From 27e0b5dabb8dd252243b909687fe69552f043c00 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 31 Jan 2024 19:56:04 +0000 Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#1155) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [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](https://github.com/pre-commit/pre-commit-hooks/compare/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](https://github.com/pre-commit/mirrors-mypy/compare/v1.5.1...v1.7.0) - [github.com/PyCQA/pylint: v3.0.0a7 → v3.0.1](https://github.com/PyCQA/pylint/compare/v3.0.0a7...v3.0.1) - [github.com/pre-commit/mirrors-prettier: v3.0.3 → v3.1.0](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.3...v3.1.0) - [github.com/asottile/pyupgrade: v3.13.0 → v3.15.0](https://github.com/asottile/pyupgrade/compare/v3.13.0...v3.15.0) * build: :arrow_up: Update `black` and `pytest` * docs: :recycle: Refactor model parameter assignment in `models.py` * ci: :construction: Add pre-commit setup and caching * fix: :memo: Fix model parameter assignment * build: :arrow_up: Update dtale version to 3.9.0 * fix: :green_heart: 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 --- .github/workflows/python-ci.yml | 15 +- .pre-commit-config.yaml | 4 +- docs/doc/models.md | 6 +- poetry.lock | 892 ++++++++++-------- pyproject.toml | 4 +- spectrafit/__init__.py | 1 - spectrafit/api/cmd_model.py | 1 - spectrafit/api/models_model.py | 1 - spectrafit/api/notebook_model.py | 1 - spectrafit/api/pptx_model.py | 1 + spectrafit/api/report_model.py | 1 + spectrafit/api/rixs_model.py | 1 - spectrafit/api/test/test_cmd_model.py | 1 - spectrafit/api/test/test_file_model.py | 1 + spectrafit/api/test/test_pptx_model.py | 1 + spectrafit/api/tools_model.py | 1 - spectrafit/app/app.py | 1 - spectrafit/app/test/test_app.py | 1 + spectrafit/models.py | 6 +- spectrafit/plotting.py | 1 + spectrafit/plugins/color_schemas.py | 1 + spectrafit/plugins/converter.py | 1 + spectrafit/plugins/file_converter.py | 1 + spectrafit/plugins/pptx_converter.py | 1 + .../plugins/test/test_rixs_visualizer.py | 1 - spectrafit/report.py | 1 + spectrafit/spectrafit.py | 1 + spectrafit/test/test_plot.py | 1 + spectrafit/test/test_report.py | 1 + spectrafit/test/test_tools.py | 1 + spectrafit/tools.py | 8 +- spectrafit/utilities/test/test_transformer.py | 1 + spectrafit/utilities/transformer.py | 1 + tools/spectra_generator.py | 1 + vendor/docker-stacks | 2 +- vendor/lmfit-py | 2 +- 36 files changed, 531 insertions(+), 435 deletions(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 8382858be..1fd4946b6 100644 --- a/.github/workflows/python-ci.yml +++ b/.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/action@v3.0.0 + run: | + pre-commit run --all-files --color=always build: name: Python ${{ matrix.python-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} needs: pre-commit diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 78d877bef..d87404f41 100644 --- a/.pre-commit-config.yaml +++ b/.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: diff --git a/docs/doc/models.md b/docs/doc/models.md index af1c1f24c..e6f04c867 100644 --- a/docs/doc/models.md +++ b/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])][ - 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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" diff --git a/spectrafit/__init__.py b/spectrafit/__init__.py index ccf424bae..e43089f90 100644 --- a/spectrafit/__init__.py +++ b/spectrafit/__init__.py @@ -5,5 +5,4 @@ SpectraFit uses [Semantic Versioning](https://semver.org/). """ - __version__ = "1.0.0" diff --git a/spectrafit/api/cmd_model.py b/spectrafit/api/cmd_model.py index 3e45d3a3e..13bf74c79 100644 --- a/spectrafit/api/cmd_model.py +++ b/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 diff --git a/spectrafit/api/models_model.py b/spectrafit/api/models_model.py index f1d30913c..5edcc9044 100644 --- a/spectrafit/api/models_model.py +++ b/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 diff --git a/spectrafit/api/notebook_model.py b/spectrafit/api/notebook_model.py index 2f0235c22..414aadfb7 100644 --- a/spectrafit/api/notebook_model.py +++ b/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 diff --git a/spectrafit/api/pptx_model.py b/spectrafit/api/pptx_model.py index 88471acd8..bf93dea4c 100644 --- a/spectrafit/api/pptx_model.py +++ b/spectrafit/api/pptx_model.py @@ -1,4 +1,5 @@ """PPTXModel class for SpectraFit API.""" + import re import tempfile diff --git a/spectrafit/api/report_model.py b/spectrafit/api/report_model.py index 4f78062f7..3c5c781a8 100644 --- a/spectrafit/api/report_model.py +++ b/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 diff --git a/spectrafit/api/rixs_model.py b/spectrafit/api/rixs_model.py index e1f54856d..37e916cf0 100644 --- a/spectrafit/api/rixs_model.py +++ b/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 diff --git a/spectrafit/api/test/test_cmd_model.py b/spectrafit/api/test/test_cmd_model.py index 59779eaa7..76b9d96a4 100644 --- a/spectrafit/api/test/test_cmd_model.py +++ b/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 diff --git a/spectrafit/api/test/test_file_model.py b/spectrafit/api/test/test_file_model.py index 15a857309..5b1f71d2a 100644 --- a/spectrafit/api/test/test_file_model.py +++ b/spectrafit/api/test/test_file_model.py @@ -1,4 +1,5 @@ """Test the file model.""" + import pytest from spectrafit.api.file_model import DataFileAPI diff --git a/spectrafit/api/test/test_pptx_model.py b/spectrafit/api/test/test_pptx_model.py index db7f1c827..bc13fa771 100644 --- a/spectrafit/api/test/test_pptx_model.py +++ b/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 diff --git a/spectrafit/api/tools_model.py b/spectrafit/api/tools_model.py index 8181d9fb9..7b055d7dd 100644 --- a/spectrafit/api/tools_model.py +++ b/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 diff --git a/spectrafit/app/app.py b/spectrafit/app/app.py index 5f432462a..12c0a79f6 100644 --- a/spectrafit/app/app.py +++ b/spectrafit/app/app.py @@ -1,6 +1,5 @@ """Starting jupyter lab as a app.""" - import sys from jupyterlab.labapp import main diff --git a/spectrafit/app/test/test_app.py b/spectrafit/app/test/test_app.py index e1744ca91..b13c49da2 100644 --- a/spectrafit/app/test/test_app.py +++ b/spectrafit/app/test/test_app.py @@ -1,4 +1,5 @@ """Test of the Jupiter plugin app.""" + from unittest import mock diff --git a/spectrafit/models.py b/spectrafit/models.py index 75900bc4e..c27cacf6a 100644 --- a/spectrafit/models.py +++ b/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 diff --git a/spectrafit/plotting.py b/spectrafit/plotting.py index 51a985e0d..33b71b083 100644 --- a/spectrafit/plotting.py +++ b/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 diff --git a/spectrafit/plugins/color_schemas.py b/spectrafit/plugins/color_schemas.py index b48ecd210..0eee7c2ce 100644 --- a/spectrafit/plugins/color_schemas.py +++ b/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 diff --git a/spectrafit/plugins/converter.py b/spectrafit/plugins/converter.py index 12cc78d87..dafb8c856 100644 --- a/spectrafit/plugins/converter.py +++ b/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 diff --git a/spectrafit/plugins/file_converter.py b/spectrafit/plugins/file_converter.py index e3b0560cb..632308d67 100644 --- a/spectrafit/plugins/file_converter.py +++ b/spectrafit/plugins/file_converter.py @@ -1,4 +1,5 @@ """Convert the input and output files to the preferred file format.""" + import argparse import json diff --git a/spectrafit/plugins/pptx_converter.py b/spectrafit/plugins/pptx_converter.py index 45df7113a..d2b067045 100644 --- a/spectrafit/plugins/pptx_converter.py +++ b/spectrafit/plugins/pptx_converter.py @@ -1,4 +1,5 @@ """Convert the lock file to a powerpoint presentation.""" + import argparse from pathlib import Path diff --git a/spectrafit/plugins/test/test_rixs_visualizer.py b/spectrafit/plugins/test/test_rixs_visualizer.py index c00cdad10..2ee2b3234 100644 --- a/spectrafit/plugins/test/test_rixs_visualizer.py +++ b/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 diff --git a/spectrafit/report.py b/spectrafit/report.py index c75fae83a..65c7b9375 100644 --- a/spectrafit/report.py +++ b/spectrafit/report.py @@ -1,4 +1,5 @@ """Fit-Results as Report.""" + import pprint import sys diff --git a/spectrafit/spectrafit.py b/spectrafit/spectrafit.py index 9cad8da91..952c9ff5b 100644 --- a/spectrafit/spectrafit.py +++ b/spectrafit/spectrafit.py @@ -1,4 +1,5 @@ """SpectraFit, the command line tool for fitting.""" + import argparse from typing import Any diff --git a/spectrafit/test/test_plot.py b/spectrafit/test/test_plot.py index 608c3bfd1..3e5586a4f 100644 --- a/spectrafit/test/test_plot.py +++ b/spectrafit/test/test_plot.py @@ -1,4 +1,5 @@ """Pytest of the plotting features of spectrafit.""" + import pandas as pd from matplotlib import pyplot diff --git a/spectrafit/test/test_report.py b/spectrafit/test/test_report.py index 6e4cfb866..f96f176b4 100644 --- a/spectrafit/test/test_report.py +++ b/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 diff --git a/spectrafit/test/test_tools.py b/spectrafit/test/test_tools.py index a369a134f..90797312b 100644 --- a/spectrafit/test/test_tools.py +++ b/spectrafit/test/test_tools.py @@ -1,4 +1,5 @@ """Pytest of tools model.""" + import gzip import pickle diff --git a/spectrafit/tools.py b/spectrafit/tools.py index 451b934e5..1f2ce59a9 100644 --- a/spectrafit/tools.py +++ b/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) } ) diff --git a/spectrafit/utilities/test/test_transformer.py b/spectrafit/utilities/test/test_transformer.py index 22e037145..2e194f2ea 100644 --- a/spectrafit/utilities/test/test_transformer.py +++ b/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 diff --git a/spectrafit/utilities/transformer.py b/spectrafit/utilities/transformer.py index 8eb47376a..99e6dbfa1 100644 --- a/spectrafit/utilities/transformer.py +++ b/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 diff --git a/tools/spectra_generator.py b/tools/spectra_generator.py index ed8897867..cce69b470 100644 --- a/tools/spectra_generator.py +++ b/tools/spectra_generator.py @@ -1,4 +1,5 @@ """Tools for generating spectra for testing.""" + import math from pathlib import Path diff --git a/vendor/docker-stacks b/vendor/docker-stacks index 7a5990be1..bfe5f2091 160000 --- a/vendor/docker-stacks +++ b/vendor/docker-stacks @@ -1 +1 @@ -Subproject commit 7a5990be1f90766de2d59194bdec73327b0885c0 +Subproject commit bfe5f20914d0b049c10f65392ac7c9371f3406be diff --git a/vendor/lmfit-py b/vendor/lmfit-py index 6096c3a36..8b2038a16 160000 --- a/vendor/lmfit-py +++ b/vendor/lmfit-py @@ -1 +1 @@ -Subproject commit 6096c3a360ce12cca7301673c8ed8fc738eb792b +Subproject commit 8b2038a16cf3ce87c25c35d224093ce3e8dc2af3