new tool: orthodb #51959
new tool: orthodb #51959
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/orthodb/meta.yaml (2)
9-14: Consider removing run_exports configuration.The
run_exportssection is typically used for compiled libraries where ABI compatibility matters. For a pure Python package, this configuration is unnecessary and can be safely removed.build: number: 0 noarch: python - run_exports: - - {{ pin_subpackage('orthodb', max_pin="x") }}
31-34: Consider adding more comprehensive tests.While the basic import test is good, consider adding more functional tests to verify the API's basic operations. For example:
- Test API connection
- Verify basic query functionality
- Check error handling
test: commands: - python -c 'import orthodb; api=orthodb.OdbAPI();' + - python -c 'import orthodb; api=orthodb.OdbAPI(); api.ping()' + - python -c 'import orthodb; help(orthodb)'
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📒 Files selected for processing (2)
recipes/orthodb/build.sh(1 hunks)recipes/orthodb/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/orthodb/build.sh
🧰 Additional context used
🪛 yamllint
recipes/orthodb/meta.yaml
[error] 30-30: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/orthodb/meta.yaml (4)
1-8: LGTM: Package metadata is well-structured.
The package metadata section follows conda packaging best practices with proper use of Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
15-18: LGTM: Source configuration is correct.
The source URL and checksum are properly configured for GitLab source distribution.
45-51: LGTM: Extra metadata is well-documented.
The extra section includes appropriate identifiers (biotools, DOI, PMID) and correctly lists the recipe maintainer.
35-44: Verify LICENSE file existence.
The meta.yaml references a LICENSE file, but we should verify its existence in the source package.
✅ Verification successful
LICENSE file exists in the source package
The LICENSE file is present in the source package at orthodb_py-0.9.0/LICENSE, confirming the correct reference in meta.yaml.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify the LICENSE file exists in the package
curl -sL https://gitlab.com/ezlab/orthodb_py/-/archive/0.9.0/orthodb_py-0.9.0.tar.gz | tar tz | grep -i license
Length of output: 138
recipes/orthodb/meta.yaml
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| requirements: | ||
| build: | ||
| - python >=3.9 | ||
| - bash >=4.1 | ||
| host: | ||
| - python >=3.9 | ||
| - pip | ||
| - bash >=4.1 | ||
| run: | ||
| - python >=3.9 | ||
| - bash >=4.1 | ||
|
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💡 Codebase verification
Remove unnecessary Bash dependency requirements
The package only uses Bash in the build script with a simple pip install command that doesn't require any Bash-specific features. The build.sh could easily use sh instead. The Bash dependency in all sections (build, host, run) is unnecessary since:
- The package itself is a pure Python package
- The build script doesn't use any Bash-specific features
- No other shell scripts or Bash usage was found in the package
Please remove the Bash requirements from all sections and fix the trailing whitespace on line 30.
🔗 Analysis chain
Verify Bash dependency requirement.
The inclusion of Bash >=4.1 as a requirement in all sections (build, host, run) is unusual for a Python package. Please verify if this is actually needed for the package functionality.
Also, there's a trailing whitespace on line 30 that should be removed.
Let me generate additional scripts to check for bash script usage specifically in the orthodb package.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the package actually uses bash in its code
rg -l 'subprocess.*bash|os.system.*bash' || echo "No direct bash usage found"
# Check if there are any shell scripts in the package
ast-grep --pattern 'from subprocess import|import subprocess'
Length of output: 11022
Script:
#!/bin/bash
# Check for shell scripts in the orthodb package directory
fd -e sh . recipes/orthodb/
# Check for bash shebang in any files
rg '^#!.*bash' recipes/orthodb/
# Check build.sh and any other scripts for bash-specific features
cat recipes/orthodb/build.sh || echo "No build.sh found"
Length of output: 226
🧰 Tools
🪛 yamllint
[error] 30-30: trailing spaces
(trailing-spaces)
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/orthodb/meta.yaml (2)
19-27: Simplify requirements sectionFor a pure Python package using
noarch: python, thebuildsection requirements are unnecessary. Thehostandrunsections are sufficient.requirements: - build: - - python >=3.9 host: - python >=3.9 - pip run: - python >=3.9
28-31: Enhance test coverage and fix formatting
- The current test only verifies import and API instantiation. Consider adding more comprehensive tests:
- Verify basic API functionality
- Test error handling
- Remove trailing whitespace on line 30
test: commands: - - python -c 'import orthodb; api=orthodb.OdbAPI();' + - python -c 'import orthodb; api=orthodb.OdbAPI();' + - python -c 'from orthodb import __version__; assert __version__ == "0.9.0"'
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📒 Files selected for processing (1)
recipes/orthodb/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/orthodb/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/orthodb/meta.yaml (4)
1-8: LGTM! Package metadata is well-structured and follows conda packaging conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
15-18: LGTM! Source configuration is correct and follows best practices.
32-41: LGTM! Package metadata is complete and well-documented.
42-48: LGTM! Extra metadata is properly formatted with appropriate identifiers.
| build: | ||
| number: 0 | ||
| noarch: python | ||
| run_exports: | ||
| - {{ pin_subpackage('orthodb', max_pin="x") }} | ||
|
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🛠️ Refactor suggestion
Remove unnecessary run_exports configuration
The run_exports section is typically used for compiled libraries where ABI compatibility matters. For a pure Python package, this configuration is unnecessary and could potentially constrain downstream packages unnecessarily.
build:
number: 0
noarch: python
- run_exports:
- - {{ pin_subpackage('orthodb', max_pin="x") }}📝 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.
| build: | |
| number: 0 | |
| noarch: python | |
| run_exports: | |
| - {{ pin_subpackage('orthodb', max_pin="x") }} | |
| build: | |
| number: 0 | |
| noarch: python |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/orthodb/meta.yaml (1)
32-34: Consider adding offline test casesThe current test creates an API instance which might fail in environments without network access. Consider adding offline tests that verify the package installation without requiring API connectivity.
test: commands: - - python -c 'import orthodb; api=orthodb.OdbAPI();' + - python -c 'import orthodb' + - python -c 'from orthodb import OdbAPI'
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📒 Files selected for processing (1)
recipes/orthodb/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/orthodb/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/orthodb/meta.yaml (4)
12-13: Remove unnecessary run_exports configuration
The run_exports section is typically used for compiled libraries where ABI compatibility matters. For a pure Python package, this configuration is unnecessary and could potentially constrain downstream packages unnecessarily.
19-31: Verify Python version constraint
The Python >=3.9 requirement seems restrictive. Let's verify if this constraint is actually needed by the package.
#!/bin/bash
# Description: Check for Python version requirements in the package
# Test: Look for version-specific features or explicit version checks
rg -l 'python_requires|requires-python' || echo "No explicit Python version requirement found in package"
ast-grep --pattern 'if sys.version_info $$$:'15-17: Verify source URL accessibility and checksum
The source URL and checksum configuration look correct. Let's verify the accessibility and integrity of the source.
✅ Verification successful
The previous script didn't execute properly. Let's try again with a focused verification of the source configuration.
Source URL and checksum configuration verified successfully
The verification confirms:
- The source URL is accessible (HTTP 200 response)
- The URL template correctly uses the version variable (0.9.0)
- The sha256 checksum is properly defined
- The source configuration follows the expected format for GitLab archives
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify source URL accessibility and checksum
# Test: Check if the URL is accessible and returns expected content
curl -sI "https://gitlab.com/ezlab/orthodb_py/-/archive/0.9.0/orthodb_py-0.9.0.tar.gz" | head -n1
Length of output: 5530
Script:
#!/bin/bash
# Let's verify the source URL and checksum properly
curl -sI "https://gitlab.com/ezlab/orthodb_py/-/archive/0.9.0/orthodb_py-0.9.0.tar.gz" | head -n1
# Also check if we can find the version and sha256 values in meta.yaml
cat recipes/orthodb/meta.yaml
Length of output: 1313
40-40: Verify license file existence
Let's verify that the LICENSE file is included in the source package.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/orthodb/meta.yaml (1)
30-34: Consider adding more comprehensive tests.While the basic import tests are good, consider adding tests that verify API functionality, such as:
- Testing connection to the API
- Basic query operations
test: commands: - python -c 'import orthodb' - python -c 'from orthodb import OdbAPI' + - python -c 'api = OdbAPI(); api.ping()' # Add basic connectivity test if available
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/orthodb/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/orthodb/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/orthodb/meta.yaml (5)
1-8: LGTM! Package metadata follows best practices.
The package metadata section is well-structured using Jinja2 variables for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-12: LGTM! Build configuration is appropriate.
The build configuration correctly specifies this as a pure Python package with noarch: python.
35-44: LGTM! Package metadata is complete.
The about section provides all necessary metadata including license, documentation, and development URLs.
45-51: LGTM! Extra metadata is well-documented.
The extra section properly includes relevant identifiers (biotools, DOI, PMID) and maintainer information.
13-16: Verify if package is available on PyPI.
While the GitLab source is valid, if the package is available on PyPI, it would be preferred to use that as the source.
✅ Verification successful
GitLab source is appropriate as package is not available on PyPI
The verification shows that:
- The package is not available on PyPI (null response from PyPI API)
- The GitLab source URL is accessible and valid (HTTP 200 response)
Therefore, using the GitLab repository as the source is the correct approach here.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if package exists on PyPI
curl -s "https://pypi.org/pypi/orthodb/json" | jq -r '.info.version' || echo "Not found on PyPI"
# Verify the GitLab URL is accessible
curl -sI "https://gitlab.com/ezlab/orthodb_py/-/archive/0.9.0/orthodb_py-0.9.0.tar.gz" | head -n1
Length of output: 181
recipes/orthodb/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - python >=3.4 | ||
| - pip | ||
| - setuptools | ||
| host: | ||
| - python >=3.4 | ||
| - pip | ||
| - setuptools | ||
| run: | ||
| - python >=3.4 | ||
| - requests | ||
|
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🛠️ Refactor suggestion
Consider updating minimum Python version requirement.
Python 3.4 reached end-of-life in March 2019. Consider updating to a more recent minimum version (e.g., >=3.7) for better security and feature support.
build:
- python >=3.4
+ - python >=3.7
- pip
- setuptools
host:
- python >=3.4
+ - python >=3.7
- pip
- setuptools
run:
- python >=3.4
+ - python >=3.7
- requestsCommittable suggestion skipped: line range outside the PR's diff.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/orthodb/meta.yaml (2)
29-30: Consider adding version constraint for requestsThe
requestspackage is specified without version constraints. Consider adding a minimum version requirement to ensure compatibility and security updates.run: - python >=3.7 - - requests + - requests >=2.25.0
32-35: Consider adding functional API testsThe current tests only verify imports. Consider adding basic API functionality tests to ensure the package works as expected.
Example test to add:
test: commands: - python -c 'import orthodb' - python -c 'from orthodb import OdbAPI' + - python -c 'api = OdbAPI(); assert api.get_version() is not None'
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/orthodb/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/orthodb/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/orthodb/meta.yaml (1)
15-17: Verify package name in source URL
The source URL uses orthodb_py while the package name is orthodb. Please verify if this is intentional and if the URL will remain stable.
✅ Verification successful
Source URL is valid and accessible
The GitLab source URL is correct and accessible. The package name difference (orthodb_py vs orthodb) is intentional - it's common for Python packages to have different repository names than their installation names. The HTTP 200 response confirms the URL is stable and working.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify if the URL is accessible and returns the expected content
curl -sI "https://gitlab.com/ezlab/orthodb_py/-/archive/0.9.0/orthodb_py-0.9.0.tar.gz" | head -n1
Length of output: 109
| home: https://www.ezlab.org/orthodb_v12_userguide.html | ||
| license: GPL3 | ||
| license_family: GPL3 | ||
| license_file: LICENSE |
There was a problem hiding this comment.
Add license file to the files section
The license_file is specified but there's no files section to ensure it's included in the package.
Add this section after the source section:
files:
- LICENSE
Add new tool prthodb