feat: Update dependencies to latest versions #1010
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| @@ -7,21 +7,21 @@ conda-forge-pinning=2024.06.01.05.54.15 | |||
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| # basics | |||
| python=3.10.* | |||
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I'm too afraid to bump python to 3.12 ... but if someone says its a good idea, please let me know!
| mamba=1.5.* | ||
| boa=0.17.* | ||
| #boa=0.17.* |
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Are we using this one? This one is currently blocked by conda-forge/boa-feedstock#85
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Looks like the boa imports were all removed in #980
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| #boa=0.17.* |
WalkthroughThe pull request introduces several changes across multiple files. In the GitHub Actions workflow file In the The Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- .github/workflows/GithubActionTests.yml (2 hunks)
- bioconda_utils/bioconda_utils-requirements.txt (2 hunks)
- versioneer.py (1 hunks)
🧰 Additional context used
🪛 LanguageTool
bioconda_utils/bioconda_utils-requirements.txt
[uncategorized] ~17-~17: Interjections are usually punctuated.
Context: ...reaming=0.11.* mamba=1.5.* #boa=0.17.* argh=0.31.* # CLI colorlog...(INTERJECTIONS_PUNCTUATION)
🔇 Additional comments (13)
bioconda_utils/bioconda_utils-requirements.txt (7)
10-10: LGTM: conda and conda-build version updatesThe updates to conda (24.9.) and conda-build (24.9.) are minor version increments. These updates likely include bug fixes and improvements while maintaining compatibility. Keeping these versions in sync is a good practice.
Also applies to: 12-12
24-24: LGTM: networkx version updateThe networkx version has been updated from 3.3.* to 3.4.. This minor version update is consistent with the comment indicating that networkx>3.3 requires python>=3.10, which aligns with the python version specified in this file (python=3.10.). This update is appropriate and maintains compatibility.
47-47: LGTM: aioftp version updateThe aioftp version has been updated from 0.22.* to 0.23.*. This minor version update likely includes improvements and bug fixes. The change appears to be appropriate and should maintain compatibility with the project's requirements.
23-23: Consider deprecation: pyaml version updateThe pyaml version has been updated from 24.04.* to 24.09.*. This minor version update is likely beneficial. However, the comment suggests that pyaml might be deprecated in the future. It may be worth considering if this dependency is still necessary or if there are plans to replace it.
Please run the following script to check for any deprecation notices or alternatives:
#!/bin/bash # Description: Check for deprecation notices or alternatives for pyaml # Test: Search for deprecation notices or alternatives gh search issues "pyaml deprecation" --repo yaml/pyyaml gh search issues "pyaml alternative" --repo yaml/pyyaml
49-49: Review dependency necessity: cachetools version updateThe cachetools version has been updated from 5.3.* to 5.5.*. This minor version update likely includes improvements and bug fixes. However, the comment "(NEEDED?)" raises a question about the necessity of this dependency. While the update itself is fine, it might be worth reviewing whether this dependency is still required for the project.
Please run the following script to check for the usage of cachetools in the project:
13-13: Verify compatibility: conda-index version updateThe conda-index version has been updated from 0.4.* to 0.5.*. This minor version increment may introduce new features or significant changes. While this update is likely beneficial, it's important to ensure compatibility with the project's requirements and other dependencies.
Please run the following script to check for any potential compatibility issues:
✅ Verification successful
| @@ -43,10 +43,10 @@ aiohttp=3.9.* # HTTP lib | |||
| aiohttp-jinja2 # jinja2 renderer for aiohttp.web | |||
| aiohttp-session # | |||
| aiohttp-security # | |||
| aiofiles=23.* # async open | |||
| aioftp=0.22.* # FTP lib | |||
| aiofiles=24.* # async open | |||
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💡 Codebase verification
aiofiles updated to version 24.1.0 with Potential Breaking Changes
The aiofiles dependency has been updated from version 23.* to 24.1.0. This major version update includes the following changes that may impact the project's compatibility:
- Dropped Python 3.7 Support: Ensure that the project is using Python 3.8 or higher. If your project still relies on Python 3.7, you will need to upgrade the Python version or revert
aiofilesto version 23.2.1. - Updated Async Idioms: The removal of
types.coroutineand makingAiofilesContextManagerawaitable may require refactoring your asynchronous code to align with the new patterns introduced in this version.
Please review your project's Python version and asynchronous I/O implementations to ensure compatibility with aiofiles 24.1.0.
🔗 Analysis chain
Review changelog: aiofiles major version update
The aiofiles version has been updated from 23.* to 24.*. This major version update may include significant changes or potential breaking changes. While keeping dependencies up-to-date is important, it's crucial to review the changelog for any breaking changes that might affect the project's async I/O operations.
Please run the following script to review the changelog and check for any breaking changes:
Action Required: Verify aiofiles 24. Release Details*
The previous attempt to verify the aiofiles 24.* release targeted the wrong repository and did not provide the necessary information. Please run the following script to accurately review the aiofiles changelog and check for any breaking changes:
Action Required: Verify the Existence of aiofiles 24. Release*
The previous script incorrectly targeted the 'conda/conda-package-streaming' repository and failed to find the aiofiles 24.* release. Please run the following script to list all releases in the 'Tinche/aiofiles' repository and identify the correct release tag:
Action Required: Review aiofiles 24.1.0 Changelog for Breaking Changes
The aiofiles has been updated to version 24.1.0. To ensure compatibility and identify any potential breaking changes introduced in this major version update, please run the following script to review the changelog:
Action Required: Review aiofiles v24.1.0 Changelog for Breaking Changes
The aiofiles has been updated to version 24.1.0. To ensure compatibility and identify any potential breaking changes introduced in this major version update, please run the following script to review the changelog:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Review changelog and check for breaking changes in aiofiles 24.*
# Test: Search for breaking changes
gh search issues "aiofiles 24 breaking change" --repo Tinche/aiofiles
# Display changelog
echo "Please review the following changelog:"
gh release view --repo Tinche/aiofiles 24.0.0
Length of output: 269
Script:
#!/bin/bash
# Description: Review changelog and check for breaking changes in aiofiles 24.*
# Search for breaking changes in issues
gh search issues "aiofiles 24 breaking change" --repo Tinche/aiofiles
# Display changelog for version 24.0.0
echo "Please review the following changelog:"
gh release view --repo Tinche/aiofiles 24.0.0
Length of output: 224
Script:
#!/bin/bash
# Description: List all releases in the Tinche/aiofiles repository to verify aiofiles 24.* release
# List all releases
gh release list --repo Tinche/aiofiles
# Optionally, search for releases matching 24.*
gh release list --repo Tinche/aiofiles | grep '^v?24\.'
Length of output: 215
Script:
#!/bin/bash
# Description: Fetch and review the changelog for aiofiles 24.1.0 to identify breaking changes
# Display changelog for version 24.1.0
echo "Fetching changelog for aiofiles v24.1.0..."
gh release view --repo Tinche/aiofiles 24.1.0
Length of output: 160
Script:
#!/bin/bash
# Description: Fetch and review the changelog for aiofiles v24.1.0 to identify breaking changes
# Display changelog for version v24.1.0
echo "Fetching changelog for aiofiles v24.1.0..."
gh release view --repo Tinche/aiofiles v24.1.0
Length of output: 956
| # the top of versioneer.py for instructions on writing your setup.cfg . | ||
| setup_cfg = os.path.join(root, "setup.cfg") | ||
| parser = configparser.SafeConfigParser() | ||
| parser = configparser.ConfigParser() | ||
| with open(setup_cfg, "r") as f: | ||
| parser.readfp(f) | ||
| parser.read_file(f) |
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🛠️ Refactor suggestion
Consider updating error handling for better robustness
While the changes to use ConfigParser and read_file are excellent, it might be beneficial to update the error handling in this function. Consider catching specific exceptions that might be raised by the new methods, such as configparser.Error or its subclasses, to provide more precise error messages and improve the overall robustness of the function.
Here's a suggested improvement:
try:
parser = configparser.ConfigParser()
with open(setup_cfg, "r") as f:
parser.read_file(f)
except configparser.Error as e:
print(f"Error parsing {setup_cfg}: {e}", file=sys.stderr)
return 1
except IOError as e:
print(f"Error reading {setup_cfg}: {e}", file=sys.stderr)
return 1
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