Standardise package structure and add tests (#57)

* Standardise tooling and package structure

* Add more assertions to the cellfinder xml reader test

* remove boilerplate comment

* Move cellfinder dir reader into workflows directory

* remove unused function

* restructure tests

* Add more assertions for writer test

* Expand cellfinder xml writer tests

* Test loading other files

* Add unit tests

* Add test for layer naming

* Move xml test data

* Add brainreg reader tests

* Add whole brain cell detection & registration tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* lint

* Remove check for executables

* replace np.random.random with Generator

* Update GH workflow

* Update tests/tests/test_integration/test_cellfinder_reader.py

Co-authored-by: Alessandro Felder <[email protected]>

* update pre-commit

* update pre-commit

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>

.github/workflows/test_and_deploy.yml

@@ -1,18 +1,18 @@
-name: Test (and Deploy on tag)
+name: tests
 
 on:
   push:
     branches:
-    - main
+      - '*'
     tags:
       - '*'
   pull_request:
 
 jobs:
   linting:
-      runs-on: ubuntu-latest
-      steps:
-        - uses: neuroinformatics-unit/actions/lint@v2
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
 
   manifest:
     name: Check Manifest
@@ -21,43 +21,39 @@ jobs:
       - uses: neuroinformatics-unit/actions/check_manifest@v2
 
   test:
+    needs: [linting, manifest]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
-    needs: [linting,manifest]
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
       matrix:
-        # Run across a mixture of Python versions and operating systems
+        # Run all supported Python versions on linux
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
         include:
-        - os: ubuntu-latest
-          python-version: "3.11"
         - os: macos-latest
           python-version: "3.10"
         - os: windows-latest
-          python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.8"
+          python-version: "3.10"
 
     steps:
-      # these libraries enable testing on Qt on linux
-      - uses: tlambert03/setup-qt-libs@v1
       # Run tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
 
-  build_sdist_wheel:
-    name: Build source distribution and wheel
+  build_sdist_wheels:
+    name: Build source distribution
     needs: [test]
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses:  neuroinformatics-unit/actions/build_sdist_wheels@v2
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+
 
   upload_all:
     name: Publish build distributions
-    needs: [build_sdist_wheel]
-    if: github.event_name == 'push' && github.ref_type == 'tag'
+    needs: [build_sdist_wheels]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/download-artifact@v3

.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

@@ -7,7 +7,6 @@ repos:
       rev: v4.5.0
       hooks:
           - id: check-docstring-first
-          - id: check-executables-have-shebangs
           - id: check-merge-conflict
           - id: check-toml
           - id: end-of-file-fixer
@@ -16,7 +15,7 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.6
+      rev: v0.1.7
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
@@ -29,3 +28,9 @@ repos:
           - 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