[pre-commit.ci] pre-commit autoupdate (#1155)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black.git: 23.12.1 → 24.1.1](https://github.com/psf/black.git/compare/23.12.1...24.1.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/psf/black.git: 23.9.1 → 23.11.0](https://github.com/psf/black.git/compare/23.9.1...23.11.0)
- [github.com/pre-commit/mirrors-mypy: v1.5.1 → v1.7.0](pre-commit/mirrors-mypy@v1.5.1...v1.7.0)
- [github.com/PyCQA/pylint: v3.0.0a7 → v3.0.1](pylint-dev/pylint@v3.0.0a7...v3.0.1)
- [github.com/pre-commit/mirrors-prettier: v3.0.3 → v3.1.0](pre-commit/mirrors-prettier@v3.0.3...v3.1.0)
- [github.com/asottile/pyupgrade: v3.13.0 → v3.15.0](asottile/pyupgrade@v3.13.0...v3.15.0)

* build: ⬆️ Update `black` and `pytest`

* docs: ♻️ Refactor model parameter assignment in `models.py`

* ci: 🚧 Add pre-commit setup and caching

* fix: 📝 Fix model parameter assignment

* build: ⬆️ Update dtale version to 3.9.0

* fix: 💚 Update pre-commit-config.yaml and models.md

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Anselm Hahn <[email protected]>

.github/workflows/python-ci.yml

@@ -15,8 +15,21 @@ jobs:
         uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v5
+      - name: Install pre-commit
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit
+          pip freeze --local
+      - name: Cash pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-pre-commit-${{ hashFiles('**/.pre-commit-config.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-pre-commit-
       - name: Pre-commit
-        uses: pre-commit/[email protected]
+        run: |
+          pre-commit run --all-files --color=always
   build:
     name: Python ${{ matrix.python-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     needs: pre-commit

.pre-commit-config.yaml

@@ -19,14 +19,14 @@ repos:
         args: ["--maxkb=1000"]
         exclude: \.ipynb
   - repo: https://github.com/psf/black.git
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
       - id: black
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.16.0
     hooks:
       - id: blacken-docs
-        additional_dependencies: [black>=23.12.1]
+        additional_dependencies: [black>=24.1.1]
   - repo: https://github.com/PyCQA/isort.git
     rev: 5.13.2
     hooks:

docs/doc/models.md

@@ -26,9 +26,9 @@
         model = model.lower()
         if model.split("_")[0] not in __implemented_models__:
             raise KeyError(f"{model} is not supported")
-        peak_kwargs[(model.split("_")[-1], model.split("_")[0])][
-            model.split("_")[1]
-        ] = params[model]
+        peak_kwargs[(model.split("_")[-1], model.split("_")[0])][model.split("_")[1]] = (
+            params[model]
+        )
 
     for key, _kwarg in peak_kwargs.items():
         if key[1] == "my_new_model":

pyproject.toml

@@ -68,7 +68,7 @@ jupyterlab = { version = ">=3.5.2,<5.0.0", optional = true }
 plotly = { version = "^5.14.0", optional = true }
 itables = { version = "^1.3.4", optional = true }
 kaleido = { version = "0.2.1", optional = true }
-dtale = { version = "^2.8.1", optional = true }
+dtale = { version = "^3.9.0", optional = true }
 networkx = { extras = [
   "all",
 ], version = "^3.0", optional = true }
@@ -82,7 +82,7 @@ python-pptx = { version = "^0.6.22", optional = true }
 [tool.poetry.group.dev.dependencies]
 pylint = "^2.16.1"
 mypy = "^1.1.1"
-black = { extras = ["jupyter"], version = ">=22.8,<24.0" }
+black = { extras = ["jupyter"], version = "^24.0" }
 blacken-docs = "^1.12.1"
 isort = "^5.10.1"
 pre-commit = "^3.2.0"

spectrafit/__init__.py

@@ -5,5 +5,4 @@
     SpectraFit uses [Semantic Versioning](https://semver.org/).
 """
 
-
 __version__ = "1.0.0"

spectrafit/api/cmd_model.py

@@ -1,6 +1,5 @@
 """Reference model for the API of the command line interface."""
 
-
 from datetime import datetime
 from getpass import getuser
 from hashlib import sha256

spectrafit/api/models_model.py

@@ -1,6 +1,5 @@
 """Reference model for the API of the models distributions."""
 
-
 from typing import Callable
 from typing import List
 from typing import Optional

spectrafit/api/notebook_model.py

@@ -1,6 +1,5 @@
 """Reference model for the API of the Jupyter Notebook interface."""
 
-
 from typing import List
 from typing import Optional
 from typing import Tuple

spectrafit/api/pptx_model.py

@@ -1,4 +1,5 @@
 """PPTXModel class for SpectraFit API."""
+
 import re
 import tempfile
 

spectrafit/api/report_model.py

@@ -1,4 +1,5 @@
 """Reference model for the API of the Jupyter Notebook report."""
+
 from typing import Any
 from typing import Dict
 from typing import Hashable

spectrafit/api/rixs_model.py

@@ -1,6 +1,5 @@
 """Reference model for the API of the Jupyter Notebook interface."""
 
-
 from typing import Any
 from typing import Optional
 from typing import Tuple

spectrafit/api/test/test_cmd_model.py

@@ -1,6 +1,5 @@
 """Test of CMD and Tool Model."""
 
-
 from getpass import getuser
 from hashlib import sha256
 from socket import gethostname

spectrafit/api/test/test_file_model.py

@@ -1,4 +1,5 @@
 """Test the file model."""
+
 import pytest
 
 from spectrafit.api.file_model import DataFileAPI

spectrafit/api/test/test_pptx_model.py

@@ -1,4 +1,5 @@
 """Test the pptx_model module."""
+
 from math import isclose
 from typing import Tuple
 from typing import Type

spectrafit/api/tools_model.py

@@ -1,6 +1,5 @@
 """Reference model for the API of the SpectraFit tools."""
 
-
 from typing import Any
 from typing import Dict
 from typing import List

spectrafit/app/app.py

@@ -1,6 +1,5 @@
 """Starting jupyter lab as a app."""
 
-
 import sys
 
 from jupyterlab.labapp import main

spectrafit/app/test/test_app.py

@@ -1,4 +1,5 @@
 """Test of the Jupiter plugin app."""
+
 from unittest import mock
 
 

spectrafit/models.py

@@ -1,4 +1,5 @@
 """Minimization models for curve fitting."""
+
 from collections import defaultdict
 from dataclasses import dataclass
 from math import log
@@ -563,10 +564,7 @@ def polynom3(
             NDArray[np.float64]: Third order polynomial function of `x`
         """
         return np.array(
-            coefficient0
-            + coefficient1 * x
-            + coefficient2 * x**2
-            + coefficient3 * x**3
+            coefficient0 + coefficient1 * x + coefficient2 * x**2 + coefficient3 * x**3
         )
 
     @staticmethod

spectrafit/plotting.py

@@ -7,6 +7,7 @@
     this, you can comment out the line `matplotlib.font_manager._rebuild()` in
     the `plotting.py` file.
 """
+
 from typing import Any
 from typing import Dict
 from typing import Optional

spectrafit/plugins/color_schemas.py

@@ -1,4 +1,5 @@
 """Color themes for the Plots in Jupyter Notebooks."""
+
 from typing import List
 
 from spectrafit.api.notebook_model import ColorAPI

spectrafit/plugins/converter.py

@@ -1,4 +1,5 @@
 """Abstract base class for the converter plugins."""
+
 from abc import ABC
 from abc import abstractmethod
 from pathlib import Path

spectrafit/plugins/file_converter.py

@@ -1,4 +1,5 @@
 """Convert the input and output files to the preferred file format."""
+
 import argparse
 import json
 

spectrafit/plugins/pptx_converter.py

@@ -1,4 +1,5 @@
 """Convert the lock file to a powerpoint presentation."""
+
 import argparse
 
 from pathlib import Path

spectrafit/plugins/test/test_rixs_visualizer.py

@@ -1,6 +1,5 @@
 """Test of the RIXS Visualizer."""
 
-
 from pathlib import Path
 from typing import Any
 from typing import Tuple

spectrafit/report.py

@@ -1,4 +1,5 @@
 """Fit-Results as Report."""
+
 import pprint
 import sys
 

spectrafit/spectrafit.py

@@ -1,4 +1,5 @@
 """SpectraFit, the command line tool for fitting."""
+
 import argparse
 
 from typing import Any

spectrafit/test/test_plot.py

@@ -1,4 +1,5 @@
 """Pytest of the plotting features of spectrafit."""
+
 import pandas as pd
 
 from matplotlib import pyplot

spectrafit/test/test_report.py

@@ -1,4 +1,5 @@
 """Pytest of report model."""
+
 from math import isclose
 from typing import Any
 from typing import Dict

spectrafit/test/test_tools.py

@@ -1,4 +1,5 @@
 """Pytest of tools model."""
+
 import gzip
 import pickle
 

spectrafit/tools.py

@@ -253,9 +253,11 @@ def rename_columns(self, df: pd.DataFrame) -> pd.DataFrame:
         if self.args["global_"]:
             return df.rename(
                 columns={
-                    col: ColumnNamesAPI().energy
-                    if i == 0
-                    else f"{ColumnNamesAPI().intensity}_{i}"
+                    col: (
+                        ColumnNamesAPI().energy
+                        if i == 0
+                        else f"{ColumnNamesAPI().intensity}_{i}"
+                    )
                     for i, col in enumerate(df.columns)
                 }
             )

spectrafit/utilities/test/test_transformer.py

@@ -1,4 +1,5 @@
 """Test of the jupyter plugin."""
+
 from typing import Any
 from typing import Dict
 from typing import List

spectrafit/utilities/transformer.py

@@ -1,4 +1,5 @@
 """Transformer functions for the SpectraFit."""
+
 from typing import Any
 from typing import Dict
 from typing import List

tools/spectra_generator.py

@@ -1,4 +1,5 @@
 """Tools for generating spectra for testing."""
+
 import math
 
 from pathlib import Path