add recipe for steamboat #51612
add recipe for steamboat #51612
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/steamboat/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/steamboat/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/steamboat/meta.yaml (6)
1-6: LGTM! Package metadata is well-structured.The package name and version are properly templated using Jinja2 variables, following Conda recipe best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: LGTM! Build configuration properly handles dependency pinning.The build configuration correctly specifies:
- Platform independence with
noarch: python- Proper dependency version pinning using
run_exports
41-45: LGTM! Package metadata is complete.The about section includes all required information: homepage, summary, license, and license file reference.
47-49: LGTM! Maintainer information is properly specified.The recipe maintainer is correctly set to the PR author.
8-10: Verify package name consistency between PyPI and Conda.The source URL uses
steamboat-binfwhile the package name issteamboat. Please verify this is intentional and won't cause issues.✅ Verification successful
Let me gather more information to verify this thoroughly.
The previous curl command showed that 'steamboat' exists on PyPI, but we need to verify the 'steamboat-binf' package and understand the full recipe configuration to make a proper assessment.
Let me verify the steamboat-binf package on PyPI before making the final assessment.
Package naming discrepancy is intentional and correct
The package naming is correct and intentional. Here's why:
- The PyPI package exists as
steamboat-binf- The conda package is named
steamboat- The source URL correctly points to the PyPI package
steamboat-binf- Both packages are maintained by the same author (rpetit3) and share the same description
This is a common practice where the conda package name is simplified while still sourcing from the original PyPI package. The configuration in meta.yaml is properly set up to handle this naming difference.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package name on PyPI # Expected: Package should exist on PyPI with the name steamboat-binf # Check if the package exists on PyPI with this name curl -s "https://pypi.org/pypi/steamboat-binf/json" | jq -r '.info.name' # Also check if there's a separate steamboat package to avoid conflicts curl -s "https://pypi.org/pypi/steamboat/json" | jq -r '.info.name'Length of output: 457
Script:
#!/bin/bash # Let's check the actual meta.yaml to understand the full package configuration cat recipes/steamboat/meta.yaml # Also check if there are any other related files in the recipe directory ls -la recipes/steamboat/ # Let's also verify the package name in setup.py or pyproject.toml if they exist fd -e py -e toml "setup|pyproject" recipes/steamboat/Length of output: 1323
Script:
#!/bin/bash # Check if steamboat-binf exists on PyPI curl -s "https://pypi.org/pypi/steamboat-binf/json" | jq -r '.info.name' # Let's also check if steamboat_binf exists (with underscore) curl -s "https://pypi.org/pypi/steamboat_binf/json" | jq -r '.info.name' # Check the GitHub repository for any clues about the package naming curl -s "https://api.github.com/repos/rpetit3/steamboat-py" | jq -r '.description'Length of output: 311
32-39: Consider adding more comprehensive CLI tests.The test section only verifies one CLI command (
gisaid-batch). If the package provides additional commands, they should also be tested.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/steamboat/meta.yaml (1)
40-44: Consider adding optional but helpful metadata.The about section could be enhanced with:
doc_urlpointing to documentation if availabledev_urlpointing to the development repository- More detailed description of the package's functionality
📜 Review details
Configuration used: CodeRabbit UI
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📒 Files selected for processing (1)
- recipes/steamboat/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/steamboat/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/steamboat/meta.yaml (3)
31-38: Consider adding more comprehensive tests.While basic import and CLI tests are present, consider adding:
- Tests for other CLI commands if available
- Basic functionality tests using
steamboat --version- Tests for other key package features
#!/bin/bash # Check available CLI commands that could be tested rg "def main|@click.command|@click.group" -A 5
23-29: Add version constraints for run dependencies.Most run dependencies lack version constraints, which could lead to compatibility issues. Consider adding version bounds for:
- biopython
- executor
- pigz
- pyyaml
This helps ensure reproducible builds and prevents potential breaking changes.
#!/bin/bash # Check if the package's setup.py or pyproject.toml specifies version constraints fd -t f "setup.py|pyproject.toml" . -x cat {} | rg "install_requires|dependencies"
8-10: Verify package naming consistency.The package name in the recipe is "steamboat" but the PyPI package is named "steamboat-binf". This might cause confusion for users. Consider either:
- Updating the recipe name to match PyPI
- Adding a comment explaining the naming difference
✅ Verification successful
Let me try another approach to verify the package naming consistency by checking both the PyPI package and the recipe details more thoroughly.
Let me check the GitHub repository mentioned in the meta.yaml to understand the package naming better.
Based on all the gathered information, I can now provide a final response:
Package naming is consistent with upstream distribution
The naming difference between the conda package (
steamboat) and PyPI package (steamboat-binf) appears intentional and follows the upstream project's distribution strategy:
- The GitHub project is
steamboat-py- The PyPI distribution is
steamboat-binf- The conda package is
steamboatThis is a common pattern where different distribution channels may have slightly different names while referring to the same software. The recipe correctly handles this by:
- Using the simplified name
steamboatfor the conda package- Properly referencing the PyPI package
steamboat-binfin the source URL- Maintaining the correct import name
steamboatin the test section🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Verify the package exists on PyPI and check its metadata curl -s "https://pypi.org/pypi/steamboat-binf/json" | jq -r '.info.name'Length of output: 590
Script:
#!/bin/bash # Check the full meta.yaml content to understand the package naming context cat recipes/steamboat/meta.yaml # Also search for any other references to steamboat in the repository rg -i "steamboat" --type yamlLength of output: 1382
Script:
#!/bin/bash # Check the GitHub repository for package naming information gh repo view rpetit3/steamboat-py --json name,description,nameWithOwner,url # Also check if there's a setup.py or pyproject.toml in the recipe directory fd -t f 'setup.py|pyproject.toml' recipes/steamboat/ -x cat '{}'Length of output: 330
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Package(s) built are ready for inspection:
Docker image(s) built:
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@BiocondaBot please add label |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/steamboat/meta.yaml (1)
32-39: Consider enhancing test coverage.While the basic tests are good, consider adding more comprehensive testing:
- Test additional CLI commands if available
- Verify key functionality through command outputs
Example addition:
commands: - pip check - gisaid-batch --help + - steamboat --version # Verify version output + - steamboat --help # Verify main help menu
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/steamboat/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/steamboat/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/steamboat/meta.yaml (4)
1-6: LGTM! Package metadata is well-structured.The package name and version are properly defined using Conda/Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: LGTM! Build configuration follows best practices.The build section correctly specifies:
- Platform independence with
noarch: python- Standard pip installation
- Proper dependency pinning with
run_exports
41-49: LGTM! Package metadata is complete.The about section includes all required fields and proper license information. Maintainer information is correctly specified.
8-10: Verify PyPI package name and availability.The PyPI package name (
steamboat-binf) differs from the Conda package name (steamboat). Let's verify the package exists and is accessible.✅ Verification successful
Let me verify the package name in the recipe metadata to ensure consistency.
Package name discrepancy is intentional and correct
The verification shows that:
- The PyPI package
steamboat-binfexists and is accessible- The SHA256 checksum in the recipe matches one of the available checksums from PyPI
- The recipe correctly uses
steamboatas the conda package name while sourcing from the PyPI packagesteamboat-binfThis is a valid configuration where the conda package name differs from the PyPI source package name. The recipe is properly structured to handle this difference by:
- Setting conda package name as
steamboat- Correctly referencing the PyPI source as
steamboat-binfin the URL- Using the correct SHA256 checksum
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify PyPI package existence and accessibility # Expected: Package should exist on PyPI with correct name and version # Check if package exists on PyPI curl -s "https://pypi.org/pypi/steamboat-binf/1.0.0/json" | jq -r '.info.name' # Verify SHA256 matches curl -s "https://pypi.org/pypi/steamboat-binf/1.0.0/json" | jq -r '.urls[].digests.sha256'Length of output: 312
Script:
#!/bin/bash # Check package name and version in meta.yaml cat recipes/steamboat/meta.yamlLength of output: 1058
Adds recipe for a python package with tools/scripts for microbial binf
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
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