content: [build-system]
  requires = ["setuptools>=61.0.0", "wheel"]
  build-backend = "setuptools.build_meta"
  
  [project]
  name="domainator"
  authors = [
      {name = "Sean Johnson", email = "sjohnson@neb.com"},
      {name = "Andrew Ge"},
      {name = "Yu-Cheng Lin"},
      {name = "Zhiyi Sun"}
  ]
  description="A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering."
  readme = "README.md"
  requires-python = ">=3.9"
  
  classifiers=[
      "Programming Language :: Python :: 3",
  ]
  license = {file = "LICENSE.txt"}
  dynamic = ["version"]
  dependencies = [
      "pandas >=2.1.0",
      "seaborn >=0.13.0",
      "scipy >=1.11.2",
      "pyhmmer >=0.10.2 ",
      "umap-learn >=0.5.4",
      "h5py >=3.9.0",
      "jsonargparse >=4.18.0",
      "psutil >=5.9.6",
      "tqdm >=4.65.0",
      "pyrodigal >=3.0.1",
      "bashplotlib >=0.6.5",
      "requests >=2.31.0"
  ]
  
  [project.optional-dependencies]
  test = ["pytest >=7.4.2", 
          "pytest-datadir~=1.4.1"]
  # add dependency for Foldseek/ESM2 related stuff.
  
  [project.urls]
  Bug_Tracker = "https://github.com/nebiolabs/domainator/issues"
  
  
  [tool.setuptools]
  package-dir = {"" = "src"}
  
  
  [tool.setuptools.dynamic]
  version = {attr = "domainator.__version__"}
  
  [project.scripts]
  "build_projection.py" = "domainator:build_projection._entrypoint"
  "build_ssn.py" = "domainator:build_ssn._entrypoint"
  "build_tree.py" = "domainator:build_tree._entrypoint"
  "color_genbank.py" = "domainator:color_genbank._entrypoint"
  "color_table_to_legend.py" = "domainator:color_table_to_legend._entrypoint"
  "compare_contigs.py" = "domainator:compare_contigs._entrypoint"
  "deduplicate_genbank.py" = "domainator:deduplicate_genbank._entrypoint"
  "domain_search.py" = "domainator:domain_search._entrypoint"
  "domainate.py" = "domainator:domainate._entrypoint"
  "domainator_db_download.py" = "domainator:domainator_db_download._entrypoint"
  "enum_report.py" = "domainator:enum_report._entrypoint"
  "extract_domains.py" = "domainator:extract_domains._entrypoint"
  "extract_peptides.py" = "domainator:extract_peptides._entrypoint"
  "extract_unannotated.py" = "domainator:extract_unannotated._entrypoint"
  "filter_domains.py" = "domainator:filter_domains._entrypoint"
  "genbank_to_fasta.py" = "domainator:genbank_to_fasta._entrypoint"
  "hmmer_build.py" = "domainator:hmmer_build._entrypoint"
  "hmmer_compare.py" = "domainator:hmmer_compare._entrypoint"
  "hmmer_report.py" = "domainator:hmmer_report._entrypoint"
  "hmmer_search.py" = "domainator:hmmer_search._entrypoint"
  "hmmer_select.py" = "domainator:hmmer_select._entrypoint"
  "matrix_report.py" = "domainator:matrix_report._entrypoint"
  "partition_seqfile.py" = "domainator:partition_seqfile._entrypoint"
  "select_by_cds.py" = "domainator:select_by_cds._entrypoint"
  "select_by_contig.py" = "domainator:select_by_contig._entrypoint"
  "seq_dist.py" = "domainator:seq_dist._entrypoint"
  "summary_report.py" = "domainator:summary_report._entrypoint"
  "transform_matrix.py" = "domainator:transform_matrix._entrypoint"
  "plot_contigs.py" = "domainator:plot_contigs._entrypoint"
  "trim_contigs.py" = "domainator:trim_contigs._entrypoint"