Use mypy for type checking (#249)

* add typechecking with mypy

* typecheck packages without __init__

* reformat code

* add mypy to lock file

* resolve circular dependencies and fix bugs

* refactor

* add typecheck to CI

* change initial value to None

* test if CI passes without typecheck

* add type check to CI

* git status to CI for more output

* ignore mypy cache

* reformat code

* add assertion for non optional parameter

* remove redundant imports

.github/workflows/main.yml

@@ -34,6 +34,10 @@ jobs:
 
     - name: Lint code
       run: poetry run pylint -j4 wkcuber
+
+    - name: Check typing
+      run: |
+        ./typecheck.sh
       
     - name: Python tests
       run: poetry run pytest tests

.gitignore

@@ -99,4 +99,7 @@ testdata/WT1_wkw
 testdata/tiff_mag_2_reference
 
 # VSCode
-.vscode/
+.vscode/
+
+# MyPy
+.mypy_cache/

pyproject.toml

@@ -18,6 +18,7 @@ natsort = "^6.2.0"
 psutil = "^5.6.7"
 nibabel = "^2.5.1"
 scikit-image = "^0.16.2"
+mypy = "^0.770"
 
 [tool.poetry.dev-dependencies]
 pylint = "^2.6.0"

setup.cfg

@@ -0,0 +1,5 @@
+[mypy]
+ignore_missing_imports = True
+
+[mypy-wkcuber.vendor.*]
+ignore_errors = True

tests/test_downsampling.py

@@ -1,4 +1,6 @@
 import logging
+from typing import Tuple
+
 import numpy as np
 from wkcuber.downsampling import (
     InterpolationModes,
@@ -20,7 +22,9 @@
 target_info = WkwDatasetInfo("testoutput/WT1_wkw", "color", 2, wkw.Header(np.uint8))
 
 
-def read_wkw(wkw_info, offset, size):
+def read_wkw(
+    wkw_info: WkwDatasetInfo, offset: Tuple[int, int, int], size: Tuple[int, int, int]
+):
     with open_wkw(wkw_info) as wkw_dataset:
         return wkw_dataset.read(offset, size)
 
@@ -120,7 +124,7 @@ def downsample_test_helper(use_compress):
 
     assert np.all(
         target_buffer
-        == downsample_cube(source_buffer, (2, 2, 2), InterpolationModes.MAX)
+        == downsample_cube(source_buffer, [2, 2, 2], InterpolationModes.MAX)
     )
 
 
@@ -180,7 +184,7 @@ def test_downsample_multi_channel():
     for channel_index in range(num_channels):
         channels.append(
             downsample_cube(
-                source_data[channel_index], (2, 2, 2), InterpolationModes.MAX
+                source_data[channel_index], [2, 2, 2], InterpolationModes.MAX
             )
         )
     joined_buffer = np.stack(channels)

typecheck.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+set -eEuo pipefail
+python -m mypy wkcuber --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages

wkcuber/__main__.py

@@ -4,9 +4,10 @@
 from .metadata import write_webknossos_metadata, refresh_metadata
 from .utils import add_isotropic_flag, setup_logging, add_scale_flag
 from .mag import Mag
+from argparse import Namespace, ArgumentParser
 
 
-def create_parser():
+def create_parser() -> ArgumentParser:
     parser = create_cubing_parser()
 
     parser.add_argument(
@@ -32,7 +33,7 @@ def create_parser():
     return parser
 
 
-def main(args):
+def main(args: Namespace) -> None:
     setup_logging(args)
 
     bounding_box = cubing(
@@ -82,5 +83,5 @@ def main(args):
 
 
 if __name__ == "__main__":
-    parsed_args = create_parser().parse_args()
+    parsed_args: Namespace = create_parser().parse_args()
     main(parsed_args)