Clean up quality checks (#40)

* ruff instead of a range of different tools
* update python requirement and python versions on GHA
* update pre-commit config


Closes #5

.github/workflows/test_suite.yml

@@ -54,7 +54,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
@@ -74,23 +74,18 @@ jobs:
     - name: Install dependencies
       run: pip install tox pre-commit
 
-# failing on github, no size environment in tox.ini
-#    - name: Check repository size
-#      run: tox -e size
-
     - name: Run quality checks
       timeout-minutes: 5
-      run: tox -e pyroma,flake8
+      run: tox -e pyroma
 
-# failing on github
-#    - name: Run pre-commit hooks
-#      run: pre-commit run --all-files
+    - name: Run pre-commit hooks
+      run: pre-commit run --all-files
 
   docs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository

.pre-commit-config.yaml

@@ -10,31 +10,8 @@
 # `pre-commit run --all-files` as by default only changed files are checked
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-  - id: black
-    description: The uncompromising code formatter
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    name: isort (python)
-  - id: isort
-    name: isort (cython)
-    types: [cython]
-  - id: isort
-    name: isort (pyi)
-    types: [pyi]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
-  hooks:
-  - id: nbqa-black
-  - id: nbqa-pyupgrade
-    args: [--py36-plus]
-  - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax
@@ -54,11 +31,19 @@ repos:
     description: Replace or check mixed line endings
   - id: trailing-whitespace
     description: Trim trailing whitespaces
-- repo: local
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.9
   hooks:
-  - id: style
-    name: Check style
-    description: Check style
-    entry: tox -e project,flake8 --
-    language: python
-    types: [python]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml

doc/conf.py

@@ -1,7 +1,6 @@
 import os
 import sys
-
-import mock
+from unittest import mock
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -61,8 +60,12 @@
 
 
 autodoc_mock_imports = [
-    "amici", "amici.amici", "amici.petab", "amici.petab.simulations",
-    "amici.petab.parameter_mapping", "amici.petab.conditions"
+    "amici",
+    "amici.amici",
+    "amici.petab",
+    "amici.petab.simulations",
+    "amici.petab.parameter_mapping",
+    "amici.petab.conditions",
 ]
 for mod_name in autodoc_mock_imports:
     sys.modules[mod_name] = mock.MagicMock()

examples/derivative.ipynb

@@ -30,7 +30,6 @@
    ],
    "source": [
     "import numpy as np\n",
-    "import pandas as pd\n",
     "from scipy.optimize import rosen, rosen_der\n",
     "\n",
     "from fiddy import MethodId, get_derivative\n",

fiddy/derivative.py

@@ -45,6 +45,7 @@ class Derivative:
         success:
             Whether the derivative was successfully computed.
     """
+
     hide_columns = [
         "pending_computers",
         "computers",

fiddy/extensions/amici/amici.py

@@ -6,9 +6,9 @@
 import amici.petab.simulations
 import numpy as np
 import petab.v1 as petab
+from amici.petab.conditions import create_edatas
 from amici.petab.parameter_mapping import create_parameter_mapping
 from amici.petab.simulations import LLH, SLLH
-from amici.petab.conditions import create_edatas
 from petab.v1.C import LIN, LOG, LOG10
 
 from ...constants import Type

pyproject.toml

@@ -5,5 +5,28 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
-[tool.black]
+[tool.ruff]
 line-length = 79
+lint.select = [
+    "F",  # Pyflakes
+    "I",  # isort
+    # "D",  # pydocstyle (PEP 257)  FIXME enable later
+    "S",  # flake8-bandit
+    "B",  # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "T20",  # flake8-print
+    "W",  # pycodestyle Warnings
+    "E",  # pycodestyle Errors
+    "UP",  # pyupgrade
+    # "ANN",  # flakes-annotations
+]
+lint.ignore = [
+    "S101", # Use of assert detected
+    # FIXME
+    "E501", # Line too long
+    "T201", # print statement
+    "F403", # star import
+    "F401", # unused import
+]
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"

setup.cfg

@@ -27,9 +27,9 @@ classifiers =
     License :: OSI Approved :: BSD License
     Operating System :: OS Independent
     Programming Language :: Python
+    Programming Language :: Python :: 3.12
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.9
 keywords =
     finite difference
     gradient check
@@ -40,7 +40,7 @@ install_requires =
     numpy
     pandas
 
-python_requires = >=3.9
+python_requires = >=3.10
 include_package_data = True
 
 # Where is my code

tests/test_derivative.py

@@ -142,9 +142,9 @@ def test_get_derivative_relative():
     )  # cardinal direction, simplifies to this, but usually need dot product
 
     g_a = (f_a - f_0) / size
-    g_r = (f_r - f_0) / (
-        point * direction * size
-    ).sum()  # cardinal direction, simplifies to this, but usually need dot product
+    g_r = (
+        (f_r - f_0) / (point * direction * size).sum()
+    )  # cardinal direction, simplifies to this, but usually need dot product
 
     # Fiddy finite difference derivatives
     kwargs = {

tox.ini

@@ -12,7 +12,6 @@
 envlist =
     clean
     pyroma
-    flake8
     doc
 
 # Base-environment
@@ -40,23 +39,6 @@ commands =
 description =
     Check the package friendliness
 
-[testenv:flake8]
-skip_install = true
-deps =
-    flake8 >= 6.0.0
-    flake8-bandit >= 4.1.1
-    flake8-bugbear >= 23.3.23
-    flake8-colors >= 0.1.9
-    flake8-comprehensions >= 3.12.0
-    flake8-print >= 5.0.0
-    flake8-black >= 0.3.6
-    flake8-isort >= 6.0.0
-    flake8-docstrings >= 1.7.0
-commands =
-    flake8 fiddy tests
-description =
-    Run flake8 with various plugins.
-
 [testenv:doc]
 extras =
     doc