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setup.py
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setup.py
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from os import path
from setuptools import setup, find_packages
from biokit.version import __version__
here = path.abspath(path.dirname(__file__))
with open(path.join(here, "README.md")) as f:
long_description = f.read()
CLASSIFIERS = [
"Operating System :: OS Independent",
"Intended Audience :: Science/Research",
"Programming Language :: Python",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering",
]
REQUIRES = ["biopython>=1.82", "numpy>=1.24.0", "cython"]
setup(
name="jlsteenwyk-biokit",
description="",
long_description=long_description,
long_description_content_type="text/markdown",
author="Jacob L. Steenwyk",
author_email="[email protected]",
url="https://github.com/jlsteenwyk/biokit",
packages=find_packages(),
classifiers=CLASSIFIERS,
entry_points={
"console_scripts": [
"biokit = biokit.biokit:main",
"bk_alignment_length = biokit.biokit:alignment_length", # Alignment-based functions
"bk_aln_len = biokit.biokit:alignment_length",
"bk_alignment_recoding = biokit.biokit:alignment_recoding",
"bk_aln_recoding = biokit.biokit:alignment_recoding",
"bk_recode = biokit.biokit:alignment_recoding",
"bk_alignment_summary = biokit.biokit:alignment_summary",
"bk_aln_summary = biokit.biokit:alignment_summary",
"bk_consensus_sequence = biokit.biokit:consensus_sequence",
"bk_con_seq = biokit.biokit:consensus_sequence",
"bk_constant_sites = biokit.biokit:constant_sites",
"bk_con_sites = biokit.biokit:constant_sites",
"bk_parsimony_informative_sites = biokit.biokit:parsimony_informative_sites",
"bk_pi_sites = biokit.biokit:parsimony_informative_sites",
"bk_pis = biokit.biokit:parsimony_informative_sites",
"bk_position_specific_score_matrix = biokit.biokit:position_specific_score_matrix",
"bk_pssm = biokit.biokit:position_specific_score_matrix",
"bk_variable_sites = biokit.biokit:variable_sites",
"bk_var_sites = biokit.biokit:variable_sites",
"bk_vs = biokit.biokit:variable_sites",
"bk_gc_content_first_position = biokit.biokit:gc_content_first_position", # Coding sequences-based functions
"bk_gc1 = biokit.biokit:gc_content_first_position",
"bk_gc_content_second_position = biokit.biokit:gc_content_second_position",
"bk_gc2 = biokit.biokit:gc_content_second_position",
"bk_gc_content_third_position = biokit.biokit:gc_content_third_position",
"bk_gc3 = biokit.biokit:gc_content_third_position",
"bk_gene_wise_relative_synonymous_codon_usage = biokit.biokit:gene_wise_relative_synonymous_codon_usage",
"bk_gene_wise_rscu = biokit.biokit:gene_wise_relative_synonymous_codon_usage",
"bk_gw_rscu = biokit.biokit:gene_wise_relative_synonymous_codon_usage",
"bk_grscu = biokit.biokit:gene_wise_relative_synonymous_codon_usage",
"bk_relative_synonymous_codon_usage = biokit.biokit:relative_synonymous_codon_usage",
"bk_rscu = biokit.biokit:relative_synonymous_codon_usage",
"bk_translate_sequence = biokit.biokit:translate_sequence",
"bk_translate_seq = biokit.biokit:translate_sequence",
"bk_trans_seq = biokit.biokit:translate_sequence",
"bk_fastq_read_lengths = biokit.biokit:fastq_read_lengths", # FASTQ-based functions
"bk_fastq_read_lens = biokit.biokit:fastq_read_lengths",
"bk_subset_pe_fastq_reads = biokit.biokit:subset_pe_fastq_reads",
"bk_subset_pe_fastq = biokit.biokit:subset_pe_fastq_reads",
"bk_subset_se_fastq_reads = biokit.biokit:subset_se_fastq_reads",
"bk_subset_se_fastq = biokit.biokit:subset_se_fastq_reads",
"bk_trim_pe_adapters_fastq = biokit.biokit:trim_pe_adapters_fastq",
"bk_trim_pe_adapters_fastq_reads = biokit.biokit:trim_pe_adapters_fastq",
"bk_trim_pe_fastq = biokit.biokit:trim_pe_fastq",
"bk_trim_pe_fastq_reads = biokit.biokit:trim_pe_fastq",
"bk_trim_se_adapters_fastq = biokit.biokit:trim_se_adapters_fastq",
"bk_trim_se_adapters_fastq_reads = biokit.biokit:trim_se_adapters_fastq",
"bk_trim_se_fastq = biokit.biokit:trim_se_fastq",
"bk_trim_se_fastq_reads = biokit.biokit:trim_se_fastq",
"bk_gc_content = biokit.biokit:gc_content", # genomes-based functions
"bk_gc = biokit.biokit:gc_content",
"bk_genome_assembly_metrics = biokit.biokit:genome_assembly_metrics",
"bk_assembly_metrics = biokit.biokit:genome_assembly_metrics",
"bk_l50 = biokit.biokit:l50",
"bk_l90 = biokit.biokit:l90",
"bk_longest_scaffold = biokit.biokit:longest_scaffold",
"bk_longest_scaff = biokit.biokit:longest_scaffold",
"bk_longest_contig = biokit.biokit:longest_scaffold",
"bk_longest_cont = biokit.biokit:longest_scaffold",
"bk_n50 = biokit.biokit:n50",
"bk_n90 = biokit.biokit:n90",
"bk_number_of_large_scaffolds = biokit.biokit:number_of_large_scaffolds",
"bk_num_of_lrg_scaffolds = biokit.biokit:number_of_large_scaffolds",
"bk_number_of_large_contigs = biokit.biokit:number_of_large_scaffolds",
"bk_num_of_lrg_cont = biokit.biokit:number_of_large_scaffolds",
"bk_number_of_scaffolds = biokit.biokit:number_of_scaffolds",
"bk_num_of_scaffolds = biokit.biokit:number_of_scaffolds",
"bk_number_of_contigs = biokit.biokit:number_of_scaffolds",
"bk_num_of_cont = biokit.biokit:number_of_scaffolds",
"bk_sum_of_scaffold_lengths = biokit.biokit:sum_of_scaffold_lengths",
"bk_sum_of_contig_lengths = biokit.biokit:sum_of_scaffold_lengths",
"bk_character_frequency = biokit.biokit:character_frequency", # text-based functions
"bk_char_freq = biokit.biokit:character_frequency",
"bk_faidx = biokit.biokit:faidx",
"bk_get_entry = biokit.biokit:faidx",
"bk_ge = biokit.biokit:faidx",
"bk_file_format_converter = biokit.biokit:file_format_converter",
"bk_format_converter = biokit.biokit:file_format_converter",
"bk_ffc = biokit.biokit:file_format_converter",
"bk_multiple_line_to_single_line_fasta = biokit.biokit:multiple_line_to_single_line_fasta",
"bk_ml2sl = biokit.biokit:multiple_line_to_single_line_fasta",
"bk_remove_short_sequences = biokit.biokit:remove_short_sequences",
"bk_remove_short_seqs = biokit.biokit:remove_short_sequences",
"bk_remove_fasta_entry = biokit.biokit:remove_fasta_entry",
"bk_rename_fasta_entries = biokit.biokit:rename_fasta_entries",
"bk_rename_fasta = biokit.biokit:rename_fasta_entries",
"bk_reorder_by_sequence_length = biokit.biokit:reorder_by_sequence_length",
"bk_reorder_by_seq_len = biokit.biokit:reorder_by_sequence_length",
"bk_sequence_complement = biokit.biokit:sequence_complement",
"bk_seq_comp = biokit.biokit:sequence_complement",
"bk_sequence_length = biokit.biokit:sequence_length",
"bk_seq_len = biokit.biokit:sequence_length",
"bk_single_line_to_multiple_line_fasta = biokit.biokit:single_line_to_multiple_line_fasta",
"bk_sl2ml = biokit.biokit:single_line_to_multiple_line_fasta",
]
},
version=__version__,
include_package_data=True,
install_requires=REQUIRES,
)
# push new version to pypi
# rm -rf dist
# python setup.py sdist bdist_wheel --universal
# twine upload dist/* -r pypi
# then push to anaconda