fix plugin name and test fixture

formats/image-dimension-stacking-plugin/.bumpversion.cfg → formats/image-dimension-stacking-tool/.bumpversion.cfg

@@ -26,4 +26,4 @@ replace = version = "{new_version}"
 
 [bumpversion:file:plugin.json]
 
-[bumpversion:file:src/polus/plugins/formats/image_dimension_stacking/__init__.py]
+[bumpversion:file:src/polus/images/formats/image_dimension_stacking/__init__.py]

formats/image-dimension-stacking-plugin/Dockerfile → formats/image-dimension-stacking-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.3
+FROM polusai/bfio:2.3.6
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
@@ -17,5 +17,5 @@ COPY src ${EXEC_DIR}/src
 RUN pip3 install ${EXEC_DIR} --no-cache-dir
 
 # Default command. Additional arguments are provided through the command line
-ENTRYPOINT ["python3", "-m", "polus.plugins.formats.image_dimension_stacking"]
+ENTRYPOINT ["python3", "-m", "polus.images.formats.image_dimension_stacking"]
 CMD ["--help"]

formats/image-dimension-stacking-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/image-dimension-stacking-tool:${version}

formats/image-dimension-stacking-plugin/plugin.json → formats/image-dimension-stacking-tool/plugin.json

@@ -5,13 +5,13 @@
   "description": "Stacking of image dimensions (c, z, t) to create a multidimensional image.",
   "author": "Nick Schaub ([email protected]), Hamdah Shafqat Abbasi ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
-  "repository": "https://github.com/PolusAI/polus-plugins",
+  "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
-  "containerId": "polusai/image-dimension-stacking-plugin:0.1.1-dev",
+  "containerId": "polusai/image-dimension-stacking-tool:0.1.1-dev",
   "baseCommand": [
     "python3",
     "-m",
-    "polus.plugins.formats.image_dimension_stacking"
+    "polus.images.formats.image_dimension_stacking"
   ],
   "inputs": {
     "inpDir": {

formats/image-dimension-stacking-plugin/pyproject.toml → formats/image-dimension-stacking-tool/pyproject.toml

@@ -1,8 +1,9 @@
 [tool.poetry]
-name = "polus-plugins-formats-image-dimension-stacking"
+name = "polus-images-formats-image-dimension-stacking"
 version = "0.1.1-dev"
 description = "Stacking multi-dimensional images"
 authors = [
+           "Nick Schaub <[email protected]>",
            "Hamdah Shafqat abbasi <[email protected]>"
            ]
 readme = "README.md"

formats/image-dimension-stacking-plugin/src/polus/plugins/formats/image_dimension_stacking/__main__.py → 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")

formats/image-dimension-stacking-plugin/tests/fixture.py → 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."""

formats/image-dimension-stacking-plugin/tests/test_cli.py → 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()

formats/image-dimension-stacking-plugin/tests/test_dimension_stacking.py → 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: