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Update sdeper to 1.6.3 #51501

Merged
merged 1 commit into from
Oct 20, 2024
Merged

Update sdeper to 1.6.3 #51501

merged 1 commit into from
Oct 20, 2024

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Update sdeper: 1.6.21.6.3

install with bioconda Conda

Info Link or Description
Recipe recipes/sdeper (click to view/edit other files)
Summary Spatial Deconvolution method with Platform Effect Removal
Home https://az7jh2.github.io/SDePER/
Releases https://pypi.org/pypi/sdeper/json
Recipe Maintainer(s) @az7jh2

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Oct 20, 2024
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coderabbitai bot commented Oct 20, 2024

📝 Walkthrough

Walkthrough

The pull request involves an update to the recipe file for the SDePER package located in recipes/sdeper/meta.yaml. The primary changes include an increment in the version number from "1.6.2" to "1.6.3" and an update to the SHA256 checksum corresponding to the new version. The checksum has been modified to ensure integrity and authenticity of the source tarball, changing from 271371a6cdd717244c96ce7ba0c6e282f9cd85112048aac3a0ab40975724a1e4 to 2b77042525519a1de5c07956e562fe2f0173e411a921826c4ab6b6ca1f5d6e10. All other elements of the recipe, including package metadata, source URL, build specifications, requirements, test commands, and additional package information, remain unchanged.

Possibly related PRs


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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/sdeper/meta.yaml (1)

Dependency Versions Verification

There are discrepancies between the dependencies specified in meta.yaml and those listed in PyPI for SDePER 1.6.3:

  • matplotlib-base ==3.5.2 in meta.yaml vs matplotlib==3.5.2 on PyPI
  • tensorflow-base 2.15.0 cpu_* in meta.yaml vs tensorflow-cpu==2.15.0 on PyPI
  • libopencv ==4.9.0 headless_* and opencv ==4.9.0 in meta.yaml vs opencv-python-headless==4.9.0.80 on PyPI

Please update the meta.yaml to match the PyPI dependency specifications to ensure compatibility.

🔗 Analysis chain

Line range hint 25-46: Verify dependency versions compatibility.

The requirements section specifies versions for various dependencies. It's important to ensure that these versions are still compatible with SDePER 1.6.3. Please verify that no updates to dependency versions are needed for this new release.

You can check the package's setup.py or requirements.txt file in the SDePER 1.6.3 source code to confirm if any dependency versions have changed. Here's a script to help with this verification:

Please compare the output of this script with the requirements listed in the recipe to ensure all versions are up-to-date.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for changes in dependency versions

# Download the package
curl -L -o sdeper-1.6.3.tar.gz https://pypi.io/packages/source/s/sdeper/sdeper-1.6.3.tar.gz

# Extract the package
tar -xzf sdeper-1.6.3.tar.gz

# Check for setup.py or requirements.txt
if [ -f sdeper-1.6.3/setup.py ]; then
    echo "Contents of setup.py:"
    cat sdeper-1.6.3/setup.py
elif [ -f sdeper-1.6.3/requirements.txt ]; then
    echo "Contents of requirements.txt:"
    cat sdeper-1.6.3/requirements.txt
else
    echo "Neither setup.py nor requirements.txt found."
fi

# Clean up
rm -rf sdeper-1.6.3 sdeper-1.6.3.tar.gz

Length of output: 1175


Script:

#!/bin/bash
# Description: Verify the integrity and contents of the downloaded sdeper-1.6.3.tar.gz

# Check if the file exists
if [ ! -f sdeper-1.6.3.tar.gz ]; then
    echo "sdeper-1.6.3.tar.gz does not exist."
    exit 1
fi

# Verify the file type
file sdeper-1.6.3.tar.gz

# Attempt to list the contents without extracting
tar -tzf sdeper-1.6.3.tar.gz > tar_contents.txt 2>/dev/null

if [ $? -ne 0 ]; then
    echo "The tar.gz file is corrupted or not a valid archive."
    exit 1
fi

echo "Contents of sdeper-1.6.3.tar.gz:"
cat tar_contents.txt

# Check for alternative dependency files
if grep -q "pyproject.toml" tar_contents.txt; then
    echo "Found pyproject.toml in the archive."
else
    echo "No pyproject.toml found in the archive."
fi

# Clean up
rm -f tar_contents.txt

Length of output: 126


Script:

#!/bin/bash
# Description: List all available versions of sdeper on PyPI

curl -s https://pypi.org/pypi/sdeper/json | jq -r '.releases | keys[]' | sort -V

Length of output: 172


Script:

#!/bin/bash
# Description: List all distribution files for sdeper version 1.6.3 on PyPI

# Fetch the JSON metadata for sdeper 1.6.3
curl -s https://pypi.org/pypi/sdeper/1.6.3/json | jq -r '.urls[] | {filename: .filename, packagetype: .packagetype, url: .url}'

Length of output: 565


Script:

#!/bin/bash
# Description: Extract dependencies for sdeper version 1.6.3 from PyPI

# Fetch the JSON metadata for sdeper 1.6.3
curl -s https://pypi.org/pypi/sdeper/1.6.3/json | jq -r '.info.requires_dist // "No dependencies listed."'

Length of output: 477

🧰 Tools
🪛 yamllint

[error] 3-3: syntax error: found character '%' that cannot start any token

(syntax)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 0242e47 and 944c4d2.

📒 Files selected for processing (1)
  • recipes/sdeper/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (2)
recipes/sdeper/meta.yaml (2)

4-4: Version update looks good.

The version has been correctly updated from 1.6.2 to 1.6.3, which is consistent with the PR objectives.


12-12: Verify the SHA256 checksum.

The SHA256 checksum has been updated, which is necessary for the new version. However, we should verify that this checksum is correct for the SDePER 1.6.3 package.

To verify the checksum, you can run the following script:

@martin-g martin-g merged commit 8dd05cc into master Oct 20, 2024
7 checks passed
@martin-g martin-g deleted the bump/sdeper branch October 20, 2024 12:33
@coderabbitai coderabbitai bot mentioned this pull request Oct 21, 2024
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2 participants