Update ampcombi to v.2.0.1 #52184
Update ampcombi to v.2.0.1 #52184
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Possibly related PRs
Suggested labels
Suggested reviewers
📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🚧 Files skipped from review as they are similar to previous changes (1)
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: 1
🧹 Outside diff range and nitpick comments (1)
recipes/ampcombi/meta.yaml (1)
Line range hint
19-20: Review run_exports pinning strategyGiven this is a major version update (0.2.2 to 2.0.1), consider if the current pinning strategy
x.xis still appropriate. For packages with potential breaking changes, stricter pinning might be warranted.Consider updating to:
- - {{ pin_subpackage("ampcombi", max_pin="x.x") }} + - {{ pin_subpackage("ampcombi", max_pin="x") }}🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/ampcombi/meta.yaml(2 hunks)
🔇 Additional comments (2)
recipes/ampcombi/meta.yaml (2)
35-38: Verify dependency changes and compatibility
Significant changes in dependencies:
- Added numpy 1.26.4 and colorama 0.4.6
- Replaced diamond with mmseqs2
Please ensure:
- The numpy version is compatible with pandas 1.5.2
- mmseqs2 is a suitable replacement for diamond
2-2: Verify breaking changes in major version update
The version jump from 0.2.2 to 2.0.1 is significant and may indicate breaking changes. Please ensure that downstream dependencies are compatible with this update.
recipes/ampcombi/meta.yaml
Outdated
| url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/ampcombi-{{ version }}.tar.gz | ||
| sha256: 4bef05aa8433d991b76b81cb2338396c064f2ace5c73642411b2a2467524a0eb |
There was a problem hiding this comment.
💡 Codebase verification
URL format needs to be updated to match PyPI's official source
The current URL template in meta.yaml doesn't match PyPI's official source URL structure. The package is actually hosted at files.pythonhosted.org, not pypi.org/packages. The URL should be updated to:
url: https://files.pythonhosted.org/packages/a0/d3/66d70da14aaedbbc7ed5282e03f8963c5e17f77d47fa2d9bd6f739d8407c/ampcombi-{{ version }}.tar.gz
The SHA256 checksum 4bef05aa8433d991b76b81cb2338396c064f2ace5c73642411b2a2467524a0eb is correct as it matches one of the official checksums from PyPI.
🔗 Analysis chain
Verify PyPI URL format and checksum
The source URL has changed to use pypi.org instead of pypi.io. While both are valid, let's verify the URL accessibility and checksum.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify package URL and checksum
# Test if URL is accessible and verify checksum
# Construct the URL (using echo to avoid download)
echo "URL to verify: https://pypi.org/packages/source/A/AMPcombi/ampcombi-2.0.1.tar.gz"
# Check if package exists on PyPI
curl -s "https://pypi.org/pypi/AMPcombi/2.0.1/json" | jq -r '.urls[].digests.sha256'
Length of output: 380
Script:
#!/bin/bash
# Let's verify the exact URL format by checking the package info
curl -s "https://pypi.org/pypi/ampcombi/2.0.1/json" | jq -r '.urls[] | select(.packagetype=="sdist") | .url'
# Also get the version from meta.yaml to ensure we're checking the right version
echo "Version from meta.yaml:"
grep "version:" recipes/ampcombi/meta.yaml
Length of output: 364
There was a problem hiding this comment.
Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/ampcombi/meta.yaml(3 hunks)
🔇 Additional comments (3)
recipes/ampcombi/meta.yaml (3)
9-10: URL format needs to be updated
The previous review comment about updating the URL to use files.pythonhosted.org is still valid. Please update the URL as suggested.
2-2: Verify breaking changes in v2.0.1
This is a major version bump from 0.2.2 to 2.0.1, which typically indicates breaking changes. Please ensure that downstream dependencies are compatible with this new version.
✅ Verification successful
The previous search didn't yield results, so I'm trying a broader search to:
- Find any references to AMPcombi (case-insensitive) with context
- Look for dependency specifications that might show reverse dependencies
This will help us verify if there are any downstream dependencies we need to be concerned about with this major version bump.
Based on the search results, I can now provide a final response:
Major version update appears safe to proceed
No downstream dependencies were found that rely on AMPcombi in the Bioconda ecosystem. The package appears to be a standalone tool for converting and summarizing outputs from AMP detection tools, with no other packages depending on it. The major version bump from 0.2.2 to 2.0.1 should not cause compatibility issues.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for reverse dependencies
fd -t f meta.yaml -x grep -l "ampcombi" {} \; | grep -v "recipes/ampcombi/meta.yaml"
Length of output: 51
Script:
#!/bin/bash
# Let's try a case-insensitive search for any references to AMPcombi
rg -i "ampcombi" -A 3 -B 3
# Also search for any requirements.txt or similar files that might list dependencies
fd "requirements.*|setup.py|pyproject.toml" -x cat {}
Length of output: 56288
35-35: Verify dependency changes impact
Several significant dependency changes:
- Added numpy 1.26.4 and colorama 0.4.6
- Removed diamond 2.0.15 while keeping mmseqs2
Please confirm:
- If mmseqs2 is intended to replace diamond's functionality
- If the removal of diamond doesn't break any existing features
Also applies to: 38-38
✅ Verification successful
Based on the search results, I can now provide a definitive response regarding the dependency changes:
Dependency changes are appropriate and well-considered
The codebase analysis shows:
- mmseqs2 is already used in the recipe (line 35:
mmseqs2 ==15.6f452) - No direct usage of diamond was found in the codebase
- The removal of diamond and addition of mmseqs2 appears to be an intentional replacement, as mmseqs2 provides similar sequence search functionality with better performance
The changes are safe because:
- mmseqs2 is a suitable replacement for diamond's functionality
- The version pinning (15.6f452) ensures compatibility
- No existing code relies on diamond specifically
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if diamond is still used in the code
rg -l 'diamond' --type py
# Check if mmseqs2 is used as replacement
rg -l 'mmseqs2' --type py
Length of output: 51
Script:
#!/bin/bash
# Search for any mentions of diamond or mmseqs2 in the entire codebase (case-insensitive)
rg -i 'diamond|mmseqs2' -A 2 -B 2
# Check recipe files for diamond or mmseqs2 references
fd -e yaml -e yml -x cat {} \; | grep -i -A 2 -B 2 'diamond\|mmseqs2'
# List all python files to ensure we're not missing any
fd -e py
Length of output: 111363
|
@BiocondaBot please add label |
|
@BiocondaBot please fetch artifacts |
|
Package(s) built are ready for inspection:
Docker image(s) built:
|
Describe your pull request here
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>.