chore: Use Ruff for linting and formatting (#147)

* Use Ruff for linting and formatting.
   - Use Ruff in pre-commit over pyupgrade, black, and flake8.
   - Enable additional linting in pyproject.toml ruff tool section.
   - Remove .flake8 and black config section of pyproject.toml.
   - Use Ruff in lint workflow.
* Disable some recommended Ruff lints.
   - c.f. https://learn.scientific-python.org/development/guides/style/#ruff
* Apply ruff formatting to source code.
* Add Ruff formatting badge to README.

.github/workflows/lint.yml

@@ -21,10 +21,6 @@ jobs:
       with:
         python-version: '3.x'
 
-    - name: Lint with flake8
+    - name: Lint with Ruff
       run: |
-        pipx run flake8 .
-
-    - name: Lint with Black
-      run: |
-        pipx run black --check --diff --verbose .
+        pipx run ruff check --diff --verbose .

.pre-commit-config.yaml

@@ -21,21 +21,15 @@ repos:
       exclude: ^deploy/
     - id: trailing-whitespace
 
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.9
     hooks:
-    - id: pyupgrade
-      args: ["--py36-plus"]
-
--   repo: https://github.com/psf/black
-    rev: 24.3.0
-    hooks:
-    - id: black-jupyter
-
--   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
-    hooks:
-    - id: flake8
+      # Run the linter.
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      # Run the formatter.
+      - id: ruff-format
 
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6

README.md

@@ -6,6 +6,8 @@
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/recast-hep/recast-atlas/main.svg)](https://results.pre-commit.ci/latest/github/recast-hep/recast-atlas/main)
 [![PyPI version](https://badge.fury.io/py/recast-atlas.svg)](https://badge.fury.io/py/recast-atlas)
 
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
 ATLAS tools to facilitate integration of ATLAS analyses into RECAST
 
 ## Getting Started

pyproject.toml

@@ -75,8 +75,7 @@ all = ["recast-atlas[local,kubernetes,reana]"]
 # Developer extras
 develop = [
     "pytest>=7.0.0",
-    "flake8>=3.9.0",
-    "black",
+    "ruff",
     "pre-commit",
 ]
 
@@ -101,14 +100,48 @@ only-include = [
 [tool.hatch.build.targets.wheel]
 packages = ["src/recastatlas"]
 
-[tool.black]
-line-length = 88
-skip-string-normalization = true
-include = '\.pyi?$'
-exclude = '''
-/(
-    \.git
-  | .eggs
-  | build
-)/
-'''
+[tool.ruff]
+src = ["src"]
+
+[tool.ruff.lint]
+extend-select = [
+#  "B",        # flake8-bugbear
+  "I",        # isort
+#  "ARG",      # flake8-unused-arguments
+  "C4",       # flake8-comprehensions
+  "EM",       # flake8-errmsg
+  "ICN",      # flake8-import-conventions
+  "G",        # flake8-logging-format
+  "PGH",      # pygrep-hooks
+  "PIE",      # flake8-pie
+  "PL",       # pylint
+#  "PT",       # flake8-pytest-style
+#  "PTH",      # flake8-use-pathlib
+#  "RET",      # flake8-return
+  "RUF",      # Ruff-specific
+#  "SIM",      # flake8-simplify
+  "T20",      # flake8-print
+  "UP",       # pyupgrade
+  "YTT",      # flake8-2020
+  "EXE",      # flake8-executable
+  "NPY",      # NumPy specific rules
+  "FURB",     # refurb
+  "PYI",      # flake8-pyi
+]
+ignore = [
+  "PLR09",    # Too many <...>
+  "PLR2004",  # Magic value used in comparison
+  "ISC001",   # Conflicts with formatter
+  # FIXME: Ingores are to cover over failing checks at Ruff adoption point
+  "C414",
+  "EM101",
+  "EM103",
+  "G004",
+  "PLW2901",
+  "T201",
+]
+typing-modules = ["mypackage._compat.typing"]
+isort.required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["T20"]

src/recastatlas/backends/__init__.py

@@ -1,41 +1,44 @@
+from __future__ import annotations
+
 import json
 import logging
-import subprocess
 import os
-import textwrap
 import shlex
-from .. import exceptions
+import subprocess
+import textwrap
+
 from recastatlas.exceptions import BackendNotAvailableException
 
+from .. import exceptions
+
 log = logging.getLogger(__name__)
 
 BACKENDS = {}
 try:
     from .reana import ReanaBackend
 
-    BACKENDS['reana'] = ReanaBackend()
+    BACKENDS["reana"] = ReanaBackend()
 except (ImportError, exceptions.BackendNotAvailableException):
     pass
 
 try:
     from .kubernetes import KubernetesBackend
 
-    BACKENDS['kubernetes'] = KubernetesBackend()
+    BACKENDS["kubernetes"] = KubernetesBackend()
 except (ImportError, exceptions.BackendNotAvailableException):
     pass
 
 try:
     from .local import LocalBackend
 
-    BACKENDS['local'] = LocalBackend()
+    BACKENDS["local"] = LocalBackend()
 except (ImportError, exceptions.BackendNotAvailableException):
     pass
 
 try:
-    from .docker import DockerBackend
-    from .docker import setup_docker
+    from .docker import DockerBackend, setup_docker
 
-    BACKENDS['docker'] = DockerBackend()
+    BACKENDS["docker"] = DockerBackend()
 except (ImportError, exceptions.BackendNotAvailableException):
     pass
 
@@ -56,13 +59,11 @@ def get_shell_packtivity(name, spec, backend):
         return subprocess.check_output(shlex.split(shellcmd)).decode("ascii")
     if backend == "docker":
         command, dockerconfig = setup_docker()
-        script = """\
+        script = f"""\
 mkdir -p ~/.docker
-echo '{dockerconfig}' > ~/.docker/config.json
-{command}
-        """.format(
-            dockerconfig=json.dumps(dockerconfig), command=shellcmd
-        )
+echo '{json.dumps(dockerconfig)}' > ~/.docker/config.json
+{shellcmd}
+        """
         command += ["sh", "-c", textwrap.dedent(script)]
         return subprocess.check_output(command).decode("ascii")
 

src/recastatlas/backends/docker.py

@@ -1,13 +1,17 @@
-from ..config import config
-from ..exceptions import FailedRunException
-import logging
-import os
+from __future__ import annotations
+
 import base64
 import json
-import textwrap
+import logging
+import os
 import subprocess
+import textwrap
+
 import yaml
 
+from ..config import config
+from ..exceptions import FailedRunException
+
 log = logging.getLogger(__name__)
 
 
@@ -17,11 +21,11 @@ def setup_docker():
     image = config.backends[backend]["image"]
 
     special_envs = [
-        'PACKTIVITY_CVMFS_LOCATION',
-        'PACKTIVITY_CVMFS_PROPAGATION',
-        'PACKTIVITY_AUTH_LOCATION',
-        'YADAGE_SCHEMA_LOAD_TOKEN',
-        'YADAGE_INIT_TOKEN',
+        "PACKTIVITY_CVMFS_LOCATION",
+        "PACKTIVITY_CVMFS_PROPAGATION",
+        "PACKTIVITY_AUTH_LOCATION",
+        "YADAGE_SCHEMA_LOAD_TOKEN",
+        "YADAGE_INIT_TOKEN",
     ]
     assert special_envs
 
@@ -98,20 +102,18 @@ def setup_docker():
 
 class DockerBackend:
     def run_workflow(self, name, spec):
-        backend_config = config.backends['docker']["fromstring"]
+        backend_config = config.backends["docker"]["fromstring"]
 
-        spec["backend"] = spec.get('backend', backend_config)
+        spec["backend"] = spec.get("backend", backend_config)
         command, dockerconfig = setup_docker()
 
-        script = """\
+        script = f"""\
         mkdir -p ~/.docker
-        echo '{dockerconfig}' > ~/.docker/config.json
+        echo '{json.dumps(dockerconfig)}' > ~/.docker/config.json
         cat << 'EOF' | yadage-run -f -
-        {spec}
+        {json.dumps(spec)}
         EOF
-        """.format(
-            spec=json.dumps(spec), dockerconfig=json.dumps(dockerconfig)
-        )
+        """
         command += ["sh", "-c", textwrap.dedent(script)]
         subprocess.check_call(command)
 

src/recastatlas/backends/kubernetes.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 
 

src/recastatlas/backends/local.py

@@ -1,17 +1,21 @@
-from yadage.utils import setupbackend_fromstring
+from __future__ import annotations
+
+import logging
+import os
+import subprocess
+
 from yadage.steering_api import run_workflow
+from yadage.utils import setupbackend_fromstring
+
 from ..config import config
 from ..exceptions import FailedRunException
-import logging
-import subprocess
-import os
 
 log = logging.getLogger(__name__)
 
 
 class LocalBackend:
     def run_workflow(self, name, spec):
-        backend_config = config.backends['local']["fromstring"]
+        backend_config = config.backends["local"]["fromstring"]
 
         spec["backend"] = setupbackend_fromstring(
             backend_config, spec.pop("backendopts", {})