Switch from black/isort/... to ruff (#99)

Replace black/isort/... by ruff. Run `pre-commit run --all-files`. Some additional rules should be enabled, but that will require additional effort. --------- Co-authored-by: Dilan Pathirana <[email protected]>
PEtab-dev · Nov 12, 2024 · 44a555a · 44a555a
1 parent ec9a5a6
commit 44a555a
Show file tree

Hide file tree

Showing 35 changed files with 866 additions and 944 deletions.
diff --git a/.flake8 b/.flake8
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,31 +4,8 @@
 # `pre-commit run --all-files` as by default only changed files are checked
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.10.0
-  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: 1.7.0
-  hooks:
-    - id: nbqa-black
-    - id: nbqa-pyupgrade
-      args: [--py36-plus]
-    - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax
@@ -44,3 +21,19 @@ repos:
     description: Fix empty lines at ends of files
   - id: detect-private-key
     description: Detects the presence of private keys
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.9
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml
diff --git a/doc/conf.py b/doc/conf.py
@@ -2,15 +2,19 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
+from __future__ import annotations
 
 import inspect
 
+import sphinx
+
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'PEtab Select'
-copyright = '2023, The PEtab Select developers'
-author = 'The PEtab Select developers'
+project = "PEtab Select"
+copyright = "2024, The PEtab Select developers"
+author = "The PEtab Select developers"
+
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -29,8 +33,8 @@
     "sphinx_autodoc_typehints",
 ]
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 intersphinx_mapping = {
@@ -53,7 +57,7 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 # html_static_path = ['_static']
 html_logo = "logo/logo-wide.svg"
 
@@ -73,5 +77,5 @@ def autodoc_skip_member(app, what, name, obj, skip, options):
     return None
 
 
-def setup(app: "sphinx.application.Sphinx"):
+def setup(app: sphinx.application.Sphinx):
     app.connect("autodoc-skip-member", autodoc_skip_member, priority=0)
diff --git a/doc/examples/example_cli_famos.ipynb b/doc/examples/example_cli_famos.ipynb
@@ -32,9 +32,7 @@
     "from pathlib import Path\n",
     "\n",
     "from example_cli_famos_helpers import (\n",
-    "    expected_criterion_values,\n",
     "    parse_summary_to_progress_list,\n",
-    "    petab_select_problem_yaml,\n",
     ")\n",
     "\n",
     "output_path = Path().resolve() / \"output_famos\"\n",
@@ -50,16 +48,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "import pandas as pd\n",
-    "import petab\n",
+    "from petab_select import Method\n",
     "\n",
-    "import petab_select\n",
-    "from petab_select import ESTIMATE, FamosCandidateSpace, Method, Model\n",
-    "from petab_select.constants import Criterion\n",
-    "from petab_select.model import default_compare\n",
-    "\n",
-    "state = str(output_path / 'state.dill')\n",
+    "state = str(output_path / \"state.dill\")\n",
     "\n",
     "# Each iteration of model selection is described as a 2-tuple here.\n",
     "# First value is the model selection method.\n",
@@ -231,7 +222,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "progress_list = parse_summary_to_progress_list(output_path / 'summary.tsv')"
+    "progress_list = parse_summary_to_progress_list(output_path / \"summary.tsv\")"
    ]
   },
   {

diff --git a/doc/examples/example_cli_famos_calibration_tool.py b/doc/examples/example_cli_famos_calibration_tool.py
@@ -1,10 +1,8 @@
 import sys
 
-import pandas as pd
 from example_cli_famos_helpers import calibrate
 
 import petab_select
-from petab_select import ESTIMATE, Criterion, Model
 
 models_yaml = sys.argv[1]
 calibrated_models_yaml = sys.argv[2]
@@ -24,6 +22,6 @@
     (predecessor_model_hash,) = predecessor_model_hashes
 else:
     print(
-        'The models of this iteration somehow have different predecessor models.\n'
-        + '\n'.join(predecessor_model_hashes)
+        "The models of this iteration somehow have different predecessor models.\n"
+        + "\n".join(predecessor_model_hashes)
     )
diff --git a/doc/examples/example_cli_famos_helpers.py b/doc/examples/example_cli_famos_helpers.py
@@ -1,11 +1,10 @@
 from pathlib import Path
-from typing import List, Tuple
 
 import pandas as pd
 from more_itertools import one
 
 import petab_select
-from petab_select import ESTIMATE, MODEL_HASH, Criterion, Method, Model
+from petab_select import MODEL_HASH, Criterion, Method, Model
 
 input_path = (
     Path(__file__).resolve().parent.parent.parent
@@ -43,9 +42,9 @@ def calibrate(
 
 def parse_summary_to_progress_list(
     summary_tsv: str,
-) -> List[Tuple[Method, set]]:
+) -> list[tuple[Method, set]]:
     """Get progress information from the summary file."""
-    df_raw = pd.read_csv(summary_tsv, sep='\t')
+    df_raw = pd.read_csv(summary_tsv, sep="\t")
     df = df_raw.loc[~pd.isnull(df_raw["predecessor change"])]
 
     parameter_list = list(

diff --git a/doc/examples/workflow_cli.ipynb b/doc/examples/workflow_cli.ipynb
@@ -147,7 +147,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'uncalibrated_models_1.yaml') as f:\n",
+    "with open(output_path / \"uncalibrated_models_1.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -261,7 +261,7 @@
     }
    ],
    "source": [
-    "with open('model_selection/calibrated_models_1.yaml') as f:\n",
+    "with open(\"model_selection/calibrated_models_1.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -362,7 +362,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'uncalibrated_models_2.yaml') as f:\n",
+    "with open(output_path / \"uncalibrated_models_2.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -441,7 +441,7 @@
     }
    ],
    "source": [
-    "with open('model_selection/calibrated_M1_4.yaml') as f:\n",
+    "with open(\"model_selection/calibrated_M1_4.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -501,7 +501,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'uncalibrated_models_3.yaml') as f:\n",
+    "with open(output_path / \"uncalibrated_models_3.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -566,7 +566,7 @@
     }
    ],
    "source": [
-    "with open('model_selection/calibrated_M1_7.yaml') as f:\n",
+    "with open(\"model_selection/calibrated_M1_7.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -605,7 +605,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'uncalibrated_models_4.yaml') as f:\n",
+    "with open(output_path / \"uncalibrated_models_4.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -699,7 +699,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'uncalibrated_models_5.yaml') as f:\n",
+    "with open(output_path / \"uncalibrated_models_5.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },
@@ -765,7 +765,7 @@
     }
    ],
    "source": [
-    "with open(output_path / 'best_model.yaml') as f:\n",
+    "with open(output_path / \"best_model.yaml\") as f:\n",
     "    print(f.read())"
    ]
   },

diff --git a/doc/examples/workflow_python.ipynb b/doc/examples/workflow_python.ipynb
@@ -46,31 +46,30 @@
    ],
    "source": [
     "import petab_select\n",
-    "from petab_select import ForwardCandidateSpace, Model\n",
+    "from petab_select import Model\n",
     "from petab_select.constants import (\n",
     "    CANDIDATE_SPACE,\n",
     "    MODELS,\n",
-    "    TERMINATE,\n",
     "    UNCALIBRATED_MODELS,\n",
     ")\n",
     "\n",
-    "BOLD_TEXT = '\\033[1m'\n",
-    "NORMAL_TEXT = '\\033[0m'\n",
+    "BOLD_TEXT = \"\\033[1m\"\n",
+    "NORMAL_TEXT = \"\\033[0m\"\n",
     "\n",
     "# Load the PEtab Select problem.\n",
     "select_problem = petab_select.Problem.from_yaml(\n",
-    "    'model_selection/petab_select_problem.yaml'\n",
+    "    \"model_selection/petab_select_problem.yaml\"\n",
     ")\n",
     "# Fake criterion values as a surrogate for a model calibration tool.\n",
     "fake_criterion = {\n",
-    "    'M1_0': 200,\n",
-    "    'M1_1': 150,\n",
-    "    'M1_2': 140,\n",
-    "    'M1_3': 130,\n",
-    "    'M1_4': -40,\n",
-    "    'M1_5': -70,\n",
-    "    'M1_6': -110,\n",
-    "    'M1_7': 50,\n",
+    "    \"M1_0\": 200,\n",
+    "    \"M1_1\": 150,\n",
+    "    \"M1_2\": 140,\n",
+    "    \"M1_3\": 130,\n",
+    "    \"M1_4\": -40,\n",
+    "    \"M1_5\": -70,\n",
+    "    \"M1_6\": -110,\n",
+    "    \"M1_7\": 50,\n",
     "}\n",
     "\n",
     "\n",
@@ -327,7 +326,7 @@
     "\n",
     "for candidate_model in iteration_results[MODELS].values():\n",
     "    if candidate_model.get_hash() == local_best_model.get_hash():\n",
-    "        print(BOLD_TEXT + 'BEST MODEL OF CURRENT ITERATION' + NORMAL_TEXT)\n",
+    "        print(BOLD_TEXT + \"BEST MODEL OF CURRENT ITERATION\" + NORMAL_TEXT)\n",
     "    print_model(candidate_model)"
    ]
   },
@@ -377,7 +376,7 @@
     "\n",
     "for candidate_model in iteration_results[MODELS].values():\n",
     "    if candidate_model.get_hash() == local_best_model.get_hash():\n",
-    "        print(BOLD_TEXT + 'BEST MODEL OF CURRENT ITERATION' + NORMAL_TEXT)\n",
+    "        print(BOLD_TEXT + \"BEST MODEL OF CURRENT ITERATION\" + NORMAL_TEXT)\n",
     "    print_model(candidate_model)"
    ]
   },
@@ -420,7 +419,7 @@
     "\n",
     "for candidate_model in iteration_results[MODELS].values():\n",
     "    if candidate_model.get_hash() == local_best_model.get_hash():\n",
-    "        print(BOLD_TEXT + 'BEST MODEL OF CURRENT ITERATION' + NORMAL_TEXT)\n",
+    "        print(BOLD_TEXT + \"BEST MODEL OF CURRENT ITERATION\" + NORMAL_TEXT)\n",
     "    print_model(candidate_model)"
    ]
   },
@@ -467,7 +466,7 @@
     }
    ],
    "source": [
-    "print(f'Number of candidate models: {len(iteration_results[MODELS])}.')"
+    "print(f\"Number of candidate models: {len(iteration_results[MODELS])}.\")"
    ]
   },
   {

diff --git a/petab_select/__init__.py b/petab_select/__init__.py
@@ -15,5 +15,5 @@
 __all__ = [
     x
     for x in dir(sys.modules[__name__])
-    if not x.startswith('_') and x != 'sys'
+    if not x.startswith("_") and x != "sys"
 ]