🧰 Use pyproject-fmt

.pre-commit-config.yaml

@@ -18,6 +18,11 @@ repos:
       - id: fix-encoding-pragma
         args: [--remove]
 
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "1.3.0"
+    hooks:
+      - id: pyproject-fmt
+
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.15.0
     hooks:

pyproject.toml

@@ -7,116 +7,111 @@ requires = [
 [project]
 name = "pyglotaran"
 description = "The Glotaran fitting engine."
+readme = "README.md"
+license = { text = "LGPL-3.0" }
 authors = [
   { name = "Joern Weissenborn", email = "joern.weissenborn@gmail.com" },
   { name = "Joris Snellenburg", email = "j.snellenburg@gmail.com" },
   { name = "Ivo van Stokkum", email = "i.h.m.van.stokkum@vu.nl" },
 ]
-license = { text = "LGPL-3.0" }
+requires-python = ">=3.10, <3.12"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Education",
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
   "Natural Language :: English",
   "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
   "Topic :: Scientific/Engineering",
   "Topic :: Scientific/Engineering :: Chemistry",
   "Topic :: Scientific/Engineering :: Physics",
 ]
-requires-python = ">=3.10, <3.12"
+dynamic = [
+  "version",
+]
 dependencies = [
   "asteval!=0.9.28,>=0.9.22",
   "netCDF4>=1.5.7",
-  "numba>=0.55.0",
-  "numpy>=1.21.2,<1.25",
+  "numba>=0.55",
+  "numpy<1.25,>=1.21.2",
   "odfpy>=1.4.1",
   "openpyxl>=3.0.10",
   "pandas>=1.3.4",
-  "pydantic>=2.0",
+  "pydantic>=2",
   "ruamel.yaml>=0.17.17",
   "scipy>=1.7.2",
   "sdtfile>=2020.8.3",
   "tabulate>=0.8.9",
-  "xarray>=2022.3.0",
+  "xarray>=2022.3",
+]
+[project.optional-dependencies]
+dev = [
+  "pyglotaran[docs,test]",
+]
+docs = [
+  # documentation dependencies
+  "IPython>=7.2",
+  "Jinja2<3.1.0",
+  "jupyterlab>=3",
+  "matplotlib>=3",
+  "myst-parser>=0.12",
+  "nbsphinx>=0.8.1", # notebook docs
+  "nbval>=0.9.6",
+  "numpydoc>=0.8",
+  "Sphinx>=3.2",
+  "sphinx-click>=3.0.1",
+  "sphinx-copybutton>=0.3",
+  "sphinx-last-updated-by-git>=0.3",
+  "sphinx-rtd-theme>=1.2",
+  "sphinxcontrib-jquery>=4.1", # Needed for the search to work Ref.: https://github.com/readthedocs/sphinx_rtd_theme/issues/1434
+]
+extras = [
+  "pyglotaran-extras>=0.5",
+]
+full = [
+  "pyglotaran[extras]",
+]
+test = [
+  "coverage[toml]",
+  "pluggy>=0.7",
+  "pytest>=3.7.1",
+  "pytest-allclose>=1",
+  "pytest-benchmark>=3.1.1",
+  "pytest-cov>=2.5.1",
+  "pytest-env>=0.6.2",
+  "pytest-runner>=2.11.1",
+  "types-dataclasses>=0.1.7",
 ]
-dynamic = ["version"]
-
-[project.readme]
-file = "README.md"
-content-type = "text/markdown"
-
 [project.urls]
-Homepage = "https://github.com/glotaran/pyglotaran"
-"Glotaran Ecosystem" = "https://glotaran.org"
-Documentation = "https://pyglotaran.readthedocs.io"
 Changelog = "https://pyglotaran.readthedocs.io/en/latest/changelog.html"
+Documentation = "https://pyglotaran.readthedocs.io"
+"Glotaran Ecosystem" = "https://glotaran.org"
+Homepage = "https://github.com/glotaran/pyglotaran"
 Source = "https://github.com/glotaran/pyglotaran"
 Tracker = "https://github.com/glotaran/pyglotaran/issues"
-
+[project.scripts]
+glotaran = "glotaran.cli.main:main"
 [project.entry-points."glotaran.plugins.data_io"]
 ascii = "glotaran.builtin.io.ascii.wavelength_time_explicit_file"
-sdt = "glotaran.builtin.io.sdt.sdt_file_reader"
 nc = "glotaran.builtin.io.netCDF.netCDF"
+sdt = "glotaran.builtin.io.sdt.sdt_file_reader"
 yml = "glotaran.builtin.io.yml.yml"
-
 [project.entry-points."glotaran.plugins.elements"]
 baseline = "glotaran.builtin.elements.baseline"
 clp_guide = "glotaran.builtin.elements.clp_guide"
 coherent_artifact = "glotaran.builtin.elements.coherent_artifact"
 damped_oscillation = "glotaran.builtin.elements.damped_oscillation"
 kinetic = "glotaran.builtin.elements.kinetic"
 spectral = "glotaran.builtin.elements.spectral"
-
 [project.entry-points."glotaran.plugins.project_io"]
 csv = "glotaran.builtin.io.pandas.csv"
 tsv = "glotaran.builtin.io.pandas.tsv"
 xlsx = "glotaran.builtin.io.pandas.xlsx"
 xsx = "glotaran.builtin.io.pandas.xlsx"
 
-[project.optional-dependencies]
-docs = [
-  # documentation dependencies
-  "Sphinx>=3.2.0",
-  "sphinx-click>=3.0.1",
-  "sphinx-rtd-theme>=1.2.0",
-  # Needed for the search to work
-  # Ref.: https://github.com/readthedocs/sphinx_rtd_theme/issues/1434
-  "sphinxcontrib-jquery>=4.1",
-  "sphinx-copybutton>=0.3.0",
-  "myst-parser>=0.12.0",
-  "numpydoc>=0.8.0",
-  # notebook docs
-  "nbsphinx>=0.8.1",
-  "sphinx-last-updated-by-git>=0.3.0",
-  "jupyterlab>=3.0.0",
-  "matplotlib>=3.0.0",
-  "IPython>=7.2.0",
-  "nbval>=0.9.6",
-  "Jinja2<3.1.0",
-]
-test = [
-  "pytest>=3.7.1",
-  "pluggy>=0.7",
-  "coverage[toml]",
-  "pytest-cov>=2.5.1",
-  "pytest-env>=0.6.2",
-  "pytest-runner>=2.11.1",
-  "pytest-benchmark>=3.1.1",
-  "pytest-allclose>=1.0.0",
-  "types-dataclasses>=0.1.7",
-]
-dev = [
-  "pyglotaran[docs,test]",
-]
-extras = ["pyglotaran-extras>=0.5.0"]
-full = ["pyglotaran[extras]"]
-
-[project.scripts]
-glotaran = "glotaran.cli.main:main"
-
 [tool.hatch.version]
 path = "glotaran/__init__.py"
 
@@ -129,7 +124,6 @@ only-include = ["glotaran"]
 [tool.hatch.envs.default]
 features = ["dev"]
 
-
 [tool.black]
 line-length = 99
 target-version = ['py38']
@@ -148,7 +142,6 @@ exclude = '''
 )/
 '''
 
-
 [tool.ruff]
 
 select = [
@@ -245,7 +238,6 @@ unfixable = ["F401"]
 # Needs a full rewrite anyway
 "glotaran/builtin/io/ascii/wavelength_time_explicit_file.py" = ["PTH"]
 
-
 [tool.isort]
 profile = "hug"
 src_paths = ["glotaran"]
@@ -255,14 +247,21 @@ known_first_party = ["glotaran", "tests"]
 force_single_line = true
 remove_redundant_aliases = true
 
-[tool.interrogate]
-exclude = ["setup.py", "docs", "tests", "benchmark/*"]
-ignore-init-module = true
-fail-under = 63
-
-[tool.nbqa.addopts]
-flake8 = ["--extend-ignore=E402,F404"]
-
+[tool.pytest.ini_options]
+# env = [
+#   "DEACTIVATE_GTA_PLUGINS=1",
+#   # Uncomment the following lines to deactivate pyglotaran all plugins
+#   # Uncomment "env =" and "COMPARE_RESULTS_LOCAL" and set it to a local folder
+#   # with results to use as a reference in lieu of the comparison-results branch
+#   # in the pyglotaran-examples git repository
+#   "COMPARE_RESULTS_LOCAL=~/local_results/", # On *nix
+#   "COMPARE_RESULTS_LOCAL=%USERPROFILE%/local_results/", # On Windows
+# ]
+# Uncomment to ignore deprecation warnings coming from pyglotaran
+# (this helps to see the warnings from dependencies)
+# filterwarnings = [
+#   "ignore:.+glotaran:GlotaranApiDeprecationWarning",
+# ]
 
 [tool.coverage.run]
 branch = true
@@ -293,23 +292,6 @@ exclude_lines = [
   'if TYPE_CHECKING:',
 ]
 
-[tool.pytest.ini_options]
-# env = [
-#   "DEACTIVATE_GTA_PLUGINS=1",
-#   # Uncomment the following lines to deactivate pyglotaran all plugins
-#   # Uncomment "env =" and "COMPARE_RESULTS_LOCAL" and set it to a local folder
-#   # with results to use as a reference in lieu of the comparison-results branch
-#   # in the pyglotaran-examples git repository
-#   "COMPARE_RESULTS_LOCAL=~/local_results/", # On *nix
-#   "COMPARE_RESULTS_LOCAL=%USERPROFILE%/local_results/", # On Windows
-# ]
-# Uncomment to ignore deprecation warnings coming from pyglotaran
-# (this helps to see the warnings from dependencies)
-# filterwarnings = [
-#   "ignore:.+glotaran:GlotaranApiDeprecationWarning",
-# ]
-
-
 [tool.mypy]
 plugins = "pydantic.mypy"
 ignore_missing_imports = true
@@ -335,3 +317,11 @@ ignore_errors = true
 [[tool.mypy.overrides]]
 module = "benchmark.*"
 ignore_errors = true
+
+[tool.interrogate]
+exclude = ["setup.py", "docs", "tests", "benchmark/*"]
+ignore-init-module = true
+fail-under = 63
+
+[tool.nbqa.addopts]
+flake8 = ["--extend-ignore=E402,F404"]