add recipe for sizemeup #51033
add recipe for sizemeup #51033
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (6)
recipes/sizemeup/build.sh (3)
5-6: LGTM: Proper installation of sizemeup library.The installation command is correct and uses appropriate flags for isolated installation. However, consider adding error handling to ensure the installation was successful.
You could add error handling like this:
-$PYTHON -m pip install --no-deps --ignore-installed -vv . +$PYTHON -m pip install --no-deps --ignore-installed -vv . || exit 1This will cause the script to exit if the installation fails, preventing further execution with an incomplete setup.
8-11: LGTM: Proper setup of executable and wrapper.The script correctly sets up the main executable and wrapper. However, consider adding error checking for critical operations.
You could add error handling for critical operations:
-chmod 755 bin/sizemeup-bioconda -mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main -cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup +chmod 755 bin/sizemeup-bioconda || exit 1 +mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main || exit 1 +cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup || exit 1This ensures that the script exits if any of these critical operations fail.
13-14: LGTM: Proper copying of genome size database.The script correctly copies the genome size database to the shared directory. However, consider adding a check to ensure the file exists before copying.
You could add a check for the database file:
-cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup +if [ -f data/sizemeup-sizes.txt ]; then + cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup || exit 1 +else + echo "Error: Genome size database file not found" >&2 + exit 1 +fiThis ensures that the script exits with an informative error message if the database file is missing.
recipes/sizemeup/meta.yaml (3)
1-10: LGTM! Consider using Jinja2 variable for GitHub repository.The package and source sections are well-defined. The use of Jinja2 variables for the package name and version is a good practice.
Consider defining a Jinja2 variable for the GitHub repository to make future updates easier. For example:
{% set name = "sizemeup" %} {% set version = "1.0.0" %} {% set github_repo = "rpetit3/sizemeup" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/{{ github_repo }}/archive/v{{ version }}.tar.gz sha256: f8307bd4c9fb7b404046c87e18f1811daeefe9e8d431c0ea55e6adc004008338🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-16: Consider removing the run_exports section.The build section is mostly well-defined. However, the
run_exportssection might not be necessary for this Python package.For Python packages,
run_exportsis typically not needed unless the package provides compiled extensions or is meant to be linked against. Consider removing therun_exportssection:build: number: 0 noarch: genericIf there's a specific reason for including
run_exports, please clarify its necessity for this package.
46-48: LGTM! Add a newline at the end of the file.The extra section correctly lists the recipe maintainer.
Add a newline at the end of the file to comply with YAML best practices and resolve the linter warning:
extra: recipe-maintainers: - rpetit3 +🧰 Tools
🪛 yamllint
[error] 48-48: no new line character at the end of file
(new-line-at-end-of-file)
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📒 Files selected for processing (2)
- recipes/sizemeup/build.sh (1 hunks)
- recipes/sizemeup/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/sizemeup/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: no new line character at the end of file
(new-line-at-end-of-file)
🔇 Additional comments (3)
recipes/sizemeup/build.sh (1)
1-3: LGTM: Correct shebang and directory setup.The script starts with the correct shebang for a bash script and properly creates the necessary directories using the
$PREFIXvariable, which is consistent with Bioconda's build system.recipes/sizemeup/meta.yaml (2)
40-44: LGTM! About section is well-defined.The about section provides all the necessary information, including the home page URL, a concise summary, and correct license details.
1-2: Note: Ignore the YAML syntax error for Jinja2 templates.The YAML linter reports a syntax error for the '%' characters at the beginning of the file. This is a false positive, as these are valid Jinja2 template markers used in Conda recipes.
No action is required to address this linter warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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| #!/bin/bash | ||
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| mkdir -p $PREFIX/bin ${PREFIX}/share/sizemeup | ||
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| # Install sizemup library | ||
| $PYTHON -m pip install --no-deps --ignore-installed -vv . | ||
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| # move main executable, and replace with wrapper | ||
| chmod 755 bin/sizemeup-bioconda | ||
| mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main | ||
| cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup | ||
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| # Copy genome size database (~100kb) | ||
| cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup |
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🛠️ Refactor suggestion
Consider adding overall error handling and logging.
While the script is functional and follows Bioconda conventions, it could benefit from some overall improvements:
- Add a logging mechanism to track the progress of the installation.
- Implement overall error handling to catch and report any unexpected issues.
- Consider adding a cleanup function to handle interruptions gracefully.
Here's an example of how you could implement these improvements:
#!/bin/bash
set -e # Exit immediately if a command exits with a non-zero status.
log() {
echo "[$(date +'%Y-%m-%d %H:%M:%S')] $1"
}
cleanup() {
log "Cleaning up..."
# Add any necessary cleanup steps here
}
trap cleanup EXIT
log "Starting sizemeup installation"
mkdir -p $PREFIX/bin ${PREFIX}/share/sizemeup
log "Created necessary directories"
log "Installing sizemeup library"
$PYTHON -m pip install --no-deps --ignore-installed -vv . || { log "Failed to install sizemeup library"; exit 1; }
log "Setting up executable and wrapper"
chmod 755 bin/sizemeup-bioconda || { log "Failed to set permissions for sizemeup-bioconda"; exit 1; }
mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main || { log "Failed to move sizemeup executable"; exit 1; }
cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup || { log "Failed to copy sizemeup-bioconda wrapper"; exit 1; }
log "Copying genome size database"
if [ -f data/sizemeup-sizes.txt ]; then
cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup || { log "Failed to copy genome size database"; exit 1; }
else
log "Error: Genome size database file not found"
exit 1
fi
log "sizemeup installation completed successfully"This version of the script includes logging, error handling, and a cleanup function to make the installation process more robust and easier to debug.
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I'm going to pass on this recommendation as it makes the build.sh way more complex then it really needs to be
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@rpetit3, understood, thank you for letting me know.
(_/)
( •_•)
💧
✏️ Learnings added
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/build.sh:1-14
Timestamp: 2024-09-29T21:59:41.620Z
Learning: In build scripts like `build.sh`, prefer simplicity and avoid adding unnecessary complexity such as detailed logging and error handling beyond what's necessary.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
| test: | ||
| imports: | ||
| - sizemeup | ||
| commands: | ||
| - pip check | ||
| - sizemeup --version | ||
| - sizemeup --help | ||
| - sizemeup --species "Staphylococcus aureus" | ||
| - sizemeup-build --help | ||
| requires: | ||
| - pip |
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💡 Codebase verification
Remove undefined sizemeup-build command from test scripts
The sizemeup-build command is referenced in the test commands but does not exist in the codebase or documentation. Please remove this command from the test section to avoid confusion and potential test failures.
- File: recipes/sizemeup/meta.yaml
- Lines: 28-38
🔗 Analysis chain
LGTM! Please clarify the sizemeup-build command.
The test section is well-defined and comprehensive, covering import checks, pip check, and various CLI functionalities.
Could you please provide more information about the sizemeup-build command? It's not mentioned in the package summary, and it would be helpful to understand its purpose and ensure it's documented in the package's README or documentation.
To verify the existence and purpose of this command, we can check the project's documentation:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for sizemeup-build documentation
rg -i 'sizemeup-build' README.md || echo "No mention of sizemeup-build in README.md"
Length of output: 125
Script:
#!/bin/bash
# Description: Search for the implementation of 'sizemeup-build' in the codebase
rg -i 'sizemeup-build' src/ || echo "sizemeup-build command not found in the src directory"
Length of output: 189
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AI growing pains, sizemeup-build does actually exist
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@rpetit3 Thank you for the clarification! I apologize for the oversight. I'll make sure to remember that sizemeup-build does indeed exist in the package.
(>_<) Sorry for the confusion.
✏️ Learnings added
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/meta.yaml:28-38
Timestamp: 2024-09-29T21:58:52.201Z
Learning: The `sizemeup-build` command exists in the `sizemeup` package and should be included in the test scripts where applicable.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/sizemeup/meta.yaml (1)
1-48: Overall, the recipe is well-structured but requires a few adjustments.The sizemeup recipe is generally well-constructed and aligns with the PR objectives. However, there are a few areas that need attention:
- Adjust the Python version constraint and host requirements as suggested in the requirements section.
- Remove the
sizemeup-buildcommand from the test section.Once these changes are made, the recipe should be ready for inclusion in Bioconda. Please make the necessary adjustments and update the PR.
After making the changes:
- Ensure all tests pass.
- Issue the command
@BiocondaBot please add labelwhen the PR is ready for merging.Thank you for contributing to Bioconda!
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (1)
- recipes/sizemeup/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/sizemeup/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/sizemeup/meta.yaml (6)
1-10: LGTM! Package and source sections are well-defined.The package name, version, source URL, and SHA256 checksum are correctly specified. The use of Jinja2 variables for the package name and version is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-17: LGTM! Build section is well-configured.The build section is correctly set up with:
- Appropriate build number (0 for a new package).
- noarch: generic, which is suitable for Python packages without compiled extensions.
- Proper use of run_exports for dependency management.
40-44: LGTM! About section is complete and accurate.The about section provides all necessary metadata, including:
- Home page URL
- Concise summary of the tool's purpose
- License type (MIT)
- License file location
This information aligns well with the PR objectives and Bioconda guidelines.
46-48: LGTM! Extra section correctly specifies the recipe maintainer.The extra section properly lists rpetit3 as the recipe maintainer, which aligns with the PR submitter information.
18-26:⚠️ Potential issueReconsider Python version constraint and host requirements.
The requirements section needs adjustments to ensure broader compatibility and align with Bioconda best practices:
The Python version constraint of >=3.12 is very recent and might limit the package's usability. Consider using a lower minimum version, such as >=3.7 or >=3.8, unless there's a specific need for Python 3.12 features.
The inclusion of
poetryin the host requirements is unusual for a Bioconda recipe. Typically,poetryis used for development and packaging, not for installation in the conda environment. Consider removing it unless it's absolutely necessary for the build process.Suggested changes:
requirements: host: - python >=3.7 - pip run: - python >=3.7 - requests - rich-click >=1.6.0If there are specific reasons for the current choices, please provide more context.
28-38:⚠️ Potential issueRemove undefined
sizemeup-buildcommand from test scriptsThe
sizemeup-buildcommand is referenced in the test commands but does not exist in the codebase or documentation. Please remove this command from the test section to avoid confusion and potential test failures.Suggested change:
test: imports: - sizemeup commands: - pip check - sizemeup --version - sizemeup --help - sizemeup --species "Staphylococcus aureus" requires: - pip
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@BiocondaBot please add label |
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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Testing CondaThe built in test confirmed conda is working DockerNeed to fix issue on sizemeup end |
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Actionable comments posted: 1
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📒 Files selected for processing (1)
- recipes/sizemeup/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/sizemeup/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/sizemeup/meta.yaml (6)
1-10: LGTM: Package and source information are well-defined.The package name, version, source URL, and SHA256 checksum are correctly specified. This ensures proper identification and integrity of the package source.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-16: LGTM: Build configuration is appropriate.The build section is well-configured:
- Build number is correctly set to 0 for the initial release.
- The package is correctly marked as
noarch: generic, which is suitable for Python packages without compiled extensions.- The use of
run_exportsis a good practice for managing dependencies across different builds.
28-38: LGTM: Comprehensive test section.The test section is well-defined and thorough:
- It includes import checks to ensure the package can be imported correctly.
- The
pip checkcommand verifies that all dependencies are satisfied.- Various CLI functionalities are tested, including version display, help command, and a specific use case.
- The
sizemeup-buildcommand is included, which has been confirmed to exist by the package author.This comprehensive set of tests helps ensure the package's functionality and integrity.
40-44: LGTM: About section is complete and accurate.The about section provides all necessary metadata:
- The home page URL is correctly specified.
- The summary accurately describes the tool's purpose.
- The license (MIT) is clearly stated.
- The license file location is provided.
This information aligns well with the PR objectives and provides users with essential details about the package.
46-48: LGTM: Maintainer information is correctly specified.The extra section correctly identifies rpetit3 as the recipe maintainer, which aligns with the PR author information.
1-1: Note on static analysis warning.The yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 template syntax commonly used in conda recipes. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/sizemeup/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3.12 | ||
| - poetry | ||
| - pip | ||
| run: | ||
| - python >=3.12 | ||
| - requests | ||
| - rich-click >=1.6.0 |
There was a problem hiding this comment.
Consider adjusting Python version constraint and host requirements.
While the requirements are generally well-defined, there are two points to consider:
-
The Python version constraint of >=3.12 is very recent and might limit the package's usability. Unless there's a specific need for Python 3.12 features, consider using a lower minimum version, such as >=3.7 or >=3.8, to ensure broader compatibility.
-
The inclusion of
poetryin the host requirements is unusual for a Bioconda recipe. Typically,poetryis used for development and packaging, not for installation in the conda environment. Consider removing it unless it's absolutely necessary for the build process.
Suggested changes:
requirements:
host:
- python >=3.7
- pip
run:
- python >=3.7
- requests
- rich-click >=1.6.0If there are specific reasons for the current choices, please provide more context.
There was a problem hiding this comment.
This one should include poetry
There was a problem hiding this comment.
@rpetit3, understood regarding including poetry in the host requirements. If sizemeup requires poetry for its build process, then including it is appropriate.
Regarding the Python version constraint of >=3.12, is that intentional? Since Python 3.12 is very recent, setting a lower minimum version like >=3.7 or >=3.8 might help reach a broader user base, unless sizemeup specifically requires features introduced in Python 3.12.
✏️ Learnings added
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/meta.yaml:0-0
Timestamp: 2024-09-29T22:52:49.536Z
Learning: The `sizemeup` package requires `poetry` in the host requirements for its build process.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
🧠 Learnings used
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/meta.yaml:28-38
Timestamp: 2024-09-29T21:58:52.399Z
Learning: The `sizemeup-build` command exists in the `sizemeup` package and should be included in the test scripts where applicable.
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/sizemeup/meta.yaml (1)
18-26: Consider removing poetry from host requirements.The requirements are generally well-defined, but there's one point to consider:
The inclusion of
poetryin the host requirements is unusual for a Bioconda recipe. Typically,poetryis used for development and packaging, not for installation in the conda environment. Consider removing it unless it's absolutely necessary for the build process.Suggested change:
requirements: host: - python >=3.7 - pip run: - python >=3.7 - requests - rich-click >=1.6.0If there's a specific reason for including
poetry, please provide more context.
📜 Review details
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📒 Files selected for processing (1)
- recipes/sizemeup/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/sizemeup/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/sizemeup/meta.yaml (5)
1-10: LGTM! Package and source information are well-defined.The package name, version, source URL, and SHA256 checksum are correctly specified. The use of Jinja2 variables for the package name and version is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-16: LGTM! Build settings are appropriate.The build configuration is well-defined:
- The build number is correctly set to 0 for a new package.
- The
noarch: genericsetting is appropriate for a Python package without compiled extensions.- The use of
run_exportswithpin_subpackageis a good practice for managing dependencies across minor version updates.
40-44: LGTM! About section is complete and accurate.The about section provides all necessary metadata:
- The home page correctly points to the GitHub repository.
- The summary accurately describes the tool's purpose.
- The license (MIT) is specified along with the license file location.
This information aligns well with the PR objectives and the package's GitHub repository.
46-48: LGTM! Maintainer information is correct.The extra section correctly specifies rpetit3 as the recipe maintainer, which matches the PR submitter.
1-48: Overall, the recipe is well-constructed with a few minor issues to address.The
meta.yamlfile for the sizemeup package is generally well-defined and follows Bioconda guidelines. Here's a summary of the review:
- Package, source, and build sections are correctly specified.
- Requirements are mostly appropriate, but consider removing
poetryfrom host requirements unless it's necessary for the build process.- The test section is comprehensive, but the specific use case test might fail due to a permission error. Consider adjusting this test as suggested in the previous comment.
- About and extra sections provide accurate metadata and maintainer information.
Once these minor issues are addressed, the recipe should be ready for inclusion in Bioconda. Great work on creating this recipe for sizemeup!
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| test: | ||
| imports: | ||
| - sizemeup | ||
| commands: | ||
| - pip check | ||
| - sizemeup --version | ||
| - sizemeup --help | ||
| - sizemeup --species "Staphylococcus aureus" | ||
| - sizemeup-build --help | ||
| requires: | ||
| - pip |
There was a problem hiding this comment.
Consider adjusting the specific use case test.
The test section is comprehensive and well-structured. However, there's a potential issue to address:
The specific use case test on line 35:
- sizemeup --species "Staphylococcus aureus"might fail due to the permission error mentioned in the PR comments. This error occurs when the tool attempts to write the output file.
Consider modifying this test to avoid the permission issue. You could:
- Add a temporary directory with write permissions for the test.
- Use a
--dry-runoption if available, to skip file writing. - Redirect the output to
/dev/nullor a temporary file.
For example:
- sizemeup --species "Staphylococcus aureus" --output /tmp/sizemeup_test_output.txtor
- sizemeup --species "Staphylococcus aureus" > /dev/nullPlease choose the most appropriate option based on the tool's capabilities and the desired test coverage.
There was a problem hiding this comment.
This does not affect the tests and was corrected in the source of sizemeup
There was a problem hiding this comment.
@rpetit3, thank you for the clarification. It's great to hear that the permission issue has been corrected in the source of sizemeup and does not affect the tests.
(・_・)?
✏️ Learnings added
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/meta.yaml:28-38
Timestamp: 2024-09-29T22:53:18.469Z
Learning: The permission issue in 'sizemeup --species "Staphylococcus aureus"' has been corrected in the source of sizemeup and does not affect the tests.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
🧠 Learnings used
Learnt from: rpetit3
PR: bioconda/bioconda-recipes#51033
File: recipes/sizemeup/meta.yaml:28-38
Timestamp: 2024-09-29T21:58:52.399Z
Learning: The `sizemeup-build` command exists in the `sizemeup` package and should be included in the test scripts where applicable.
If you found this review helpful, would you consider giving us a shout-out on X?
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Package(s) built are ready for inspection:
Docker image(s) built:
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Testing again Good to go! |
This PR adds a recipe for sizemeup a simple tool to get genome sizes based on species names
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
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@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
sizemeuplibrary.sizemeup, detailing package information and dependencies.Bug Fixes
Documentation