Add recipe for HELIANO, a tool for the detection of helitrons in diverse genomes #51129
Conversation
📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe changes update the Heliano package to version 1.2.1, reflected in the Changes
Suggested reviewers
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 5
🧹 Outside diff range and nitpick comments (6)
recipes/heliano/meta.yaml (1)
48-53: Consider removing trailing spaces in the description.There are trailing spaces at the end of some lines in the description. While these might be intentional for formatting, it's generally good practice to remove them to avoid potential issues with different YAML parsers.
You can remove the trailing spaces from lines 49-51 and 53 in the description section.
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
recipes/heliano/build.sh (5)
1-11: LGTM! Consider adding error handling for directory creation.The script setup and path definition look good. The use of environment variables for paths enhances portability, and creating necessary directories is essential.
Consider adding error handling for the
mkdircommands to ensure the script exits if directory creation fails:-mkdir -p ${PREFIX}/bin -mkdir -p ${PACKAGE_HOME} +mkdir -p ${PREFIX}/bin || exit 1 +mkdir -p ${PACKAGE_HOME} || exit 1🧰 Tools
🪛 Shellcheck
[warning] 7-7: SCRIT_DIR_PATH appears unused. Verify use (or export if used externally).
(SC2034)
13-14: Consider using a more selective copying approach.While copying all files ensures nothing is missed, it might include unnecessary files. Consider using a more selective approach to copy only the required files.
You could use a list of required files or directories:
required_files=("heliano.py" "heliano_cons.py" "heliano_bcheck.R" "heliano_fisher.R" "RepHel.hmm" "tclcv.txt" "SplitJoint.R" "Sort.sh") for file in "${required_files[@]}"; do cp "$file" "${PACKAGE_HOME}/" || exit 1 done
16-31: LGTM! Consider adding error handling for sed commands.The file path definition and sed replacement section looks good. Defining file paths as variables and using
sedfor path replacement are effective practices.Consider adding error handling for the
sedcommands to ensure the script exits if any replacement fails:-sed -i.bak "s|_INTERPRETERPYTHON_PATH_|${myPYTHON_PATH}|" ${PACKAGE_HOME}/heliano.py +sed -i.bak "s|_INTERPRETERPYTHON_PATH_|${myPYTHON_PATH}|" ${PACKAGE_HOME}/heliano.py || exit 1Apply this change to all
sedcommands in this section.
33-37: LGTM! Consider adding error handling for file operations.The file permission setting section looks good. Copying scripts and setting executable permissions are necessary steps for proper package setup.
Consider adding error handling for the
cpandchmodcommands:-cp ${PACKAGE_HOME}/heliano.py ${PACKAGE_HOME}/heliano -cp ${PACKAGE_HOME}/heliano_cons.py ${PACKAGE_HOME}/heliano_cons -chmod +x ${PACKAGE_HOME}/heliano -chmod +x ${PACKAGE_HOME}/heliano_cons +cp ${PACKAGE_HOME}/heliano.py ${PACKAGE_HOME}/heliano || exit 1 +cp ${PACKAGE_HOME}/heliano_cons.py ${PACKAGE_HOME}/heliano_cons || exit 1 +chmod +x ${PACKAGE_HOME}/heliano || exit 1 +chmod +x ${PACKAGE_HOME}/heliano_cons || exit 1
48-48: Enhance the success message for clarity.While providing feedback about the installation success is good, the message could be more informative.
Consider updating the success message to provide more specific information:
-echo "Succeed! Please find programs in bin/ directory." +echo "Installation successful! The 'heliano' and 'heliano_cons' programs are now available in ${PREFIX}/bin."This message clearly indicates which programs were installed and their exact location.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/build.sh (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/heliano/build.sh
[warning] 7-7: SCRIT_DIR_PATH appears unused. Verify use (or export if used externally).
(SC2034)
[warning] 43-43: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
🔇 Additional comments (5)
recipes/heliano/meta.yaml (5)
1-7: LGTM: Package metadata is well-defined.The package name, version, and SHA256 checksum are correctly specified. Good use of Jinja2 variables and proper lowercasing of the package name.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source configuration is correct.The source URL and SHA256 checksum are properly defined. Using a GitHub release tarball is good practice for reproducibility.
13-17: LGTM: Build configuration is well-defined.The build section is correctly configured:
- Build number is set to 0 for a new package.
run_exportsis properly used withpin_subpackage, which is crucial for dependency management as mentioned in the PR objectives.noarch: genericis appropriate for this type of package.
42-52: LGTM: About section is comprehensive and well-structured.The about section provides all necessary information:
- Home and development URLs are correctly specified.
- License (GPL-3) is properly declared with a reference to the license file.
- The summary and description provide a clear overview of the tool's purpose and functionality.
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
54-56: LGTM: Extra section includes DOI for citation.The inclusion of a DOI in the extra section is excellent practice for academic software, enabling proper citation in scientific literature.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/heliano/meta.yaml (2)
42-51: LGTM: About section is comprehensive. Minor formatting suggestion.The about section provides all necessary information and follows Bioconda guidelines. The description is informative and clearly explains the tool's purpose.
Consider removing trailing spaces at the end of lines 48-50 and 52 to adhere to YAML best practices.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
1-55: Address minor YAML linting issues.The yamllint tool reported some issues:
The error about the '%' character at the start of the file can be safely ignored. This is a false positive due to the use of Jinja2 templating, which is standard in Bioconda recipes.
There are trailing spaces at the end of some lines (48-50, 52). Consider removing these trailing spaces to improve YAML formatting.
Would you like assistance in removing the trailing spaces?
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
recipes/heliano/build.sh (1)
15-30: Consider cleaning up sed backup files.The path fixing section looks good and systematically replaces placeholders. However, the sed commands create backup files (.bak) which are not cleaned up. If these backups are not needed, consider adding a cleanup step or using sed without creating backups.
You could add the following line at the end of this section to remove the backup files:
rm ${PACKAGE_HOME}/*.bakAlternatively, you can modify the sed commands to not create backups by using the -i option without an extension, like this:
sed -i "s|_INTERPRETERPYTHON_PATH_|${myPYTHON_PATH}|" ${PACKAGE_HOME}/heliano.pyThis approach would eliminate the need for cleanup.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/build.sh (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/heliano/build.sh
[warning] 42-42: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (10)
recipes/heliano/meta.yaml (5)
1-11: LGTM: Package and source sections are well-defined.The package metadata and source information are correctly specified. The use of Jinja2 variables for version and checksum is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section adheres to Bioconda guidelines.The build section is well-defined:
- The build number is correctly set to 0 for a new package.
- The
run_exportsspecification ensures dependency versions are locked, as recommended in the PR objectives.- The
noarch: genericspecification is appropriate for this type of package.
53-55: LGTM: Extra section includes DOI.The inclusion of the DOI in the extra section is excellent practice for academic software. This will help users properly cite the tool in their work.
19-35: 🛠️ Refactor suggestionConsider relaxing Python version constraint and adding version specifications for dependencies.
As mentioned in a previous review, there are some improvements that can be made to the requirements section:
The Python version is strictly pinned to 3.9. Unless there's a specific reason for this, consider allowing a range of Python versions (e.g.,
python >=3.7,<4) to increase compatibility.Add version constraints to key dependencies to ensure compatibility. For example:
- biopython >=1.78 - pybedtools >=0.8 - r-base >=4.0Verify if any build requirements are needed. If not, consider adding a comment explaining why only run requirements are specified.
Would you like assistance in implementing these changes?
37-40: 🛠️ Refactor suggestionEnhance test section with more comprehensive tests.
As suggested in a previous review, the test section can be improved:
- Remove the
df -hcommand as it's not directly related to testing the package functionality.- Add more comprehensive tests to verify the package's core functionality. For example:
test: commands: - heliano -h - heliano --version - python -c "import heliano; print(heliano.__version__)" # Add a simple functional test if possibleWould you like assistance in implementing these changes or creating more specific test cases based on the package's functionality?
recipes/heliano/build.sh (5)
1-13: LGTM: Initial setup is well-structured.The script's initial setup is clear and follows good practices. It properly defines the package home directory and creates the necessary directory structure.
32-37: LGTM: File permissions are set correctly.This section appropriately copies the Python scripts and sets the correct executable permissions.
46-46: LGTM: Clear success message.The final echo statement provides a clear and informative success message, indicating where users can find the installed programs.
38-39:⚠️ Potential issueImplement a proper disk space check.
The current
df -hcommand only displays disk space information without verifying if there's sufficient space available. As suggested in a previous review, consider implementing a more robust check to ensure adequate disk space before proceeding with the installation.Here's a reminder of the suggested implementation:
# Check for at least 1GB of free space MIN_SPACE=1000000 # 1GB in KB FREE_SPACE=$(df -k "${PREFIX}" | awk 'NR==2 {print $4}') if [ "${FREE_SPACE}" -lt "${MIN_SPACE}" ]; then echo "Error: Insufficient disk space. At least 1GB required." exit 1 fiReplace the existing
df -hcommand with this code block to perform an actual verification of available disk space.
41-44:⚠️ Potential issueImprove symbolic link creation process.
The current implementation of symbolic link creation can be enhanced for better reliability and consistency. Consider the following improvements:
- Add error checking when changing directory, as suggested by the static analysis tool.
- Use full paths for symbolic links to avoid potential issues with the current working directory.
Here's a suggested refactor, incorporating previous review comments and addressing the static analysis hint:
# Create symbolic links in the bin directory cd ${PREFIX}/bin || exit 1 ln -sf ${PACKAGE_HOME}/heliano heliano || exit 1 ln -sf ${PACKAGE_HOME}/heliano_cons heliano_cons || exit 1This approach ensures that the symbolic links are created correctly, with proper error handling for the directory change.
🧰 Tools
🪛 Shellcheck
[warning] 42-42: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
1-54: Address minor YAML formatting issues.The yamllint tool has identified some minor formatting issues:
There are trailing spaces on lines 47-49 and 51. Please remove these trailing spaces to improve the file's formatting.
The tool reports a syntax error on line 1 for the '%' character. This is a false positive as the '%' is part of the Jinja2 template syntax used in Bioconda recipes. You can safely ignore this warning.
Addressing the trailing spaces will improve the overall quality of the YAML file.
Would you like assistance in removing the trailing spaces?
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
🔇 Additional comments (6)
recipes/heliano/meta.yaml (6)
1-11: LGTM: Package and source sections are well-defined.The package name, version, and SHA256 checksum are correctly defined using Jinja2 variables. The source URL points to the appropriate GitHub release. This structure follows best practices for Bioconda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section is correctly configured.The build section is well-structured:
- Build number is appropriately set to 0 for a new package.
- The use of
run_exportswithpin_subpackagealigns with the PR objectives for version locking.- The
noarch: genericsetting is correct for a package without compiled code.This configuration helps ensure consistency across different platforms and prevents potential API, ABI, and CLI breakage.
42-50: LGTM: About section is comprehensive and informative.The about section is well-structured and provides valuable information:
- Home and development URLs are correctly specified.
- The summary succinctly describes the tool's purpose.
- The description offers a detailed explanation of Helitron-like elements and the tool's functionality.
This information will be helpful for users looking to understand and use the package.
🧰 Tools
🪛 yamllint
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
52-54: LGTM: Extra section includes DOI identifier.The inclusion of the DOI (Digital Object Identifier) in the extra section is excellent. This practice:
- Facilitates proper citation of the software in academic contexts.
- Enhances the discoverability and recognition of the tool in scientific literature.
The format of the DOI appears to be correct.
19-35: 🛠️ Refactor suggestionConsider relaxing Python version constraint and adding version specifications for dependencies.
The requirements section is comprehensive, but there are a few suggestions for improvement:
The Python version is strictly pinned to 3.9. Unless there's a specific reason for this, consider allowing a range of Python versions (e.g.,
python >=3.7,<4) to increase compatibility.Consider adding version constraints to some of the key dependencies to ensure compatibility. For example:
- biopython >=1.78 - pybedtools >=0.8 - r-base >=4.0Verify if any build requirements are needed. If not, it might be worth adding a comment explaining why only run requirements are specified.
These changes will help ensure long-term compatibility and make the recipe more robust.
Would you like assistance in implementing these changes?
37-40: 🛠️ Refactor suggestionEnhance test section with more comprehensive tests.
The current test section can be improved:
- Remove the
df -hcommand as it's not directly related to testing the package functionality.- Add more comprehensive tests to verify the package's core functionality. For example:
test: commands: - heliano -h - heliano --version - python -c "import heliano; print(heliano.__version__)" # Add a simple functional test if possibleThese changes will provide better assurance that the package is installed and functioning correctly.
Would you like assistance in implementing these changes or creating more specific test cases based on the package's functionality?
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
42-52: LGTM: Comprehensive about section with minor formatting suggestion.The about section provides excellent metadata for the package, including URLs, license information, and a detailed description.
Minor suggestion: Remove trailing spaces from the description lines to adhere to YAML best practices.
Would you like assistance in removing the trailing spaces?
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
🔇 Additional comments (6)
recipes/heliano/meta.yaml (6)
1-11: LGTM: Package and source sections are well-defined.The package metadata and source information are correctly specified. Good use of Jinja2 templating for version and checksum.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section is well-configured.The build section adheres to Bioconda guidelines. The use of
run_exportswithpin_subpackageis excellent for version locking, as mentioned in the PR objectives. Thenoarch: genericspecification is appropriate for this package.
54-56: LGTM: Extra section with DOI.The inclusion of the DOI in the extra section is excellent. This allows for proper academic citation of the software.
1-1: Note on static analysis warning.The static analysis tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive. The use of Jinja2 templating ({% ... %}) is correct and necessary in Bioconda recipe files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
19-35: 🛠️ Refactor suggestionConsider relaxing Python version constraint and adding version specifications for dependencies.
The requirements section is comprehensive, but there are a few suggestions:
The Python version is strictly pinned to 3.9. Unless there's a specific reason for this, consider allowing a range of Python versions (e.g.,
python >=3.7,<4) to increase compatibility.Consider adding version constraints to some of the key dependencies to ensure compatibility. For example:
- biopython >=1.78 - pybedtools >=0.8 - r-base >=4.0Verify if any build requirements are needed. If not, it might be worth adding a comment explaining why only run requirements are specified.
Would you like assistance in implementing these changes?
37-40: 🛠️ Refactor suggestionEnhance test section with more comprehensive tests.
The current test section can be improved:
- Remove the
df -hcommand as it's not directly related to testing the package functionality.- Add more comprehensive tests to verify the package's core functionality. For example:
test: commands: - heliano -h - heliano --version - python -c "import heliano; print(heliano.__version__)" # Add a simple functional test if possibleWould you like assistance in implementing these changes or creating more specific test cases based on the package's functionality?
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/heliano/meta.yaml (2)
42-56: LGTM: Comprehensive metadata provided. Minor formatting issue to address.The about and extra sections provide thorough metadata for the package, including URLs, license information, a detailed description, and a DOI for academic referencing. This is excellent for users and citation purposes.
However, there are trailing spaces in the description that should be removed:
- Line 49
- Line 50
- Line 51
- Line 53
Consider using a YAML linter to catch these formatting issues in the future.
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
1-56: Summary: Good initial recipe, some refinements neededOverall, this is a well-structured recipe for the HELIANO tool. Here's a summary of the suggested improvements:
- Relax the Python version constraint to improve compatibility.
- Add version specifications for key dependencies.
- Enhance the test section with more comprehensive tests.
- Remove trailing spaces in the description.
Once these changes are implemented, the recipe will be in excellent shape and ready for inclusion in the Bioconda repository.
Next steps:
- Address the suggested changes.
- Run
conda-buildlocally to ensure the recipe builds successfully.- Update the PR with the changes.
- Once all tests pass and you're ready for merging, comment with
@BiocondaBot please add labelas mentioned in the PR description.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
🔇 Additional comments (5)
recipes/heliano/meta.yaml (5)
1-7: LGTM: Package metadata is well-defined.The package metadata section is correctly structured using Jinja2 variables for maintainability. The package name is appropriately lowercased in the package section, adhering to Conda naming conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source section properly defines the URL for the GitHub release tarball and includes the SHA256 checksum for verification, which is a good security practice.
13-17: LGTM: Build section is well-configured.The build section is correctly set up with:
- An initial build number of 0.
- Proper use of
run_exportswithpin_subpackagefor dependency management.- The
noarch: genericspecification, which is appropriate for this type of package.
19-35: 🛠️ Refactor suggestionConsider relaxing Python version constraint and adding version specifications for dependencies.
The requirements section is comprehensive, but there are a few suggestions:
The Python version is strictly pinned to 3.9. Unless there's a specific reason for this, consider allowing a range of Python versions (e.g.,
python >=3.7,<4) to increase compatibility.Consider adding version constraints to some of the key dependencies to ensure compatibility. For example:
- biopython >=1.78 - pybedtools >=0.8 - r-base >=4.0Verify if any build requirements are needed. If not, it might be worth adding a comment explaining why only run requirements are specified.
37-40: 🛠️ Refactor suggestionEnhance test section with more comprehensive tests.
The current test section can be improved:
- Remove the
df -hcommand as it's not directly related to testing the package functionality.- Add more comprehensive tests to verify the package's core functionality. For example:
test: commands: - heliano -h - heliano --version - python -c "import heliano; print(heliano.__version__)" # Add a simple functional test if possible
|
Having trouble regarding the When trying to run the test, I have tried:
@bioconda/core any other ideas for this one? I'm sure I've just missed something silly... |
|
Reposting for @TobyBaril to enable pings (courtesy of the BiocondaBot):
When trying to run the test, I have tried:
@bioconda/core any other ideas for this one? I'm sure I've just missed something silly... |
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
47-52: Consider removing trailing spaces in the description.The YAML linter detected trailing spaces in the description section. While these might be intentional for formatting, it's generally a good practice to remove them to avoid potential issues with different YAML parsers.
Would you like assistance in removing these trailing spaces?
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (5)
recipes/heliano/meta.yaml (5)
1-7: LGTM: Package information is well-defined.The package name, version, and SHA256 checksum are correctly defined using Jinja2 variables. The package section properly uses these variables, ensuring consistency and maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source URL and SHA256 checksum are properly defined. The use of the version variable in the URL is a good practice for maintainability.
13-17: LGTM: Build section is well-configured.The build number, run exports, and noarch specification are correctly set. The use of
pin_subpackagefor run exports is a good practice for ensuring consistency across dependent packages.
42-51: LGTM: About section is comprehensive and well-defined.The about section provides all necessary information, including home and dev URLs, license, summary, and a detailed description. The content is informative and appropriate for the package.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
53-55: LGTM: Extra section includes relevant identifier.The inclusion of the DOI in the extra section is a good practice for academic software, allowing proper citation of the tool.
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
48-53: Remove trailing spaces in the description.There are trailing spaces at the end of some lines in the description. While these don't affect functionality, it's good practice to remove them for consistency and to adhere to YAML best practices.
You can remove the trailing spaces from lines 49-51 and 53 in the description section.
🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/LICENSE.txt (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 LanguageTool
recipes/heliano/LICENSE.txt
[style] ~18-~18: To make your writing flow more naturally, try moving ‘also’ before the verb.
Context: ...ic License for most of our software; it applies also to any other work released this way by ...(ALSO_PLACEMENT)
[style] ~23-~23: Consider using only “Public” to avoid wordiness.
Context: ...e referring to freedom, not price. Our General Public Licenses are designed to make sure that...(GENERAL_XX)
[typographical] ~47-~47: The conjunction “so that” does not require a comma.
Context: ...t modified versions be marked as changed, so that their problems will not be attributed e...(SO_THAT_UNNECESSARY_COMMA)
[uncategorized] ~189-~189: ‘To effect’ means ‘to cause’. Did you mean “affected”?
Context: ...res to the extent such circumvention is effected by exercising rights under this License...(EFFECT_AFFECT)
[style] ~189-~189: ‘with respect to’ might be wordy. Consider a shorter alternative.
Context: ...by exercising rights under this License with respect to the covered work, and you disclaim any ...(EN_WORDINESS_PREMIUM_WITH_RESPECT_TO)
[style] ~419-~419: ‘prior to’ might be wordy. Consider a shorter alternative.
Context: ... the violation by some reasonable means prior to 60 days after the cessation. Moreove...(EN_WORDINESS_PREMIUM_PRIOR_TO)
[style] ~426-~426: ‘prior to’ might be wordy. Consider a shorter alternative.
Context: ...ight holder, and you cure the violation prior to 30 days after your receipt of the notic...(EN_WORDINESS_PREMIUM_PRIOR_TO)
[style] ~437-~437: Consider a shorter alternative to avoid wordiness.
Context: ...are not required to accept this License in order to receive or run a copy of the Program. ...(IN_ORDER_TO_PREMIUM)
[style] ~439-~439: To make your writing clearer, consider a shorter, more direct phrase.
Context: ...tion of a covered work occurring solely as a consequence of using peer-to-peer transmission to rece...(AS_A_CONSEQUENCE_OF)
[style] ~481-~481: To make your writing clearer, consider a shorter, more direct phrase.
Context: ...ude claims that would be infringed only as a consequence of further modification of the contributor...(AS_A_CONSEQUENCE_OF)
[grammar] ~494-~494: ‘an’ may be redundant when used with the uncountable noun ‘permission’.
Context: ...nated, not to enforce a patent (such as an express permission to practice a patent or covenant not to...(A_UNCOUNTABLE_NOUN)
[grammar] ~507-~507: The verb ‘rely’ requires the preposition ‘on’ (or ‘upon’).
Context: ...e to downstream recipients. "Knowingly relying" means you have actual knowledge that, ...(RELY_ON)
[misspelling] ~508-~508: Did you mean “you're” (short for ‘you are’)?
Context: ...ledge that, but for the patent license, your conveying the covered work in a country...(YOUR)
[uncategorized] ~528-~528: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...conveying the work, and under which the third party grants, to any of the parties who would...(EN_COMPOUND_ADJECTIVE_INTERNAL)
[style] ~534-~534: ‘prior to’ might be wordy. Consider a shorter alternative.
Context: ...nt, or that patent license was granted, prior to 28 March 2007. Nothing in this Licen...(EN_WORDINESS_PREMIUM_PRIOR_TO)
[style] ~545-~545: ‘So as to’ expresses purpose and is used in formal texts. Consider using “to”.
Context: ...e. If you cannot convey a covered work so as to satisfy simultaneously your obligations...(SO_AS_TO)
[typographical] ~631-~631: Conjunctions like ‘and’ should not follow semicolons. Consider using a comma, or removing the conjunction.
Context: ...ectively state the exclusion of warranty; and each file should have at least the "copyrigh...(CONJUNCTION_AFTER_SEMICOLON)
[style] ~662-~662: This phrase is redundant (‘I’ stands for ‘interface’). Use simply “GUI”.
Context: ...am's commands might be different; for a GUI interface, you would use an "about box". You s...(ACRONYM_TAUTOLOGY)
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/heliano/meta.yaml (4)
1-11: LGTM: Package and source sections are well-defined.The package metadata and source information are correctly specified. The use of Jinja2 variables for the package name and version is a good practice for maintainability. The inclusion of a SHA256 checksum enhances security by verifying the integrity of the downloaded source.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section is well-configured.The build section is correctly formatted. The use of
run_exportsis good practice for ensuring consistent versioning. Thenoarch: genericspecification is appropriate for this package, as it doesn't include compiled extensions.
42-52: LGTM: About section is comprehensive and well-formatted.The about section provides detailed information about the package, including home and dev URLs, license information, and a comprehensive description. The use of
{{ RECIPE_DIR }}/LICENSE.txtfor the license file is correct and addresses the issue mentioned in the PR comments.The license file issue has been resolved as per the previous suggestion. The
license_file: {{ RECIPE_DIR }}/LICENSE.txtline ensures that the license file is included with the package, even if it's missing from the source distribution.🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
54-56: LGTM: Extra section includes DOI identifier.The inclusion of a DOI identifier in the extra section is good practice for academic software. This allows for proper citation of the package in scientific literature.
|
@BiocondaBot please add label |
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
recipes/heliano/build.sh (1)
12-13: Consider explicitly listing files to copy.While copying all files from the current directory to
${PACKAGE_HOME}works, it might include unnecessary files. Consider explicitly listing the required files to copy for better control and clarity.Example:
cp -f heliano.py heliano_cons.py RepHel.hmm tclcv.txt heliano_bcheck.R heliano_fisher.R SplitJoint.R Sort.sh ${PACKAGE_HOME}/recipes/heliano/meta.yaml (1)
49-53: Remove trailing spaces.There are trailing spaces on lines 49-51 and 53. While these don't affect functionality, removing them improves code cleanliness.
Apply this diff to remove the trailing spaces:
- Helitron-like elements (HLE1 and HLE2) are DNA transposons. - They have been found in diverse species and seem to play significant roles in the evolution of host genomes. - Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements. - + Helitron-like elements (HLE1 and HLE2) are DNA transposons. + They have been found in diverse species and seem to play significant roles in the evolution of host genomes. + Although known for over twenty years, Helitron sequences are still challenging to identify. + Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/build.sh (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/heliano/build.sh
[warning] 41-41: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
[error] 53-53: trailing spaces
(trailing-spaces)
🔇 Additional comments (10)
recipes/heliano/build.sh (5)
1-10: LGTM: Good script setup and directory creation.The script starts with proper shebang, enables command tracing, and correctly defines paths using environment variables. The creation of necessary directories at the beginning is a good practice.
15-29: LGTM: Proper path definition and placeholder replacement.The script correctly defines paths for required files and uses sed to replace placeholders in heliano.py with actual paths. This approach ensures proper dependency resolution.
37-38: Improve disk space check for actual verification.The current disk space check doesn't actually verify if there's enough space available. Consider implementing a more robust check as suggested in the previous review:
# Check for at least 1GB of free space MIN_SPACE=1000000 # 1GB in KB FREE_SPACE=$(df -k "${PREFIX}" | awk 'NR==2 {print $4}') if [ "${FREE_SPACE}" -lt "${MIN_SPACE}" ]; then echo "Error: Insufficient disk space. At least 1GB required." exit 1 fiThis will ensure that there's at least 1GB of free space before proceeding with the installation.
45-45: LGTM: Appropriate success message.The final echo statement provides a clear and informative success message, indicating where the installed programs can be found.
40-43:⚠️ Potential issueRefactor symbolic link creation for better reliability.
The current implementation of symbolic link creation can be improved:
- Add error checking when changing directory (addressing the static analysis hint).
- Use full paths for symbolic links to avoid potential issues with the current working directory.
Here's a suggested refactor:
# Create symbolic links in the bin directory ln -sf ${PACKAGE_HOME}/heliano ${PREFIX}/bin/heliano || exit 1 ln -sf ${PACKAGE_HOME}/heliano_cons ${PREFIX}/bin/heliano_cons || exit 1This approach ensures that the symbolic links are created correctly regardless of the current working directory and handles potential failures.
🧰 Tools
🪛 Shellcheck
[warning] 41-41: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/heliano/meta.yaml (5)
1-7: Package metadata looks good.The package name, version, and SHA256 checksum are correctly defined using Jinja2 variables. This approach enhances maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: Source information is correctly specified.The source URL and SHA256 checksum are properly defined. The use of the version variable in the URL is a good practice for maintainability.
13-17: Build section is well-defined.The build number, run exports, and noarch specification are all correctly set. The use of run exports is a good practice for maintaining consistency across dependent packages.
42-52: About section is well-defined and informative.The home and dev URLs, license information, and description are all correctly specified. The license file specification using
{{ RECIPE_DIR }}/LICENSE.txtaddresses the issue mentioned in the PR comments. The description provides a good overview of the tool's purpose and functionality.🧰 Tools
🪛 yamllint
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
54-56: Extra section is correctly specified.The inclusion of the DOI identifier is a good practice for academic software, allowing proper citation of the tool.
There was a problem hiding this comment.
Actionable comments posted: 7
🧹 Outside diff range and nitpick comments (2)
recipes/heliano/build.sh (1)
3-3: Consider conditionally enabling debug mode.The
set -xcommand is useful for debugging but may produce excessive output in a production environment. Consider making it conditional:# Enable debug mode only if DEBUG environment variable is set if [[ -n "${DEBUG}" ]]; then set -x fiThis allows you to enable debugging when needed without modifying the script.
recipes/heliano/meta.yaml (1)
47-52: Consider removing trailing spaces in the description.There are trailing spaces at the end of some lines in the description. While these might be intentional for formatting, it's generally good practice to remove them to avoid potential issues with different YAML parsers or editors. Consider trimming these trailing spaces if they're not necessary for the desired formatting.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/build.sh (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/heliano/build.sh
[warning] 39-39: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/heliano/meta.yaml (4)
1-11: LGTM: Package and source sections are well-defined.The package name, version, and SHA256 checksum are correctly defined using Jinja2 variables. The source URL is properly constructed using the version variable, which is a good practice for maintainability. The inclusion of the SHA256 checksum ensures the integrity of the downloaded source.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-17: LGTM: Build section is correctly configured.The build section is well-defined:
- The build number is correctly set to 0 for a new package.
- The use of
run_exportswithpin_subpackageis a good practice for version pinning.- The
noarch: genericsetting is appropriate for a package that doesn't contain compiled code.
41-51: LGTM: About section is comprehensive and well-defined.The about section provides all necessary metadata:
- Home and dev URLs are correctly specified.
- License information is properly included, with the license file correctly referenced using the RECIPE_DIR variable.
- The description provides a good overview of the tool's purpose and functionality.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
53-55: LGTM: Extra section includes DOI identifier.The inclusion of the DOI identifier is excellent practice for academic software, as it allows for proper citation and tracking of the tool's usage in scientific literature.
Co-authored-by: Martin Grigorov <[email protected]>
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
47-55: Remove trailing spaces in the description.The yamllint tool has flagged trailing spaces in the description. While these don't affect functionality, it's good practice to remove them for cleaner code. Consider removing the trailing spaces from lines 48-50 and 52.
Would you like me to provide a cleaned-up version of the description without trailing spaces?
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/heliano/build.sh (1 hunks)
- recipes/heliano/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/heliano/build.sh
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/heliano/meta.yaml (3)
1-7: LGTM: Package metadata is well-defined.The package metadata is correctly defined using Jinja2 variables, which is a good practice for maintainability. The package name is properly lowercased, and the version matches the information provided in the PR objectives.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source URL is properly structured for a GitHub release, and the use of the version variable in the URL is good for maintainability. The inclusion of the SHA256 checksum ensures the integrity and security of the downloaded package.
13-17: LGTM: Build section is well-configured.The build section is correctly set up with an initial build number of 0. The use of
run_exportswithpin_subpackageis a good practice for dependency management. Thenoarch: genericspecification is appropriate for this type of package.
|
Thanks for the suggestions / refinements @martin-g! |
There was a problem hiding this comment.
Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/heliano/meta.yaml (4)
1-7: LGTM: Package metadata is well-defined.The package metadata section is correctly structured using Jinja2 templating. The package name, version, and SHA256 checksum are properly defined, which is crucial for package identification and integrity verification.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source section properly defines the URL for the GitHub release tarball and correctly references the SHA256 checksum. This ensures that the correct version of the package is downloaded and its integrity is verified.
40-54: LGTM: About and extra sections are well-defined.The about and extra sections provide comprehensive metadata for the package:
- The home and dev_url links are correctly specified.
- The summary and description provide clear information about the tool's purpose.
- The license and license_file are properly defined.
- The inclusion of a DOI in the extra section is excellent for academic citation.
It's great to see that the LICENSE.txt issue has been resolved. The current structure ensures that the license information is correctly packaged with the tool.
🧰 Tools
🪛 yamllint
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
1-54: Overall, the meta.yaml file is well-structured and comprehensive.Great job on creating this Conda package recipe for HELIANO. The file follows best practices and provides a solid foundation for packaging the tool. Here's a summary of the review:
- Package metadata and source information are correctly defined.
- The build section could benefit from adding
noarch: python.- Consider adding version constraints to key dependencies for better reproducibility.
- The test section could be enhanced with more comprehensive tests.
- The about and extra sections provide excellent metadata, including the resolved LICENSE.txt issue and DOI for citation.
These minor improvements will further enhance the quality and robustness of the package. Let me know if you need any assistance in implementing the suggested changes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
47-52: Minor: Remove trailing spaces in the description.The YAML linter detected trailing spaces in the description section. While this doesn't affect functionality, removing them improves code cleanliness. Consider trimming trailing spaces from lines 48-50 and 52.
Would you like assistance in removing these trailing spaces?
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/heliano/meta.yaml (4)
1-7: LGTM: Package metadata is well-defined.The package metadata is correctly defined using Jinja2 variables, which is a good practice for maintainability. The package name is properly lowercased, and the version is set correctly.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source configuration is correct.The source URL is properly formatted using the version variable, and the SHA256 checksum is correctly implemented for download verification, which is a good security practice.
13-17: LGTM: Build configuration is well-structured.The build section is correctly configured:
- The build number is set to 0, which is appropriate for a new package.
- The
noarch: pythonsetting is correctly used for a Python package without compiled extensions.- The
run_exportsdirective is properly implemented to ensure consistent versioning across dependent packages.
41-55: LGTM: About and extra sections are well-defined.The about and extra sections are comprehensive and well-structured:
- Home and dev URLs are correctly specified.
- The license and license file are properly defined.
- The description provides a clear overview of the tool's purpose.
- The inclusion of a DOI in the extra section is excellent for academic referencing.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
46-51: Remove trailing spaces in the description.There are trailing spaces at the end of lines 47-51 in the description. While they don't affect functionality, removing them improves code cleanliness.
Would you like assistance in removing these trailing spaces?
🧰 Tools
🪛 yamllint
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/heliano/meta.yaml (3)
1-7: LGTM: Package information is well-defined.The package information is correctly specified using Jinja2 variables, which is a good practice for maintainability. The package name is appropriately lowercased.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source URL and SHA256 checksum are properly defined. The use of the version variable in the URL is good for maintainability.
40-54: LGTM: About and extra sections are well-defined.The about section provides comprehensive information about the package, including appropriate URLs, license details, and a descriptive summary. The inclusion of the DOI in the extra section is valuable for academic referencing.
🧰 Tools
🪛 yamllint
[error] 47-47: trailing spaces
(trailing-spaces)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 51-51: trailing spaces
(trailing-spaces)
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/heliano/meta.yaml (1)
48-52: Remove trailing spaces for better code cleanliness.There are trailing spaces on lines 48-50 and 52. While these don't affect functionality, removing them improves code cleanliness. Consider using an editor with a trailing space highlighter or trimmer to avoid this in the future.
Would you like assistance in removing these trailing spaces?
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/heliano/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/heliano/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/heliano/meta.yaml (4)
1-7: LGTM: Package metadata updated correctly.The package version has been properly updated to 1.2.1, and the SHA256 checksum has been updated accordingly. The use of Jinja2 variables for name and version is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information updated correctly.The source URL has been properly updated to reflect the new version 1.2.1. The use of Jinja2 variables for version and SHA256 ensures consistency throughout the recipe.
13-17: Consider reviewing thenoarch: genericspecification.The build section is mostly correct, with the build number reset to 0 for the new version and the
run_exportssection properly configured. However, thenoarch: genericspecification is unusual for Python packages. Typically, Python packages usenoarch: python. Please review ifgenericis intentional or if it should be changed topython.Would you like assistance in determining the appropriate
noarchspecification for this package?
41-55: LGTM: About section improved and license file specified.The changes in the about section are well-implemented:
- The license file specification has been added, addressing a previous issue.
- The description has been expanded, providing more context about Helitron-like elements and the tool's functionality.
- The DOI identifier is correctly included in the extra section for academic referencing.
These improvements enhance the package metadata and provide better information for users.
🧰 Tools
🪛 yamllint
[error] 48-48: trailing spaces
(trailing-spaces)
[error] 49-49: trailing spaces
(trailing-spaces)
[error] 50-50: trailing spaces
(trailing-spaces)
[error] 52-52: trailing spaces
(trailing-spaces)
Describe your pull request here
Recipe to add HELIANO to bioconda
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
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.