How to use the pyani.pyani_tools.termcolor function in pyani

# Add dependency citations
    logger.info(termcolor("DEPENDENCIES", bold=True))
    dep_citations = [
        "The authors of pyani gratefully acknowledge its dependence on",
        "the following bioinformatics software:",
        f"\t{termcolor('MUMmer3', 'cyan')}: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway,",
        "\tC. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software",
        "\tfor comparing large genomes' Genome Biology 5:R12",
        f"\t{termcolor('BLAST+', 'cyan')}: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J.,",
        "\tBealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.'",
        "\tBMC Bioinformatics 10:421.",
        f"\t{termcolor('BLAST', 'cyan')}: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J.,",
        "\tZhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST:",
        "\ta new generation of protein database search programs.' Nucleic Acids Res.",
        "\t25:3389-3402",
        f"\t{termcolor('Biopython', 'cyan')}: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A,",
        "\tFriedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL",
        "\t(2009) Biopython: freely available Python tools for computational",
        "\tmolecular biology and bioinformatics. Bioinformatics, 25, 1422-1423",
    ]
    for line in dep_citations:
        logger.info(line)

# skipped downloads (and define a helper tuple for collating skipped
    # genome information)
    classes = []
    labels = []
    skippedlist = []
    Skipped = namedtuple("Skipped", "taxon_id accession organism strain url dltype")

    # Download contigs and hashes for each assembly UID in the list
    # On completion of this loop, each assembly in the list will either be
    # downloaded or skipped (with skipped genome information preserved in
    # skippedlist), and class/label info will be collated, ready for writing
    # to file.
    # Summary information is reported to the logger for each eSummary that
    # can be recovered
    for tid, uids in asm_dict.items():
        logger.info(termcolor("Downloading contigs for Taxon ID %s", "blue"), uids)
        for uid in uids:
            # Obtain eSummary
            logger.info(
                termcolor("Retrieving eSummary information for UID %s", "cyan"), uid
            )
            esummary, filestem = download.get_ncbi_esummary(uid, args.retries, api_key)
            logger.debug("NCBI eSummary:\n%s\n%s", esummary, filestem)
            uid_class = download.get_ncbi_classification(esummary)

            # Report summary
            outstr = "\n\t".join(
                [
                    f"Species Taxid: {esummary['SpeciesTaxid']}",
                    f"TaxID: {esummary['Taxid']}",
                    f"Accession: {esummary['AssemblyAccession']}",
                    f"Name: {esummary['AssemblyName']}",

logger.info(termcolor("CITATION INFO", bold=True))
    for line in CITATION_INFO:
        logger.info(line)

    # Add dependency citations
    logger.info(termcolor("DEPENDENCIES", bold=True))
    dep_citations = [
        "The authors of pyani gratefully acknowledge its dependence on",
        "the following bioinformatics software:",
        f"\t{termcolor('MUMmer3', 'cyan')}: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway,",
        "\tC. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software",
        "\tfor comparing large genomes' Genome Biology 5:R12",
        f"\t{termcolor('BLAST+', 'cyan')}: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J.,",
        "\tBealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.'",
        "\tBMC Bioinformatics 10:421.",
        f"\t{termcolor('BLAST', 'cyan')}: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J.,",
        "\tZhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST:",
        "\ta new generation of protein database search programs.' Nucleic Acids Res.",
        "\t25:3389-3402",
        f"\t{termcolor('Biopython', 'cyan')}: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A,",
        "\tFriedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL",
        "\t(2009) Biopython: freely available Python tools for computational",
        "\tmolecular biology and bioinformatics. Bioinformatics, 25, 1422-1423",
    ]
    for line in dep_citations:
        logger.info(line)

def add_log_headers():
    """Add headers to log output."""
    logger = logging.getLogger(__name__)

    # Add citation information to log
    logger.info(termcolor("CITATION INFO", bold=True))
    for line in CITATION_INFO:
        logger.info(line)

    # Add dependency citations
    logger.info(termcolor("DEPENDENCIES", bold=True))
    dep_citations = [
        "The authors of pyani gratefully acknowledge its dependence on",
        "the following bioinformatics software:",
        f"\t{termcolor('MUMmer3', 'cyan')}: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway,",
        "\tC. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software",
        "\tfor comparing large genomes' Genome Biology 5:R12",
        f"\t{termcolor('BLAST+', 'cyan')}: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J.,",
        "\tBealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.'",
        "\tBMC Bioinformatics 10:421.",
        f"\t{termcolor('BLAST', 'cyan')}: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J.,",
        "\tZhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST:",
        "\ta new generation of protein database search programs.' Nucleic Acids Res.",
        "\t25:3389-3402",
        f"\t{termcolor('Biopython', 'cyan')}: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A,",
        "\tFriedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL",
        "\t(2009) Biopython: freely available Python tools for computational",
        "\tmolecular biology and bioinformatics. Bioinformatics, 25, 1422-1423",
    ]
    for line in dep_citations:
        logger.info(line)

import logging
import sys
import time

from typing import List, Optional

from pyani.pyani_tools import termcolor

from .logger import config_logger
from .parsers import parse_cmdline
from .. import __version__


CITATION_INFO = [
    termcolor(
        "If you use pyani in your work, please cite the following publication:",
        "green",
    ),
    termcolor(
        "\tPritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G.,", "yellow",
    ),
    termcolor(
        "\t& Toth, I.K. (2016) 'Genomics and taxonomy in diagnostics for", "yellow"
    ),
    termcolor(
        "\tfood security: soft-rotting enterobacterial plant pathogens.'", "yellow"
    ),
    termcolor(
        "\tAnalytical Methods, 8(1), 12–24. http://doi.org/10.1039/C5AY02550H",
        "yellow",
    ),

The intended outcomes are:
    outdir doesn't exist: create outdir
    outdir exists: raise exception
    outdir exists, --force only: remove the directory tree
    outdir exists, --force --noclobber: continue with existing directory tree

    So long as the outdir is created with this function, we need only check
    for args.noclobber elsewhere to see how to proceed when a file exists.
    """
    # Create logger
    logger = logging.getLogger(__name__)
    logger.info("Creating output directory %s", outdir)

    if force:
        logger.warning(termcolor("Output directory overwrite forced", "red"))
        if outdir.is_dir() and noclobber is False:
            logger.warning(termcolor("Clobbering existing directory %s", "red"), outdir)
            shutil.rmtree(outdir)
    outdir.mkdir(parents=True, exist_ok=force)

def add_log_headers():
    """Add headers to log output."""
    logger = logging.getLogger(__name__)

    # Add citation information to log
    logger.info(termcolor("CITATION INFO", bold=True))
    for line in CITATION_INFO:
        logger.info(line)

    # Add dependency citations
    logger.info(termcolor("DEPENDENCIES", bold=True))
    dep_citations = [
        "The authors of pyani gratefully acknowledge its dependence on",
        "the following bioinformatics software:",
        f"\t{termcolor('MUMmer3', 'cyan')}: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway,",
        "\tC. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software",
        "\tfor comparing large genomes' Genome Biology 5:R12",
        f"\t{termcolor('BLAST+', 'cyan')}: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J.,",
        "\tBealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.'",
        "\tBMC Bioinformatics 10:421.",
        f"\t{termcolor('BLAST', 'cyan')}: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J.,",
        "\tZhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST:",
        "\ta new generation of protein database search programs.' Nucleic Acids Res.",
        "\t25:3389-3402",
        f"\t{termcolor('Biopython', 'cyan')}: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A,",
        "\tFriedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL",
        "\t(2009) Biopython: freely available Python tools for computational",

def subcmd_classify(args: Namespace) -> int:
    """Generate classifications for an analysis.

    :param args:  Namespace, command-line arguments
    """
    logger = logging.getLogger(__name__)

    # Tell the user what's going on
    logger.info(
        termcolor("Generating classification for ANI run: %s", "red"), args.run_id
    )
    logger.info("\tWriting output to: %s", args.outdir)
    logger.info(termcolor("\tCoverage threshold: %s", "cyan"), args.cov_min)
    logger.info(
        termcolor("\tInitial minimum identity threshold: %s", "cyan"), args.id_min
    )

    # Get results data for the specified run
    logger.info("Acquiring results for run: %s", args.run_id)
    logger.debug("Connecting to database: %s", args.dbpath)
    session = pyani_orm.get_session(args.dbpath)
    logger.debug("Retrieving results matrices")
    results = (
        session.query(pyani_orm.Run).filter(pyani_orm.Run.run_id == args.run_id).first()
    )
    result_label_dict = pyani_orm.get_matrix_labels_for_run(session, args.run_id)

    # Generate initial graph on basis of results
    logger.info("Constructing graph from results.")
    initgraph = pyani_classify.build_graph_from_results(
        results, result_label_dict, args.cov_min, args.id_min

We attempt to gracefully skip genomes with download errors.
    """
    # Create logger
    logger = logging.getLogger(__name__)

    if dltype == "GenBank":
        filestem = re.sub("^GCF_", "GCA_", dlfiledata.filestem)
    else:
        filestem = dlfiledata.filestem
    dlstatus = retrieve_genome_and_hash(
        filestem, dlfiledata.suffix, dlfiledata.ftpstem, outdir, timeout, disable_tqdm,
    )
    # Pylint is confused by the content of dlstatus (a namedlist)
    if dlstatus.error is not None:  # pylint: disable=no-member
        logger.warning(termcolor("%s download failed: skipping!", "magenta"), dltype)
        logger.debug(
            "Exception raised:\n%s", dlstatus.error
        )  # pylint: disable=no-member
        dlstatus.skipped = True

    return dlstatus  # pylint: disable=no-member

logger = logging.getLogger(__name__)

    # Add citation information to log
    logger.info(termcolor("CITATION INFO", bold=True))
    for line in CITATION_INFO:
        logger.info(line)

    # Add dependency citations
    logger.info(termcolor("DEPENDENCIES", bold=True))
    dep_citations = [
        "The authors of pyani gratefully acknowledge its dependence on",
        "the following bioinformatics software:",
        f"\t{termcolor('MUMmer3', 'cyan')}: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway,",
        "\tC. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software",
        "\tfor comparing large genomes' Genome Biology 5:R12",
        f"\t{termcolor('BLAST+', 'cyan')}: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J.,",
        "\tBealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.'",
        "\tBMC Bioinformatics 10:421.",
        f"\t{termcolor('BLAST', 'cyan')}: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J.,",
        "\tZhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST:",
        "\ta new generation of protein database search programs.' Nucleic Acids Res.",
        "\t25:3389-3402",
        f"\t{termcolor('Biopython', 'cyan')}: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A,",
        "\tFriedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL",
        "\t(2009) Biopython: freely available Python tools for computational",
        "\tmolecular biology and bioinformatics. Bioinformatics, 25, 1422-1423",
    ]
    for line in dep_citations:
        logger.info(line)