{% set name = "plastid" %}
{% set version = "0.6.1" %}

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

source:
  url: https://files.pythonhosted.org/packages/source/p/{{ name }}/{{ name }}-{{ version }}.tar.gz
  sha256: 7a63f8a3b760e9c91e7c6d95ff781d9a8f2f967d705fcd8555ebb1e6d3b08b7b

build:
  # We're not rebuilding old biopython versions on conda-forge for this
  skip: true  # [py > 39]
  number: 2

extra:
  skip-lints:
    - cython_must_be_in_host  # Plastid mistakenly checks for Cython at runtime (pkg_resources.DistributionNotFound)

requirements:
  build:
    - {{ compiler('c') }}
  host:
    - python
    - cython >=0.22.0
    - setuptools
    - numpy >=1.9.4,<=1.23.5 # numpy 1.24 removes np.TYPE (reported https://github.com/joshuagryphon/plastid/issues/55)
    - pysam >=0.8.4
    - termcolor
    - scipy >=0.15.1
    - pandas >=0.17.0
    - matplotlib-base >=1.4.0
    - biopython >=1.64,<1.78  # 1.78 removed Bio.Alphabet (reported https://github.com/joshuagryphon/plastid/issues/45)
    - twobitreader >=3.0.0
    - zlib
    - openssl
    - htslib
    
  run:
    - python
    - numpy <=1.23.5
    - {{ pin_compatible('pysam', max_pin='x.x.x') }}
    - setuptools
    - cython >=0.22.0
    - termcolor
    - scipy >=0.15.1
    - pandas >=0.17.0
    - matplotlib-base >=1.4.0
    - biopython >=1.64,<1.78
    - twobitreader >=3.0.0
    - zlib
    - bowtie
    - fastx_toolkit
    - htslib
test:
  imports:
    - plastid
  commands:
    - counts_in_region -h
    - cs -h
    - get_count_vectors -h
    - make_wiggle -h
    - metagene -h
    - phase_by_size -h
    - psite -h
    - crossmap -h
    - gff_parent_types -h
    - reformat_transcripts -h
    - findjuncs -h
    - slidejuncs -h

about:
  home: http://plastid.readthedocs.io/en/latest/
  license: BSD 3-Clause
  summary: plastid is a Python library for genomic analysis -- in particular, high-throughput sequencing data
