Update jbrowse2 to 2.16.0

[BiocondaBot]

Update jbrowse2: 2.15.4 → 2.16.0

Info	Link or Description
Recipe	recipes/jbrowse2 (click to view/edit other files)
Summary	The JBrowse 2 Genome Browser
Home	https://jbrowse.org/
Releases	https://github.com/GMOD/jbrowse-components/releases
Author	@GMOD

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request updates the meta.yaml file for the jbrowse2 package. The version number has been incremented from 2.15.4 to 2.16.0. Alongside this version change, the SHA256 checksum for the source file has been updated from fa0a6163dab65d1705c1968cc41adc0f6b035a8fbc572b7ddff12721b5b58642 to 5f58748cf7c3dcbaddbf87e123cfa878f0d64d3e965bd2ac9bda1b359db40dfd. Additionally, the source URL has been modified to reflect the new version, changing from https://github.com/GMOD/jbrowse-components/releases/download/v2.15.4/jbrowse-web-v2.15.4.zip to https://github.com/GMOD/jbrowse-components/releases/download/v2.16.0/jbrowse-web-v2.16.0.zip. No other modifications to the structure or content of the meta.yaml file have been made.

Possibly related PRs

• Update qtlseq to 2.2.5 #51172: The changes in this PR involve updating the meta.yaml file for the qtlseq package, including a version bump and SHA256 checksum update, similar to the version and checksum updates in the main PR for jbrowse2.
• Update qtlseq to 2.2.6 #51191: This PR also updates the meta.yaml file for the qtlseq package, reflecting a version increment and SHA256 checksum change, paralleling the updates made in the main PR.
• Update qtlseq to 2.2.8 #51471: Similar to the main PR, this PR updates the meta.yaml file for the qtlseq package, including a version change and SHA256 checksum update, indicating a consistent pattern of version management across related packages.

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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 500d734 and 531719c.

📒 Files selected for processing (1)

• recipes/jbrowse2/meta.yaml (1 hunks)

🧰 Additional context used

🪛 yamllint

recipes/jbrowse2/meta.yaml

[error] 2-2: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (3)

recipes/jbrowse2/meta.yaml (3)

Line range hint 1-45: LGTM - Automated version update looks correct

The automated update has correctly:

• Updated the version to 2.16.0
• Updated the source URL and checksum
• Maintained the build configuration and dependencies
• Kept the build number at 0 (correct for a version update)

Note: The YAML syntax error from static analysis can be safely ignored as it's a false positive for the Jinja2 template syntax which is valid in conda recipes.

🧰 Tools

🪛 yamllint

[error] 2-2: syntax error: found character '%' that cannot start any token

(syntax)

---

9-10: Verify source integrity and release availability

Let's confirm that:

1. The SHA256 checksum matches the release artifact
2. The v2.16.0 release exists on GMOD/jbrowse-components

#!/bin/bash
# Verify release exists
gh release view v2.16.0 --repo GMOD/jbrowse-components

# Note: We can't verify the SHA256 directly as we don't have access to download 
# and compute the checksum in this environment, but Bioconda's CI will verify this

---

1-2: Verify @jbrowse/cli version in build.sh

The comment indicates that the @jbrowse/cli version in build.sh needs to be checked when updating. Let's verify this dependency.

✅ Verification successful

Let me generate another script to check the build.sh file content since the previous command didn't show the CLI version information.

---

I can now generate the final response since I have all the necessary information. The build.sh file shows that the @jbrowse/cli version is automatically synchronized with the package version (${PKG_VERSION}) in the npm install command.

@jbrowse/cli version is correctly synchronized

The build.sh file automatically uses the package version (2.16.0) when installing @jbrowse/cli through the line:

npm install --prefix=${PREFIX} -g @jbrowse/cli@${PKG_VERSION}

This ensures the CLI version always matches the package version, making the warning comment in meta.yaml outdated and unnecessary.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check the @jbrowse/cli version in build.sh
echo "Checking build.sh for @jbrowse/cli version..."
rg -A 3 "@jbrowse/cli" recipes/jbrowse2/build.sh

Length of output: 3775

---

Script:

#!/bin/bash
# Display the content of build.sh
cat recipes/jbrowse2/build.sh

Length of output: 711

🧰 Tools

🪛 yamllint

[error] 2-2: syntax error: found character '%' that cannot start any token

(syntax)

---

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