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Add pykofamsearch #51537

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merged 4 commits into from
Oct 22, 2024
Merged

Add pykofamsearch #51537

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80eb1ad
Add `pykofamsearch`
apcamargo Oct 21, 2024
28a5e92
Fix run_exports
apcamargo Oct 21, 2024
5c19018
Remove `subset_serialized_models` test
apcamargo Oct 21, 2024
9198b14
Fix `subset_serialized_models` test
apcamargo Oct 22, 2024
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48 changes: 48 additions & 0 deletions recipes/pykofamsearch/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
{% set name = "pykofamsearch" %}
{% set version = "2024.10.20" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pykofamsearch-{{ version }}.tar.gz
sha256: f9455f343095327bab331a35010867d5d60f67b13bd5c2344d012e6801e48fad

build:
script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
number: 0
noarch: python
entry_points:
- pykofamsearch=pykofamsearch.pykofamsearch:main
- reformat_enzymes=pykofamsearch.reformat_enzymes:main
- reformat_pykofamsearch=pykofamsearch.reformat_pykofamsearch:main
- serialize_kofam_models=pykofamsearch.serialize_kofam_models:main
run_exports:
- {{ pin_subpackage("pykofamsearch", max_pin=None) }}
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💡 Codebase verification

Consider revising the pinning strategy for pykofamsearch.

The current max_pin=None allows any version of pykofamsearch to satisfy the dependency, which might be too permissive. Given the date-based versioning, it's advisable to implement a more restrictive pinning strategy to ensure compatibility and stability.

  • Review and define a specific pinning range that aligns with your project's compatibility requirements.
🔗 Analysis chain

LGTM: Build section is well-defined, but consider reviewing the pinning strategy.

The build script, build number, noarch specification, and entry points are all correctly defined. The run_exports section is included, which is good for maintaining consistency across dependent packages.

However, consider if max_pin=None is the desired pinning strategy for this package. This strategy means that any version of pykofamsearch will satisfy the dependency, which might be too permissive. You might want to use a more restrictive pinning strategy depending on your versioning scheme and backwards compatibility guarantees.

To help decide on the appropriate pinning strategy, you can review the package's versioning history and compatibility guarantees. Here's a script to check the available versions:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check available versions of pykofamsearch on PyPI
pip install yq
curl -s https://pypi.org/pypi/pykofamsearch/json | jq -r '.releases | keys[]' | sort -V

Length of output: 468

Script:

#!/bin/bash
# Description: Check available versions of pykofamsearch on PyPI using jq

curl -s https://pypi.org/pypi/pykofamsearch/json | jq -r '.releases | keys[]' | sort -V

Length of output: 149


requirements:
host:
- python
- pip
run:
- python
- pyhmmer >=0.10.12
- pandas >=2
- tqdm >=4

test:
commands:
- pykofamsearch --help
- reformat_enzymes --help
- reformat_pykofamsearch --help
- serialize_kofam_models --help
- subset_serialized_models --helps
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⚠️ Potential issue

Test commands look good, but there's a typo in the last command.

The approach of testing the help output for each entry point is a good basic test.

There's a typo in the last test command:

-    - subset_serialized_models --helps
+    - subset_serialized_models --help

Please correct this to ensure all tests pass.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
test:
commands:
- pykofamsearch --help
- reformat_enzymes --help
- reformat_pykofamsearch --help
- serialize_kofam_models --help
- subset_serialized_models --helps
test:
commands:
- pykofamsearch --help
- reformat_enzymes --help
- reformat_pykofamsearch --help
- serialize_kofam_models --help
- subset_serialized_models --help


about:
home: "https://github.com/jolespin/pykofamsearch"
summary: "Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer."
license: MIT
license_family: MIT
license_file: LICENSE
dev_url: "https://github.com/jolespin/pykofamsearch"
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