mandos.commands

Complexity

Total Complexity

54

Size/Duplication

Total Lines	913
Duplicated Lines	0 %

Importance

Changes

0

26 Methods

Rating	Name	Duplication	Size	Complexity
A	MiscCommands.plot_tau()	0	16	1
A	MiscCommands.calc_ecfp()	0	34	2
A	MiscCommands.search()	0	18	1
A	MiscCommands.cache_clear()	0	19	4
A	MiscCommands.export_db()	0	23	1
A	MiscCommands.plot_project()	0	9	1
A	MiscCommands.concat()	0	20	2
A	MiscCommands.cache_data()	0	19	1
A	MiscCommands.export_reify()	0	31	3
A	MiscCommands.cache_g2p()	0	16	1
A	MiscCommands.calc_tau()	0	50	1
A	MiscCommands.plot_score()	0	11	1
A	MiscCommands.fill()	0	52	1
A	MiscCommands.describe()	0	71	2
A	MiscCommands.calc_analysis()	0	14	1
A	MiscCommands.filter()	0	28	1
A	MiscCommands.export_copy()	0	27	1
A	MiscCommands.calc_psi()	0	30	1
A	MiscCommands.export_taxa()	0	37	1
A	MiscCommands.plot_phi_psi()	0	38	1
F	MiscCommands.cache_taxa()	0	53	15
A	MiscCommands.calc_score()	0	44	1
A	MiscCommands.format_phi()	0	30	3
A	MiscCommands.export_state()	0	34	3
A	MiscCommands.calc_project()	0	45	3
A	MiscCommands.serve()	0	14	1

"""
Command-line interface for mandos.
"""

from __future__ import annotations

from pathlib import Path
from typing import Optional, List

import typer

Unable to import 'typer'

from typeddfs import FileFormat

Unused FileFormat imported from typeddfs

Unable to import 'typeddfs'

from mandos.entries.docs import Documenter
from mandos.entries.searcher import InputFrame

from mandos import logger, MANDOS_SETUP
from mandos.analysis.io_defns import SimilarityDfLongForm
from mandos.analysis.concordance import ConcordanceCalculation
from mandos.analysis.distances import MatrixCalculation
from mandos.analysis.filtration import Filtration
from mandos.analysis.enrichment import EnrichmentCalculation, RealAlg, BoolAlg
from mandos.analysis.io_defns import ScoreDf
from mandos.analysis.prepping import MatrixPrep
from mandos.analysis.reification import Reifier
from mandos.entries.common_args import Arg, CommonArgs
from mandos.entries.common_args import CommonArgs as Ca

The import CommonArgs was already done on line 25. You should be able to
remove this line.

from mandos.entries.common_args import Opt
from mandos.entries.multi_searches import MultiSearch
from mandos.entries.filler import CompoundIdFiller, IdMatchFrame
from mandos.model import MandosResources
from mandos.model.utils import MiscUtils
from mandos.model.apis.g2p_api import CachingG2pApi
from mandos.model.hits import HitFrame
from mandos.model.settings import MANDOS_SETTINGS
from mandos.model.taxonomy_caches import TaxonomyFactories
from mandos.analysis.projection import UMAP

set_up = MANDOS_SETUP
DEF_SUFFIX = MANDOS_SETTINGS.default_table_suffix

if UMAP is None:
    _umap_params = {}
else:
    _umap_params = {
        k: v
        for k, v in UMAP().get_params(deep=False).items()
        if k not in {"random_state", "metric"}
    }


class _InsertedCommandListSingleton:
    commands = None


class MiscCommands:

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    @staticmethod
    def describe(

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        to: Path = Ca.doc_output,

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        style: str = Ca.doc_style,

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        width: int = Opt.val(

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            r"""
            Max line width for a single cell.

            After that, the text is wrapped.
            Only applies when writing formatted text (.txt, etc.).
            """,
            default=100,
        ),
        flatten: bool = Opt.flag(

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            r"""
            Flatten all columns into a single one.

            Only affects pretty-printing.
            """
        ),
        level: int = Opt.val(

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            r"""
            The amount of detail to output.

            - 1 : show a 1-line description

            - 2 : Show a 1-line description, plus parameter names

            - 3 : Show the full description, plus parameter names, types, and 1-line descriptions

            - 4 : Show the full description, plus parameter names types, and full descriptions

            - 5 : Same as 4, but enable --hidden and --common
            """,
            default=4,
        ),
        main_only: bool = Opt.flag(r"Only include main commands."),

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        search_only: bool = Opt.flag(r"Only include search commands."),

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        hidden: bool = Opt.flag(r"Show hidden commands."),

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        common: bool = Opt.flag(

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            r"""
            Show common arguments and options.

            Normally --log, --quiet, and --verbose are excluded,
            along with path, --key, --to, --as-of for searches,
            and the hidden flags for searches --check and --no-setup.
        """
        ),
        replace: bool = CommonArgs.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ):
        r"""
        Write documentation on commands to a file.
        """
        set_up(log, quiet, verbose)
        if level == 5:
            hidden = common = True
        default = f"commands-level{level}.txt"
        to = MiscUtils.adjust_filename(to, default, replace)
        doc = Documenter(
            level=level,
            main=main_only,
            search=search_only,
            hidden=hidden,
            common=common,
            width=width,
            flatten=flatten,
        )
        doc.document(_InsertedCommandListSingleton.commands, to, style)

    @staticmethod
    def search(

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        path: Path = Ca.compounds,

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        config: Path = Arg.in_file(

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            r"""
            TOML config file. See docs.
            """
        ),
        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        out_dir: Path = Ca.out_dir,

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    ) -> None:
        r"""
        Run multiple searches.
        """
        set_up(log, quiet, verbose)
        MultiSearch.build(path, out_dir, config).run()

    @staticmethod
    def serve(

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        port: int = Opt.val(r"Port to serve on", default=1540),

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        db: str = Opt.val("Name of the MySQL database", default="mandos"),

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Start a REST server.

        The connection information is stored in your global settings file.
        """
        set_up(log, quiet, verbose)

    @staticmethod
    def export_db(

Argument name "db" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = Ca.file_input,

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        db: str = Opt.val(r"Name of the MySQL database", default="mandos"),

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        host: str = Opt.val(

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            r"Database hostname (ignored if ``--socket`` is passed", default="127.0.0.1"
        ),
        socket: Optional[str] = Opt.val("Path to a Unix socket (if set, ``--host`` is ignored)"),

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        user: Optional[str] = Opt.val("Database username (empty if not set)"),

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        password: Optional[str] = Opt.val("Database password (empty if not set)"),

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        as_of: Optional[str] = CommonArgs.as_of,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Export to a relational database.

        Saves data from Mandos search commands to a database for serving via REST.

        See also: ``:serve``.
        """
        set_up(log, quiet, verbose)

    @staticmethod
    def fill(

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Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.compounds_to_fill,

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        to: Path = Ca.id_table_to,

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        no_pubchem: bool = Opt.flag("Do not use PubChem.", "--no-pubchem"),

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        no_chembl: bool = Opt.flag("Do not use ChEMBL.", "--no-chembl"),

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        replace: bool = Ca.replace,

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        log: Optional[Path] = Ca.log_path,

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        quiet: bool = Ca.quiet,

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        verbose: bool = Ca.verbose,

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    ) -> None:
        r"""
        Fill in missing IDs from existing compound data.

        The idea is to find a ChEMBL ID, a PubChem ID, and parent-compound InChI/InChI Key.
        Useful to check compound/ID associations before running a search.

        To be filled, each row must should have a non-null value for
        "inchikey", "chembl_id", and/or "pubchem_id".
        "inchi" will be used but not to match to PubChem and ChEMBL.

        No existing columns will be dropped or modified.
        Any conflicting column will be renamed to 'origin_<column>'.
        E.g. 'inchikey' will be renamed to 'origin_inchikey'.
        (Do not include a column beginning with 'origin_').

        Final columns (assuming --no-chembl and --no-pubchem) will include:
        inchikey, inchi, pubchem_id, chembl_id, pubchem_inch, chembl_inchi,
        pubchem_inchikey, and chembl_inchikey.
        The "inchikey" and "inchikey" columns will be the "best" available:
        chembl (preferred), then pubchem, then your source inchikey column.
        In cases where PubChem and ChEMBL differ, an error will be logged.
        You can always check the columns "origin_inchikey" (yours),
        chembl_inchikey, and pubchem_inchikey.

        The steps are:

        - If "chembl_id" or "pubchem_id" is non-null, uses that to find an InChI Key (for each).

        - Otherwise, if only "inchikey" is non-null, uses it to find ChEMBL and PubChem records.

        - Log an error if the inchikeys or inchis differ between PubChem and ChEMBL.

        - Set the final "inchi" and "inchikey" to the best choice,
          falling back to the input inchi and inchikey if they are missing.
        """
        set_up(log, quiet, verbose)
        default = str(Path(path).with_suffix("")) + "-filled" + "".join(path.suffixes)
        to = MiscUtils.adjust_filename(to, default, replace)
        df = IdMatchFrame.read_file(path)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df = CompoundIdFiller(chembl=not no_chembl, pubchem=not no_pubchem).fill(df)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df.write_file(to)

    @staticmethod
    def cache_data(

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        path: Path = Ca.compounds,

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        no_pubchem: bool = Opt.flag(r"Do not download data from PubChem", "--no-pubchem"),

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        no_chembl: bool = Opt.flag(r"Do not fetch IDs from ChEMBL", "--no_chembl"),

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Fetch and cache compound data.

        Useful to freeze data before running a search.
        """
        set_up(log, quiet, verbose)
        logger.error(f"Not implemented fully yet.")

Using an f-string that does not have any interpolated variables

        df = IdMatchFrame.read_file(path)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df = CompoundIdFiller(chembl=not no_chembl, pubchem=not no_pubchem).fill(df)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        logger.notice(f"Done caching.")

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    @staticmethod
    def export_taxa(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        taxa: str = Ca.taxa,

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        forbid: str = Opt.val(

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            r"""Exclude descendents of these taxa IDs or names (comma-separated).""", default=""
        ),
        to: Path = typer.Option(

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            None,
            help=rf"""
            Where to export.

            {Ca.output_formats}

            [default: ./<taxa>-<datetime>.{DEF_SUFFIX}]
            """,
        ),
        replace: bool = Ca.replace,

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        in_cache: bool = CommonArgs.in_cache,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ):
        """
        Export a taxonomic tree to a table.

        Writes a taxonomy of given taxa and their descendants to a table.
        """
        set_up(log, quiet, verbose)
        concat = taxa + "-" + forbid
        taxa = Ca.parse_taxa(taxa)
        forbid = Ca.parse_taxa(forbid)
        default = concat + "-" + MandosResources.start_timestamp_filesys + DEF_SUFFIX
        to = MiscUtils.adjust_filename(to, default, replace)
        my_tax = TaxonomyFactories.get_smart_taxonomy(taxa, forbid)
        my_tax = my_tax.to_df()
        to.parent.mkdir(exist_ok=True, parents=True)
        my_tax.write_file(to)

    @staticmethod
    def cache_taxa(
        taxa: str = Opt.val(

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            r"""
            Either "vertebrata", "all", or a comma-separated list of UniProt taxon IDs.

            "all" is only valid when --replace is passed;
            this will regenerate all taxonomy files that are found in the cache.
            """,
            default="",
        ),
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Prep a new taxonomy file for use in mandos.

        With --replace set, will delete any existing file.
        This can be useful to make sure your cached taxonomy is up-to-date before running.

        Downloads and converts a tab-separated file from UniProt.
        (To find manually, follow the ``All lower taxonomy nodes`` link and click ``Download``.)
        Then applies fixes and reduces the file size, creating a new file alongside.
        Puts both the raw data and fixed data in the cache under ``~/.mandos/taxonomy/``.
        """
        if taxa == "":
            logger.info("No taxa were specified. No data downloaded.")
            return
        if (
            taxa not in ["all", "vertebrata"]

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            and not taxa.replace(",", "").replace(" ", "").isdigit()

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        ):
            raise ValueError(f"Use either 'all', 'vertebrata', or a UniProt taxon ID")

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        if taxa == "all" and not replace:
            raise ValueError(f"Use --replace with taxon 'all'")

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        set_up(log, quiet, verbose)
        factory = TaxonomyFactories.from_uniprot()
        if taxa == "all" and replace:
            listed = TaxonomyFactories.list_cached_files()
            for p in listed.values():

Variable name "p" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                p.unlink()
            factory.rebuild_vertebrata()
            for t in listed.keys():

Variable name "t" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

                factory.load_dl(t)
        elif taxa == "vertebrata" and (replace or not factory.resolve_path(7742).exists()):
            factory.rebuild_vertebrata()
        elif taxa == "vertebrata":
            factory.load_vertebrate(7742)  # should usually do nothing
        else:
            for taxon in [int(t.strip()) for t in taxa.split(",")]:
                factory.delete_exact(taxon)

    @staticmethod
    def cache_g2p(
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Caches GuideToPharmacology data.

        With --replace set, will overwrite existing cached data.
        Data will generally be stored under``~/.mandos/g2p/``.
        """
        set_up(log, quiet, verbose)
        api = CachingG2pApi(MANDOS_SETTINGS.g2p_cache_path)
        api.download(force=replace)

    @staticmethod
    def cache_clear(
        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        yes: bool = CommonArgs.yes,

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    ) -> None:
        """
        Deletes all cached data.
        """
        set_up(log, quiet, verbose)
        typer.echo(f"Will recursively delete all of these paths:")

Using an f-string that does not have any interpolated variables

        for p in MANDOS_SETTINGS.all_cache_paths:

Variable name "p" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            typer.echo(f"    {p}")
        if not yes:
            typer.confirm("Delete?", abort=True)
        for p in MANDOS_SETTINGS.all_cache_paths:

Variable name "p" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            p.unlink(missing_ok=True)
        logger.notice("Deleted all cached data")

    @staticmethod
    def concat(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = Ca.input_dir,

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        to: Optional[Path] = Ca.to_single,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Concatenate Mandos annotation files into one.

        Note that ``:search`` automatically performs this;
        this is needed only if you want to combine results from multiple independent searches.
        """
        set_up(log, quiet, verbose)
        default = path / ("concat" + DEF_SUFFIX)
        to = MiscUtils.adjust_filename(to, default, replace)
        for found in path.iterdir():

The variable found seems to be unused.

            pass

    @staticmethod
    def filter(

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Argument name "by" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.to_single,

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        by: Optional[Path] = Arg.in_file(

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            r"""
            Path to a TOML (.toml) file containing filters.

            The file contains a list of ``mandos.filter`` keys,
            each containing an expression on a single column.
            This is only meant for simple, quick-and-dirty filtration.

            See the docs for more info.
            """
        ),
        to: Optional[Path] = Ca.to_single,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Filters by simple expressions.
        """
        set_up(log, quiet, verbose)
        default = str(path) + "-filter-" + by.stem + DEF_SUFFIX
        to = MiscUtils.adjust_filename(to, default, replace)
        df = HitFrame.read_file(path)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        Filtration.from_file(by).apply(df).write_file(to)

    @staticmethod
    def export_state(

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Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.file_input,

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        to: Optional[Path] = Opt.out_path(

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            """
            Path to the output file.

            Valid formats and filename suffixes are .nt and .txt with an optional .gz, .zip, or .xz.
            If only a filename suffix is provided, will use that suffix with the default directory.
            If no suffix is provided, will interpret the path as a directory and use the default filename.

This line is too long as per the coding-style (106/100).

            Will fail if the file exists and ``--replace`` is not set.

            [default: <path>-statements.nt]
        """
        ),
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Output simple N-triples statements.

        Each statement is of this form, where the InChI Key refers to the input data:

        `"InChI Key" "predicate" "object" .`
        """
        set_up(log, quiet, verbose)
        default = f"{path}-statements.nt"
        to = MiscUtils.adjust_filename(to, default, replace)
        hits = HitFrame.read_file(path).to_hits()
        with to.open() as f:

Variable name "f" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            for hit in hits:
                f.write(hit.to_triple.n_triples)

    @staticmethod
    def export_reify(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = Ca.file_input,

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        to: Optional[Path] = Opt.out_path(

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            r"""
            Path to the output file.

            The filename suffix should be either .nt (N-triples) or .ttl (Turtle),
            with an optional .gz, .zip, or .xz.
            If only a filename suffix is provided, will use that suffix with the default directory.
            If no suffix is provided, will interpret the path as a directory but use the default filename.

This line is too long as per the coding-style (106/100).

            Will fail if the file exists and ``--replace`` is not set.

            [default: <path>-reified.nt]
            """
        ),
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Outputs reified semantic triples.
        """
        set_up(log, quiet, verbose)
        default = f"{path}-reified.nt"
        to = MiscUtils.adjust_filename(to, default, replace)
        hits = HitFrame.read_file(path).to_hits()
        with to.open() as f:

Variable name "f" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

            for triple in Reifier().reify(hits):
                f.write(triple.n_triples)

    @staticmethod
    def export_copy(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = Ca.file_input,

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        to: Optional[Path] = Opt.out_path(

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            rf"""
            Path to the output file.

            {Ca.output_formats}

            [default: <path.parent>/export{DEF_SUFFIX}]
        """
        ),
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Copies and/or converts annotation files.

        Example: ``:export:copy --to .snappy`` to highly compress a data set.
        """
        set_up(log, quiet, verbose)
        default = path.parent / DEF_SUFFIX
        to = MiscUtils.adjust_filename(to, default, replace)
        df = HitFrame.read_file(path)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df.write_file(to)

    @staticmethod
    def calc_analysis(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = Ca.file_input,

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        phi: Path = Ca.input_matrix,

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        scores: Path = Ca.alpha_input,

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        seed: int = Ca.seed,

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        samples: int = Ca.boot,

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        to: Optional[Path] = Ca.misc_out_dir,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Shorthand for multiple calculations and plots.

        Generates n-triple statements and reified n-triples.
        Calculates correlation and enrichment using ``scores``,
        psi matrices (one per variable), and concordance between psi and tau matrices (tau).
        Plots UMAP of psi variables, enrichment bar plots, correlation violin plots,
        phi-vs-psi scatter and line plots, and phi-vs-psi (tau) violin plots.
        """

    @staticmethod
    def calc_score(

Too many arguments (12/5)

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This function exceeds the maximum number of variables (16/15).

Argument name "on" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.file_input,

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        scores: Path = Ca.alpha_input,

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        bool_alg: Optional[str] = Opt.val(

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            rf"""
            Algorithm to use for scores starting with 'is_'.

            Allowed values: {Ca.list(BoolAlg)}
            """,
            default="alpha",
        ),
        real_alg: Optional[str] = Opt.val(

Wrong hanging indentation before block (add 4 spaces).

            rf"""
            Algorithm to use for scores starting with 'score_'.

            Allowed values: {Ca.list(RealAlg)}
            """,
            default="weighted",
        ),
        on: bool = Ca.on,

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        boot: int = Ca.boot,

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        seed: int = Ca.seed,

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        to: Optional[Path] = Ca.alpha_to,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        """
        Compare annotations to user-supplied values.

        Calculates correlation between provided scores and object/predicate pairs.
        For booleans, compares annotations for hits and non-hits.
        See the docs for more info.
        """
        set_up(log, quiet, verbose)
        default = f"{path}-{scores.name}{DEF_SUFFIX}"
        to = MiscUtils.adjust_filename(to, default, replace)
        hits = HitFrame.read_file(path)
        scores = ScoreDf.read_file(scores)
        calculator = EnrichmentCalculation(bool_alg, real_alg, boot, seed)
        df = calculator.calculate(hits, scores)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df.write_file(to)

    @staticmethod
    def calc_psi(

Too many arguments (7/5)

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.file_input,

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        algorithm: str = Opt.val(

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            r"""
            The algorithm for calculating similarity between annotation sets.

            Currently, only "j" (J') is supported. Refer to the docs for the equation.
            """,
            default="j",
        ),
        to: Path = Ca.output_matrix,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Calculate a similarity matrix from annotations.

        The data are output as a dataframe (CSV by default), where rows and columns correspond
        to compounds, and the cell i,j is the overlap J' in annotations between compounds i and j.
        """
        set_up(log, quiet, verbose)
        default = path.parent / (algorithm + DEF_SUFFIX)
        to = MiscUtils.adjust_filename(to, default, replace)
        hits = HitFrame.read_file(path).to_hits()
        calculator = MatrixCalculation.create(algorithm)
        matrix = calculator.calc_all(hits)
        matrix.write_file(to)

    @staticmethod
    def calc_ecfp(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

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        path: Path = CommonArgs.compounds,

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        radius: int = Opt.val(r"""Radius of the ECFP fingerprint.""", default=4),

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        n_bits: int = Opt.val(r"""Number of bits.""", default=2048),

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        psi: bool = Opt.flag(

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            r"""Use "psi" as the type in the resulting matrix instead of "phi"."""
        ),
        to: Path = Ca.output_matrix,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Compute a similarity matrix from ECFP fingerprints.

        Requires rdkit to be installed.

        This is a bit faster than computing using a search and then calculating with ``:calc:psi``.
        Values range from 0 (no overlap) to 1 (identical).
        The type will be "phi" -- in contrast to using :calc:phi.
        See ``:calc:phi`` for more info.
        This is most useful for comparing a phenotypic phi against pure structural similarity.
        """
        set_up(log, quiet, verbose)
        name = f"ecfp{radius}-n{n_bits}"
        default = path.parent / (name + DEF_SUFFIX)
        to = MiscUtils.adjust_filename(to, default, replace)
        df = InputFrame.read_file(path)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        kind = "psi" if psi else "phi"
        short = MatrixPrep.ecfp_matrix(df, radius, n_bits)
        long_form = MatrixPrep(kind, False, False, False).create({name: short})
        long_form.write_file(to)

    @staticmethod
    def calc_tau(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Too many arguments (10/5)

        phi: Path = Ca.input_matrix,

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        psi: Path = Ca.input_matrix,

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        algorithm: str = Opt.val(

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            r"""
            The algorithm for calculating concordance.

            Currently, only "tau" is supported.
            This calculation is a modified Kendall’s  τ-a, where disconcordant ignores ties.
            See the docs for more info.
            """,
            default="tau",
        ),
        seed: int = Ca.seed,

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        samples: int = Ca.boot,

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        to: Optional[Path] = Opt.out_file(

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            rf"""
            The path to a table for output.

            {Ca.output_formats}

            [default: <input-path.parent>/<algorithm>-concordance.{DEF_SUFFIX}]
            """,
        ),
        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ) -> None:
        r"""
        Calculate correlation between matrices.

        Values are calculated over bootstrap, outputting a table.

        Phi is typically a phenotypic matrix, and psi a matrix from Mandos.
        This command is designed to calculate the similarity between compound annotations
        (from Mandos) and some user-input compound–compound similarity matrix.
        (For example, vectors from a high-content cell screen.
        See ``:calc:correlation`` or ``:calc:enrichment`` if you have a single variable,
        such as a hit or lead-like score.
        """
        set_up(log, quiet, verbose)
        default = phi.parent / f"{psi.stem}-{algorithm}{DEF_SUFFIX}"
        to = MiscUtils.adjust_filename(to, default, replace)
        phi = SimilarityDfLongForm.read_file(phi)
        psi = SimilarityDfLongForm.read_file(psi)
        calculator = ConcordanceCalculation.create(algorithm, phi, psi, samples, seed)
        concordance = calculator.calc_all(phi, psi)
        concordance.write_file(to)

    @staticmethod
    def calc_project(

Too many arguments (9/5)

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        psi_matrix: Path = Ca.input_matrix,

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The argument psi_matrix seems to be unused.

        algorithm: str = Opt.val(

Wrong hanging indentation before block (add 4 spaces).

            r"""
            Projection algorithm.

            Currently only "umap" is supported.
            """,
            default="umap",
        ),
        seed: str = Opt.val(

Wrong hanging indentation before block (add 4 spaces).

The argument seed seems to be unused.

            r"""
            Random seed (integer or 'none').

            Setting to 'none' may increase performance.
            """,
            default=0,
        ),
        params: str = Opt.val(

Wrong hanging indentation before block (add 4 spaces).

The argument params seems to be unused.

            rf"""
            Parameters fed to the algorithm.

            This is a comma-separated list of key=value pairs.
            For example: ``n_neighbors=4,n_components=12,min_dist=0.8``
            Supports all UMAP parameters except random_state and metric:

            {Ca.definition_list(_umap_params) if UMAP else "<list is unavailable>"}
            """,
            default="",
        ),
        to: Optional[Path] = Ca.project_to,

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        replace: bool = Ca.replace,

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        log: Optional[Path] = CommonArgs.log_path,

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The argument log seems to be unused.

        quiet: bool = CommonArgs.quiet,

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The argument quiet seems to be unused.

        verbose: bool = CommonArgs.verbose,

The argument verbose seems to be unused.

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    ) -> None:
        r"""
        Calculate compound UMAP from psi matrices.

        The input should probably be calculated from ``:calc:matrix``.
        Saves a table of the UMAP coordinates.
        """
        if algorithm == "umap" and UMAP is None:
            raise ImportError(f"UMAP is not available")

Using an f-string that does not have any interpolated variables

    @staticmethod
    def format_phi(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Too many arguments (10/5)

        matrices: List[Path] = Ca.input_matrix_short_form,

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        kind: str = Ca.var_type,

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        to: Path = Ca.output_matrix,

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        replace: bool = Ca.replace,

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        normalize: bool = Opt.flag(

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            r"""Rescale values to between 0 and 1 by (v-min) / (max-min). (Performed after negation.)"""

This line is too long as per the coding-style (104/100).

        ),
        log10: bool = Opt.val(r"""Rescales values by log10. (Performed after normalization.)"""),

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        invert: bool = Opt.val(r"""Multiplies the values by -1. (Performed first.)"""),

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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    ):
        r"""
        Convert phi matrices to one long-form matrix.

        The keys will be derived from the filenames.
        """
        set_up(log, quiet, verbose)
        default = "."
        if to is None:
            try:
                default = next(iter({mx.parent for mx in matrices}))
            except StopIteration:
                logger.warning(f"Outputting to {default}")
        to = MiscUtils.adjust_filename(to, default, replace)
        long_form = MatrixPrep(kind, normalize, log10, invert).from_files(matrices)
        long_form.write_file(to)

    @staticmethod
    def plot_project(

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        umap_df: Path = Ca.project_input,

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        style: Optional[Path] = Ca.style_for_compounds,

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        color_col: Optional[str] = Ca.color_col,

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        marker_col: Optional[str] = Ca.marker_col,

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        to: Optional[Path] = Ca.plot_to,

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    ) -> None:
        r"""
        Plot UMAP, etc. of compounds from psi matrices.

        Will plot one variable (psi) per column.
        """

    @staticmethod
    def plot_score(

Argument name "ci" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Too many arguments (7/5)

        path: Path = Ca.input_correlation,

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        kind: str = Ca.plot_kind,

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        style: Optional[Path] = Ca.style_for_pairs,

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        color_col: Optional[str] = Ca.color_col,

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        marker_col: Optional[str] = Ca.marker_col,

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        ci: float = Ca.ci,

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        to: Optional[Path] = Ca.plot_to,

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    ) -> None:
        r"""
        Plot correlation to scores.

        Visualizes the correlation between predicate/object pairs and user-supplied scores.
        Will output one figure (file) per scoring function.
        Will plot (psi, score-fn) pairs over a grid,
        one row per scoring function and column per psi.
        """

    @staticmethod
    def plot_phi_psi(

Too many arguments (9/5)

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Argument name "ci" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.input_matrix,

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        join: Optional[bool] = Opt.flag(

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            r"""
            Pool all psi variables into a single column with multiple plots.
            """
        ),
        kind: str = Opt.val(

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            r"""
            Either 'points', 'lines', or 'points+lines'.

            - points: Scatter plots of (phi, psi) values.

            - lines: Plot a linear interpolation.

            - ci: Plot a linear interpolation with a confidence band.

            - points+lines: Both 'points' and 'lines'.
            """,
            "--type",
        ),
        ci: float = Ca.ci,

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        sort_by: str = Opt.val(

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            r"""
            Which axis to sort by: 'phi'/'x' or 'psi'/'y'.

            Sorting by psi values (y-axis) makes it easier to compare psi variables,
            while sorting by phi values (x-axis) makes it easier to compare phi variables.
            """,
            default="psi",
        ),
        style: Optional[Path] = Ca.style_for_psi,

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        color_col: Optional[str] = Ca.color_col,

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        marker_col: Optional[str] = Ca.marker_col,

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        to: Optional[Path] = Ca.plot_to,

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    ) -> None:
        r"""
        Plot line plots of phi against psi.

        Plots scatter plots of (phi, psi) values, sorted by phi values.
        All plots are log/log (all similarity values should be scaled from 0 to 1).

        For each unique phi matrix and psi matrix, flattens the matrices and plots
        the flattened (n choose 2 - n) pairs of each jointly, phi mapped to the y-axis
        and psi mapped to the x-axis.

        Without --split:

        Will show values for all psi variables together.
        If ``--color`` is not set, will choose a palette.
        Works best with ``--type lines``.

        With --split:

        Will plot each (phi, psi) pair over a grid, one plot per cell:
        One row per phi and one column per psi.
        """

    @staticmethod
    def plot_tau(

Too many arguments (6/5)

Argument name "to" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        path: Path = Ca.input_matrix,

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        split: bool = Opt.flag(

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            r"""
            Split each violin into phi #1 on the left and phi #2 on the right.

            Useful to compare two phi variables. Requires exactly 2.
            """
        ),
        style: Optional[Path] = Ca.style_for_psi,

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        color_col: Optional[str] = Ca.color_col,

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        marker_col: Optional[str] = Ca.marker_col,

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        to: Optional[Path] = Ca.plot_to,

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    ) -> None:
        r"""
        Plot violin plots from tau values.

        The input data should be generated by ``:calc:phi-vs-psi.tau``.

        Will plot each (phi, psi) pair over a grid, one row per phi and one column per psi
        (unless ``--split`` is set).
        """


__all__ = ["MiscCommands"]