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Bump pyfastani to v0.6.0 #51550

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merged 4 commits into from
Oct 22, 2024
Merged

Bump pyfastani to v0.6.0 #51550

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61c7437
Update pyfastani to 0.6.0
BiocondaBot Oct 22, 2024
253c9ba
pyfastani: add aarch64/arm64 builds
martin-g Oct 22, 2024
63e7950
Update `pyfastani` recipe to use new `scikit-build-core` build
althonos Oct 22, 2024
aeac548
clean up recipe
mencian Oct 22, 2024
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23 changes: 14 additions & 9 deletions recipes/pyfastani/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,34 +1,34 @@
{% set name = "pyfastani" %}
{% set version = "0.5.1" %}
{% set version = "0.6.0" %}

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

source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
sha256: ad6c28303290a2389c29ed20db8266bbc4bf89a5b1bf64a7514d1bc9c6ba2d92
sha256: 255e890d3ee6bbd051bb94d71a5245703b254be1ff2b5dc6789d28b715ec5fa9

build:
number: 1
skip: True #[py2k]
script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
number: 0
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
run_exports:
- {{ pin_subpackage(name, max_pin="x.x") }}

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- cmake >=3.20
- make
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💡 Codebase verification

Based on the meta.yaml contents, I can now generate the final response:

Build system transition requirements need adjustment

The recipe shows a mismatch between the declared build requirements and the actual build command:

  • While cmake >=3.20, make, and scikit-build-core are added as requirements, the build script still uses pip's direct installation: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
  • This should be updated to use scikit-build-core's build mechanism instead

Required changes:

  • Update build script section to use scikit-build-core's recommended installation method
  • Keep the current requirements as they are correct for scikit-build-core
🔗 Analysis chain

Verify build system transition requirements.

The transition from setuptools to scikit-build-core looks correct with appropriate dependencies:

  • Added cmake >=3.20 and make for build
  • Added scikit-build-core to host requirements

Let's verify the build system requirements:

Also applies to: 29-29

Let me generate additional scripts to verify the build system transition properly.

The previous script had issues and mixed up with fastani instead of pyfastani. Let's examine the actual recipe and build configuration to verify the transition properly.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if any setuptools references remain in the recipe
rg -i 'setuptools' recipes/pyfastani/

# Verify scikit-build-core is the standard build system for this version
curl -s https://pypi.org/pypi/pyfastani/0.6.0/json | jq -r '.info.requires_dist[]' | grep -i 'scikit-build-core'

Length of output: 481

Script:

#!/bin/bash
# Check build system related files and configurations
cat recipes/pyfastani/meta.yaml

# Check if there are any pyproject.toml references that might indicate build system
fd pyproject.toml recipes/pyfastani/ --exec cat {}

# Look for any setup related files
fd -e py -e cfg setup recipes/pyfastani/ --exec cat {}

Length of output: 1354

host:
- python
- pip
- cython
- setuptools
- zlib
- scikit-build-core
run:
- python
- zlib

test:
imports:
Expand All @@ -39,10 +39,15 @@ test:
about:
home: https://github.com/althonos/pyfastani
license: MIT
license_family: MIT
license_file: COPYING
summary: Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation..
doc_url: https://pyfastani.readthedocs.org/
summary: "Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation."
doc_url: https://pyfastani.readthedocs.org
dev_url: https://github.com/althonos/pyfastani

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
recipe-maintainers:
- althonos