Update NORDic to 2.5.0 #51719
Update NORDic to 2.5.0 #51719
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request includes modifications to the Nordic recipes across three files. The Possibly related PRs
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Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/nordic/LICENSE (2 hunks)
- recipes/nordic/meta.yaml (4 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/nordic/LICENSE
🔇 Additional comments (3)
recipes/nordic/meta.yaml (3)
3-3: LGTM: Version update follows semantic versioningThe version bump from 2.4.4 to 2.5.0 indicates a feature release while maintaining backward compatibility.
24-27: LGTM: Build configuration is appropriateThe build number reset to 0 is correct for a new version, and the run_exports section properly pins the package version, following Bioconda guidelines for ABI compatibility.
46-46: 🛠️ Refactor suggestionConsider relaxing the strict omnipath version pin
The exact version pin (
==1.0.6) for omnipath might be too restrictive and could cause dependency resolution issues. Unless there's a specific compatibility requirement, consider using a more flexible constraint like>=1.0.6,<2.0.0.✅ Verification successful
Let me gather more information about the omnipath package usage in the repository.
Let me check the upstream repository to see if there's any specific version requirement for omnipath.
Let me try one final verification to check the repository and package history.
Based on the gathered information, I can now provide the final response:
Keep the strict omnipath version pin as is
The exact version pin (
==1.0.6) appears to be intentional as:
- This is the only recipe in the repository using the Python omnipath package
- Other packages using omnipath-related dependencies (like bioconductor-omnipathr) also use strict version constraints
- The package is used in both host and run requirements with the same version, suggesting specific compatibility needs
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if other recipes in bioconda use strict pinning for omnipath rg -l 'omnipath\s*==\s*[\d\.]+' --type yamlLength of output: 70
Script:
#!/bin/bash # Check for any omnipath dependency specifications in yaml files rg 'omnipath' --type yaml -A 2 -B 2 # Also check if there's any specific reason mentioned in the recipe cat recipes/nordic/meta.yamlLength of output: 6039
Script:
#!/bin/bash # Check setup.py or requirements files in the NORDic package source for omnipath version requirements cd NORDic-2.5.0 2>/dev/null && find . -type f -name "setup.py" -o -name "requirements.txt" -o -name "pyproject.toml" | while read file; do cat "$file"; done # Also check if there are any version-specific imports or compatibility notes in the source code rg -l "import.*omnipath|from.*omnipath"Length of output: 59
Script:
#!/bin/bash # Check commit history for any mentions of omnipath version requirements git log -p | rg -i "omnipath.*version|version.*omnipath" # Check if there are any issues or pull requests mentioning omnipath version requirements gh issue list --search "omnipath version" --limit 100 2>/dev/null gh pr list --search "omnipath version" --limit 100 2>/dev/null # Look for any documentation files that might mention omnipath requirements rg -l "omnipath" --type mdLength of output: 194
recipes/nordic/meta.yaml
Outdated
| - numpy >=1.22.4 | ||
| - omnipath >=1.0.6 | ||
| - numpy <2.0.0 |
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Remove duplicate numpy requirement
There are two numpy requirements in the host section. The first one (>=1.22.4) appears to be outdated.
Apply this diff to remove the duplicate:
- matplotlib-base
- - numpy >=1.22.4
- numpy <2.0.0📝 Committable suggestion
‼️ IMPORTANT
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.
| - numpy >=1.22.4 | |
| - omnipath >=1.0.6 | |
| - numpy <2.0.0 | |
| - numpy <2.0.0 |
recipes/nordic/meta.yaml
Outdated
| - numpy >=1.22.4 | ||
| - omnipath >=1.0.6 | ||
| - numpy <2.0.0 |
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Remove duplicate numpy requirement in run section
Similar to the host section, there are duplicate numpy requirements in the run section.
Apply this diff to remove the duplicate:
- matplotlib-base
- - numpy >=1.22.4
- numpy <2.0.0📝 Committable suggestion
‼️ IMPORTANT
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.
| - numpy >=1.22.4 | |
| - omnipath >=1.0.6 | |
| - numpy <2.0.0 | |
| - matplotlib-base | |
| - numpy <2.0.0 |
|
The double requirement on NumPy is needed for the package to be functional. |
|
You can combine the numpy requiremente something like |
Thank you, I will update the PR then. |
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/nordic/build.sh (1 hunks)
- recipes/nordic/meta.yaml (3 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/nordic/meta.yaml
🧰 Additional context used
🪛 Shellcheck
recipes/nordic/build.sh
[warning] 21-21: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🔇 Additional comments (1)
recipes/nordic/build.sh (1)
21-21: Verify the NORDic directory path.
The path has been updated to match the new version 2.5.0. Let's verify this matches the actual package structure.
✅ Verification successful
The NORDic directory path is correctly specified
The meta.yaml confirms that the source package will be downloaded as "nordic-2.5.0.tar.gz" and extracted to the "NORDic-2.5.0" folder, matching exactly with the path used in build.sh. The version and folder name are properly templated using Jinja2 variables:
folder: "{{ ucname }}-{{ version }}" # expands to "NORDic-2.5.0"🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the NORDic directory structure in the source package
# Expected: Directory name should match the version
# Test: Check if the directory exists in the package
fd -t d "NORDic-2.5.0"
Length of output: 22
Script:
#!/bin/bash
# Let's check the content of the build.sh file to understand the context better
cat recipes/nordic/build.sh
# Also search for any NORDic related files/directories
fd -t d "NORDic"
Length of output: 550
Script:
#!/bin/bash
# Let's check the meta.yaml to verify the source information and version
cat recipes/nordic/meta.yaml
# Also check if there are any patches or additional files in the recipe directory
ls -la recipes/nordic/
Length of output: 2997
🧰 Tools
🪛 Shellcheck
[warning] 21-21: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
| cd ${SRC_DIR}"/NORDic-2.5.0/" | ||
|
|
||
| "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv No newline at end of file | ||
| "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv |
There was a problem hiding this comment.
Add error handling for directory change.
The cd command should handle potential failures to prevent silent errors in the build process.
Apply this diff to add error handling:
-cd ${SRC_DIR}"/NORDic-2.5.0/"
+cd ${SRC_DIR}"/NORDic-2.5.0/" || exit 1
"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv📝 Committable suggestion
‼️ IMPORTANT
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.
| cd ${SRC_DIR}"/NORDic-2.5.0/" | |
| "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv | |
| \ No newline at end of file | |
| "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv | |
| cd ${SRC_DIR}"/NORDic-2.5.0/" || exit 1 | |
| "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv |
🧰 Tools
🪛 Shellcheck
[warning] 21-21: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
Update NORDic to 2.5.0
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