From 3703c4ac8f48110667c27c245ffbba00e1e1807c Mon Sep 17 00:00:00 2001
From: sfmig <33267254+sfmig@users.noreply.github.com>
Date: Sat, 16 Dec 2023 13:49:16 +0000
Subject: [PATCH] rename cellfinder workflow to avoid circular import issue

---
 benchmarks/cellfinder_core.py                          |  8 +++-----
 .../{cellfinder_core.py => cellfinder.py}              |  0
 pyproject.toml                                         |  2 +-
 tests/cellfinder_core/conftest.py                      |  2 +-
 .../test_integration/test_cellfinder.py                |  4 ++--
 tests/cellfinder_core/test_unit/test_cellfinder.py     | 10 +++-------
 6 files changed, 10 insertions(+), 16 deletions(-)
 rename brainglobe_workflows/cellfinder_core/{cellfinder_core.py => cellfinder.py} (100%)

diff --git a/benchmarks/cellfinder_core.py b/benchmarks/cellfinder_core.py
index 8cc7186a..717cc085 100644
--- a/benchmarks/cellfinder_core.py
+++ b/benchmarks/cellfinder_core.py
@@ -7,16 +7,14 @@
 from cellfinder_core.main import main as cellfinder_run
 from cellfinder_core.tools.IO import read_with_dask
 
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder_core.cellfinder import (
     CellfinderConfig,
     run_workflow_from_cellfinder_run,
 )
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder_core.cellfinder import (
     setup as setup_cellfinder_workflow,
 )
-from brainglobe_workflows.utils import (
-    DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
-)
+from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
 
 
 class TimeBenchmarkPrepGIN:
diff --git a/brainglobe_workflows/cellfinder_core/cellfinder_core.py b/brainglobe_workflows/cellfinder_core/cellfinder.py
similarity index 100%
rename from brainglobe_workflows/cellfinder_core/cellfinder_core.py
rename to brainglobe_workflows/cellfinder_core/cellfinder.py
diff --git a/pyproject.toml b/pyproject.toml
index f7ce8d62..0c464945 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,7 +81,7 @@ napari = [
 "Source Code" = "https://github.com/brainglobe/brainglobe-workflows"
 
 [project.scripts]
-cellfinder-workflow = "brainglobe_workflows.cellfinder_core.cellfinder_core:main_app_wrapper"
+cellfinder-workflow = "brainglobe_workflows.cellfinder_core.cellfinder:main_app_wrapper"
 cellfinder = "brainglobe_workflows.cellfinder_brainreg.main:main"
 
 [build-system]
diff --git a/tests/cellfinder_core/conftest.py b/tests/cellfinder_core/conftest.py
index 7e115705..749d83d3 100644
--- a/tests/cellfinder_core/conftest.py
+++ b/tests/cellfinder_core/conftest.py
@@ -5,7 +5,7 @@
 import pooch
 import pytest
 
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder_core.cellfinder import (
     read_cellfinder_config,
 )
 
diff --git a/tests/cellfinder_core/test_integration/test_cellfinder.py b/tests/cellfinder_core/test_integration/test_cellfinder.py
index 38063ddb..1bd120ba 100644
--- a/tests/cellfinder_core/test_integration/test_cellfinder.py
+++ b/tests/cellfinder_core/test_integration/test_cellfinder.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from brainglobe_workflows.cellfinder_core.cellfinder_core import main
+from brainglobe_workflows.cellfinder_core.cellfinder import main
 
 
 @pytest.mark.parametrize(
@@ -87,7 +87,7 @@ def test_script(
         Path(__file__).resolve().parents[3]
         / "brainglobe_workflows"
         / "cellfinder_core"
-        / "cellfinder_core.py"
+        / "cellfinder.py"
     )
     subprocess_input = [
         sys.executable,
diff --git a/tests/cellfinder_core/test_unit/test_cellfinder.py b/tests/cellfinder_core/test_unit/test_cellfinder.py
index ee339de3..87f65623 100644
--- a/tests/cellfinder_core/test_unit/test_cellfinder.py
+++ b/tests/cellfinder_core/test_unit/test_cellfinder.py
@@ -6,16 +6,14 @@
 import pooch
 import pytest
 
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder_core.cellfinder import (
     CellfinderConfig,
     add_signal_and_background_files,
     read_cellfinder_config,
     run_workflow_from_cellfinder_run,
     setup_workflow,
 )
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
-    setup as setup_full,
-)
+from brainglobe_workflows.cellfinder_core.cellfinder import setup as setup_full
 from brainglobe_workflows.utils import setup_logger
 
 
@@ -29,9 +27,7 @@ def default_input_config_cellfinder() -> Path:
         Path to default input config
 
     """
-    from brainglobe_workflows.utils import (
-        DEFAULT_JSON_CONFIG_PATH_CELLFINDER,
-    )
+    from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER
 
     return DEFAULT_JSON_CONFIG_PATH_CELLFINDER