add sipros #51091
add sipros #51091
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces several new files to the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (9)
recipes/sipros/build.sh (5)
4-6: Consider a more selective approach to setting executable permissionsWhile creating the bin directory and copying files is correct, making all files in the bin directory executable (line 5) might be too broad. Some files may not require execution permissions.
Consider modifying line 5 to only set executable permissions for specific files that need it. For example:
-chmod u+x bin/* +chmod u+x bin/file1 bin/file2 # List only the files that need to be executableThis approach is more secure and follows the principle of least privilege.
8-9: Add existence checks for directories before copyingWhile copying the EnsembleScripts and V4Scripts directories to $PREFIX is likely correct, it's good practice to verify that these directories exist before attempting to copy them.
Consider adding existence checks:
+[ -d "EnsembleScripts" ] && cp -r EnsembleScripts "$PREFIX" || echo "Warning: EnsembleScripts directory not found" +[ -d "V4Scripts" ] && cp -r V4Scripts "$PREFIX" || echo "Warning: V4Scripts directory not found" -cp -r EnsembleScripts "$PREFIX" -cp -r V4Scripts "$PREFIX"This change will make the script more robust and provide helpful warnings if the directories are missing.
11-11: Add existence check for configTemplates directory before copyingSimilar to the previous comment, it's a good practice to verify that the configTemplates directory exists before attempting to copy it.
Consider modifying the line as follows:
-cp -r configTemplates "$PREFIX" +[ -d "configTemplates" ] && cp -r configTemplates "$PREFIX" || echo "Warning: configTemplates directory not found"This change will make the script more robust and provide a helpful warning if the directory is missing.
13-14: LGTM: Proper handling of Raxport script, consider adding a commentThe copying and permission setting for the Raxport script is correct. However, it would be helpful to add a comment explaining the purpose of this script, especially since it's coming from $RECIPE_DIR and not the original package.
Consider adding a comment before these lines:
+# Copy custom Raxport script and make it executable cp $RECIPE_DIR/Raxport.sh "$PREFIX/bin/Raxport" chmod +x "$PREFIX/bin/Raxport"This will help future maintainers understand the purpose of this custom script.
1-14: Overall: Good build script with room for minor improvementsThe build script correctly installs the sipros package components, including binaries, scripts, and configuration templates. It also handles a custom Raxport script appropriately.
To further improve the script:
Consider adding error handling and logging. For example:
log_error() { echo "ERROR: $1" >&2 } # Use this function for critical operations cp -r bin/* "$PREFIX/bin" || log_error "Failed to copy binaries"Add a clean-up function to handle any temporary files or rollback partially completed operations in case of failure:
cleanup() { # Add clean-up logic here echo "Cleaning up..." } trap cleanup EXITConsider adding a simple check to ensure $PREFIX is set:
[ -z "$PREFIX" ] && { echo "ERROR: PREFIX is not set"; exit 1; }These additions will make the script more robust and easier to maintain.
recipes/sipros/Raxport.sh (2)
3-8: LGTM: Robust symlink resolution with a minor optimization opportunity.The symlink resolution logic is well-implemented and handles both absolute and relative symlinks correctly. This ensures that the script can determine its true location regardless of how it's invoked.
Consider using
readlink -f(if available on your target systems) to simplify the symlink resolution:DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"This would replace the entire while loop, making the script more concise. However, note that
readlink -fis not available on all systems (e.g., macOS), so the current implementation is more portable.
9-9: LGTM: Correct execution of .NET executable with room for error handling.The script correctly executes the
Raxport.exeusingmono, leveraging the resolved directory path and properly forwarding all arguments.Consider adding basic error handling to improve robustness:
if [ ! -f "$DIR/Raxport.exe" ]; then echo "Error: Raxport.exe not found in $DIR" >&2 exit 1 fi if ! command -v mono &> /dev/null; then echo "Error: mono runtime not found" >&2 exit 1 fi mono "$DIR/Raxport.exe" "$@"This addition would check for the existence of
Raxport.exeand the availability of themonoruntime before attempting to execute, providing more informative error messages if something is missing.recipes/sipros/meta.yaml (2)
1-6: Consider using Semantic Versioning (SemVer) for the version number.The current version "4.01" doesn't strictly follow the Semantic Versioning (SemVer) format. Consider changing it to "4.1.0" to align with SemVer practices, which can help with dependency management and version comparisons.
-{% set version = "4.01" %} +{% set version = "4.1.0" %}🧰 Tools
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12-18: Remove redundantskipparameter and trailing space.The
skip: Falseline is redundant as it's the default behavior. Also, there's a trailing space on line 18 that should be removed.Apply this diff to clean up the build section:
build: noarch: generic number: 0 - skip: False run_exports: - {{ pin_subpackage('sipros', max_pin="x") }} -🧰 Tools
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[error] 18-18: trailing spaces
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📒 Files selected for processing (4)
- recipes/sipros/LICENSE (1 hunks)
- recipes/sipros/Raxport.sh (1 hunks)
- recipes/sipros/build.sh (1 hunks)
- recipes/sipros/meta.yaml (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/sipros/LICENSE
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recipes/sipros/meta.yaml
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🔇 Additional comments (7)
recipes/sipros/build.sh (1)
1-3: LGTM: Proper script setupThe script starts with the correct shebang and uses
set -e, which is a good practice to ensure the script stops on any error.recipes/sipros/Raxport.sh (1)
1-2: LGTM: Proper shebang and source file resolution.The script starts with the correct shebang and properly initializes the
SOURCEvariable usingBASH_SOURCE[0]. This approach ensures the script can determine its own location, which is crucial for the subsequent operations.recipes/sipros/meta.yaml (5)
8-10: Source section looks good!The use of a GitHub release URL with the version variable and the inclusion of a SHA256 checksum for integrity verification are both good practices.
30-37: Test section looks comprehensive!The test commands cover various executables and Python scripts, which is good for ensuring the package is correctly installed and functional. The use of $CONDA_PREFIX in the Python script paths is correct.
19-28:⚠️ Potential issueUpdate Python version and review dependency constraints.
- Python 2.7 is no longer supported. Consider updating to a supported Python 3 version.
- Some package version constraints might be too restrictive. Review if these specific versions are necessary or if they can be relaxed.
- There are no build-time dependencies specified. Ensure this is intentional and add them if needed.
Here's a suggested update for the Python dependency:
- - python =2.7 + - python >=3.7To check if the package is compatible with Python 3, run:
#!/bin/bash # Check for Python version compatibility rg -i 'python' recipes/sipros/meta.yaml ast-grep --lang python --pattern 'print $_' .This will help identify any Python 2-specific syntax that needs updating.
48-54: Verify the DOI.The DOI (10.1186/s40168-024-01866-1) appears to be for a future publication (2024). Please verify if this is correct or if it's a typo.
To check the validity of the DOI, you can use the following command:
If the DOI is valid, the command should return a HTTP 200 status. If not, it might return a 404 or another error code.
✅ Verification successful
DOI is valid and correctly points to an existing resource.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check DOI validity curl -sI "https://doi.org/10.1186/s40168-024-01866-1" | grep -i "HTTP/"Length of output: 189
Script:
#!/bin/bash # Check DOI validity by following redirects curl -sI -L "https://doi.org/10.1186/s40168-024-01866-1" | grep -i "HTTP/"Length of output: 97
39-46:⚠️ Potential issueAddress LICENSE file inclusion.
The comment suggests that the LICENSE file is included in the recipe folder because it's not in the release. This is unusual and should be addressed.
Consider the following actions:
- Open an issue in the upstream repository (https://github.com/thepanlab/Sipros4) to include the LICENSE file in future releases.
- Ensure the LICENSE file is properly included in the recipe folder for now.
To check if the LICENSE file is present in the recipe folder, run:
If the file is not found, it needs to be added to the recipe folder.
✅ Verification successful
LICENSE file is correctly included in the recipe folder.
The
recipes/sipros/LICENSEfile is present as required.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for LICENSE file in the recipe folder ls recipes/sipros/LICENSELength of output: 189
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#!/bin/bash # Check for LICENSE file in the recipe folder ls recipes/sipros/LICENSELength of output: 50
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/sipros/meta.yaml (3)
1-6: Consider using Semantic Versioning (SemVer) for the version number.The current version "4.01" doesn't strictly follow the Semantic Versioning (SemVer) format. Consider changing it to "4.1.0" to align with SemVer guidelines, which use the format MAJOR.MINOR.PATCH.
This change would improve version clarity and help with dependency management.
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12-18: LGTM: Build section is well-defined, with a minor formatting issue.The build section is correctly configured with
noarch: genericand appropriaterun_exportsfor version pinning.However, there's a minor formatting issue:
Remove the trailing space on line 18 to improve code cleanliness:
run_exports: - {{ pin_subpackage('sipros', max_pin="x") }} - +🧰 Tools
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[error] 18-18: trailing spaces
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30-37: LGTM: Comprehensive test section with a suggestion for improvement.The test section is well-defined with a good range of commands to verify the installation of various components.
For improved robustness, consider using the
$PREFIXenvironment variable instead of$CONDA_PREFIXin the Python script test commands. This ensures compatibility across different conda-based package managers:- - python $CONDA_PREFIX/EnsembleScripts/sipros_psm_tabulating.py -v - - python $CONDA_PREFIX/V4Scripts/sipros_peptides_filtering.py -v + - python $PREFIX/EnsembleScripts/sipros_psm_tabulating.py -v + - python $PREFIX/V4Scripts/sipros_peptides_filtering.py -vThis change makes the recipe more portable across different conda-based environments.
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📒 Files selected for processing (1)
- recipes/sipros/meta.yaml (1 hunks)
🧰 Additional context used
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recipes/sipros/meta.yaml
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🔇 Additional comments (4)
recipes/sipros/meta.yaml (4)
8-10: LGTM: Source section is well-defined.The source section correctly uses a GitHub release URL with Jinja2 templating for the version. The inclusion of a SHA256 checksum is a good practice for ensuring package integrity.
48-54: LGTM: Well-defined extra section with maintainers and identifiers.The extra section properly includes recipe maintainers and relevant identifiers (biotools and DOI). This information is valuable for users and follows Bioconda best practices.
19-28:⚠️ Potential issueUpdate Python dependency and consider adding build-time requirements.
The recipe specifies Python 2.7, which has reached its end-of-life and is no longer supported. This may pose security risks and compatibility issues. Consider updating to a supported Python version (e.g., 3.7+) if possible.
The recipe only specifies runtime dependencies. If there are any build-time dependencies required for compiling or setting up the package, they should be added under a
host:section.Here's a suggested update to the requirements section:
requirements: host: - python >=3.7 # Add any build-time dependencies here run: - bioconductor-biostrings - mono - numpy - python >=3.7 - r-base - r-stringr - r-tidyr - scikit-learnPlease verify the compatibility of the package with Python 3 before making this change. If Python 2.7 is absolutely required, consider adding a comment explaining why, and ensure all other dependencies are compatible with this Python version.
To check if the package is compatible with Python 3, you can run:
This will search for any explicit mentions of Python 2 in the source code, which might indicate potential compatibility issues.
✅ Verification successful
Verified: Python 2 usage not detected; updating Python dependency is appropriate.
The verification process found no references to Python 2 in the
.pyfiles of the codebase. Therefore, updating the Python dependency from 2.7 to a supported version (e.g., 3.7+) is appropriate and should not introduce compatibility issues.
- No Python 2 dependencies detected in the source code.
🏁 Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash # Check for Python 3 compatibility in the source code rg -i 'python\s*2' --type pyLength of output: 124
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#!/bin/bash # Check for Python 2 compatibility in the source code rg -i 'python\s*2' --type pyLength of output: 30
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#!/bin/bash # Check for Python 2 compatibility in the source code rg -i 'python\s*2' --type pyLength of output: 30
39-46: LGTM: Comprehensive about section with a note on the license file.The about section is well-defined with all necessary information. However, there's a note about including the license file in the recipe folder due to an issue with the upstream repository.
To ensure this is addressed properly:
- Verify that the LICENSE file is indeed included in the recipe folder.
- Consider opening an issue in the upstream repository to include the LICENSE file in future releases.
You can verify the presence of the LICENSE file with:
If the LICENSE file is missing, please add it to the recipe folder and update the
license_fileentry to use the local path.✅ Verification successful
Please run the following corrected shell script to verify if the
LICENSEfile exists in the recipe folder:
Verified: LICENSE file is present in the recipe folder.
The
LICENSEfile is correctly included in therecipes/sipros/directory as required.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if LICENSE file exists in the recipe folder if [ -f "recipes/sipros/LICENSE" ]; then echo "LICENSE file found in the recipe folder." else echo "LICENSE file not found in the recipe folder." fiLength of output: 124
Script:
# #!/bin/bash # Check if LICENSE file exists in the recipe folder if [ -f "recipes/sipros/LICENSE" ]; then echo "LICENSE file found in the recipe folder." else echo "LICENSE file not found in the recipe folder." fiLength of output: 126
|
@bioconda-bot please add label |
Co-authored-by: M Bernt <m.bernt@ufz.de>
|
Anything to add @xyz1396 ? Or should we merge as it is. |
I am trying to symlink the python scripts. Could I add it after the merge? |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (8)
recipes/sipros/copyConfigTemplate.sh (2)
1-7: LGTM with a suggestion for improvementThe initial setup looks good. The shebang is correct, and the OUTPUT_PATH logic is sound. However, consider adding input validation for the OUTPUT_PATH to ensure it's a valid directory.
You could add a check like this after line 7:
if [ ! -d "$OUTPUT_PATH" ]; then echo "Error: $OUTPUT_PATH is not a valid directory" exit 1 fi
1-16: Add documentation and consider further enhancementsThe script serves its purpose of copying configuration templates based on user input. However, there are a few areas for improvement:
- Add a comment block at the beginning of the script explaining its purpose, usage, and the significance of the configuration templates.
- Consider implementing the robustness and error handling improvements suggested in the previous comments.
- You might want to add logging or more detailed error messages to aid in troubleshooting.
Overall, the script is a good start but could benefit from these enhancements to make it more robust and maintainable.
recipes/sipros/build.sh (3)
9-13: Consider adding error checking for directory copying operations.While the copying of script directories is correct, it might be beneficial to add error checking to ensure the directories exist before attempting to copy them. This can prevent silent failures if the source directories are missing.
Consider adding checks like this before each copy operation:
if [ ! -d "EnsembleScripts" ]; then echo "Error: EnsembleScripts directory not found" exit 1 fi
15-25: LGTM: Proper handling of Python scripts with a minor optimization suggestion.The processing of Python scripts, including adding shebang lines and creating symbolic links, is done correctly. The naming convention for the links is clear and consistent.
Consider combining the two loops for Python scripts to reduce code duplication:
for dir in EnsembleScripts V4Scripts; do for script in "$PREFIX/$dir"/*.py; do baseName=$(basename "$script" .py) sed -i '1i#!/usr/bin/env python\n' "$script" ln -s "$script" "$PREFIX/bin/${dir}_$baseName" done doneThis approach is more maintainable and easier to extend if needed.
33-35: LGTM: Proper final file operations with a minor consistency suggestion.The copying of additional scripts and setting of execute permissions are done correctly.
For consistency, consider using quotes around $PREFIX in the last line:
chmod u+x "$PREFIX"/bin/*This maintains consistency with the usage in previous lines and is a good practice when dealing with variables that might contain spaces.
recipes/sipros/meta.yaml (3)
12-17: Remove redundantskip: Falseline.The build section is well-defined with appropriate noarch setting and run_exports for subpackage pinning. However, the
skip: Falseline is redundant and can be safely removed.Apply this diff to remove the redundant line:
build: noarch: generic number: 0 - skip: False run_exports: - {{ pin_subpackage('sipros', max_pin="x") }}
30-40: Improve test command consistency and consider symlinking scripts.The test commands provide good coverage of the package components. However, there are some inconsistencies in naming conventions (e.g.,
EnsembleScripts_vsV4Scripts_). Additionally, as suggested in the past review comments, consider symlinking Python scripts to$PREFIX/binor using Python entry points for easier access.
- Standardize the naming conventions for test commands.
- Implement symlinking or Python entry points as suggested in the past review comments.
Example of using Python entry points in the
build.shscript:#!/bin/bash # ... other build steps ... # Create entry points for Python scripts cat << EOF >> $PREFIX/bin/sipros_psm_tabulating #!/bin/bash python $PREFIX/EnsembleScripts/sipros_psm_tabulating.py "\$@" EOF chmod +x $PREFIX/bin/sipros_psm_tabulating # Repeat for other scripts...Then update the test commands to use these entry points:
test: commands: - configGenerator -h - SiprosEnsembleOMP --help - SiprosV4OMP --help - Raxport -h - sipros_psm_tabulating -v - sipros_peptides_filtering -v - getSpectraCountInEachFT -help - refineProteinFDR -help - copyConfigTemplate -SIPThis approach allows users to call the scripts directly by their names without using
$CONDA_PREFIX.Would you like assistance in implementing these changes or creating a GitHub issue to track this task?
18-18: Remove trailing spaces.There are trailing spaces on this line that should be removed.
Apply this diff to remove the trailing spaces:
- +🧰 Tools
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[error] 18-18: trailing spaces
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📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- recipes/sipros/build.sh (1 hunks)
- recipes/sipros/copyConfigTemplate.sh (1 hunks)
- recipes/sipros/meta.yaml (1 hunks)
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recipes/sipros/meta.yaml
[error] 18-18: trailing spaces
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🔇 Additional comments (7)
recipes/sipros/build.sh (3)
1-7: LGTM: Proper script setup and initial file operations.The script starts with the correct shebang line and uses
set -efor error handling, which are good practices. The initial directory creation and file copying operations are appropriate for the build process.
27-31: LGTM: Proper handling of R scripts.The processing of R scripts, including adding the correct shebang lines and creating symbolic links, is done correctly. The approach is consistent with the Python script processing, which is good for maintainability.
1-35: Overall, the build script is well-structured and functional.The script successfully sets up the sipros package, copying necessary files, processing Python and R scripts, and setting appropriate permissions. The suggestions provided in the review are minor optimizations for error handling, code reduction, and consistency. These improvements would enhance the script's robustness and maintainability, but the current implementation is already functional and follows good practices.
recipes/sipros/meta.yaml (4)
1-10: LGTM: Package and source information are well-defined.The package name and version are correctly set using Jinja2 templating, which is good for maintainability. The source URL and SHA256 checksum are properly specified, ensuring integrity during package installation.
🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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51-57: LGTM: Extra section is well-defined.The extra section includes appropriate recipe maintainers and identifiers. The inclusion of the biotools identifier and DOI enhances the package's discoverability and citability.
42-49:⚠️ Potential issueFollow up on LICENSE file inclusion in the upstream repository.
The about section is well-defined with comprehensive information. However, the comment about including the LICENSE file in the recipe folder indicates an issue with the upstream repository.
Follow up with the upstream repository (https://github.com/thepanlab/Sipros4) to include the LICENSE file in their releases. This will allow you to remove the LICENSE file from the recipe folder and update the
license_fileentry accordingly.To verify if the issue has been resolved, you can run:
#!/bin/bash # Check if the LICENSE file is present in the latest release latest_release=$(gh api repos/thepanlab/Sipros4/releases/latest --jq .tag_name) gh api repos/thepanlab/Sipros4/contents/LICENSE?ref=$latest_releaseIf the issue is still present, consider opening a GitHub issue in the upstream repository to address this.
19-28:⚠️ Potential issueUpdate dependencies and add build requirements.
The requirements section has some issues:
- The package uses Python 2.7, which is no longer supported. Consider updating to a modern Python version.
- The numpy and scikit-learn versions are outdated. Update these to more recent versions for better compatibility and security.
- There are no build-time dependencies specified, which is unusual for a package with compiled components.
Consider applying these changes:
- Update Python dependency to a supported version (e.g.,
python >=3.7).- Update numpy and scikit-learn to more recent versions.
- Add a
hostsection for build-time dependencies.Example diff:
requirements: + host: + - python >=3.7 + - pip run: - bioconductor-biostrings - mono - - numpy =1.16 - - python =2.7 + - numpy >=1.19 + - python >=3.7 - r-base - r-stringr - r-tidyr - - scikit-learn =0.20.3 + - scikit-learn >=0.24Please verify compatibility with these updated versions before applying the changes.
To check for any compatibility issues with the suggested updates, you can run:
There was a problem hiding this comment.
Thanks @xyz1396 . I think the suggested refactoring could be useful.
Let me know if I should merge as it is, or if you want to integrate the suggestion.
Co-authored-by: M Bernt <m.bernt@ufz.de>
|
Thanks a lot for all the work @xyz1396 I can start now to work on a Galaxy integration. Let me know if you have any wishes regarding this. |
Feel free to tag me when creating the PR, and I'll assist with it. |
add sipros for sip proteomics
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