Add ruff rules for notebook.

pyproject.toml

@@ -0,0 +1,142 @@
+[tool.versioningit.vcs]
+method = "git"
+default-tag = "0.0.1"
+
+[tool.cibuildwheel.linux]
+archs = ["auto64"]
+skip = ["*musllinux*"]
+before-all = "ln -s /usr/lib64/libgfortran.so.5 /usr/lib64/libgfortran.so.3"
+
+[tool.cibuildwheel.macos]
+repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} --ignore-missing-dependencies"
+
+[tool.ruff]
+target-version = "py39"
+line-length = 120
+extend-include = ["*.ipynb"]
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+  # Rule families
+  "ANN",  # flake8-annotations (not ready, require types for ALL args)
+  "ARG",  # Check for unused function arguments
+  "BLE",  # General catch of Exception
+  "C90",  # Check for functions with a high McCabe complexity
+  "COM",  # flake8-commas (conflict with line wrapper)
+  "CPY",  # Missing copyright notice at top of file (need preview mode)
+  "EM",   # Format nice error messages
+  "ERA",  # Check for commented-out code
+  "FIX",  # Check for FIXME, TODO and other developer notes
+  "FURB", # refurb (need preview mode, too many preview errors)
+  "G",    # validate logging format strings
+  "INP",  # Ban PEP-420 implicit namespace packages
+  "N",    # pep8-naming (many var/arg names are intended)
+  "NPY",  # NumPy-specific rules (TODO: enable this)
+  "PTH",  # Prefer pathlib over os.path
+  "S",    # flake8-bandit (TODO: enable this)
+  "SLF",  # Access "private" class members
+  "T20",  # Check for print/pprint
+  "TD",   # TODO tags related
+
+  # Single rules
+  "B023",    # Function definition does not bind loop variable
+  "B028",    # No explicit stacklevel keyword argument found
+  "B904",    # Within an except clause, raise exceptions with ...
+  "C408",    # unnecessary-collection-call
+  "D105",    # Missing docstring in magic method
+  "D205",    # 1 blank line required between summary line and description
+  "D212",    # Multi-line docstring summary should start at the first line
+  "DTZ003",  # TODO: fix this (issue #3791)
+  "FBT001",  # Boolean-typed positional argument in function definition
+  "FBT002",  # Boolean default positional argument in function
+  "PD901",   # pandas-df-variable-name
+  "PERF203", # try-except-in-loop
+  "PERF401", # manual-list-comprehension
+  "PLR0911", # too many return statements
+  "PLR0912", # too many branches
+  "PLR0913", # too many arguments
+  "PLR0915", # too many statements
+  "PLR2004", # magic values in comparison
+  "PLW2901", # Outer for loop variable overwritten by inner assignment target
+  "PT013",   # pytest-incorrect-pytest-import
+  "SIM105",  # Use contextlib.suppress() instead of try-except-pass
+  "TRY003",  # Avoid specifying long messages outside the exception class
+  "TRY300",  # Checks for return statements in try blocks
+  "TRY301",  # Checks for raise statements within try blocks
+]
+pydocstyle.convention = "google"
+isort.required-imports = ["from __future__ import annotations"]
+isort.split-on-trailing-comma = false
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]
+"tests/**" = ["ANN201", "D", "PLR0124"]
+"src/pymatgen/analysis/*" = ["D"]
+"src/pymatgen/io/*" = ["D"]
+"dev_scripts/*" = ["D"]
+
+[tool.pytest.ini_options]
+addopts = "--durations=30 --quiet -r xXs --color=yes -p no:warnings --import-mode=importlib"
+
+[tool.coverage.run]
+parallel = true
+omit = [
+    "pymatgen/cli/feff_plot_cross_section.py",
+    "pymatgen/cli/feff_plot_dos.py",
+    "pymatgen/cli/pmg_config.py",
+    "pymatgen/cli/pmg_plot.py",
+    "pymatgen/cli/pmg_potcar.py",
+    "pymatgen/cli/pmg_query.py",
+    "pymatgen/dao.py",
+]
+
+[tool.coverage.report]
+exclude_also = [
+    "@deprecated",
+    "@np.deprecate",
+    "def __repr__",
+    "except ImportError:",
+    "if 0:",
+    "if TYPE_CHECKING:",
+    "if __name__ == .__main__.:",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "if typing.TYPE_CHECKING:",
+    "pragma: no cover",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "show_plot",
+]
+
+[tool.mypy]
+ignore_missing_imports = true
+namespace_packages = true
+explicit_package_bases = true
+no_implicit_optional = false
+disable_error_code = "annotation-unchecked"
+
+[[tool.mypy.overrides]]
+module = ["requests.*", "tabulate.*"]
+ignore_missing_imports = true
+
+[tool.codespell]
+ignore-words-list = """
+titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo,nax,coo,
+coul,ser,leary,thre,fase,rute,reson,titels,ges,scalr,strat,
+struc,hda,nin,ons,pres,kno,loos,lamda,lew,atomate,nempty
+"""
+skip = "pymatgen/analysis/aflow_prototypes.json"
+check-filenames = true
+
+[tool.pyright]
+typeCheckingMode = "off"
+reportPossiblyUnboundVariable = true
+reportUnboundVariable = true
+reportMissingImports = false
+reportMissingModuleSource = false
+reportInvalidTypeForm = false
+exclude = ["**/tests"]