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Add converters to SnakeBidsApp #421

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merged 2 commits into from
May 9, 2024
Merged

Add converters to SnakeBidsApp #421

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9e086bf
Add converters to SnakeBidsApp
pvandyken May 1, 2024
ad0b495
Add test
pvandyken May 9, 2024
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11 changes: 8 additions & 3 deletions snakebids/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
bidsapp.app([plugins.SnakemakeBidsApp(...)])

"""

from __future__ import annotations

import logging
Expand Down Expand Up @@ -69,12 +70,16 @@ class SnakeBidsApp:
DEPRECATED: no-op, use version plugin instead
"""

snakemake_dir: Path
snakemake_dir: Path = attrs.field(converter=Path)
plugins: list[Callable[[SnakeBidsApp], None | SnakeBidsApp]] = attrs.Factory(list)
skip_parse_args: bool = False
_parser: Any = attrs.field(default=None, alias="parser")
configfile_path: Path | None = None
snakefile_path: Path | None = None
configfile_path: Path | None = attrs.field(
default=None, converter=attrs.converters.optional(Path)
)
snakefile_path: Path | None = attrs.field(
default=None, converter=attrs.converters.optional(Path)
)
_config: Any = attrs.field(default=None, alias="config")
version: str | None = None
args: Any = None
Expand Down
19 changes: 18 additions & 1 deletion snakebids/tests/test_app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,6 @@ def test_arguments_carried_forward(mocker: MockerFixture):
from snakebids.app import sb_plugins
from snakebids.bidsapp import run

mocker.stopall()
mocker.patch.object(run, "_Runner")
snakemake = mocker.spy(sb_plugins, "SnakemakeBidsApp")
SnakeBidsApp(
Expand All @@ -55,6 +54,24 @@ def test_arguments_carried_forward(mocker: MockerFixture):
)


def test_str_converted_to_path(mocker: MockerFixture):
from snakebids.app import sb_plugins
from snakebids.bidsapp import run

mocker.patch.object(run, "_Runner")
snakemake = mocker.spy(sb_plugins, "SnakemakeBidsApp")
SnakeBidsApp(
"",
configfile_path="config",
snakefile_path="Snakefile",
).run_snakemake()
snakemake.assert_called_once_with(
snakemake_dir=Path(),
configfile_path=Path("config"),
snakefile_path=Path("Snakefile"),
)


def test_plugins_carried_forward(mocker: MockerFixture):
from snakebids.app import bidsapp
from snakebids.bidsapp import run
Expand Down