Add standard pre-commit config + linting CI job (#17)

* Add standard pre-commit config

* Add GH actions linting job

.github/workflows/test_and_deploy.yml

@@ -6,6 +6,10 @@ name: tests
 on: [push, pull_request]
 
 jobs:
+  linting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: brainglobe/actions/lint@v1
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}

.pre-commit-config.yaml

@@ -1,12 +1,32 @@
 repos:
--   repo: https://github.com/python/black
-    rev: 20.8b1
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
     hooks:
-    - id: black
-      pass_filenames: true
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
+      - id: isort
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
     hooks:
-    - id: flake8
-      pass_filenames: true
-#      exclude: __init__.py
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+        exclude: setup.cfg # bump2version fix
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.931
+    hooks:
+      - id: mypy
+        additional_dependencies:
+            - types-setuptools

README.md

@@ -13,9 +13,9 @@ Visualise cellfinder and brainreg results with napari
 
 
 ## Installation
-This package is likely already installed 
-(e.g. with cellfinder, brainreg or another napari plugin), but if you want to 
-install it again, either use the napari plugin install GUI or you can 
+This package is likely already installed
+(e.g. with cellfinder, brainreg or another napari plugin), but if you want to
+install it again, either use the napari plugin install GUI or you can
 install `brainglobe-napari-io` via [pip]:
 
     pip install brainglobe-napari-io
@@ -26,7 +26,7 @@ install `brainglobe-napari-io` via [pip]:
 ### brainreg
 #### Sample space
 Drag your [brainreg](https://github.com/brainglobe/brainreg) output directory (the one with the log file) onto the napari window.
-    
+
 Various images should then open, including:
 * `Registered image` - the image used for registration, downsampled to atlas resolution
 * `atlas_name` - e.g. `allen_mouse_25um` the atlas labels, warped to your sample brain
@@ -42,8 +42,8 @@ _N.B. If you use a high resolution atlas (such as `allen_mouse_10um`), then the
 
 
 #### Atlas space
-`napari-brainreg` also comes with an additional plugin, for visualising your data 
-in atlas space. 
+`napari-brainreg` also comes with an additional plugin, for visualising your data
+in atlas space.
 
 This is typically only used in other software, but you can enable it yourself:
 * Open napari
@@ -61,9 +61,9 @@ This is typically only used in other software, but you can enable it yourself:
 * Load your raw data (drag and drop the data directories into napari, one at a time)
 * Drag and drop your cellfinder output directory into napari.
 
-The plugin will then load your detected cells (in yellow) and the rejected cell 
-candidates (in blue). If you carried out registration, then these results will be 
-overlaid (similarly to the loading brainreg data, but transformed to the 
+The plugin will then load your detected cells (in yellow) and the rejected cell
+candidates (in blue). If you carried out registration, then these results will be
+overlaid (similarly to the loading brainreg data, but transformed to the
 coordinate space of your raw data).
 
 ![load_data](https://raw.githubusercontent.com/brainglobe/brainglobe-napari-io/master/resources/load_data.gif)

brainglobe_napari_io/brainreg/reader_dir.py

@@ -1,7 +1,8 @@
-import os
 import json
-import tifffile
+import os
 from pathlib import Path
+
+import tifffile
 from bg_atlasapi.bg_atlas import BrainGlobeAtlas
 
 from .utils import is_brainreg_dir, load_additional_downsampled_channels

brainglobe_napari_io/brainreg/reader_dir_standard_space.py

@@ -1,7 +1,8 @@
-import os
 import json
-import tifffile
+import os
 from pathlib import Path
+
+import tifffile
 from bg_atlasapi.bg_atlas import BrainGlobeAtlas
 
 from .utils import is_brainreg_dir, load_additional_downsampled_channels

brainglobe_napari_io/brainreg/utils.py

@@ -1,4 +1,5 @@
 import os
+
 import tifffile
 
 
@@ -45,12 +46,9 @@ def load_additional_downsampled_channels(
         ):
 
             print(
-                f"Found additional downsampled image: {file.name}, "
-                f"adding to viewer"
-            )
-            name = file.name.strip(search_string).strip(extension) + (
-                " (downsampled)"
+                f"Found additional downsampled image: {file.name}, " f"adding to viewer"
             )
+            name = file.name.strip(search_string).strip(extension) + (" (downsampled)")
             layers.append(
                 (
                     tifffile.imread(file),

brainglobe_napari_io/cellfinder/reader_dir.py

@@ -9,14 +9,14 @@
 Replace code below accordingly.  For complete documentation see:
 https://napari.org/docs/plugins/for_plugin_developers.html
 """
+import json
 import os
 import sys
-import json
-import bg_space as bgs
 from pathlib import Path
 
-from ..brainreg.reader_dir import reader_function as brainreg_reader
+import bg_space as bgs
 
+from ..brainreg.reader_dir import reader_function as brainreg_reader
 from .utils import load_cells
 
 
@@ -110,16 +110,12 @@ def reader_function(path, point_size=15, opacity=0.6, symbol="ring"):
             )
 
     else:
-        layers = load_cells_from_file(
-            path, layers, point_size, opacity, symbol
-        )
+        layers = load_cells_from_file(path, layers, point_size, opacity, symbol)
 
     return layers
 
 
-def load_cells_from_file(
-    path, layers, point_size, opacity, symbol, channel=None
-):
+def load_cells_from_file(path, layers, point_size, opacity, symbol, channel=None):
     classified_cells_path = path / "points" / "cell_classification.xml"
     layers = load_cells(
         layers,
@@ -139,9 +135,7 @@ def load_registration(layers, registration_directory, metadata):
     registration_layers = remove_downsampled_images(registration_layers)
     atlas = get_atlas(registration_layers)
 
-    registration_layers = scale_reorient_layers(
-        registration_layers, atlas, metadata
-    )
+    registration_layers = scale_reorient_layers(registration_layers, atlas, metadata)
     layers.extend(registration_layers)
     return layers
 
@@ -181,13 +175,9 @@ def reorient_registration_layers(layers, atlas, metadata):
     return new_layers
 
 
-def reorient_registration_layer(
-    layer, atlas_orientation, raw_data_orientation
-):
+def reorient_registration_layer(layer, atlas_orientation, raw_data_orientation):
     layer = list(layer)
-    layer[0] = bgs.map_stack_to(
-        atlas_orientation, raw_data_orientation, layer[0]
-    )
+    layer[0] = bgs.map_stack_to(atlas_orientation, raw_data_orientation, layer[0])
     layer = tuple(layer)
     return layer
 

brainglobe_napari_io/cellfinder/reader_xml.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-
 from xml.etree import ElementTree
 
 from .utils import load_cells

brainglobe_napari_io/cellfinder/writer_xml.py

@@ -1,7 +1,7 @@
-from typing import List, Tuple, Dict, Any
+from typing import Any, Dict, List, Tuple
 
-from imlib.IO.cells import save_cells
 from imlib.cells.cells import Cell
+from imlib.IO.cells import save_cells
 from napari.types import FullLayerData
 from napari.utils.notifications import show_info
 

brainglobe_napari_io/plugins.py

@@ -1,9 +1,4 @@
-from brainglobe_napari_io.cellfinder.reader_xml import cellfinder_read_xml
-from brainglobe_napari_io.cellfinder.reader_dir import cellfinder_read_dir
-
 from brainglobe_napari_io.brainreg.reader_dir import brainreg_read_dir
-
-from brainglobe_napari_io.cellfinder.writer_xml import (
-    cellfinder_write_xml,
-    cellfinder_write_multiple_xml,
-)
+from brainglobe_napari_io.cellfinder.reader_dir import cellfinder_read_dir
+from brainglobe_napari_io.cellfinder.reader_xml import cellfinder_read_xml
+from brainglobe_napari_io.cellfinder.writer_xml import write_multiple_points_to_xml

brainglobe_napari_io/tests/test_cellfinder_reader.py

@@ -15,8 +15,8 @@ def test_reader_xml():
     assert reader_xml.cellfinder_read_xml(str(xml_file.resolve())) is not None
     layers = reader_xml.xml_reader(xml_file)
 
-    for l in layers:
-        assert len(l) == 3
-        assert isinstance(l[0], np.ndarray)
-        assert isinstance(l[1], dict)
-        assert isinstance(l[2], str)
+    for layer in layers:
+        assert len(layer) == 3
+        assert isinstance(layer[0], np.ndarray)
+        assert isinstance(layer[1], dict)
+        assert isinstance(layer[2], str)

brainglobe_napari_io/tests/test_cellfinder_writer.py

@@ -2,10 +2,7 @@
 
 import numpy as np
 
-from brainglobe_napari_io.cellfinder import (
-    reader_xml,
-    writer_xml,
-)
+from brainglobe_napari_io.cellfinder import reader_xml, writer_xml
 
 test_data_dir = pathlib.Path(__file__) / ".." / "data"
 

pyproject.toml

@@ -1,7 +1,6 @@
 [tool.black]
-target-version = ['py36', 'py37', 'py38']
+target-version = ['py36', 'py37', 'py38', 'py39', 'py310']
 skip-string-normalization = false
-line-length = 79
 exclude = '''
 (
   /(
@@ -18,4 +17,8 @@ exclude = '''
     | examples
   )/
 )
-'''
+'''
+
+
+[tool.isort]
+profile = "black"

setup.cfg

@@ -4,14 +4,14 @@ commit = True
 tag = True
 tag_name = {new_version}
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<rc>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}-{release}{rc}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:release]
 optional_value = prod
 first_value = rc
-values = 
+values =
 	rc
 	prod
 

setup.py

@@ -1,6 +1,7 @@
-from setuptools import setup, find_packages
 from os import path
 
+from setuptools import find_packages, setup
+
 this_directory = path.abspath(path.dirname(__file__))
 with open(path.join(this_directory, "README.md"), encoding="utf-8") as f:
     long_description = f.read()