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Update emu-pca to 1.1 #52035

Merged
merged 3 commits into from
Nov 11, 2024
Merged

Update emu-pca to 1.1 #52035

merged 3 commits into from
Nov 11, 2024

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Update emu-pca: 1.01.1

install with bioconda Conda

Info Link or Description
Recipe recipes/emu-pca (click to view/edit other files)
Summary EM-PCA for Ultra-low Coverage Sequencing Data.
Home https://github.com/Rosemeis/emu
Releases https://github.com/Rosemeis/emu/tags
Author @Rosemeis

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 10, 2024
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coderabbitai bot commented Nov 10, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request includes updates to the meta.yaml file for the emu-pca package. Key changes involve incrementing the package version from "1.0" to "1.1" and modifying the source URL to reflect the new version tag, changing it from v1.0 to v1.1. The checksum method has been updated from MD5 to SHA256, with the new hash value specified as a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb. Additionally, the build number has been reset from 1 to 0, and a new entry skip: True # [py < 310] has been added under the build section. The installation script has been modified to include the --no-cache-dir option, and the verbosity level has been increased from -vv to -vvv. An entry_points section has also been introduced, defining the entry point for the package. The overall structure of the file, including package requirements and test commands, remains unchanged.

Possibly related PRs


📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 0ab902d and e12e6b7.

📒 Files selected for processing (2)
  • recipes/emu-pca/build_failure.osx-64.yaml (0 hunks)
  • recipes/emu-pca/meta.yaml (1 hunks)
💤 Files with no reviewable changes (1)
  • recipes/emu-pca/build_failure.osx-64.yaml
🔇 Additional comments (5)
recipes/emu-pca/meta.yaml (5)

2-2: LGTM: Version update matches PR objectives

The version bump from 1.0 to 1.1 aligns with the PR's stated purpose.


16-16: LGTM: Improved pip install flags

The addition of --no-cache-dir and increased verbosity (-vvv) will help with build reproducibility and debugging.


17-18: Verify entry point functionality

The new entry point configuration needs verification to ensure it matches the package's main function.

#!/bin/bash
# Description: Verify the entry point matches the package structure

# Check if the main module exists and contains the main function
curl -sL https://github.com/Rosemeis/emu/archive/refs/tags/v1.1.tar.gz | \
  tar xz --to-stdout "emu-1.1/emu/main.py" 2>/dev/null | \
  rg "def main"

9-10: Verify source archive checksum

The switch from MD5 to SHA256 is a security improvement. Let's verify the checksum matches the source archive.


13-14: Verify Python version constraint impact

The new constraint skip: True # [py < 310] means this package will only be available for Python 3.10+. This is a potentially breaking change for users on older Python versions.


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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/emu-pca/meta.yaml (1)

Dependencies have changed and need to be updated

The build dependencies in v1.1 have significant changes compared to v1.0:

  • Requires newer versions: setuptools >= 61.0, cython > 3.0.0, numpy > 2.0.0
  • Removed dependency: scipy is no longer required
  • More strict version constraints are now specified

The current recipe needs to be updated to:

  1. Add version constraints for Cython and NumPy in host section
  2. Remove unnecessary dependencies
🔗 Analysis chain

Line range hint 18-29: Verify dependency requirements for new version

Let's confirm that the dependency requirements haven't changed in version 1.1.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any dependency changes in the new version
# Compare setup.py/requirements.txt between versions

# Check for requirements files in both versions
curl -sL https://github.com/Rosemeis/emu/archive/refs/tags/v1.0.tar.gz | tar xz -O "*/setup.py" > v1.0_setup.py
curl -sL https://github.com/Rosemeis/emu/archive/refs/tags/v1.1.tar.gz | tar xz -O "*/setup.py" > v1.1_setup.py
diff v1.0_setup.py v1.1_setup.py || true

Length of output: 706


Script:

#!/bin/bash
# Let's try a different approach to fetch and compare the dependencies
# First, let's check if we can find any requirements or setup files in the current PR
fd -e txt -e py -e yaml -e toml "requirements|setup|pyproject" --exec cat {}

Length of output: 4993


Script:

#!/bin/bash
# Let's check the recipe directory specifically for the emu package
cat recipes/emu-pca/meta.yaml

# Also check if there are any other related files in the recipe directory
fd . recipes/emu-pca/ --exec cat {}

Length of output: 9828


Script:

#!/bin/bash
# Let's fetch the setup.py or pyproject.toml from the source repository to check dependencies
curl -sL https://github.com/Rosemeis/emu/raw/v1.1/pyproject.toml || curl -sL https://github.com/Rosemeis/emu/raw/v1.1/setup.py

# Also check the previous version for comparison
curl -sL https://github.com/Rosemeis/emu/raw/v1.0/pyproject.toml || curl -sL https://github.com/Rosemeis/emu/raw/v1.0/setup.py

Length of output: 366

🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 9168102 and 0ab902d.

📒 Files selected for processing (1)
  • recipes/emu-pca/meta.yaml (1 hunks)
🔇 Additional comments (3)
recipes/emu-pca/meta.yaml (3)

2-2: LGTM: Version update is correct

Version bump from 1.0 to 1.1 matches the PR objectives.


13-13: LGTM: Build number reset is correct

Resetting build number to 0 for the new version follows Conda packaging conventions.


10-10: Verify SHA256 checksum authenticity

The switch from MD5 to SHA256 is a security improvement. Let's verify the checksum against the source.

#!/bin/bash
# Description: Verify the SHA256 checksum of the source tarball
# Expected: Should match a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb

# Download the source and compute its checksum
curl -sL https://github.com/Rosemeis/emu/archive/refs/tags/v1.1.tar.gz | sha256sum

@mencian mencian merged commit 8ded147 into master Nov 11, 2024
6 checks passed
@mencian mencian deleted the bump/emu_pca branch November 11, 2024 16:58
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2 participants