Update ntedit to 2.1.0 #52248
Update ntedit to 2.1.0 #52248
Conversation
📝 WalkthroughWalkthroughThe pull request introduces modifications to the Possibly related PRs
Suggested labels
Suggested reviewers
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: 0
🧹 Outside diff range and nitpick comments (1)
recipes/ntedit/meta.yaml (1)
Line range hint
18-26: Consider build system optimizationThe recipe includes multiple build systems (cmake, make, automake, autoconf, meson, ninja). Consider documenting which build system is primarily used and if all are necessary. This could help reduce build dependencies and complexity.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/ntedit/meta.yaml(3 hunks)
🔇 Additional comments (3)
recipes/ntedit/meta.yaml (3)
2-2: Version update looks good!
The version bump to 2.1.0 matches the PR objectives and follows semantic versioning. The existing run_exports section with max_pin="x" will help maintain ABI compatibility with downstream dependencies.
15-15: Verify source integrity
Let's verify the source tarball and its checksum.
35-35: Verify dependency change impact
The replacement of nthits with ntstat is a significant change. Let's verify:
- The dependency change is documented in upstream
- The availability of ntstat in Bioconda
✅ Verification successful
Dependency change appears to be valid
Based on the verification results:
- The
ntstatpackage is available in Bioconda with version 1.0.1, as evidenced by its recipe inrecipes/ntstat/meta.yaml - The package is from the same organization (bcgsc) as ntEdit
- The dependency is properly versioned (>=1.0.1)
- The package provides k-mer frequency and depth analysis functionality, which aligns with ntEdit's genome assembly polishing purpose
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify ntstat package availability and version in Bioconda
# Check if ntstat is available in Bioconda
conda search -c bioconda ntstat
# Check for any recipes that might be affected by this change
fd -t f meta.yaml -x rg -l "nthits|ntstat" {}
Length of output: 291
Script:
#!/bin/bash
# Let's check the content of ntstat recipe and its version
cat recipes/ntstat/meta.yaml
# Check ntedit recipe for any documentation about the dependency change
cat recipes/ntedit/meta.yaml
# Check if there are any recent changes to these files
git log --oneline -n 5 recipes/ntstat/meta.yaml recipes/ntedit/meta.yaml
Length of output: 2323
Script:
#!/bin/bash
# Let's check the upstream repository's changelog or release notes for documentation about this change
curl -sL https://raw.githubusercontent.com/bcgsc/ntEdit/v2.1.0/CHANGELOG.md || true
# Let's also check if nthits was previously a dependency
git show HEAD^ recipes/ntedit/meta.yaml
Length of output: 135
|
Pending building ntStat recipe for osx-arm64 and linux-aarch64 |
Updating ntEdit to 2.1.0, updating dependency
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>.