diff --git a/formats/image-dimension-stacking-plugin/build-docker.sh b/formats/image-dimension-stacking-plugin/build-docker.sh deleted file mode 100644 index 92c2b410b..000000000 --- a/formats/image-dimension-stacking-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(", "Hamdah Shafqat abbasi " ] readme = "README.md" diff --git a/formats/image-dimension-stacking-plugin/run-plugin.sh b/formats/image-dimension-stacking-tool/run-plugin.sh similarity index 100% rename from formats/image-dimension-stacking-plugin/run-plugin.sh rename to formats/image-dimension-stacking-tool/run-plugin.sh diff --git a/formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__init__.py b/formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__init__.py similarity index 100% rename from formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__init__.py rename to formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__init__.py diff --git a/formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__main__.py b/formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__main__.py similarity index 97% rename from formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__main__.py rename to formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__main__.py index 01bb16482..165eb6c20 100644 --- a/formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__main__.py +++ b/formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__main__.py @@ -7,7 +7,7 @@ from typing import Any import filepattern as fp -import polus.plugins.formats.image_dimension_stacking.dimension_stacking as st +import polus.images.formats.image_dimension_stacking.dimension_stacking as st import typer warnings.filterwarnings("ignore") diff --git a/formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/dimension_stacking.py b/formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/dimension_stacking.py similarity index 100% rename from formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/dimension_stacking.py rename to formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/dimension_stacking.py diff --git a/formats/image-dimension-stacking-plugin/tests/__init__.py b/formats/image-dimension-stacking-tool/tests/__init__.py similarity index 100% rename from formats/image-dimension-stacking-plugin/tests/__init__.py rename to formats/image-dimension-stacking-tool/tests/__init__.py diff --git a/formats/image-dimension-stacking-plugin/tests/fixture.py b/formats/image-dimension-stacking-tool/tests/conftest.py similarity index 92% rename from formats/image-dimension-stacking-plugin/tests/fixture.py rename to formats/image-dimension-stacking-tool/tests/conftest.py index 3257e3b42..e3ab84b29 100644 --- a/formats/image-dimension-stacking-plugin/tests/fixture.py +++ b/formats/image-dimension-stacking-tool/tests/conftest.py @@ -22,6 +22,17 @@ def clean_directories() -> None: shutil.rmtree(d) +def pytest_addoption(parser: pytest.Parser) -> None: + """Add options to pytest.""" + parser.addoption( + "--downloads", + action="store_true", + dest="downloads", + default=False, + help="run tests that download large data files", + ) + + @pytest.fixture() def output_directory() -> Union[str, Path]: """Create output directory.""" diff --git a/formats/image-dimension-stacking-plugin/tests/test_cli.py b/formats/image-dimension-stacking-tool/tests/test_cli.py similarity index 89% rename from formats/image-dimension-stacking-plugin/tests/test_cli.py rename to formats/image-dimension-stacking-tool/tests/test_cli.py index 08179e288..8d4972777 100644 --- a/formats/image-dimension-stacking-plugin/tests/test_cli.py +++ b/formats/image-dimension-stacking-tool/tests/test_cli.py @@ -1,7 +1,8 @@ """Test Command line Tool.""" from typer.testing import CliRunner -from polus.plugins.formats.image_dimension_stacking.__main__ import app -from tests.fixture import * +from polus.images.formats.image_dimension_stacking.__main__ import app +from pathlib import Path +from typing import Union def test_cli(synthetic_images: tuple[Union[str, Path]], output_directory: Path) -> None: @@ -22,7 +23,6 @@ def test_cli(synthetic_images: tuple[Union[str, Path]], output_directory: Path) ) assert result.exit_code == 0 - clean_directories() def test_multipattern_cli( @@ -46,7 +46,6 @@ def test_multipattern_cli( ) assert result.exit_code == 0 - clean_directories() def test_short_cli( @@ -68,6 +67,3 @@ def test_short_cli( ) assert result.exit_code == 0 - - -clean_directories() diff --git a/formats/image-dimension-stacking-plugin/tests/test_dimension_stacking.py b/formats/image-dimension-stacking-tool/tests/test_dimension_stacking.py similarity index 90% rename from formats/image-dimension-stacking-plugin/tests/test_dimension_stacking.py rename to formats/image-dimension-stacking-tool/tests/test_dimension_stacking.py index af9e64ed2..2cd39dca4 100644 --- a/formats/image-dimension-stacking-plugin/tests/test_dimension_stacking.py +++ b/formats/image-dimension-stacking-tool/tests/test_dimension_stacking.py @@ -2,12 +2,12 @@ from pathlib import Path from typing import Union -import polus.plugins.formats.image_dimension_stacking.dimension_stacking as ds +import polus.images.formats.image_dimension_stacking.dimension_stacking as ds from bfio import BioReader from bfio import BioWriter -from tests.fixture import * # noqa: F403 -from tests.fixture import clean_directories +from .conftest import * # noqa:F403 +from .conftest import clean_directories def test_dimension_stacking( @@ -39,7 +39,6 @@ def test_dimension_stacking( assert total_dimensions == br.Z if variable == "t": assert total_dimensions == br.T - clean_directories() def test_write_image_stack( @@ -61,7 +60,6 @@ def test_write_image_stack( ds.write_image_stack(file=file, di=0, group_by=variable, bw=bw) total_dimensions = 10 assert len(list(output_directory.iterdir())) == total_dimensions - clean_directories() def test_z_distance(synthetic_images: tuple[Union[str, Path], str, str]) -> None: