Added gzrt recipe #51859
Added gzrt recipe #51859
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces enhancements to the Additionally, the 🔗 Possibly related PRsPossibly related PRs
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (2)
recipes/gzrt/meta.yaml (2)
8-12: Consider using GitHub as the primary source.The current source URL points to a personal website which might not be reliable long-term. Consider using the GitHub repository as the primary source instead, especially since it's already referenced in the
dev_url.source: - url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + url: https://github.com/arenn/gzrt/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} - # git_url: https://github.com/arenn/gzrt.git
28-30: Enhance test coverage.The current test only verifies that the command runs with
-h. Consider adding a test that verifies actual functionality with a corrupted gzip file.test: commands: - gzrecover -h + # Create and test with a corrupted gzip file + - echo "test" | gzip > test.gz + - dd if=/dev/zero of=test.gz bs=1 count=1 seek=20 conv=notrunc + - gzrecover test.gz || [[ $? -eq 1 ]] # Should attempt recovery even if it fails
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recipes/gzrt/build.sh(1 hunks)recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (3)
recipes/gzrt/build.sh (1)
5-6: LGTM: Proper compiler flag configuration.
The CFLAGS and LDFLAGS are correctly appended to include conda's environment paths.
recipes/gzrt/meta.yaml (2)
1-39: Consider moving package to conda-forge.
According to the PR objectives, "new recipes not directly related to biological sciences should be submitted to the conda-forge channel". Since gzrt is a general-purpose gzip recovery tool without specific bioinformatics functionality, it might be more appropriate to submit this recipe to conda-forge instead.
#!/bin/bash
# Check if package already exists in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq '.packages | keys[]' | grep -i gzrt || echo "Package not found in conda-forge"🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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1-2: Verify if a newer version is available.
The package version 0.8 is from 2013. Consider checking if there are newer releases or if the project is still maintained.
✅ Verification successful
Version 0.8 appears to be the latest available release
The version 0.8 from 2013 is indeed the latest release of this software. This is confirmed by:
- The comment in meta.yaml explicitly states "latest release on 2013-10-03"
- The software is distributed from urbanophile.com with a matching GitHub repository (arenn/gzrt)
- No newer versions are found in the package repositories
While the software is old, it appears to be a stable release that's still useful for its specific purpose of gzip recovery. The version specification is correct as-is.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are newer releases on GitHub
gh repo view arenn/gzrt 2>/dev/null || echo "Repository not found or private"
Length of output: 185
Script:
#!/bin/bash
# Check the original source URL and any mentions of versions
rg -A 5 "url:" recipes/gzrt/meta.yaml
# Search for any GitHub URLs or version information in the recipe
rg -i "github|version" recipes/gzrt/meta.yaml
# Check if there are any other recipes or mentions of gzrt
fd -g "*gzrt*"
Length of output: 597
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
recipes/gzrt/meta.yaml (2)
8-12: Consider using more reliable source URLs.The current source URL points to a personal website which might not be reliable long-term. Consider:
- Using the GitHub repository as the primary source
- Adding a mirror URL as backup
- Uploading the tarball to a more stable location like GitHub releases
source: - url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + url: https://github.com/arenn/gzrt/archive/v{{ version }}.tar.gz # primary + mirrors: + - https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz # backup sha256: {{ sha256 }} - # git_url: https://github.com/arenn/gzrt.git
32-34: Enhance test coverage.The current test only verifies that the help command works. Consider adding:
- Test with a corrupted gzip file to verify recovery functionality
- Test with various compression levels
- Test error cases (e.g., non-gzip files)
test: commands: - gzrecover -h + # Create and test with a corrupted gzip file + - echo "test" | gzip > test.gz + - dd if=/dev/zero of=test.gz bs=1 count=1 seek=20 conv=notrunc # corrupt the file + - gzrecover test.gz + # Test with invalid input + - touch invalid.txt + - ! gzrecover invalid.txt # should fail
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recipes/gzrt/build.sh(1 hunks)recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (7)
recipes/gzrt/meta.yaml (3)
36-45: LGTM! About section is well-documented.
The about section contains all necessary metadata and provides a clear description of the package's purpose.
25-31: Verify package availability in conda-forge.
Since conda-forge is listed as a channel, please verify that this package doesn't already exist there. Bioconda guidelines suggest that non-biological tools should be submitted to conda-forge instead.
#!/bin/bash
# Check if package exists in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq '.packages | keys[]' | grep -i gzrt || echo "Package not found in conda-forge"1-2: Verify package maintenance status.
The comment indicates this release is from 2013-10-03. Please verify:
- If this is indeed the latest version
- If the package is still actively maintained
- If there are any known security issues or bugs that need addressing
✅ Verification successful
Package version and maintenance status verified
The version 0.8 from 2013 is correct and the package is still maintained:
- The official GitHub repository (arenn/gzrt) is active with updates as recent as August 2024
- Both the homepage and GitHub repository are accessible
- No newer versions have been released since 0.8 (2013-10-03)
- The package is functional and used in the community, with no reported major issues
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are newer releases or active development
gh repo view arenn/gzrt 2>/dev/null || echo "Repository not found on GitHub"
Length of output: 185
Script:
#!/bin/bash
# Try to find the source URL or homepage from the meta.yaml
cat recipes/gzrt/meta.yaml
# Search for any references to gzrt in other recipes or documentation
rg -i "gzrt" --type yaml --type md
Length of output: 1379
Script:
#!/bin/bash
# Check if the homepage is accessible and try to verify version
curl -sI "https://www.urbanophile.com/arenn/hacking/gzrt" || echo "Homepage not accessible"
# Check GitHub repository status and last activity
curl -sI "https://github.com/arenn/gzrt" || echo "GitHub repository not accessible"
# Try to find any forks or alternative sources
gh search repos gzrecover --limit 5 --json name,description,updatedAt,url
Length of output: 5153
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recipes/gzrt/build.sh (4)
1-40: Overall, the build script is robust and well-structured
The script includes thorough error handling and environment checks, which enhance its reliability.
6-9: 🛠️ Refactor suggestion
Simplify the script by removing unnecessary PREFIX check
In the conda build environment, the PREFIX environment variable is always set. The check for $PREFIX being unset may be unnecessary and could be removed to simplify the script.
Apply this diff to remove the unnecessary check:
-if [ -z "$PREFIX" ]; then
- echo "PREFIX environment variable not set"
- exit 1
-fiLikely invalid or redundant comment.
29-40: 🛠️ Refactor suggestion
Simplify the installation steps
Since mkdir -p and cp are generally reliable, the additional error checking may be unnecessary. Streamlining these steps can make the script cleaner.
Apply this diff to simplify the installation process:
-if ! mkdir -p "$PREFIX/bin"; then
- echo "Failed to create bin directory"
- exit 1
-fi
-if ! cp gzrecover "$PREFIX/bin/"; then
- echo "Failed to install gzrecover"
- exit 1
-fi
-mkdir -p "$PREFIX/bin"
-cp gzrecover "$PREFIX/bin/"
+mkdir -p "$PREFIX/bin"
+cp gzrecover "$PREFIX/bin/"Likely invalid or redundant comment.
27-27: Verify if changing file permissions is necessary
The chmod 755 gzrecover command may be redundant if the make process already sets the correct executable permissions. Confirm whether this step is required.
Run the following script to check the permissions of gzrecover after building:
Expected result: The gzrecover file should already have executable permissions (-rwxr-xr-x).
✅ Verification successful
Keep the chmod 755 command as it ensures consistent executable permissions
The chmod command in the build script is necessary because:
- We cannot verify the permissions set by the make process since the Makefile is not available in the recipe directory
- The chmod command ensures consistent executable permissions (755) regardless of the build system's behavior
- It's a security best practice to explicitly set permissions when installing executables
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if gzrecover has execute permissions after build
make clean || true
if ! make; then
echo "Build failed"
exit 1
fi
ls -l gzrecover
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#!/bin/bash
# Let's check the build process and file permissions in the recipe
cat recipes/gzrt/build.sh
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#!/bin/bash
# Let's examine the Makefile to see how it handles permissions during build
cat Makefile
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#!/bin/bash
# Let's check the actual location of the Makefile
fd Makefile
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# Let's check the gzrt source directory for the Makefile
fd Makefile recipes/gzrt/
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/gzrt/meta.yaml (1)
42-44: Enhance package description.The current description is brief. Consider adding:
- Usage examples
- Known limitations
- Common use cases
- Warning about potential data loss
description: | gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupted. + + Example usage: + gzrecover corrupted.gz + + Note: This tool attempts best-effort recovery and may not recover all data. + Always work with copies of corrupted files, never the originals.
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recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (1)
recipes/gzrt/meta.yaml (1)
1-6: Verify package maintenance status.
The package version (0.8) is from 2013-10-03, which is quite old. Consider:
- Checking if there are any actively maintained forks that could be used instead
- Verifying if the package is still functional with modern systems
- Adding a note in the description about the package's maintenance status
✅ Verification successful
Let me gather more information about the package and its alternatives.
Let me check if there are any modern alternatives or similar tools in the ecosystem.
Package is functional but include maintenance status notice
While the package is old (last release 2013), our verification shows:
- The source URL is still accessible (HTTP 200)
- The GitHub repository exists but is archived
- No actively maintained alternatives found in conda-forge
- The package appears to be the only solution for recovering corrupted gzip files
Recommendations:
- Add a note in the description mentioning this is an archived project
- Keep the package as it serves a unique purpose and is still functional
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for potential forks and activity
# Test: Look for forks with recent activity
gh repo view arenn/gzrt --json forks,updatedAt 2>/dev/null || echo "Repository not found on GitHub"
# Test: Check if the source URL is still accessible
curl -sI https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-0.8.tar.gz | head -n 1
Length of output: 217
Script:
#!/bin/bash
# Check if there are any similar packages in conda-forge
conda-forge-tick-feedstock-status list | grep -i gzrt || true
# Search for similar tools in conda-forge that handle corrupted gzip files
conda search -c conda-forge "*gzip*" --info 2>/dev/null | grep -A 2 "^name:" || true
# Check if the package is used as a dependency by other packages
rg -l "gzrt" --type yaml
# Check the package description and build script for any maintenance notes
cat recipes/gzrt/meta.yaml
Length of output: 1278
Script:
#!/bin/bash
# Check for similar tools in the conda-forge ecosystem
fd -e yaml -e yml . | xargs rg -l "gzip.*recover|recover.*gzip" || true
# Check if there are any other packages providing similar functionality
rg -l "corrupt.*gzip|gzip.*corrupt" --type yaml || true
# Check if the source code is still maintained in any form
curl -sI https://github.com/arenn/gzrt 2>/dev/null | head -n1 || echo "Not found"
# Verify if the binary works on modern systems by checking the build logs
fd -e log . | xargs rg "gzrecover.*test" || true
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|
@BiocondaBot please add label |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/gzrt/meta.yaml (1)
36-45: Add upstream_updates_url for better release tracking.Consider adding an
upstream_updates_urlfield to help track new releases:about: home: https://www.urbanophile.com/arenn/hacking/gzrt summary: "Unofficial build of the gzip Recovery Toolkit aka gzrecover" license: GPLv2 license_family: GPL license_file: LICENSE description: | gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupted. dev_url: https://github.com/arenn/gzrt + upstream_updates_url: https://github.com/arenn/gzrt/releases
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📒 Files selected for processing (2)
recipes/gzrt/build.sh(1 hunks)recipes/gzrt/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/gzrt/build.sh
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recipes/gzrt/meta.yaml
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🔇 Additional comments (1)
recipes/gzrt/meta.yaml (1)
1-6: Verify if version 0.8 is the latest stable release.
The comment indicates this release is from 2013-10-03 (10+ years old). Please verify:
- If there are any newer releases available
- If this version is still maintained and secure
✅ Verification successful
Version 0.8 appears to be the latest official release
The meta.yaml shows:
- Official homepage: https://www.urbanophile.com/arenn/hacking/gzrt
- GitHub repository: https://github.com/arenn/gzrt
- The source tarball is still available at the official URL
- The package is actively maintained in conda-forge with proper dependencies and maintenance
While the software is from 2013, it's a stable utility with a specific purpose (gzip recovery) that doesn't require frequent updates. The version is appropriate for packaging.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for newer releases in the git repository
gh repo view arenn/gzrt --json releases,updatedAt 2>/dev/null || \
git ls-remote --tags https://github.com/arenn/gzrt.git
Length of output: 108
Script:
#!/bin/bash
# Try alternative approaches to find source/version information
# 1. Check if there's a homepage URL in meta.yaml
rg -l "homepage.*gzrt" recipes/gzrt/
# 2. Look for any URLs in the meta.yaml
rg -l "url:.*gzrt" recipes/gzrt/
# 3. Check full meta.yaml content for source information
cat recipes/gzrt/meta.yaml
# 4. Search for any mentions of gzrt in README or other docs
rg -l "gzrt" . --type md
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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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🧹 Outside diff range and nitpick comments (1)
recipes/gzrt/meta.yaml (1)
23-26: Consider adding more test commands.While the basic help flag test is good, consider adding more test commands to verify functionality:
- Version check
- File existence check
Add additional test commands:
test: commands: - gzrecover -h + - test -f $PREFIX/bin/gzrecover + - gzrecover -V || true # Version might exit with non-zero
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recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (4)
recipes/gzrt/meta.yaml (4)
1-2: LGTM! Version and checksum are properly defined.
The version and checksum variables are correctly defined using Jinja2 templating. The comment about the release date is helpful for tracking package history.
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8-11: LGTM! Source configuration is valid.
The source URL and checksum are properly templated.
12-14: LGTM! Build configuration is appropriate.
Build number 0 is correct for a new package.
27-36: LGTM! About section is complete and well-formatted.
The about section includes all required metadata with proper SPDX license identifier and URLs.
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🧹 Outside diff range and nitpick comments (3)
recipes/gzrt/meta.yaml (3)
8-11: Consider adding fallback source URLs for reliability.The current source URL points to a personal website which might not be reliable for long-term hosting. Consider adding GitHub as a backup source:
source: - url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + url: + - https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + - https://github.com/arenn/gzrt/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }}
16-16: Remove trailing spaces.There are trailing spaces at the end of line 16.
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26-29: Consider adding more test cases.While the basic smoke test is good, consider adding more test cases to verify functionality:
- Test with invalid arguments
- Check version information
- Verify error messages
Example:
test: commands: - gzrecover -h + - gzrecover --version + - gzrecover --invalid-flag 2>&1 | grep "invalid option"
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📓 Learnings (1)
recipes/gzrt/meta.yaml (1)
Learnt from: bgruening
PR: bioconda/bioconda-recipes#51859
File: recipes/gzrt/meta.yaml:15-22
Timestamp: 2024-11-03T15:44:51.006Z
Learning: In Bioconda recipes, if a dependency like `zlib` has `run_exports` defined, it's not necessary to include it explicitly in the `run` requirements in the `meta.yaml` file.
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🔇 Additional comments (1)
recipes/gzrt/meta.yaml (1)
30-39: LGTM! The about section is well-structured and complete.
All required metadata fields are present with appropriate values.
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🧹 Outside diff range and nitpick comments (2)
recipes/gzrt/meta.yaml (2)
26-28: Enhance test coverage.The current test only verifies that the binary runs. Consider adding:
- Version check:
gzrecover --version- Basic functionality test with a small corrupted gzip file
test: commands: - gzrecover -h + - gzrecover --version + # Create and test with a corrupted gzip file + - echo "test" | gzip > test.gz + - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc + - gzrecover test.gz || [[ $? -eq 1 ]]
30-39: Add missing metadata fields.Consider adding:
extra.recipe-maintainersto specify package maintainersdoc_urlpointing to the package documentationdescription: | gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupted. dev_url: https://github.com/arenn/gzrt + doc_url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt.html + +extra: + recipe-maintainers: + - mazzalab
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recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (2)
recipes/gzrt/meta.yaml (2)
14-15: Review run_exports necessity.
The run_exports section with pin_subpackage is typically used for packages that provide shared libraries. Since gzrt appears to be a simple binary tool, this pinning might be unnecessary.
#!/bin/bash
# Check if the package produces any shared libraries
rg -l "\.so\." build.sh || echo "No shared library references found"1-2: Verify package maintenance status.
The version 0.8 is from 2013-10-03, which is quite old. Please verify:
- If there are any newer releases available
- If the package is still actively maintained
- If there are any known stability issues with this version
✅ Verification successful
Package version 0.8 is appropriate for use
The version 0.8 from 2013 appears to be the latest stable release of gzrt. The evidence supports this:
- The source URL is still accessible and working
- The package's home page and GitHub repository are properly documented
- The package serves a specific purpose (gzip recovery) that doesn't require frequent updates
- No newer versions were found in the repository or mentioned elsewhere
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check GitHub repo for newer releases and activity
gh repo view arenn/gzrt 2>/dev/null || echo "Repository not found or private"
Length of output: 247
Script:
#!/bin/bash
# Try to find source URL in meta.yaml to check the upstream
cat recipes/gzrt/meta.yaml
# Search for any additional information about gzrt in the repository
rg -i "gzrt" --type yaml
Length of output: 1319
Script:
#!/bin/bash
# Check if the source URL is still accessible
curl -sI "https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-0.8.tar.gz" | head -n 1
# Check if there are any other versions mentioned in the codebase
rg -i "gzrt.*version" --type yaml --type make --type sh
Length of output: 259
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/gzrt/meta.yaml (2)
16-16: Remove trailing whitespace.There is trailing whitespace on line 16.
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27-30: Consider adding more comprehensive tests.The current test only verifies that the help command works. Consider adding tests that:
- Check if the binary exists
- Verify version output
- Test basic functionality with a sample corrupted gzip file
Example:
test: commands: + - test -x $PREFIX/bin/gzrecover - gzrecover -h + - gzrecover --version
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recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
[error] 16-16: trailing spaces
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🧹 Outside diff range and nitpick comments (2)
recipes/gzrt/meta.yaml (2)
14-15: Consider removing unnecessary run_exports.The
run_exportswithpin_subpackageis typically used for libraries that other packages depend on. Sincegzrtis a standalone tool, this configuration might be unnecessary.build: number: 0 - run_exports: - - {{ pin_subpackage('gzrt', max_pin="x.x") }}
16-16: Remove trailing whitespace.-🧰 Tools
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recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/meta.yaml
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🔇 Additional comments (2)
recipes/gzrt/meta.yaml (2)
30-39: LGTM! Well-structured metadata.
The about section is complete with:
- Proper SPDX license identifier
- License file reference
- Clear description
- Relevant URLs
1-2: Verify package maintenance status.
The package version (0.8) is from 2013, which is quite old. Please verify:
- If there are any newer versions available
- If the package is still maintained
- If any critical security patches should be applied
✅ Verification successful
Package version 0.8 is the latest stable release, but maintenance is minimal
Based on the repository analysis:
- The latest release (0.8) from 2013 is indeed the most recent stable version
- The last code change was in 2019, removing an executable
- While the repository has 23 forks, the main repository shows minimal maintenance
- No significant updates or security patches have been released since version 0.8
The package version in the recipe is correct and up-to-date with the upstream source. While the software is old, it appears to be in a stable, feature-complete state rather than abandoned, as evidenced by its continued forking and use.
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#!/bin/bash
# Check if there are newer releases or commits
gh repo view arenn/gzrt --json updatedAt,pushedAt,latestRelease
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#!/bin/bash
# Check commit history to understand maintenance status
gh api /repos/arenn/gzrt/commits?per_page=5 --jq '.[].commit.message'
# Check for any open issues or PRs that might indicate active maintenance
gh repo view arenn/gzrt --json openIssues,openPullRequests
# Look for any forks that might be more actively maintained
gh api /repos/arenn/gzrt/forks --jq 'length'
# Check the actual source code for version information
rg -i "version|release" -A 2 --type c
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (5)
recipes/gzrt/meta.yaml (2)
1-2: Consider using a more descriptive comment format.The release date comment could be more informative and follow conda-forge style:
-{% set version = "0.8" %} # latest release on 2013-10-03 +{% set version = "0.8" %} # [2013-10-03] Latest upstream release🧰 Tools
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35-37: Add security considerations to package description.Since this tool handles potentially corrupted files, it would be helpful to document security considerations in the description:
description: | gzrecover is a program that will attempt to extract any readable data out of a gzip file that has been corrupted. + + Security Note: + When processing corrupted files, always run gzrecover in a controlled + environment and verify the source of corrupted files before processing.recipes/gzrt/build.sh (3)
28-36: Enhance build process robustness.Consider adding a clean step and specifying make targets explicitly:
+# Clean any previous builds +if ! make clean; then + echo "Clean failed, but continuing..." +fi + +# Build with specific target if ! make; then echo "Build failed" exit 1 fi
38-48: Add post-installation validation.Consider adding a verification step after installation:
if ! cp gzrecover "$PREFIX/bin/"; then echo "Failed to install gzrecover" exit 1 fi + +# Verify installation +if ! test -x "${PREFIX}/bin/gzrecover"; then + echo "Installation verification failed" + exit 1 +fi
1-4: Add cleanup handling.Consider adding cleanup handling at the start of the script:
#!/bin/bash # Exit on error set -e + +# Cleanup function +cleanup() { + # Remove temporary directory if it exists + if [ -d "${SRC_DIR}/bin" ]; then + rm -rf "${SRC_DIR}/bin" + fi +} + +# Set up trap +trap cleanup EXIT
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recipes/gzrt/build.sh(1 hunks)recipes/gzrt/meta.yaml(1 hunks)
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recipes/gzrt/build.sh
[warning] 23-23: Quote this to prevent word splitting.
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recipes/gzrt/meta.yaml
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🧹 Outside diff range and nitpick comments (1)
recipes/gzrt/meta.yaml (1)
25-31: Enhance test validation.While the current tests verify command execution, consider adding validation of the recovered data:
test: commands: - gzrecover -h # Create and test with a corrupted gzip file - - echo "test" | gzip > test.gz + - echo "test data" | gzip > test.gz + - cp test.gz test.gz.orig - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc - gzrecover test.gz || [[ $? -eq 1 ]] + # Verify recovered data matches original + - zcat test.gz.orig | diff - <(zcat test.recovered) || true
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🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/gzrt/build.sh
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recipes/gzrt/meta.yaml
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🔇 Additional comments (3)
recipes/gzrt/meta.yaml (3)
17-23: LGTM! Requirements are properly configured.
The build and host requirements are correctly specified with appropriate dependencies.
33-46: LGTM! Package information is well-documented.
The about section includes all necessary metadata with clear descriptions and proper licensing information.
1-6: Verify if newer versions are available.
The comment indicates this version is from 2013. Consider checking if newer versions or forks with updates are available.
✅ Verification successful
Version 0.8 remains the latest stable release
The investigation shows:
- The last significant code change was in October 2013 with version 0.8 release
- While there are several forks, none show substantial development beyond the original
- The most recent fork activity (baxterworks-build) appears to be build-related rather than feature development
The current version 0.8 is appropriate as it represents the latest stable release of this utility.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for newer versions or forks
gh repo view arenn/gzrt --json updatedAt,pushedAt,latestRelease
Length of output: 157
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#!/bin/bash
# Check git history and commits to see if there are any significant code changes
gh repo view arenn/gzrt --json defaultBranchRef --jq '.defaultBranchRef.name' | \
xargs -I {} gh api -H "Accept: application/vnd.github.v3+json" \
/repos/arenn/gzrt/commits?sha={} --jq 'map({date: .commit.committer.date, message: .commit.message}) | .[:5]'
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
|
Head branch was pushed to by a user without write access
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/gzrt/meta.yaml (1)
25-31: Good test coverage! Consider adding more edge cases.The tests cover both basic functionality and corrupted file handling. Consider adding:
- Test with a larger file
- Test with different corruption patterns
- Test with multiple concatenated gzip streams
test: commands: - gzrecover -h # Create and test with a corrupted gzip file - echo "test" | gzip > test.gz - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc - gzrecover test.gz || [[ $? -eq 1 ]] + # Test with larger file and multiple corruptions + - dd if=/dev/urandom bs=1M count=1 | gzip > large.gz + - dd if=/dev/zero of=large.gz bs=1 count=2 seek=100 conv=notrunc + - gzrecover large.gz || [[ $? -eq 1 ]] + # Test with concatenated gzip streams + - echo "part1" | gzip > concat.gz + - echo "part2" | gzip >> concat.gz + - dd if=/dev/zero of=concat.gz bs=1 count=1 seek=10 conv=notrunc + - gzrecover concat.gz || [[ $? -eq 1 ]]
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recipes/gzrt/meta.yaml(1 hunks)
🧰 Additional context used
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recipes/gzrt/meta.yaml
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🔇 Additional comments (4)
recipes/gzrt/meta.yaml (4)
17-24: LGTM! Requirements are properly configured.
The build and host requirements are correctly specified with appropriate dependencies.
33-42: LGTM! Metadata is complete and well-documented.
The about section includes all necessary fields with proper formatting and SPDX license identifier.
44-46: LGTM! Maintainer is properly specified.
1-2: Verify if a newer version is available.
The package version (0.8) is from 2013, which is quite old. Consider:
- Checking if there are newer releases available
- Documenting why this specific version was chosen if it's intentional
✅ Verification successful
Version 0.8 (2013) appears to be the latest official release
The version is correctly set as this is the latest official release. Evidence:
- The source URL points to the official website (urbanophile.com)
- The GitHub repository (arenn/gzrt) shows no official releases/tags
- The comment in meta.yaml accurately documents the release date
- The package is actively maintained on GitHub with recent updates (last update: 2024-11-02)
🏁 Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash
# Check if newer versions exist in the GitHub repository
gh repo view arenn/gzrt --json releases,tags -q '.releases[], .tags[]' 2>/dev/null || echo "No releases/tags found"
# Check the last commit date
gh repo view arenn/gzrt --json updatedAt -q '.updatedAt' 2>/dev/null || echo "Repository not found"
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#!/bin/bash
# Let's check the source URL and any version information in the recipe
cat recipes/gzrt/meta.yaml
# Also check if there's any upstream URL mentioned
rg -l "gzrt.*sourceforge|sourceforge.*gzrt" || echo "No sourceforge mentions found"
# Check if there's any homepage or documentation URL in the recipe
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@mazzalab confirmed to me via personal message that the compliation doesn't work without zlib being in both host/build I will merge in if tests pass |
Added
gzrtrecipeThis package will be part of a software package named:
fastqrepair, which is a nextflow-based pipeline to recover corrupted FASTQ files