Rename cellfinder_core to cellfinder (#95)

* rename benchmarks module

* rename cellfinder_core refs to cellfinder only

* fix line length

* Merge branch 'main' into smg/rename_cellfinder_workflow

.gitignore

@@ -133,5 +133,3 @@ pip-wheel-metadata/
 .asv/
 benchmarks/results/*
 benchmarks/html/*
-# ignore bare repository cloned by asv
-brainglobe-workflows

benchmarks/cellfinder_core.py → benchmarks/cellfinder.py

@@ -8,11 +8,11 @@
 from cellfinder.core.tools.IO import read_with_dask
 from cellfinder.core.tools.prep import prep_models
 
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder.cellfinder import (
     CellfinderConfig,
     run_workflow_from_cellfinder_run,
 )
-from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+from brainglobe_workflows.cellfinder.cellfinder import (
     setup as setup_cellfinder_workflow,
 )
 from brainglobe_workflows.utils import DEFAULT_JSON_CONFIG_PATH_CELLFINDER

brainglobe_workflows/cellfinder_core/cellfinder_core.py → brainglobe_workflows/cellfinder/cellfinder.py

@@ -3,17 +3,13 @@
 It receives as an (optional) command line input the path to a configuration
 json file, that holds the values of the required parameters for the workflow.
 
+    python brainglobe_workflows/cellfinder.py --config path/to/config.json
+
 If no input json file is passed as a configuration, the default
 configuration defined at brainglobe_workflows/cellfinder/default_config.json
 is used.
 
-Example usage:
- - to pass a custom configuration, run (from the cellfinder_main.py
-   parent directory):
-    python cellfinder_core.py --config path/to/input/config.json
- - to use the default configuration, run
-    python cellfinder_core.py
-
+    python brainglobe_workflows/cellfinder.py
 
 """
 
@@ -81,7 +77,7 @@ class CellfinderConfig:
 
     # install path: default path for downloaded and output data
     _install_path: Pathlike = (
-        Path.home() / ".brainglobe" / "workflows" / "cellfinder_core"
+        Path.home() / ".brainglobe" / "workflows" / "cellfinder"
     )
 
     # input data paths

brainglobe_workflows/utils.py

@@ -74,7 +74,7 @@ def config_parser(
             To launch the cellfinder workflow with default parameters, run:
                 `cellfinder-workflow`.
             The default parameters are those specifed in brainglobe_workflows/
-            cellfinder_core/configs/cellfinder.json.
+            cellfinder/configs/cellfinder.json.
 
 
             To launch the cellfinder workflow with a specific set of input

tests/cellfinder_core/conftest.py

@@ -85,7 +85,7 @@ def GIN_default_location() -> Path:
         Path.home()
         / ".brainglobe"
         / "workflows"
-        / "cellfinder_core"
+        / "cellfinder"
         / "cellfinder_test_data"
     )
 

tests/cellfinder_core/test_integration/test_cellfinder.py

@@ -11,7 +11,7 @@ def test_main():
     """
     # import inside the test function so that required functions are
     # monkeypatched first
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import main
+    from brainglobe_workflows.cellfinder.cellfinder import main
 
     # run main
     cfg = main()
@@ -42,7 +42,7 @@ def test_main_w_inputs(
     request : pytest.FixtureRequest
         Pytest fixture to enable requesting fixtures by name
     """
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import main
+    from brainglobe_workflows.cellfinder.cellfinder import main
 
     # run main
     cfg = main(str(request.getfixturevalue(input_config)))

tests/cellfinder_core/test_unit/test_cellfinder.py

@@ -200,7 +200,7 @@ def test_add_input_paths(
         Pytest fixture to enable requesting fixtures by name
     """
 
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         CellfinderConfig,
     )
 
@@ -245,7 +245,7 @@ def test_read_cellfinder_config(
         Pytest fixture to enable requesting fixtures by name
 
     """
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         read_cellfinder_config,
     )
 
@@ -318,10 +318,10 @@ def test_setup(
     request : pytest.FixtureRequest
         Pytest fixture to enable requesting fixtures by name
     """
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         CellfinderConfig,
     )
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         setup as setup_workflow,
     )
 
@@ -358,10 +358,10 @@ def test_run_workflow_from_cellfinder_run(
     request : pytest.FixtureRequest
         Pytest fixture to enable requesting fixtures by name
     """
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         run_workflow_from_cellfinder_run,
     )
-    from brainglobe_workflows.cellfinder_core.cellfinder_core import (
+    from brainglobe_workflows.cellfinder.cellfinder import (
         setup as setup_workflow,
     )