Update nextclade to 3.9.0

[nextstrain-bot]

Update nextclade: 3.8.2 → 3.9.0.

Home	https://github.com/nextstrain/nextclade
Summary	Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Recipe maintainers	@pvanheus, @corneliusroemer, @ivan-aksamentov

@BiocondaBot please add label

@BiocondaBot please fetch artifacts

Note: this pull request is submitted automatically, triggered by a release in nextstrain/nextclade repo. If you want to get in touch, please ping recipe maintainers and/or someone from @nextstrain/core team.

[nextstrain-bot]

@BiocondaBot please add label

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces an update to the meta.yaml file for the nextclade package. The primary change is the increment of the version number from "3.8.2" to "3.9.0". Along with this version change, the SHA256 checksums for various binaries have been updated to ensure they match the new version. Specifically, the checksums have been altered for the Linux x86_64, AArch64 Linux, macOS x86_64, and macOS AArch64 binaries. This update does not include any modifications to the logic, error handling, or control flow within the package, focusing solely on versioning and checksum validation.

Possibly related PRs

• Update architeuthis to 0.3.1 #50970: Involves updating the version and SHA256 checksum in the meta.yaml file, similar to the changes in the main PR for the nextclade package.
• Update metabolabpy to 0.9.53 #51094: Updates the version and SHA256 checksum in the meta.yaml file, reflecting a similar type of change as seen in the main PR.
• upd orthologer to 3.4.2 #51128: Updates the version and SHA256 checksum in the meta.yaml file, paralleling the changes made in the main PR.
• Update nf-core to 3.0.0 #51249: Includes updates to the version and SHA256 checksum in the meta.yaml file, aligning with the updates in the main PR.
• Update nf-core to 3.0.1 #51272: Updates the version and SHA256 checksum in the meta.yaml file, similar to the changes made in the main PR.
• Update nf-core to 3.0.2 #51333: Involves updating the version and SHA256 checksum in the meta.yaml file, reflecting the same type of changes as in the main PR.

Suggested labels

autobump, new version

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between abe5345 and 2e62f9b.

📒 Files selected for processing (1)

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

🧰 Additional context used

🔇 Additional comments (6)

recipes/nextclade/meta.yaml (6)

2-2: Version update looks good.

The version has been correctly updated to 3.9.0, which aligns with the PR objective.

---

10-10: SHA256 checksum updated for Linux x86_64.

The checksum has been updated, which is necessary for the new version. However, we should verify its correctness.

To verify the checksum, you can run:

Compare the output with the checksum in the recipe.

---

1-16: Summary of changes and final verification.

All changes in this file are consistent with updating Nextclade to version 3.9.0. The version number and SHA256 checksums for all platforms have been updated appropriately. No other modifications were made, which is correct for a version update.

As a final verification step, it's recommended to:

1. Confirm that the version number (3.9.0) matches the latest release on the Nextclade GitHub repository.
2. Verify all SHA256 checksums using the provided curl commands in the previous comments.
3. Ensure that no other changes are needed in the recipe for this version update (e.g., dependencies, build number reset).

To verify that no unexpected changes were made, you can run:

This command should produce no output if there are no unexpected changes.

✅ Verification successful

[/run_scripts]

---

Verification Successful: No Unexpected Changes Detected

The recipes/nextclade/meta.yaml file has only been updated to version 3.9.0 with corresponding SHA256 checksums for all supported platforms. No other changes were found, ensuring the update is precise and controlled.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check for any changes other than version and checksums
grep -vE "version = |sha256: " recipes/nextclade/meta.yaml | diff - <(curl -sL https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/recipes/nextclade/meta.yaml | grep -vE "version = |sha256: ")

Length of output: 265

---

Script:

#!/bin/bash
# Check for any changes other than version and checksums by using temporary files
LOCAL_TMP=$(mktemp)
REMOTE_TMP=$(mktemp)

# Extract relevant lines from local meta.yaml
grep -vE "version = |sha256: " recipes/nextclade/meta.yaml > "$LOCAL_TMP"

# Fetch and extract relevant lines from remote meta.yaml
curl -sL https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/recipes/nextclade/meta.yaml | grep -vE "version = |sha256: " > "$REMOTE_TMP"

# Compare the two files
diff "$LOCAL_TMP" "$REMOTE_TMP"

# Clean up temporary files
rm "$LOCAL_TMP" "$REMOTE_TMP"

Length of output: 376

🧰 Tools

🪛 yamllint

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

(syntax)

---

14-14: SHA256 checksum updated for macOS x86_64.

The checksum has been updated, which is necessary for the new version. However, we should verify its correctness.

To verify the checksum, you can run:

Compare the output with the checksum in the recipe.

---

16-16: SHA256 checksum updated for macOS AArch64.

The checksum has been updated, which is necessary for the new version. However, we should verify its correctness.

To verify the checksum, you can run:

Compare the output with the checksum in the recipe.

---

12-12: SHA256 checksum updated for AArch64 Linux.

The checksum has been updated, which is necessary for the new version. However, we should verify its correctness.

To verify the checksum, you can run:

Compare the output with the checksum in the recipe.

---

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