add pre-commit and apply

.flake8

@@ -1,4 +1,5 @@
 [flake8]
+max-line-length = 120
 extend-ignore = E203,C901
 exclude =
     .git,

.pre-commit-config.yaml

@@ -0,0 +1,73 @@
+default_language_version:
+  python: python3
+
+ci:
+  autofix_prs: true
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit suggestions"
+  autoupdate_schedule: quarterly
+  # submodules: true
+
+repos:
+# todo: let's enable also al these but as separate PR
+#  - repo: https://github.com/pre-commit/pre-commit-hooks
+#    rev: v4.5.0
+#    hooks:
+#      - id: end-of-file-fixer
+#      - id: trailing-whitespace
+#      - id: check-json
+#      - id: check-yaml
+#      - id: check-toml
+#      - id: check-docstring-first
+#      - id: check-executables-have-shebangs
+#      - id: check-case-conflict
+#      - id: check-added-large-files
+#      - id: detect-private-key
+
+# todo: another great hook
+#  - repo: https://github.com/crate-ci/typos
+#    rev: v1.16.26
+#    hooks:
+#      - id: typos
+#        # empty to do not write fixes
+#        args: []
+#        exclude: pyproject.toml
+
+#  - repo: https://github.com/PyCQA/docformatter
+#    rev: v1.7.5
+#    hooks:
+#      - id: docformatter
+#        additional_dependencies: [tomli]
+#        args: ["--in-place"]
+
+#  - repo: https://github.com/psf/black-pre-commit-mirror
+#    rev: 24.1.1
+#    hooks:
+#      - id: black
+#        name: Format code
+#        args:
+#          - "--skip-string-normalization"
+
+# todo: unify formatting all GH actions files
+#  - repo: https://github.com/pre-commit/mirrors-prettier
+#    rev: v3.1.0
+#    hooks:
+#      - id: prettier
+#        # https://prettier.io/docs/en/options.html#print-width
+#        args: ["--print-width=120"]
+
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.8.0
+#    hooks:
+#      - id: mypy
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+
+# todo: replacement for flake8
+#  - repo: https://github.com/astral-sh/ruff-pre-commit
+#    rev: v0.1.9
+#    hooks:
+#      - id: ruff
+#        args: ["--fix"]

tests/requirements.txt

@@ -4,15 +4,6 @@ pytest
 coverage
 pytest-cov
 birch
-# linting and code quality; todo: remove after precommint lands
-bandit
-flake8
-pylint
-safety
-# type checking; todo: remove after precommint lands
-mypy
-types-setuptools
-pandas-stubs
 # to connect to the test mongodb server
 pymongo
 dnspython

tests/test_quality.py

@@ -2,14 +2,7 @@
 import subprocess
 
 
-def test_flake8():
-    """Flake8 linter passes with no warnings or errors."""
-    command = ['flake8']
-    parameters = ['--max-line-length=120', 'cachier', 'tests']
-    subprocess.check_call(command + parameters)
-
-
-@pytest.mark.skip
+@pytest.mark.skip  # todo: dead check, so let's replace it with Ruff
 def test_pylint():
     """Pylint linter passes with no warnings or errors."""
     command = ['pylint']

tests/test_security.py

@@ -2,7 +2,7 @@
 import subprocess
 
 
-@pytest.mark.skip
+@pytest.mark.skip  # todo: dead check, so let's replace it with Ruff
 def test_bandit():
     """Bandit security scan passes with no warnings or errors."""
     command = ['bandit']
@@ -12,7 +12,7 @@ def test_bandit():
     subprocess.check_call(command + parameters)
 
 
-@pytest.mark.skip
+@pytest.mark.skip  # todo: dead check, so let's enable it in separate PR within pre-commit
 def test_safety():
     """Safety security scan passes with no warnings or errors."""
     command = ['safety']