconda # Check the latest version of VITAP for any mentions of prodigal rg 'prodigal' --type yaml
10-10: Verify the SHA256 checksum.The SHA256 checksum has been updated for the new version. Please ensure that this checksum is correct for the v.1.7 tarball.
To verify the SHA256 checksum, you can run the following script:
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Could somebody help me review this pull? Thanks. |
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@tomkinsc Could you help to review this pull as one of the members of Bioconda? Many thanks. |
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🧹 Outside diff range and nitpick comments (1)
recipes/vitap/meta.yaml (1)
50-50: Minor: Remove trailing spaces.The static analysis tool detected trailing spaces on this line. While this is a minor issue, it's good practice to remove them for consistency.
You can remove the trailing spaces to resolve this minor formatting issue.
🧰 Tools
🪛 yamllint
[error] 50-50: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/vitap/meta.yaml (3 hunks)
🧰 Additional context used
🪛 yamllint
recipes/vitap/meta.yaml
[error] 50-50: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/vitap/meta.yaml (4)
13-13: Build number increment is correct.The build number has been properly incremented from 0 to 1, which is the correct practice when updating the package version.
49-49: Description update looks good.The change from "classification" to "taxonomic assignments" in the description maintains the overall meaning while potentially improving clarity. This update aligns well with the tool's purpose.
Line range hint
1-11: LGTM! Version and source updates look good.The version has been correctly updated to 1.7, and the source URL has been adjusted accordingly. The SHA256 checksum has been updated, which is necessary for the new version.
To ensure the integrity of the package, please verify the SHA256 checksum using the following script:
#!/bin/bash # Description: Verify the SHA256 checksum of the source tarball # Download the tarball curl -L https://github.com/DrKaiyangZheng/VITAP/archive/refs/tags/v.1.7.tar.gz -o vitap-1.7.tar.gz # Calculate and display the SHA256 checksum echo "Calculated SHA256:" sha256sum vitap-1.7.tar.gz echo "Expected SHA256:" echo "9b33447b2ca4f459ba856dbeb4947bee6b8dab9b158a9d0a3c8b863f66c086d5" # Clean up rm vitap-1.7.tar.gz
35-35: Dependency update and indentation corrections.The indentation for the
diamondandentrez-directdependencies has been corrected, which improves the YAML file structure. However, the change fromprodigal-gvtoprodigalrequires clarification.Could you please clarify the reason for changing from
prodigal-gvtoprodigal? Is this a package name update, or a switch to a different package? If it's a different package, please ensure that it provides the same functionality required by VITAP.To verify the availability and version of the
prodigalpackage, you can run the following command:
Update VITAP v.1.5 to v.1.7