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Update pybigtools to 0.2.2 #50026

Merged
merged 3 commits into from
Nov 5, 2024
Merged

Update pybigtools to 0.2.2 #50026

merged 3 commits into from
Nov 5, 2024

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@BiocondaBot BiocondaBot commented Aug 13, 2024

Update pybigtools: 0.2.00.2.2

install with bioconda Conda

Info Link or Description
Recipe recipes/pybigtools (click to view/edit other files)
Summary pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O
Home https://github.com/jackh726/bigtools
Releases https://pypi.org/pypi/pybigtools/json

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Aug 13, 2024
@BiocondaBot BiocondaBot changed the title Update pybigtools to 0.2.1 Update pybigtools to 0.2.2 Nov 4, 2024
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coderabbitai bot commented Nov 4, 2024

📝 Walkthrough

Walkthrough

The pull request includes modifications to two files: build.sh and meta.yaml within the pybigtools package. In build.sh, several lines related to SSH-based Git connections and temporary directory usage on macOS have been removed. Specifically, the script no longer sets the CARGO_NET_GIT_FETCH_WITH_CLI and CARGO_HOME environment variables, which were previously used to address SSH connection issues with Rust's cargo. The custom HOME directory export for macOS has also been eliminated, while the core functionalities for deployment targets, symbolic links, and file movements remain unchanged. In meta.yaml, the version has been updated from 0.2.0 to 0.2.2, and the SHA256 checksum has been revised. The build number has been altered from 1 to 0, and formatting adjustments have been made to the URLs in the about section. Additionally, support for the osx-arm64 platform has been added under the extra section.

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Suggested reviewers

  • martin-g: Suggested reviewer for the changes made in this pull request.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/pybigtools/build.sh (1)

Line range hint 1-37: Consider enhancing build script robustness.

The build script handles complex operations including platform-specific configurations and file movements. Consider these improvements:

  1. Add validation for successful wheel creation before installation
  2. Add error handling for the pyproject.toml move operation
  3. Consider adding a cleanup trap for the macOS tool symlinks

Example enhancement:

 # The wheels don't seem to install as expected unless pyproject.toml is moved back into the source dir.
-mv pyproject.toml pybigtools/
+if [ ! -f pyproject.toml ]; then
+    echo "ERROR: pyproject.toml not found"
+    exit 1
+fi
+mv pyproject.toml pybigtools/ || { echo "Failed to move pyproject.toml"; exit 1; }
 
 # Run maturin build to produce *.whl files.
 maturin build -m pybigtools/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip
+
+# Verify wheel creation
+if [ ! -f pybigtools/target/wheels/*.whl ]; then
+    echo "ERROR: Wheel file not created"
+    exit 1
+fi
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between ee6d0f1 and 983084e.

📒 Files selected for processing (2)
  • recipes/pybigtools/build.sh (1 hunks)
  • recipes/pybigtools/meta.yaml (3 hunks)
🔇 Additional comments (6)
recipes/pybigtools/meta.yaml (4)

14-14: LGTM: Build number reset.

Resetting the build number to 0 for a new version is the correct practice.


35-35: LGTM: URL formatting improvements.

The addition of quotes around URLs in the about section improves consistency and readability.

Also applies to: 40-41


46-46: LGTM: Enhanced platform support.

Adding osx-arm64 platform support is a valuable enhancement that extends compatibility to Apple Silicon machines.


2-3: ⚠️ Potential issue

Version mismatch with PR objectives.

The PR description indicates an update to version 0.2.1, but the recipe shows version 0.2.2. Please verify if this is intentional or if the version needs to be adjusted to match the PR objectives.

Let's verify the latest version on PyPI:

✅ Verification successful

Version update to 0.2.2 is correct and matches PyPI

The version update to 0.2.2 in the recipe is correct as it matches the latest version available on PyPI. While the PR description mentioned updating to 0.2.1, it appears that version 0.2.2 was released during the update process, and the bot correctly updated to the latest available version. This is expected behavior for automated version updates.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check the latest version of pybigtools on PyPI
curl -s https://pypi.org/pypi/pybigtools/json | jq -r '.info.version'

Length of output: 75

recipes/pybigtools/build.sh (2)

37-37: Verify LICENSE file location.

The LICENSE file is being moved from pybigtools/LICENSE to the root directory. Let's verify that this path is correct and the file exists.

#!/bin/bash
# Verify the LICENSE file exists in the expected location
if [ -f "pybigtools/LICENSE" ]; then
    echo "LICENSE file exists in the expected location"
else
    echo "WARNING: LICENSE file not found in pybigtools/LICENSE"
    # Search for LICENSE file in other locations
    fd -i license
fi

Line range hint 8-10: Verify MacOS deployment target compatibility.

Setting MACOSX_DEPLOYMENT_TARGET=12.7 might be too restrictive as it requires macOS Monterey or newer. Consider using a lower version (e.g., 10.15) to support older macOS versions unless there's a specific requirement for 12.7.

@mencian mencian merged commit c2c357d into master Nov 5, 2024
6 checks passed
@mencian mencian deleted the bump/pybigtools branch November 5, 2024 02:11
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