Merge branch 'main' into issue-46-gitignore

.github/workflows/python-package.yml

@@ -18,31 +18,20 @@ jobs:
       with:
         python-version: "3.10"
         cache: pip
-        cache-dependency-path: '**/setup.cfg'
+        cache-dependency-path: '**/pyproject.yaml'
 
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --use-deprecated=legacy-resolver -e .[dev]
 
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    - name: Format check with isort
+    - name: Lint with Ruff
       run: |
-        isort --check src
+        ruff check .
 
-    - name: Format check with black
+    - name: Format check with Ruff
       run: |
-        black --check src
-
-    - name: Security check with bandit
-      run: |
-        bandit -ll -r src
+        ruff format --check .
 
   test:
     runs-on: ubuntu-latest
@@ -82,8 +71,8 @@ jobs:
         shasum -a 256 -c codecov.SHA256SUM
         # Upload coverage report
         chmod +x codecov
-        ./codecov        
-        
+        ./codecov
+
   deploy:
     needs:
     - cqa

.pre-commit-config.yaml

@@ -1,23 +1,14 @@
 repos:
 - repo: local
   hooks:
-    -  id: flake8
-       name: flake8
-       entry: flake8
-       language: system
-       types: [python]
     -  id: pyright
        name: pyright
        entry: pyright
        language: system
        types: [python]
-    -  id: isort
-       name: isort
-       entry: isort
-       language: system
-       types: [python]
-    -  id: black
-       name: black
-       entry: black
-       language: system
-       types: [python]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff
+    - id: ruff-format
+      args: [ --check ]

Makefile

@@ -81,16 +81,14 @@ tox:
 
 #=> cqa: execute code quality tests
 cqa:
-	flake8 src --show-source --statistics
-	pyright
-	isort --check src --profile black
-	black --check src
-	bandit -ll -r src
+	ruff format --check
+	ruff check
 
 #=> reformat: reformat code
 .PHONY: reformat
 reformat:
-	pre-commit
+	ruff check --fix
+	ruff format
 
 ############################################################################
 #= UTILITY TARGETS
@@ -136,13 +134,13 @@ distclean: cleanest
 
 ## <LICENSE>
 ## Copyright 2023 Source Code Committers
-## 
+##
 ## Licensed under the Apache License, Version 2.0 (the "License");
 ## you may not use this file except in compliance with the License.
 ## You may obtain a copy of the License at
-## 
+##
 ##     http://www.apache.org/licenses/LICENSE-2.0
-## 
+##
 ## Unless required by applicable law or agreed to in writing, software
 ## distributed under the License is distributed on an "AS IS" BASIS,
 ## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

README.md

@@ -46,11 +46,11 @@ Try it:
     $ python3 -m biocommons.example
     Marvin says:
     There's only one life-form as intelligent as me within thirty parsecs...
-           
-    $ marvin-quote 
+
+    $ marvin-quote
     Marvin says:
     You think you've got problems? What are you supposed to do if you...
-    
+
     $ ipython
     >>> from biocommons.example import __version__, get_quote_from_marvin
     >>> __version__
@@ -73,5 +73,5 @@ Try it:
 
 ## DevOps
 
-* Quality tools: Code reformatting with black and isort
+* Quality tools: Code linting and reformatting with Ruff
 * GitHub Actions for testing and packaging

pyproject.toml

@@ -23,19 +23,15 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-	"bandit ~= 1.7",
-	"black ~= 22.3",
 	"build ~= 0.8",
-	"flake8 ~= 4.0",
 	"ipython ~= 8.4",
-	"isort ~= 5.10",
 	"mypy-extensions ~= 1.0",
 	"pre-commit ~= 3.4",
-	"pylint ~= 2.14",
 	"pytest-cov ~= 4.1",
 	"pytest-optional-tests",
 	"pytest ~= 7.1",
 	"pyright~=1.1",
+	"ruff == 0.4.4",
 	"tox ~= 3.25",
 	"vcrpy",
 ]
@@ -123,21 +119,64 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 100
-
-[tool.isort]
-profile = "black"
-src_paths = ["src", "tests"]
-
-
 [tool.pyright]
 include = ["src", "tests"]
 
+[tool.ruff]
+src = ["src", "tests"]
+line-length = 100
 
-[tool.pylint.'MESSAGES CONTROL']
-disable = "R0913"
-
+[tool.ruff.lint]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "YTT",  # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PL",  # https://docs.astral.sh/ruff/rules/#pylint-pl
+    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
+    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+fixable = [
+    "F401",
+    "F541",
+    "I",
+    "D",
+    "UP",
+    "B",
+    "C4",
+    "EM",
+    "PIE",
+    "PT",
+    "RSE",
+    "RET",
+    "SIM",
+    "PERF",
+    "RUF",
+]
+ignore = [
+    # ignore for compatibility with formatter
+    "W191", "E111", "E114", "E117", "S321",
+    # other
+    "PLR0913",
+]
 
-[tool.pylint.format]
-max-line-length = 100
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["S101"]

src/biocommons/example/marvin.py

@@ -36,7 +36,7 @@ def get_quote() -> str:
     """
     _logger.info("Getting quote from Marvin")
 
-    quote = random.choice(quotes)
+    quote = random.choice(quotes)  # noqa: S311
 
     _logger.info("Got quote from Marvin (len=%s)", len(quote))
 

src/biocommons/example/marvin_adjacent_test.py

@@ -5,4 +5,4 @@
 
 def test_get_quote():
     """test get_quote"""
-    assert get_quote() is not None
+    assert get_quote() is not None  # noqa: S101

src/biocommons/example/tests/conftest.py

@@ -4,7 +4,7 @@
 import yaml
 
 
-@pytest.fixture
+@pytest.fixture()
 def all_quotes():
     quotes_stream = importlib.resources.files("example").joinpath("quotes.yaml").read_text()
     return yaml.load(quotes_stream, Loader=yaml.SafeLoader)["quotes"]

src/biocommons/example/tests/marvin_subdir_test.py

@@ -6,4 +6,4 @@
 def test_get_quote(all_quotes):
     """test get_quote"""
     # NB: all_quotes argument is a test fixture; see ./conftest.py
-    assert get_quote() in all_quotes
+    assert get_quote() in all_quotes  # noqa: S101