<commit_before>{% set version = "0.7.0" %}

package:
  name: mykrobe
  version: {{ version }}

source:
  url: https://github.com/Mykrobe-tools/mykrobe/archive/v{{ version }}.tar.gz
  sha256: c1fba091bf72f95112211d53d5610297b4bcbca135592585ce2cde3e98156ef0

build:
  number: 3
  skip: True  # [py2k]
  entry_points:
    - mykrobe = mykrobe.cli:main

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
  host:
    - python
    - pip
    - zlib
    - wget
    - numpy
    - cython
    - mongoengine
    - pyvcf
    - biopython
  run:
    - python
    - mongodb >3.0
    - wget
    - zlib
    - numpy
    - mongoengine
    - pyvcf
    - biopython

test:
  imports:
    - numpy
    - mongoengine
    - vcf
    - Bio
    - mykrobe

  commands:
    - mykrobe --version
    - mykrobe --help
    - mykrobe predict --help
    - mykrobe variants --help
    - mykrobe genotype --help
    - 'mccortex31 2>&1 | head -n2 | grep "^usage: "'<commit_msg>[ci skip] Merge PR 19912<commit_after>{% set version = "0.7.0" %}

package:
  name: mykrobe
  version: {{ version }}

source:
  url: https://github.com/Mykrobe-tools/mykrobe/archive/v{{ version }}.tar.gz
  sha256: c1fba091bf72f95112211d53d5610297b4bcbca135592585ce2cde3e98156ef0

build:
  number: 4
  skip: True  # [py2k]
  entry_points:
    - mykrobe = mykrobe.cli:main

requirements:
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
  host:
    - python
    - pip
    - zlib
    - wget
    - numpy
    - cython
    # mongoenine pin can be dropped in newer release of mykrobe
    - mongoengine <=0.18.2
    - pyvcf
    - biopython
  run:
    - python
    - mongodb >3.0
    - wget
    - zlib
    - numpy
    - mongoengine
    - pyvcf
    - biopython

test:
  imports:
    - numpy
    - mongoengine
    - vcf
    - Bio
    - mykrobe

  commands:
    - mykrobe --version
    - mykrobe --help
    - mykrobe predict --help
    - mykrobe variants --help
    - mykrobe genotype --help
    - 'mccortex31 2>&1 | head -n2 | grep "^usage: "'
{'fraction_non_alphanumeric': 0.12699203187250996, 'fraction_numerical': 0.0602589641434263, 'mean_word_length': 1.9414348462664714, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 7, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3594383', 'n_tokens_mistral': 869, 'n_tokens_neox': 797, 'n_words': 167}