grayskull_links

grayskull.defopt.conda-forge.vs.grayskull.patch

4d3
< 
14d12
<   number: 1
16c14,15
<   script: {{ PYTHON }} -m pip install . -vv
---
>   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
>   number: 0
20,21c19
<     - pip
<     - python {{ python_min }}
---
>     - python >=3.5
23c21
<     - setuptools
---
>     - pip
25,26c23
<     - python >={{ python_min }}
<     - typing_inspect >=0.5.0
---
>     - python >=3.5
29d25
<     - colorama >=0.3.4
38d33
<     - python {{ python_min }}
48d42

grayskull.pybwa.bioconda.vs.grayskull.patch

diff meta.bioconda.yaml meta.grayskull.yaml 
9c9
<   url: https://github.com/fulcrumgenomics/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz
---
>   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pybwa-{{ version }}.tar.gz
12a13,14
>   skip: true  # [py>=400 or py2k]
>   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
14,19d15
<   skip: True  # [py < 39]
<   script: {{ PYTHON }} -m pip install . -vvv --no-deps
<   run_exports:
<     - {{ pin_subpackage('pybwa', max_pin="x") }}
<   script_env:
<     - M4=$BUILD_PREFIX/bin/m4  # [osx and arm64]
22,27d17
<   build:
<     - {{ compiler('c') }}
<     - make
<     - autoconf
<     - automake
<     - libtool
29,31c19
<     - cython
<     - pip
<     - python
---
>     - python >=3.9.0,<4.0
33,38c21,22
<     - zlib
<     - xz
<     - bzip2
<     - libdeflate
<     - libcurl
<     - openssl  # [not osx]
---
>     - cython >=3.0.11
>     - setuptools >=75.1.0
40c24
< 
---
>     - pip
42c26
<     - python
---
>     - python >=3.9.0,<4.0
45c29
<     - typing-extensions >=3.7.4  # [py < 313]
---
>     - typing_extensions >=3.7.4  # [py<313]
49a34,37
>   commands:
>     - pip check
>   requires:
>     - pip
52,58c40,44
<   home: https://github.com/fulcrumgenomics/pybwa
<   summary: "Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa."
<   license: MIT
<   license_family: MIT
<   license_file: LICENSE
<   dev_url: https://github.com/fulcrumgenomics/pybwa
<   doc_url: https://pybwa.readthedocs.io/en/latest
---
>   summary: Python bindings for BWA
>   license: BSD-3-Clause AND MIT
>   license_file:
>     - LICENSE
>     - htslib/LICENSE
63,67d48
<   additional-platforms:
<     - linux-aarch64
<     - osx-arm64
<   identifier:
<     - DOI:10.5281/zenodo.15029038

grayskull.sunbeam.bioconda.vs.grayskull.patch

5,6c5,6
<   name: "{{ name|lower }}"
<   version: "{{ version }}"
---
>   name: {{ name|lower }}
>   version: {{ version }}
9c9
<   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
---
>   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/sunbeamlib-{{ version }}.tar.gz
13c13,14
<   number: 0
---
>   entry_points:
>     - sunbeam = sunbeam.scripts.sunbeam:main
15,17c16,17
<   script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
<   run_exports:
<     - {{ pin_subpackage('sunbeamlib', max_pin="x") }}
---
>   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
>   number: 0
21,22d20
<     - pip
<     - setuptools
23a22,24
>     - setuptools >=61.0.0
>     - wheel
>     - pip
34a36
>     - pip check
35a38,39
>   requires:
>     - pip
38,40c42
<   home: https://github.com/sunbeam-labs/sunbeam
<   license: MIT
<   summary: "A robust, extensible metagenomic sequencing pipeline"
---
>   summary: A snakemake utility for metagenomic sequencing analysis
42c44,45
<   doc_url: https://sunbeam.readthedocs.io/
---
>   license: ''
>   license_file: PLEASE_ADD_LICENSE_FILE
46c49
<     - Ulthran
---
>     - nh13

meta.defopt.conda-forge.yaml

{% set name = "defopt" %}
{% set version = "6.4.0" %}


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

source:
  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/defopt-{{ version }}.tar.gz
  sha256: 359a56137b4b7dcbc051d2157e6591a09c35c4297cfc00f1ef8dbcd192d19a34

build:
  number: 1
  noarch: python
  script: {{ PYTHON }} -m pip install . -vv

requirements:
  host:
    - pip
    - python {{ python_min }}
    - setuptools-scm >=3.3
    - setuptools
  run:
    - python >={{ python_min }}
    - typing_inspect >=0.5.0
    - docutils >=0.12
    - sphinxcontrib-napoleon >=0.7.0
    - colorama >=0.3.4

test:
  imports:
    - defopt
  commands:
    - pip check
  requires:
    - pip
    - python {{ python_min }}

about:
  home: https://github.com/anntzer/defopt
  summary: Effortless argument parser
  license: MIT
  license_file: LICENSE.txt

extra:
  recipe-maintainers:
    - ickc
    - nh13

meta.defopt.grayskull.yaml

{% set name = "defopt" %}
{% set version = "6.4.0" %}

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

source:
  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/defopt-{{ version }}.tar.gz
  sha256: 359a56137b4b7dcbc051d2157e6591a09c35c4297cfc00f1ef8dbcd192d19a34

build:
  noarch: python
  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
  number: 0

requirements:
  host:
    - python >=3.5
    - setuptools-scm >=3.3
    - pip
  run:
    - python >=3.5
    - docutils >=0.12
    - sphinxcontrib-napoleon >=0.7.0

test:
  imports:
    - defopt
  commands:
    - pip check
  requires:
    - pip

about:
  home: https://github.com/anntzer/defopt
  summary: Effortless argument parser
  license: MIT
  license_file: LICENSE.txt

extra:
  recipe-maintainers:
    - nh13

meta.pybwa.bioconda.yaml

{% set name = "pybwa" %}
{% set version = "2.1.0" %}

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

source:
  url: https://github.com/fulcrumgenomics/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz
  sha256: aeb3e225323ec2d8b1aafc5121dcde08adc43b28b3711d1275c324b481a68130

build:
  number: 0
  skip: True  # [py < 39]
  script: {{ PYTHON }} -m pip install . -vvv --no-deps
  run_exports:
    - {{ pin_subpackage('pybwa', max_pin="x") }}
  script_env:
    - M4=$BUILD_PREFIX/bin/m4  # [osx and arm64]

requirements:
  build:
    - {{ compiler('c') }}
    - make
    - autoconf
    - automake
    - libtool
  host:
    - cython
    - pip
    - python
    - poetry-core
    - zlib
    - xz
    - bzip2
    - libdeflate
    - libcurl
    - openssl  # [not osx]
    - pysam >=0.22.1

  run:
    - python
    - fgpyo >=0.7.0
    - pysam >=0.22.1
    - typing-extensions >=3.7.4  # [py < 313]

test:
  imports:
    - pybwa

about:
  home: https://github.com/fulcrumgenomics/pybwa
  summary: "Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa."
  license: MIT
  license_family: MIT
  license_file: LICENSE
  dev_url: https://github.com/fulcrumgenomics/pybwa
  doc_url: https://pybwa.readthedocs.io/en/latest

extra:
  recipe-maintainers:
    - nh13
  additional-platforms:
    - linux-aarch64
    - osx-arm64
  identifier:
    - DOI:10.5281/zenodo.15029038

meta.pybwa.grayskull.yaml

{% set name = "pybwa" %}
{% set version = "2.1.0" %}

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

source:
  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pybwa-{{ version }}.tar.gz
  sha256: aeb3e225323ec2d8b1aafc5121dcde08adc43b28b3711d1275c324b481a68130

build:
  skip: true  # [py>=400 or py2k]
  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
  number: 0

requirements:
  host:
    - python >=3.9.0,<4.0
    - poetry-core
    - cython >=3.0.11
    - setuptools >=75.1.0
    - pysam >=0.22.1
    - pip
  run:
    - python >=3.9.0,<4.0
    - fgpyo >=0.7.0
    - pysam >=0.22.1
    - typing_extensions >=3.7.4  # [py<313]

test:
  imports:
    - pybwa
  commands:
    - pip check
  requires:
    - pip

about:
  summary: Python bindings for BWA
  license: BSD-3-Clause AND MIT
  license_file:
    - LICENSE
    - htslib/LICENSE

extra:
  recipe-maintainers:
    - nh13

meta.sunbeamlib.bioconda.yaml

{% set name = "sunbeamlib" %}
{% set version = "5.0.1" %}

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

source:
  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
  sha256: bbf06a4f2571ee62fb3ea8a78eef66f0f7fc1fee209cab3d50587c4f7eec3754

build:
  number: 0
  noarch: python
  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
  run_exports:
    - {{ pin_subpackage('sunbeamlib', max_pin="x") }}

requirements:
  host:
    - pip
    - setuptools
    - python >=3.11
  run:
    - python >=3.11
    - snakemake ==9.3.3
    - more-itertools ==10.7.0
    - pyyaml ==6.0.2
    - pandas ==2.2.3

test:
  imports:
    - sunbeam
  commands:
    - sunbeam --help

about:
  home: https://github.com/sunbeam-labs/sunbeam
  license: MIT
  summary: "A robust, extensible metagenomic sequencing pipeline"
  dev_url: https://github.com/sunbeam-labs/sunbeam
  doc_url: https://sunbeam.readthedocs.io/

extra:
  recipe-maintainers:
    - Ulthran

meta.sunbeamlib.grayskull.yaml

{% set name = "sunbeamlib" %}
{% set version = "5.0.1" %}

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

source:
  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/sunbeamlib-{{ version }}.tar.gz
  sha256: bbf06a4f2571ee62fb3ea8a78eef66f0f7fc1fee209cab3d50587c4f7eec3754

build:
  entry_points:
    - sunbeam = sunbeam.scripts.sunbeam:main
  noarch: python
  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
  number: 0

requirements:
  host:
    - python >=3.11
    - setuptools >=61.0.0
    - wheel
    - pip
  run:
    - python >=3.11
    - snakemake ==9.3.3
    - more-itertools ==10.7.0
    - pyyaml ==6.0.2
    - pandas ==2.2.3

test:
  imports:
    - sunbeam
  commands:
    - pip check
    - sunbeam --help
  requires:
    - pip

about:
  summary: A snakemake utility for metagenomic sequencing analysis
  dev_url: https://github.com/sunbeam-labs/sunbeam
  license: ''
  license_file: PLEASE_ADD_LICENSE_FILE

extra:
  recipe-maintainers:
    - nh13