Add pyright checking, use pre-commit for code reformatting

.pre-commit-config.yaml

@@ -6,6 +6,11 @@ repos:
        entry: flake8
        language: system
        types: [python]
+    -  id: pyright
+       name: pyright
+       entry: pyright
+       language: system
+       types: [python]
     -  id: isort
        name: isort
        entry: isort

Makefile

@@ -65,6 +65,7 @@ build: %:
 #=> cqa: execute code quality tests
 cqa:
 	flake8 src --count --select=E9,F63,F7,F82 --show-source --statistics
+	pyright
 	isort --profile black --check src
 	black --check src
 	bandit -ll -r src
@@ -93,10 +94,7 @@ tox:
 #=> reformat: reformat code with yapf and commit
 .PHONY: reformat
 reformat:
-	@if ! git diff --cached --exit-code >/dev/null; then echo "Repository not clean" 1>&2; exit 1; fi
-	black src tests
-	isort src tests
-	git commit -a -m "reformatted with black and isort"
+	pre-commit
 
 #=> rename: rename files and substitute content for new repo name
 .PHONY: rename

pyproject.toml

@@ -81,6 +81,10 @@ profile = "black"
 src_paths = ["src"]
 
 
+[tool.pyright]
+include = ["src"]
+
+
 # [tool.flake8]
 # flake8 does not support configuration in pyproject.toml
 # https://github.com/PyCQA/flake8/issues/234#issuecomment-812800832

setup.cfg

@@ -20,6 +20,7 @@ dev =
     mypy
     pre-commit~=3.4
     pylint~=2.14
+    pyright==1.1.327
     pytest-cov~=4.1
     pytest-optional-tests
     pytest~=7.1

src/biocommons/example/tests/conftest.py

@@ -1,4 +1,4 @@
-import importlib
+import importlib.resources
 
 import pytest
 import yaml