Coverage for phytest/cli.py : 100.00%
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1from pathlib import Path
2from typing import Optional
4from Bio.AlignIO import _FormatToIterator as supported_alignment_formats
5from Bio.Phylo._io import supported_formats as supported_tree_formats
6from Bio.SeqIO import _FormatToIterator as supported_sequence_formats
8supported_sequence_formats.update(supported_alignment_formats)
9import typer
11from .main import main
13app = typer.Typer()
16def sequence_format_callback(value: str):
17 if value not in supported_sequence_formats:
18 raise typer.BadParameter(
19 f"'{value}' is not a valid sequence format. Must be one of {', '.join(supported_sequence_formats.keys())}."
20 )
21 return value
24def tree_format_callback(value: str):
25 if value not in supported_tree_formats:
26 raise typer.BadParameter(
27 f"'{value}' is not a valid tree format. Must be one of {', '.join(supported_tree_formats.keys())}."
28 )
29 return value
32def data_format_callback(value: str):
33 if value not in ['csv', 'tsv', 'excel']:
34 raise typer.BadParameter(f"'{value}' is not a valid data format. Must be one of csv, tsv, excel.")
35 return value
38@app.command(context_settings={"help_option_names": ["-h", "--help"]})
39def cli(
40 testfile: Path = typer.Argument(..., help="Path to test file."),
41 sequence: Optional[Path] = typer.Option(
42 None, "--sequence", "-s", dir_okay=False, exists=True, help="Path to sequence file."
43 ),
44 sequence_format: Optional[str] = typer.Option(
45 'fasta',
46 "--sequence-format",
47 dir_okay=False,
48 exists=True,
49 help=f"{', '.join(supported_sequence_formats.keys())}.",
50 callback=sequence_format_callback,
51 ),
52 tree: Optional[Path] = typer.Option(None, "--tree", "-t", dir_okay=False, exists=True, help="Path to tree file."),
53 tree_format: Optional[str] = typer.Option(
54 'newick',
55 "--tree-format",
56 dir_okay=False,
57 exists=True,
58 help=f"{', '.join(supported_tree_formats.keys())}.",
59 callback=tree_format_callback,
60 ),
61 data: Optional[Path] = typer.Option(None, "--data", "-d", dir_okay=False, exists=True, help="Path to data file."),
62 data_format: Optional[str] = typer.Option(
63 'csv', "--data-format", dir_okay=False, exists=True, help="csv, tsv, excel.", callback=data_format_callback
64 ),
65 report: Optional[Path] = typer.Option(
66 None, "--report", "-r", dir_okay=False, exists=False, help="Path to HTML report to generate."
67 ),
68 verbose: Optional[bool] = typer.Option(False, "--verbose", "-v", help="Verbose output"),
69 expression: Optional[str] = typer.Option(
70 None, "-k", help="Only run tests which match the given substring expression."
71 ),
72 cores: Optional[str] = typer.Option(
73 None,
74 "-n",
75 help="Number of cores. Use 'auto' to spawn a number of workers processes equal to the number of available CPUs.",
76 ),
77):
78 exit_code = main(
79 testfile=testfile,
80 sequence=sequence,
81 sequence_format=sequence_format,
82 tree=tree,
83 tree_format=tree_format,
84 data=data,
85 data_format=data_format,
86 verbose=verbose,
87 report=report,
88 expression=expression,
89 cores=cores,
90 )
91 raise typer.Exit(code=exit_code)