def test_monkeypatch_data_io():
"""DataIoInterface only added to registry while context is entered."""
with monkeypatch_plugin_registry_data_io(
test_data_io={"test_dio": DummyDataIo(format_name="test")}):
assert "test_dio" in known_data_formats()
assert "test_mc" not in known_data_formats()
with monkeypatch_plugin_registry(
test_data_io={"test_full": DummyDataIo(format_name="test")}):
assert "test_full" in known_data_formats()
assert "test_full" not in known_data_formats()
def test_monkeypatch_plugin_registry_full(create_new_registry: bool):
"""Create a completely new registry."""
assert "decay" in known_megacomplex_names()
assert "yml" in known_project_formats()
assert "sdt" in known_data_formats()
with monkeypatch_plugin_registry(
test_megacomplex={"test_mc": DummyMegacomplex},
test_project_io={"test_pio": DummyProjectIo(format_name="test")},
test_data_io={"test_dio": DummyDataIo(format_name="test")},
create_new_registry=create_new_registry,
):
assert "test_mc" in known_megacomplex_names()
assert "test_pio" in known_project_formats()
assert "test_dio" in known_data_formats()
assert ("decay"
not in known_megacomplex_names()) is create_new_registry
assert ("yml" not in known_project_formats()) is create_new_registry
assert ("sdt" not in known_data_formats()) is create_new_registry
def plugin_list_cmd():
"""Prints a list of installed plugins."""
output = """
Installed Glotaran Plugins:
Models:
"""
output += "\n"
for name in known_model_names():
output += f" * {name}\n"
output += "\nData file Formats\n\n"
for reader_fmt in known_data_formats():
output += f" * .{reader_fmt}\n"
output += "\nProject file Formats\n\n"
for reader_fmt in known_project_formats():
output += f" * .{reader_fmt}\n"
click.echo(output)
def test_known_data_formats():
"""Known formats are the same as mocked register keys"""
assert sorted(known_data_formats()) == sorted(["foo", "mock"])
import typing
import click
from glotaran.analysis.optimize import optimize
from glotaran.cli.commands import util
from glotaran.io import save_result
from glotaran.plugin_system.data_io_registration import known_data_formats
from glotaran.project.scheme import Scheme
@click.option(
"--dataformat",
"-dfmt",
default=None,
type=click.Choice(known_data_formats()),
help=
"The input format of the data. Will be inferred from extension if not set.",
)
@click.option(
"--data",
"-d",
multiple=True,
type=(str, click.Path(exists=True, dir_okay=False)),
help="Path to a dataset in the form '--data DATASET_LABEL PATH_TO_DATA'",
)
@click.option(
"--out",
"-o",
default=None,
type=click.Path(file_okay=False),