Add ggcat 1.1.0 recipe #51632
Add ggcat 1.1.0 recipe #51632
Conversation
|
Warning Rate limit exceeded@Guilucand has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 0 minutes and 8 seconds before requesting another review. ⌛ How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. 🚦 How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. 📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe changes introduced in this pull request consist of two main components: a new shell script and a metadata file for the Possibly related PRs
Suggested labels
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/ggcat/build.sh (1 hunks)
- recipes/ggcat/meta.yaml (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/ggcat/build.sh
🧰 Additional context used
🪛 yamllint
recipes/ggcat/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/ggcat/meta.yaml (4)
1-6: LGTM! Package definition follows best practices.The package name and version are properly defined using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-11: LGTM! Build configuration properly handles dependency pinning.The
run_exportssection withmax_pin="x"ensures ABI compatibility by only allowing patch-level updates, which aligns with the PR objectives for preventing API/ABI breakage.
36-43: LGTM! Extra section is complete.The section properly specifies additional platforms, maintainer, and includes a DOI identifier.
19-22: 🛠️ Refactor suggestionRequirements section needs enhancement.
Consider adding:
- A
hostsection for system dependencies- A
runsection for runtime dependencies- Minimum Rust version specification
Let's verify if the package has any system dependencies:
Consider adding:
requirements: build: - {{ compiler('rust') }} - {{ compiler('c') }} + host: + # Add system dependencies if needed based on verification + run: + # Add runtime dependencies
| test: | ||
| commands: | ||
| - ggcat --help |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enhance test coverage.
The current test only verifies that the command runs. Consider adding more comprehensive tests.
Add additional test commands:
test:
commands:
- ggcat --help
+ - ggcat --version | grep {{ version }}
+ # Add basic functionality test if possibleCommittable suggestion was skipped due to low confidence.
recipes/ggcat/meta.yaml
Outdated
| source: | ||
| git_url: https://github.com/algbio/ggcat.git | ||
| git_rev: v1.1 | ||
| git_depth: 1 |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider using tarball URL instead of git_url.
While the current configuration works, using a tarball URL is preferred for Conda recipes as it's more reliable and efficient.
Replace the git source with:
- git_url: https://github.com/algbio/ggcat.git
- git_rev: v1.1
- git_depth: 1
+ url: https://github.com/algbio/ggcat/archive/refs/tags/v1.1.tar.gz
+ sha256: <checksum> # Replace with actual SHA256 checksumCommittable suggestion was skipped due to low confidence.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
There was a problem hiding this comment.
Actionable comments posted: 2
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/ggcat/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/ggcat/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/ggcat/meta.yaml (5)
1-6: LGTM!The package metadata section is well-structured using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-15: LGTM with a note.The source configuration is functional, though switching to .tar.gz format would align better with Conda packaging practices (as noted in previous reviews).
22-24: LGTM with a note.The basic test is present, though expanding test coverage would be beneficial (as noted in previous reviews).
26-33: LGTM!The about section is complete and well-formatted, incorporating all previous review suggestions.
35-42: Verify package's biological science relevance.Given that the PR objectives mention that "new recipes not directly related to biological sciences should be submitted to conda-forge", please verify that ggcat is primarily used in biological research. The presence of a bioRxiv DOI suggests it is, but explicit confirmation would be helpful.
✅ Verification successful
Let me gather more information about the package's biological relevance by checking the recipe and any associated documentation.
Let me try one more search to get the package description and summary:
Let me try one final check to look at the source repository's description and README:
Based on the gathered information, I can now provide a final response:
Package is appropriately placed in Bioconda
The package GGCAT (Compacted and colored de Bruijn graph construction and querying) is clearly relevant to biological sciences for several reasons:
- It's designed for processing raw sequencing data and building de Bruijn graphs, which are fundamental data structures in bioinformatics and genomics
- The associated paper is published in Genome Research (gr.277615.122)
- The tool is specifically designed for handling genomic sequencing data and performing biological sequence analysis
- It includes features like processing raw sequencing data and handling colored de Bruijn graphs, which are commonly used in comparative genomics and metagenomics
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for biological science relevance in the repository rg -i "bio|genom|dna|rna|sequenc" README.md # Check the paper abstract using the DOI echo "Please verify the biological relevance in the paper: https://doi.org/10.1101/gr.277615.122"Length of output: 2120
Script:
#!/bin/bash # Check package description in meta.yaml cat recipes/ggcat/meta.yaml | grep -A 5 "about:" # Search for biological terms in source code repository rg -i "genom|dna|rna|sequenc" recipes/ggcat/Length of output: 218
Script:
#!/bin/bash # Get the complete meta.yaml content to see the package description cat recipes/ggcat/meta.yaml # Also check if there's a README in the recipe directory ls -la recipes/ggcat/Length of output: 1142
Script:
#!/bin/bash # Get information from the source repository gh repo view algbio/ggcat # Try to get the README content from the source repository gh repo view algbio/ggcat --json readme --jq .readmeLength of output: 11326
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Add the recipe for ggcat, a program to build and query compacted and optionally colored de Bruijn graphs.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.