Standardise package structure and add tests

.gitignore

@@ -44,7 +44,6 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
-.napari_cache
 
 # Translations
 *.mo
@@ -66,6 +65,11 @@ docs/_build/
 # PyBuilder
 target/
 
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
 # IPython Notebook
 .ipynb_checkpoints
 
@@ -76,6 +80,4 @@ target/
 .DS_Store
 
 # written by setuptools_scm
-*/_version.py
-
-.idea/
+**/_version.py

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v4.4.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -15,17 +15,23 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.6
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.272
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.11.0
+      rev: 23.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.7.1
+      rev: v1.3.0
       hooks:
           - id: mypy
             additional_dependencies:
                 - types-setuptools
+    - repo: https://github.com/mgedmin/check-manifest
+      rev: "0.49"
+      hooks:
+          - id: check-manifest
+            args: [--no-build-isolation]
+            additional_dependencies: [setuptools-scm]

MANIFEST.in

@@ -1,10 +1,11 @@
 include LICENSE
 include README.md
 exclude tox.ini
-
+exclude .pre-commit-config.yaml
 
 exclude *.yml
 exclude *.yaml
+recursive-exclude tests *
 
 recursive-exclude brainglobe_napari_io *.xml
 include brainglobe_napari_io/napari.yaml

brainglobe_napari_io/__init__.py

@@ -1,5 +1,7 @@
-from importlib_metadata import version
+from importlib.metadata import PackageNotFoundError, version
 
-__version__ = version("brainglobe-napari-io")
-__author__ = "Adam Tyson"
-__license__ = "BSD-3-Clause"
+try:
+    __version__ = version("brainglobe-napari-io")
+except PackageNotFoundError:
+    # package is not installed
+    pass

brainglobe_napari_io/cellfinder/utils.py

@@ -20,13 +20,6 @@ def cells_df_as_np(
     return cells
 
 
-def cells_to_array(cells) -> Tuple[np.ndarray, np.ndarray]:
-    df = pd.DataFrame([c.to_dict() for c in cells])
-    points = cells_df_as_np(df[df["type"] == Cell.CELL])
-    rejected = cells_df_as_np(df[df["type"] == Cell.UNKNOWN])
-    return points, rejected
-
-
 def get_cell_arrays(cells_file: os.PathLike) -> Tuple[np.ndarray, np.ndarray]:
     df = cells_xml_to_df(str(cells_file))
 

brainglobe_napari_io/napari.yaml

@@ -10,9 +10,9 @@ contributions:
     title: Brainreg Read Directory Atlas Space
     python_name: brainglobe_napari_io.brainreg.reader_dir_atlas_space:brainreg_read_dir_atlas_space
 
-  - id: brainglobe-napari-io.cellfinder_read_dir
-    title: Cellfinder Read Directory
-    python_name: brainglobe_napari_io.cellfinder.reader_dir:cellfinder_read_dir
+  - id: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
+    title: Workflows Whole Brain Cell Detection Read Directory
+    python_name: brainglobe_napari_io.workflows.wholebrain_cell_reader_dir:wholebrain_cell_read_dir
 
   - id: brainglobe-napari-io.cellfinder_read_xml
     title: Cellfinder Read XML
@@ -34,7 +34,7 @@ contributions:
       - '*.tiff'
     accepts_directories: true
 
-  - command: brainglobe-napari-io.cellfinder_read_dir
+  - command: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
     filename_patterns:
     - '*.tif'
     accepts_directories: true