Update hmftools-amber to 4.1_beta

[scwatts]

Update hmftools-amber recipe to 4.1_beta

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Summary by CodeRabbit

• New Features

  • Updated the hmftools-amber package to version 4.1_beta, enhancing functionality and performance.
  • Improved source URL structure for easier access to the latest releases.

• Bug Fixes

  • Corrected SHA256 checksum to ensure integrity and security of the package.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request updates the meta.yaml file for the hmftools-amber package. It changes the version from "4.0.1" to "4.1_beta" and updates the SHA256 checksum accordingly. Additionally, the source URL is modified to accommodate the new versioning scheme, where "_beta" is replaced with an empty string in the URL. Other contents of the file, such as package metadata and requirements, remain unchanged.

Changes

File	Change Summary
recipes/hmftools-amber/meta.yaml	- Updated version from "4.0.1" to "4.1_beta". - Updated sha256 from "ab4934e503d..." to "ceef94ee067...". - Updated url to replace "_beta" in version for URL construction.

Possibly related PRs

• 2024.4 #50977: Updates the meta.yaml file for the biobb_structure_checking package, changing the version and SHA256 checksum.
• update Hsdecipher des #51023: Modifies the meta.yaml file for the hsdecipher package, updating the SHA256 checksum and version.
• Update Hsdfinder script #51058: Updates the meta.yaml file for the hsdfinder package with a version increment and SHA256 checksum change.
• Update Hsdfinder #51092: Changes the version and SHA256 checksum in the meta.yaml file for the hsdfinder package.
• Update Hsdecipher #51093: Updates the meta.yaml file for the hsdecipher package, changing the version and SHA256 checksum.

Suggested labels

autobump, new version

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between e9865fd and 8487a27.

📒 Files selected for processing (1)

• recipes/hmftools-amber/meta.yaml (1 hunks)

🧰 Additional context used

🪛 yamllint

recipes/hmftools-amber/meta.yaml

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

(syntax)

🔇 Additional comments (2)

recipes/hmftools-amber/meta.yaml (2)

9-9: URL updated correctly for beta version

The source URL has been updated to handle the beta version correctly. The replace("_beta", "") filter ensures that the correct filename is used for downloading the JAR file.

Let's verify that the URL is correct and the file exists:

✅ Verification successful

URL updated correctly and verified

The updated source URL successfully points to an existing JAR file. The replace("_beta", "") filter correctly formats the URL, and the file amber_v4.1_beta.jar exists at the specified location.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the existence of the JAR file at the specified URL

# Extract the version and construct the URL
version="4.1_beta"
url="https://github.com/hartwigmedical/hmftools/releases/download/amber-v${version//_beta/}/amber_v${version}.jar"

# Test: Check if the URL is accessible
if curl --output /dev/null --silent --head --fail "$url"; then
    echo "URL is valid and file exists: $url"
else
    echo "Error: File not found or URL is invalid: $url"
fi

Length of output: 510

---

1-2: Verify stability of beta version

The version has been updated to "4.1_beta" and the SHA256 checksum has been updated accordingly. These changes are consistent with the PR objective.

Please ensure that this beta version is stable enough for inclusion in the Bioconda channel. Consider the following:

1. Has this beta version been tested thoroughly?
2. Are there any known issues that might affect users?
3. Is there a plan for updating to the stable release when it becomes available?

✅ Verification successful

Beta Version Stability Verified

The beta version "4.1_beta" has been confirmed to be stable based on current checks:

• The release URL is valid and the file exists.
• No open issues or PRs related to the stability of "amber 4.1_beta" were found.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if there are any issues or discussions about the stability of this beta version.

# Test: Search for any mentions of stability issues or beta version discussions
gh issue list -R hartwigmedical/hmftools --search "in:title,body amber 4.1_beta"
gh pr list -R hartwigmedical/hmftools --search "in:title,body amber 4.1_beta"

Length of output: 510

🧰 Tools

🪛 yamllint

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

(syntax)

---

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[scwatts]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
noarch	hmftools-amber-4.1_beta-hdfd78af_0.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>

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Docker image(s) built:

Package	Tag	CI	Install with docker
hmftools-amber	4.1_beta--hdfd78af_0	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/hmftools-amber:4.1_beta--hdfd78af_0.tar.gz | docker load

[scwatts]

@BiocondaBot please add label