rename cellfinder workflow to cellfinder_core (to separate from cellf…

…inder-brainreg CLI while keeping backwards comp) WIP
brainglobe · Dec 14, 2023 · 98b46d2 · 98b46d2
1 parent 466667c
commit 98b46d2
Show file tree

Hide file tree

Showing 17 changed files with 27 additions and 15 deletions.
diff --git a/brainglobe_benchmarks/cellfinder.py → brainglobe_benchmarks/cellfinder_core.py b/brainglobe_benchmarks/cellfinder.py → brainglobe_benchmarks/cellfinder_core.py
@@ -7,12 +7,16 @@
 from cellfinder_core.main import main as cellfinder_run
 from cellfinder_core.tools.IO import read_with_dask
 
-from brainglobe_workflows.cellfinder import (
+from brainglobe_workflows.cellfinder_core.cellfinder_core import (
     CellfinderConfig,
     run_workflow_from_cellfinder_run,
 )
-from brainglobe_workflows.cellfinder import setup as setup_cellfinder_workflow
-from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
+from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    setup as setup_cellfinder_workflow,
+)
+from brainglobe_workflows.cellfinder_core.utils import (
+    DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
+)
 
 
 class TimeBenchmarkPrepGIN:

diff --git a/tests/test_integration/__init__.py → ...obe_workflows/cellfinder_core/__init__.py b/tests/test_integration/__init__.py → ...obe_workflows/cellfinder_core/__init__.py
diff --git a/brainglobe_workflows/cellfinder.py → ...kflows/cellfinder_core/cellfinder_core.py b/brainglobe_workflows/cellfinder.py → ...kflows/cellfinder_core/cellfinder_core.py
@@ -33,12 +33,12 @@
 from cellfinder_core.tools.IO import read_with_dask
 from cellfinder_core.train.train_yml import depth_type
 
-from brainglobe_workflows.utils import (
+from brainglobe_workflows.cellfinder_core.utils import (
     DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
     config_parser,
     setup_logger,
 )
-from brainglobe_workflows.utils import __name__ as LOGGER_NAME
+from brainglobe_workflows.cellfinder_core.utils import __name__ as LOGGER_NAME
 
 Pathlike = Union[str, os.PathLike]
 

diff --git a/brainglobe_workflows/utils.py → ...nglobe_workflows/cellfinder_core/utils.py b/brainglobe_workflows/utils.py → ...nglobe_workflows/cellfinder_core/utils.py
@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import List
 
-DEFAULT_JSON_CONFIGS_PATH = Path(__file__).resolve().parent / "configs"
+DEFAULT_JSON_CONFIGS_PATH = Path(__file__).resolve().parents[1] / "configs"
 
 DEFAULT_JSON_CONFIG_PATH_CELLFINDER = (
     DEFAULT_JSON_CONFIGS_PATH / "cellfinder.json"

diff --git a/...gration/brainglobe_benchmarks/__init__.py → tests/cellfinder_core/__init__.py b/...gration/brainglobe_benchmarks/__init__.py → tests/cellfinder_core/__init__.py
diff --git a/tests/conftest.py → tests/cellfinder_core/conftest.py b/tests/conftest.py → tests/cellfinder_core/conftest.py
@@ -5,7 +5,9 @@
 import pooch
 import pytest
 
-from brainglobe_workflows.cellfinder import read_cellfinder_config
+from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    read_cellfinder_config,
+)
 
 
 @pytest.fixture()
@@ -18,7 +20,7 @@ def input_configs_dir() -> Path:
     Path
         Test data directory path
     """
-    return Path(__file__).parent / "data"
+    return Path(__file__).parents[1] / "data"
 
 
 @pytest.fixture(scope="session")

diff --git a/...egration/brainglobe_workflows/__init__.py → ...lfinder_core/test_integration/__init__.py b/...egration/brainglobe_workflows/__init__.py → ...lfinder_core/test_integration/__init__.py
diff --git a/tests/test_unit/__init__.py → ...gration/brainglobe_benchmarks/__init__.py b/tests/test_unit/__init__.py → ...gration/brainglobe_benchmarks/__init__.py
diff --git a/.../brainglobe_benchmarks/test_cellfinder.py → .../brainglobe_benchmarks/test_cellfinder.py b/.../brainglobe_benchmarks/test_cellfinder.py → .../brainglobe_benchmarks/test_cellfinder.py
diff --git a/...st_unit/brainglobe_benchmarks/__init__.py → ...egration/brainglobe_workflows/__init__.py b/...st_unit/brainglobe_benchmarks/__init__.py → ...egration/brainglobe_workflows/__init__.py
diff --git a/...n/brainglobe_workflows/test_cellfinder.py → ...n/brainglobe_workflows/test_cellfinder.py b/...n/brainglobe_workflows/test_cellfinder.py → ...n/brainglobe_workflows/test_cellfinder.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from brainglobe_workflows.cellfinder import main
+from brainglobe_workflows.cellfinder_core.cellfinder_core import main
 
 
 @pytest.mark.parametrize(

diff --git a/...est_unit/brainglobe_workflows/__init__.py → tests/cellfinder_core/test_unit/__init__.py b/...est_unit/brainglobe_workflows/__init__.py → tests/cellfinder_core/test_unit/__init__.py
diff --git a/tests/cellfinder_core/test_unit/brainglobe_benchmarks/__init__.py b/tests/cellfinder_core/test_unit/brainglobe_benchmarks/__init__.py
diff --git a/tests/cellfinder_core/test_unit/brainglobe_workflows/__init__.py b/tests/cellfinder_core/test_unit/brainglobe_workflows/__init__.py
diff --git a/...est_unit/brainglobe_workflows/conftest.py → ...est_unit/brainglobe_workflows/conftest.py b/...est_unit/brainglobe_workflows/conftest.py → ...est_unit/brainglobe_workflows/conftest.py
@@ -10,6 +10,8 @@ def custom_logger_name() -> str:
     str
         Name of custom logger
     """
-    from brainglobe_workflows.utils import __name__ as logger_name
+    from brainglobe_workflows.cellfinder_core.utils import (
+        __name__ as logger_name,
+    )
 
     return logger_name
diff --git a/...t/brainglobe_workflows/test_cellfinder.py → ...t/brainglobe_workflows/test_cellfinder.py b/...t/brainglobe_workflows/test_cellfinder.py → ...t/brainglobe_workflows/test_cellfinder.py
@@ -6,15 +6,17 @@
 import pooch
 import pytest
 
-from brainglobe_workflows.cellfinder import (
+from brainglobe_workflows.cellfinder_core.cellfinder_core import (
     CellfinderConfig,
     add_signal_and_background_files,
     read_cellfinder_config,
     run_workflow_from_cellfinder_run,
     setup_workflow,
 )
-from brainglobe_workflows.cellfinder import setup as setup_full
-from brainglobe_workflows.utils import setup_logger
+from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    setup as setup_full,
+)
+from brainglobe_workflows.cellfinder_core.utils import setup_logger
 
 
 @pytest.fixture()
@@ -27,7 +29,9 @@ def default_input_config_cellfinder() -> Path:
         Path to default input config
 
     """
-    from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
+    from brainglobe_workflows.cellfinder_core.utils import (
+        DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
+    )
 
     return DEFAULT_JSON_CONFIG_PATH_CELLFINDER
 

diff --git a/...t_unit/brainglobe_workflows/test_utils.py → ...t_unit/brainglobe_workflows/test_utils.py b/...t_unit/brainglobe_workflows/test_utils.py → ...t_unit/brainglobe_workflows/test_utils.py
@@ -3,7 +3,7 @@
 
 import pytest
 
-from brainglobe_workflows.utils import (
+from brainglobe_workflows.cellfinder_core.utils import (
     DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
     config_parser,
     setup_logger,