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Fix CLI. the prev approach caused RecursionError #27

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Merged
milkschen merged 2 commits into from
Jun 22, 2025
Merged

Fix CLI. the prev approach caused RecursionError #27

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22bcd15
fix cli. the prev approach caused RecursionError
milkschen Jun 22, 2025
c2513a7
update required args for to-sam, to-vcf
milkschen Jun 22, 2025
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39 changes: 24 additions & 15 deletions chaintools_bio/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,10 @@
stats,
)

app = typer.Typer(help="Utilities for the genomic chain format")


def version_callback(value: bool):
if value:
print(f"chaintools_bio version: {__version__}")
raise typer.Exit()
app = typer.Typer(
help="Utilities for the genomic chain format",
no_args_is_help=True,
)


class CoordSystem(str, Enum):
Expand Down Expand Up @@ -87,10 +84,10 @@ def to_sam_cmd(
"", "-o", "--output", help="Path to the output SAM file"
),
target_fasta: str = typer.Option(
"", "-t", "--target-fasta", help="Path to the target FASTA file"
..., "-t", "--target-fasta", help="Path to the target FASTA file"
),
query_fasta: str = typer.Option(
"", "-q", "--query-fasta", help="Path to the query FASTA file"
..., "-q", "--query-fasta", help="Path to the query FASTA file"
),
):
"""Convert a chain file to the SAM format"""
Expand All @@ -111,10 +108,10 @@ def to_vcf_cmd(
"", "-o", "--output", help="Path to the output VCF file"
),
target_fasta: str = typer.Option(
"", "-t", "--target-fasta", help="Path to the target FASTA file"
..., "-t", "--target-fasta", help="Path to the target FASTA file"
),
query_fasta: str = typer.Option(
"", "-q", "--query-fasta", help="Path to the query FASTA file"
..., "-q", "--query-fasta", help="Path to the query FASTA file"
),
):
"""Convert a chain file to the VCF format"""
Expand Down Expand Up @@ -163,7 +160,7 @@ def annotate_cmd(
"", "-o", "--output", help="Path to the output annotated chain file"
),
bed_prefix: str = typer.Option(
..., "-b", "--bed-prefix", help="Prefix for BED output files"
"", "-b", "--bed-prefix", help="Prefix for BED output files"
),
summary: str = typer.Option(
"", "-s", "--summary", help="Path to summary output file"
Expand Down Expand Up @@ -237,12 +234,24 @@ def stats_cmd(
stats.stats(fn_chain=chain, fn_out=output)


@app.callback()
def main(
def _version_callback(value: bool):
if value:
print(f"chaintools_bio version: {__version__}")
raise typer.Exit()


@app.callback(invoke_without_command=True)
def version_callback(
version: bool = typer.Option(
None, "--version", callback=version_callback, is_eager=True
None, "--version", callback=_version_callback, is_eager=True
),
):
pass


def main():
"""Primary entry point for the CLI."""
version_callback()
app()


Expand Down