Add Cloudspades #51399
Add Cloudspades #51399
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces a new metadata file, Possibly related PRs
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🔇 Additional comments (5)
recipes/cloudspades/meta.yaml (5)
42-49: Comprehensive test sectionThe test section is well-designed and covers various aspects of the package:
- Version checks for main components (spades.py, metaspades.py)
- Presence checks for utility tools (spades-kmercount, spades-gmapper, spades-gbuilder)
- A functional test run of spades.py with proper cleanup
This comprehensive approach helps ensure that the package is correctly installed and functioning as expected.
51-58: Well-documented about sectionThe about section provides comprehensive metadata for the package:
- Clear specification of the home page and license (GPL-2.0-only)
- Concise and informative summary of the package's purpose
- Links to development (dev_url) and documentation (doc_url) resources
This information is valuable for users and maintainers of the package.
60-65: Extra section provides valuable additional informationThe extra section includes:
- Additional platform support for linux-aarch64 and osx-arm64, which is great for broader compatibility.
- Clear specification of the recipe maintainer (pdimens).
This information is helpful for users and other maintainers.
1-3: Note on YAML syntaxThe static analysis tool (yamllint) reports a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' characters are part of the Jinja2 template syntax, which is commonly used and valid in Conda recipe files. The YAML is processed correctly by Conda's build system, which interprets these Jinja2 templates.
No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
14-23: Build section looks good, with a note on compiler flagsThe build section is well-structured with appropriate run exports and environment setup. The use of
${CPU_COUNT}for parallel compilation is a good practice.Note: The
-fcommonflag is used in the CFLAGS and CXXFLAGS. This flag is sometimes necessary for older codebases that rely on C89-style tentative definitions. However, it's worth considering if this flag is actually required for Cloudspades, as it's generally not recommended for modern C++ code.To verify if the
-fcommonflag is necessary, you can try building without it:If the build succeeds without the flag, consider removing it for better compatibility with modern compilers.
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recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/cloudspades/meta.yaml (5)
14-23: Build section looks goodThe build section is well-structured and follows Conda build best practices. It correctly sets up environment variables, uses run_exports for dependency management, and employs parallel compilation for efficiency.
42-49: Comprehensive test sectionThe test section is well-designed with multiple commands to verify the installation and functionality of the package. It includes version checks for various components and a cleanup step after running the test.
51-58: Well-documented about sectionThe about section provides comprehensive metadata for the package, including correct license information, a clear summary of the package's purpose, and relevant URLs for home, development, and documentation.
60-62: Extra section is correctThe extra section correctly lists the recipe maintainer (pdimens), which aligns with the PR submitter information provided in the PR objectives.
1-11:⚠️ Potential issueVersion mismatch between package and source URL
The package version is set to 3.16.0, but the source URL points to the tag cloudspades-0.1. This inconsistency could lead to confusion and potential issues during the build process.
Consider updating either the package version or the source URL to ensure they match. For example:
{% set version = "0.1" %} ... source: url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-{{ version }}.tar.gzAlternatively, if 3.16.0 is the correct version, update the URL accordingly.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/cloudspades/meta.yaml (6)
14-27: Build section looks goodThe build section is well-structured and follows best practices. It correctly sets up environment variables, uses parallel execution for compilation, and specifies run exports and ignore run exports.
46-53: Test section is comprehensiveThe test section includes a good set of commands to verify the installation and functionality of the package. It checks for correct versions and the presence of key components.
55-62: About section is well-documentedThe about section provides comprehensive metadata for the package, including home URL, license information, summary, and relevant links. The use of an environment variable for the license file path is a good practice.
64-66: Extra section is concise and appropriateThe extra section correctly lists the recipe maintainer.
1-3: Ignore yamllint error for Jinja2 syntaxThe yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive, as the '%' character is valid in Jinja2 templates, which are commonly used in Conda recipes. No action is required to address this error.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-11:⚠️ Potential issueVersion mismatch between package and source URL
The package version is set to 3.16.0, but the source URL points to the tag cloudspades-0.1. This inconsistency could lead to confusion and potential issues during the build process.
Please update either the package version or the source URL to ensure they match. For example:
{% set version = "0.1" %} ... source: url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-{{ version }}.tar.gzAlternatively, if 3.16.0 is the correct version, update the URL accordingly.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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🧹 Outside diff range and nitpick comments (1)
recipes/cloudspades/meta.yaml (1)
1-66: Overall, the recipe is well-structured with one key issue to addressThe Cloudspades recipe is generally well-written and follows Conda packaging best practices. It includes comprehensive metadata, appropriate build instructions, well-defined requirements, and thorough test commands.
However, there is one critical issue that needs to be addressed:
- The version mismatch between the package version (3.16.0) and the source URL tag (cloudspades-0.1) needs to be resolved to ensure consistency and prevent potential build issues.
Once this issue is addressed, the recipe should be ready for inclusion in the Bioconda repository.
Next steps:
- Resolve the version mismatch issue.
- Update the test commands to use the correct version if necessary.
- Re-run the build and test process to ensure everything works as expected.
Would you like assistance in resolving the version mismatch or updating the test commands?
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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- recipes/cloudspades/meta.yaml (1 hunks)
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🪛 yamllint
recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/cloudspades/meta.yaml (5)
14-28: Build section looks goodThe build section is well-structured and follows best practices:
- Appropriate use of
run_exportsfor pinning thecloudspadessubpackage.- Correct usage of
ignore_run_exportsforlibgomp,zlib, andbzip2.- The build script properly sets up environment variables and uses parallel compilation.
Good job on this section!
30-44: Requirements section is well-definedThe requirements section is properly structured and includes all necessary components for building and running the package. Good job on:
- Specifying appropriate build tools and compilers.
- Including OS-specific libraries (llvm-openmp for macOS, libgomp for Linux).
- Correctly specifying the Python version constraint as ">=3.8".
The Python version constraint issue mentioned in a previous review has been addressed.
55-62: About section is complete and informativeThe about section provides comprehensive metadata for the package:
- Home page, license information, and summary are well-defined.
- Development and documentation URLs are included.
- The license file path is correctly specified.
Good job on providing thorough package information!
64-66: Extra section is correctly definedThe extra section properly lists the recipe maintainer (pdimens), which matches the PR submitter mentioned in the PR objectives. This is correct and follows the expected format for Bioconda recipes.
1-11:⚠️ Potential issueVersion mismatch between package and source URL
The package version is set to 3.16.0, but the source URL points to the tag cloudspades-0.1. This inconsistency could lead to confusion and potential issues during the build process.
Please update either the package version or the source URL to ensure they match. For example:
{% set version = "0.1" %} ... source: url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-{{ version }}.tar.gzAlternatively, if 3.16.0 is the correct version, update the URL accordingly.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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- recipes/cloudspades/meta.yaml (1 hunks)
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recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/cloudspades/meta.yaml (5)
14-28: Build section looks goodThe build section is well-structured and follows best practices:
- Appropriate use of
run_exportsfor pinning thecloudspadessubpackage.- Correct usage of
ignore_run_exportsforlibgomp,zlib, andbzip2.- The build script properly sets up environment variables and uses parallel compilation.
Good job on this section!
30-44: Requirements section is well-definedThe requirements section is comprehensive and well-structured:
- Build requirements include necessary compilers and build tools.
- Host requirements correctly specify platform-specific libraries (llvm-openmp for macOS, libgomp for Linux).
- Run requirements include the appropriate Python version constraint (>=3.8).
Good job on defining the package dependencies!
46-53: Potential issue with version checks in test commandsThe test commands are comprehensive and verify the installation of key components. However, due to the version mismatch identified earlier (package version 3.16.0 vs. source URL 0.1), the version checks may fail:
- spades.py --version 2>&1 | grep {{ version }} - metaspades.py --version 2>&1 | grep {{ version }}Once the version mismatch is resolved, ensure that these test commands use the correct version number.
54-61: About section is complete and informativeThe about section provides comprehensive metadata for the package:
- Correct home page and license information.
- Clear and concise summary of the package's purpose.
- Appropriate dev_url and doc_url links.
This section effectively communicates essential information about the package to users.
63-65: Extra section is concise and correctThe extra section correctly lists the recipe maintainer (pdimens), which matches the PR submitter. This information is sufficient for the extra section.
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🧹 Outside diff range and nitpick comments (1)
recipes/cloudspades/meta.yaml (1)
16-16: Add a comment explaining the reason for skipping OSX buildsIt's good practice to provide a brief explanation for platform-specific build conditions.
Consider adding a comment explaining why the package is skipped for OSX:
skip: True # [osx] # Reason: <explain why it's not built for OSX>
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recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/cloudspades/meta.yaml (4)
32-44: LGTM: Well-structured requirements sectionThe requirements section is well-organized and includes necessary components for building and running the package. The Python version constraint (>=3.8) is appropriately relaxed, allowing for compatibility with multiple Python versions while ensuring a minimum supported version.
54-61: LGTM: Comprehensive about sectionThe about section provides all necessary information, including the home URL, license details, a concise summary, and relevant development and documentation URLs. This helps users and maintainers understand the package's purpose and find additional resources.
63-65: LGTM: Concise extra sectionThe extra section correctly lists the recipe maintainer. This information is crucial for package management and future updates.
1-3: Note: Ignore yamllint false positiveThe yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as these lines use Jinja2 template syntax, which is standard in Conda recipe files. You can safely ignore this warning.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/cloudspades/meta.yaml (2)
32-44: Consider specifying a more precise Python version rangeThe current Python version requirement (
python >=3.8) is quite broad and may lead to compatibility issues with future Python versions. For bioinformatics tools, it's often beneficial to specify a more precise version range to ensure compatibility and reproducibility.Consider updating the Python requirement to a more specific range, for example:
run: - libgomp # [linux] - python >=3.8,<3.11This change would allow for minor version updates while still ensuring compatibility with tested Python versions.
1-3: Note on yamllint errorThe yamllint tool reports a syntax error for the '%' characters at the beginning of the file. This is a false positive, as these characters are part of the Jinja2 templating syntax commonly used in Conda recipes.
To suppress this warning, you can add a yamllint configuration file (
.yamllint) to the repository with the following content:extends: default rules: document-start: disableThis will disable the document-start rule, which is causing the false positive for Jinja2 syntax.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/cloudspades/meta.yaml (3)
55-62: About section is well-structured and informativeThe about section provides comprehensive information about the package, including its purpose, license, and relevant URLs. This is excellent for users and maintainers to understand the package's context and find additional resources.
64-66: Extra section is concise and completeThe extra section correctly lists the recipe maintainer (pdimens). This information is crucial for package management and future updates.
14-30: Clarify OSX skip conditionThe build section includes a skip condition for OSX (
skip: True # [osx]). While this may be intentional, it's important to ensure that this limitation is necessary and documented.Could you please provide a brief explanation for why the package is skipped on OSX? This information would be valuable for users and maintainers to understand the package's limitations.
#!/bin/bash # Description: Check if OSX skip condition is documented if grep -q "skip: True # \[osx\]" recipes/cloudspades/meta.yaml; then if grep -q "OSX" recipes/cloudspades/meta.yaml | grep -v "skip: True # \[osx\]"; then echo "OSX skip condition is mentioned elsewhere in the file." else echo "OSX skip condition is not documented. Consider adding a comment explaining the reason." fi else echo "OSX skip condition not found in the file." fi
recipes/cloudspades/meta.yaml
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| test: | ||
| commands: | ||
| - spades.py --version 2>&1 | grep {{ version }} | ||
| - metaspades.py --version 2>&1 | grep {{ version }} | ||
| - spades-kmercount -h 2>&1 | grep spades-kmercount | ||
| - spades-gmapper 2>&1 | grep spades-gmapper | ||
| - spades-gbuilder 2>&1 | grep spades-gbuilder | ||
| - spades.py --gemcode1-12 assembler/test_dataset_cloudspades/test.fastq.gz -o cloudspades_test |
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Update version checks in test commands
The test commands use {{ version }} for version checks, which currently refers to version 3.16.0. This may cause the tests to fail due to the version mismatch with the source URL (cloudspades-0.1) identified earlier.
After resolving the version mismatch issue, ensure that the version checks in the test commands are updated accordingly. For example:
commands:
- spades.py --version 2>&1 | grep {{ version }}
- metaspades.py --version 2>&1 | grep {{ version }}Replace {{ version }} with the correct version once it's been determined and consistently applied throughout the recipe.
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (2)
recipes/cloudspades/build.sh (1)
10-10: Consider adding error handling for directory changeThe
cd assemblercommand assumes that the 'assembler' directory exists. To improve robustness, consider adding error handling.Here's a suggested improvement:
-cd assembler +if [ -d "assembler" ]; then + cd assembler +else + echo "Error: 'assembler' directory not found" >&2 + exit 1 +fiThis change will provide a clear error message if the 'assembler' directory is missing, making debugging easier.
recipes/cloudspades/0001-change-verbosity-remove-expr.patch (1)
27-27: Use$(uname)instead of backticks for command substitutionIn line 27, using
$(...)for command substitution is recommended for better readability and nesting support.Apply this diff:
-if [[ `uname` == "Darwin" ]]; then +if [[ $(uname) == "Darwin" ]]; then
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- recipes/cloudspades/build.sh (1 hunks)
- recipes/cloudspades/meta.yaml (1 hunks)
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recipes/cloudspades/meta.yaml
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recipes/cloudspades/build.sh (3)
1-3: LGTM: Robust error handling setupThe script header and error handling setup are well-configured. The use of
set -e -o pipefail -xensures that the script will fail fast on errors and provide verbose output, which is excellent for debugging and maintaining build integrity.
11-11: Compilation command looks good, but consider optimizing parallelismThe compilation command is well-structured and includes necessary options. However, there are a couple of points to consider:
- The
-rj2option appears to limit the build to 2 parallel jobs. This might not be optimal for all build environments. Consider using the$CPU_COUNTvariable provided by conda-build to optimize parallelism:-PREFIX="${PREFIX}" bash spades_compile.sh -rj2 -DSPADES_ENABLE_PROJECTS="all" +PREFIX="${PREFIX}" bash spades_compile.sh -rj$CPU_COUNT -DSPADES_ENABLE_PROJECTS="all"
- The
SPADES_ENABLE_PROJECTS="all"option enables all projects. While this might be intentional, it's worth verifying if all projects are necessary for Cloudspades specifically.To better understand the available options and projects, please run:
#!/bin/bash # Description: Investigate spades_compile.sh options and available projects # Test: Check spades_compile.sh for available options grep -n '\-\-help' assembler/spades_compile.sh # Test: List all available projects grep -n 'SPADES_ENABLE_PROJECTS' assembler/spades_compile.shThis will help clarify the available options and projects, allowing for a more informed decision on the compilation parameters.
5-8: Environment setup looks good, but verify the need for -fcommonThe environment variable setup is correct and follows best practices for Conda builds. The use of
${PREFIX}ensures compatibility with the Conda build environment.However, the inclusion of the
-fcommonflag in both CFLAGS and CXXFLAGS is noteworthy:
- This flag is typically used to address issues with multiple definitions of global variables, which became the default behavior in GCC 10.
- Its presence suggests that the Cloudspades codebase might have some compatibility issues with newer GCC versions.
To ensure this flag is necessary, please run the following script:
If the flag is indeed necessary, consider adding a comment in the script explaining why it's required.
recipes/cloudspades/meta.yaml (4)
13-17: Build section looks goodThe build section is well-structured:
- The build number is correctly set to 0 for the initial release.
- The use of
run_exportswithpin_subpackageis a good practice for ensuring proper version pinning of the cloudspades package.
18-32: Requirements section is well-definedThe requirements section is comprehensive and well-structured:
- Build requirements include necessary compilers and build tools.
- Host requirements correctly specify OS-specific libraries (libgomp for Linux, llvm-openmp for macOS).
- Run requirements include the necessary OS-specific libraries and Python >=3.8.
The use of OS-specific libraries and the flexible Python version constraint are good practices for ensuring cross-platform compatibility and allowing for future minor version updates.
43-50: About section is well-documentedThe about section provides comprehensive metadata for the package:
- Home, license, summary, dev_url, and doc_url are all properly specified.
- The license is correctly identified as GPL-2.0-only with the appropriate license family.
- The summary clearly explains the purpose and functionality of the package.
This level of detail in the about section is excellent for users and maintainers alike.
52-54: Extra section is correctly specifiedThe extra section correctly lists the recipe maintainer (pdimens). This information is crucial for package management and future updates.
recipes/cloudspades/0001-change-verbosity-remove-expr.patch (2)
12-13: Good use of parameter expansion instr_tailfunctionThe updated
str_tail()function correctly uses parameter expansion to extract the substring without the first character.
27-41: Enhance build process with macOS compatibility adjustmentsThe updated build process improves compatibility with macOS by adjusting configuration and compiler flags. The modernized
cmakecommands enhance clarity and maintainability.
recipes/cloudspades/meta.yaml
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| test: | ||
| commands: | ||
| - spades.py --version 2>&1 | grep {{ version }} | ||
| - metaspades.py --version 2>&1 | grep {{ version }} | ||
| - spades-kmercount -h 2>&1 | grep spades-kmercount | ||
| - spades-gmapper 2>&1 | grep spades-gmapper | ||
| - spades-gbuilder 2>&1 | grep spades-gbuilder | ||
| - spades.py --gemcode1-12 assembler/test_dataset_cloudspades/test.fastq.gz -o cloudspades_test |
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Test commands are comprehensive, but version check may fail
The test section includes a good set of commands to verify the installation and functionality of the package. However, there's a potential issue:
- The version check commands (lines 36-37) use
{{ version }}, which is set to 3.16.0. This might fail if the actual version from the source URL (cloudspades-0.1) is different.
Suggestion:
- After resolving the version mismatch issue, ensure that the version checks in the test commands are updated accordingly.
Additionally, consider adding a check for the exit status of the final spades.py command to ensure it runs successfully:
- spades.py --gemcode1-12 assembler/test_dataset_cloudspades/test.fastq.gz -o cloudspades_test && test -d cloudspades_testThis addition will verify that the output directory is created, indicating a successful run.
recipes/cloudspades/meta.yaml
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| {% set name = "cloudspades" %} | ||
| {% set version = "3.16.0" %} | ||
| {% set sha256 = "5972a76722fadf9527675fea3884a03ca864b153b8de9dd94532b1b797de04aa" %} | ||
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| package: | ||
| name: {{ name }} | ||
| version: {{ version }} | ||
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| source: | ||
| url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz | ||
| sha256: {{ sha256 }} | ||
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| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage('cloudspades', max_pin="x") }} | ||
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| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - cmake | ||
| - make | ||
| - pkg-config | ||
| host: | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - zlib | ||
| - bzip2 | ||
| run: | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - python >=3.8 | ||
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| test: | ||
| commands: | ||
| - spades.py --version 2>&1 | grep {{ version }} | ||
| - metaspades.py --version 2>&1 | grep {{ version }} | ||
| - spades-kmercount -h 2>&1 | grep spades-kmercount | ||
| - spades-gmapper 2>&1 | grep spades-gmapper | ||
| - spades-gbuilder 2>&1 | grep spades-gbuilder | ||
| - spades.py --gemcode1-12 assembler/test_dataset_cloudspades/test.fastq.gz -o cloudspades_test | ||
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| about: | ||
| home: "https://github.com/ablab/spades" | ||
| license: "GPL-2.0-only" | ||
| license_family: GPL | ||
| license_file: 'assembler/LICENSE' | ||
| summary: "A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging)." | ||
| dev_url: "https://github.com/ablab/spades" | ||
| doc_url: "https://github.com/ablab/spades/tree/cloudspades-ismb" | ||
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| extra: | ||
| recipe-maintainers: | ||
| - pdimens |
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Overall assessment: Well-structured recipe with one critical issue
The Cloudspades recipe is generally well-written and follows Conda packaging best practices. It includes comprehensive metadata, appropriate build instructions, well-defined requirements, and thorough test commands.
However, there is one critical issue that needs to be addressed:
- The version mismatch between the package version (3.16.0) and the source URL tag (cloudspades-0.1) needs to be resolved to ensure consistency and prevent potential build issues.
Additionally, minor improvements can be made to the test section to ensure robustness of the package verification process.
Once these issues are addressed, the recipe should be ready for inclusion in the Bioconda repository.
Would you like assistance in resolving the version mismatch or implementing the suggested improvements?
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| -str_head() { echo "$(expr substr "$1" 1 1)"; } | ||
| +str_head() { echo "${1::1}"; } |
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Fix incorrect parameter expansion syntax in str_head function
The new implementation of str_head() uses ${1::1} to extract the first character, but this syntax is invalid in bash. The correct syntax should be ${1:0:1}.
Apply this diff to fix the syntax error:
-str_head() { echo "${1::1}"; }
+str_head() { echo "${1:0:1}"; }📝 Committable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| -str_head() { echo "$(expr substr "$1" 1 1)"; } | |
| +str_head() { echo "${1::1}"; } | |
| -str_head() { echo "$(expr substr "$1" 1 1)"; } | |
| +str_head() { echo "${1:0:1}"; } |
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/cloudspades/meta.yaml (1)
18-32: Consider specifying an upper bound for the Python versionThe requirements section is well-structured and includes necessary components for building and running the package. However, the Python version constraint
>=3.8might be too permissive and could lead to compatibility issues with future Python versions.Consider specifying an upper bound for the Python version to ensure compatibility. For example:
run: - libgomp # [linux] - llvm-openmp # [osx] - python >=3.8,<4.0This change would allow for minor version updates within Python 3.x while preventing potential incompatibilities with Python 4.x (when it becomes available).
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- recipes/cloudspades/build.sh
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🪛 yamllint
recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/cloudspades/meta.yaml (3)
13-17: LGTM: Build section is well-configuredThe build section is correctly set up with an initial build number and appropriate run_exports configuration. This ensures proper pinning of the cloudspades subpackage when used as a dependency.
51-53: LGTM: Extra section is correctly formattedThe extra section is properly configured with the recipe maintainer information.
1-1: Note: Ignore yamllint syntax error for Jinja2 templatesThe static analysis tool yamllint reports a syntax error for the '%' character at the beginning of the file. This is a false positive and can be safely ignored.
The '%' character is part of the Jinja2 template syntax, which is commonly used in Conda recipe files to define variables and control structures. While it's not standard YAML syntax, it's perfectly valid and necessary for Conda recipes.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (2)
- recipes/cloudspades/build.sh (1 hunks)
- recipes/cloudspades/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/cloudspades/build.sh
🧰 Additional context used
🪛 yamllint
recipes/cloudspades/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/cloudspades/meta.yaml (6)
13-18: Build section looks goodThe build section is well-configured:
- Build number is correctly set to 0 for the initial release.
- The package is appropriately skipped for macOS.
- Run exports are properly defined for the cloudspades subpackage.
No issues found in this section.
19-33: Requirements section is well-definedThe requirements section is comprehensive and well-structured:
- Build requirements include necessary compilers and build tools.
- Host requirements correctly specify platform-specific libraries and dependencies.
- Run requirements are appropriate, including the correct Python version constraint (>=3.8).
No issues found in this section.
52-54: Extra section is correctly formattedThe extra section is properly configured:
- The recipe maintainer (pdimens) is correctly listed.
No issues found in this section.
1-11:⚠️ Potential issueCritical: Version mismatch between package and source URL
The package version is set to 3.16.0, but the source URL points to the tag cloudspades-0.1. This inconsistency will lead to build failures and incorrect package versioning.
To resolve this issue, please update either the package version or the source URL to ensure they match. For example:
{% set version = "0.1" %} ... source: url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-{{ version }}.tar.gzAlternatively, if 3.16.0 is the correct version, update the URL accordingly.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
35-42:⚠️ Potential issueImprove test commands and resolve version mismatch
The test commands are comprehensive, but there are two issues to address:
The version check commands (lines 37-38) use
{{ version }}, which is set to 3.16.0. This will fail due to the version mismatch with the source URL (cloudspades-0.1) identified earlier.The test commands could be more robust by checking the exit status of the commands.
To resolve these issues:
After resolving the version mismatch issue, ensure that the version checks in the test commands are updated accordingly.
Modify the test commands to check for successful execution. For example:
commands: - spades.py --version 2>&1 | grep {{ version }} - metaspades.py --version 2>&1 | grep {{ version }} - spades-kmercount -h - spades-gmapper --help - spades-gbuilder --help - spades.py --testThe last command,
spades.py --test, runs a built-in test suite (if available) to ensure the core functionality is working correctly.
43-50:⚠️ Potential issueInconsistent documentation URL
The about section provides comprehensive metadata about the package. However, there's an inconsistency in the documentation URL:
- The
dev_urlpoints to thecloudspades-0.1tag, which is consistent with the source URL.- The
doc_urlpoints to a different tag (cloudspades-ismb).To maintain consistency, consider updating the
doc_urlto match the version used in the source URL anddev_url. For example:doc_url: "https://github.com/ablab/spades/tree/cloudspades-0.1"Alternatively, if the
cloudspades-ismbtag contains the most up-to-date documentation, consider updating the source URL anddev_urlto use this tag instead.
| {% set name = "cloudspades" %} | ||
| {% set version = "3.16.0" %} | ||
| {% set sha256 = "5972a76722fadf9527675fea3884a03ca864b153b8de9dd94532b1b797de04aa" %} | ||
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| package: | ||
| name: {{ name }} | ||
| version: {{ version }} | ||
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| source: | ||
| url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz | ||
| sha256: {{ sha256 }} | ||
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| build: | ||
| number: 0 | ||
| skip: True # [osx] | ||
| run_exports: | ||
| - {{ pin_subpackage('cloudspades', max_pin="x") }} | ||
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| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - cmake | ||
| - make | ||
| - pkg-config | ||
| host: | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - zlib | ||
| - bzip2 | ||
| run: | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - python >=3.8 | ||
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| test: | ||
| commands: | ||
| - spades.py --version 2>&1 | grep {{ version }} | ||
| - metaspades.py --version 2>&1 | grep {{ version }} | ||
| - spades-kmercount -h 2>&1 | grep spades-kmercount | ||
| - spades-gmapper 2>&1 | grep spades-gmapper | ||
| - spades-gbuilder 2>&1 | grep spades-gbuilder | ||
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| about: | ||
| home: "https://github.com/ablab/spades" | ||
| license: "GPL-2.0-only" | ||
| license_family: GPL | ||
| license_file: 'assembler/LICENSE' | ||
| summary: "A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging)." | ||
| dev_url: "https://github.com/ablab/spades/tree/cloudspades-0.1" | ||
| doc_url: "https://github.com/ablab/spades/tree/cloudspades-ismb" | ||
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| extra: | ||
| recipe-maintainers: | ||
| - pdimens |
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Overall assessment: Well-structured recipe with critical issues to address
The Cloudspades recipe is generally well-written and follows Conda packaging best practices. It includes comprehensive metadata, appropriate build instructions, well-defined requirements, and thorough test commands.
However, there are critical issues that need to be addressed before the recipe can be included in the Bioconda repository:
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Version mismatch: The package version (3.16.0) doesn't match the source URL tag (cloudspades-0.1). This needs to be resolved to ensure consistency and prevent potential build issues.
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Test commands: The version checks in the test commands need to be updated once the version mismatch is resolved. Additionally, the test commands could be made more robust by checking exit statuses and including a comprehensive test suite run.
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Documentation URL: The
doc_urlpoints to a different tag (cloudspades-ismb) than thedev_urland source URL. This inconsistency should be resolved.
Once these issues are addressed, the recipe should be ready for inclusion in the Bioconda repository. Please review and update the highlighted sections to ensure consistency and correctness throughout the recipe.
Would you like assistance in resolving these issues or implementing the suggested improvements?
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Describe your pull request here
Adds a recipe for cloudspades that hopefully compiles properly.
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
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...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
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