Update annembed to v0.1.5

[jianshu93]

Describe your pull request here

With this new release, we add our own svd algorithm to get rid of ndarray-linalg and also new logo added

---

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[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request introduces modifications to the build.sh script and the meta.yaml file for the annembed package. In the build.sh script, the cargo install command has been updated to include a new feature, simdeez_f, alongside the existing intel-mkl-static feature. This change allows the installation of the Rust package with both features while maintaining the overall structure and logic of the script. The meta.yaml file has undergone several updates: the package version has been incremented from 0.1.4 to 0.1.5, the SHA256 checksum has been updated to reflect the new version, and the summary description of the package has been revised to clarify its functionality as a non-linear dimension reduction/embedding algorithm for large-scale biological data.

Possibly related PRs

• Bump openms build to expose eigen in libopenms #51331: Updates the meta.yaml file for the OpenMS package, including versioning changes.
• [biobb_common] update 5.0.0 #51335: Updates the meta.yaml file for the biobb_common package with a version increment.
• [biobb_amber] update 5.0.0 #51430: Updates the meta.yaml file for the biobb_amber package, involving a version update.
• [biobb_analysis] update 5.0.0 #51431: Updates the meta.yaml file for the biobb_analysis package with a version increment.
• [biobb_chemistry] update 5.0.0 #51435: Updates the meta.yaml file for the biobb_chemistry package, including a version update.
• [biobb_cmip] update 5.0.0 #51453: Updates the meta.yaml file for the biobb_cmip package with a version increment.
• Update biobb_cmip to 5.0.0 #51455: Updates the meta.yaml file for the biobb_cmip package, reflecting a version change.

Suggested labels

autobump, new version

Suggested reviewers

• mencian

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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 6a9fb9c and 209a2b1.

📒 Files selected for processing (2)

• recipes/annembed/build.sh (1 hunks)
• recipes/annembed/meta.yaml (3 hunks)

🧰 Additional context used

🪛 yamllint

recipes/annembed/meta.yaml

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

(syntax)

🔇 Additional comments (7)

recipes/annembed/build.sh (2)

Line range hint 1-8: Script structure and purpose are appropriate.

This build script effectively sets up the environment for building the annembed package using Rust/cargo. It includes a workaround for SSH-based Git connections and sets the necessary environment variables. The cargo install command now includes both 'intel-mkl-static' and 'simdeez_f' features, which aligns with the PR objective of updating annembed to v0.1.5 and introducing a new SVD algorithm.

The script structure is sound and serves its purpose well. No further changes are necessary.

🧰 Tools

🪛 Shellcheck

[warning] 5-5: Declare and assign separately to avoid masking return values.

(SC2155)

---

8-8: LGTM! Verify new feature dependencies.

The addition of the 'simdeez_f' feature to the cargo install command is appropriate and aligns with the PR objective of updating annembed to v0.1.5. This change likely enables the new SVD algorithm mentioned in the PR summary.

To ensure a smooth build process, please verify if the 'simdeez_f' feature introduces any new dependencies or system requirements. You can run the following command to check for any new dependencies in the updated version:

If new dependencies are found, ensure they are properly handled in the meta.yaml file.

✅ Verification successful

Verified! No new dependencies found.

The addition of the simdeez_f feature does not introduce any new dependencies beyond those already present in annembed v0.1.5's Cargo.toml. The feature is managed through the existing hnsw_rs dependency.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for new dependencies in the updated version of annembed

# Fetch the Cargo.toml file
cargo_toml=$(curl -s https://raw.githubusercontent.com/jianshu93/annembed/v0.1.5/Cargo.toml)

# Extract and display dependencies
echo "Dependencies for annembed v0.1.5:"
echo "$cargo_toml" | awk '/^\[dependencies\]/,/^\[/' | grep -v '^\[' | sed 's/^/- /'

# Check for 'simdeez' related dependencies
echo -e "\nChecking for 'simdeez' related dependencies:"
echo "$cargo_toml" | grep -i 'simdeez'

Length of output: 9774

recipes/annembed/meta.yaml (5)

1-1: Version update looks good.

The version has been correctly updated to 0.1.5, which aligns with the PR objective.

🧰 Tools

🪛 yamllint

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

(syntax)

---

31-31: Summary update enhances clarity.

The addition of "embedding" alongside "dimension reduction" in the summary provides a more comprehensive description of the algorithm's functionality. This change improves the clarity of the package's purpose.

---

1-1: Ignore yamllint warning about '%' character.

The yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of a valid Jinja2 template syntax, which is commonly used in Conda recipe files. The syntax here is correct and necessary for setting the version variable.

🧰 Tools

🪛 yamllint

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

(syntax)

---

Line range hint 1-37: Overall, the changes look good and align with the PR objectives.

The updates to the version, SHA256 checksum, and summary description are consistent with the PR's goal of updating annembed to v0.1.5. The changes improve the clarity of the package's purpose and maintain the necessary metadata updates. Once the SHA256 checksum is verified, this file should be ready for merging.

---

14-14: Verify the updated SHA256 checksum.

The SHA256 checksum has been updated, which is expected with a new version. However, it's crucial to ensure this checksum corresponds to the correct source package for version 0.1.5.

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

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[jianshu93]

@BiocondaBot please add label

[jianshu93]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	annembed-0.1.5-hdbdd923_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
annembed	0.1.5--hdbdd923_0	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/annembed:0.1.5--hdbdd923_0.tar.gz | docker load