build(deps): first major release (#323)

- Numpy was upgraded to allow v2.0.0. - Do formatting and linting with ruff, rather than black, isort, flak8, etc. - Make mypy and docstring linting pass.
engeir · Jun 17, 2024 · 42eca94 · 42eca94
1 parent 9d9298e
commit 42eca94
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diff --git a/.mise.toml b/.mise.toml
@@ -1,2 +1,2 @@
-[tools]
-python = {version = "3.12", virtualenv = ".venv"}
+[env.'_'.python]
+venv = ".venv"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,56 +8,48 @@ repos:
         stages: [commit]
         entry: check-added-large-files
         language: system
-      - id: isort
-        name: isort
+      - id: ruff_fmt
+        name: Ruff format
         stages: [commit]
         language: system
-        entry: poetry run isort src
+        entry: ruff format
         types: [python]
-
-      - id: black
-        name: black
+      - id: ruff_check
+        name: Ruff check
         stages: [commit]
         language: system
-        entry: poetry run black src
+        entry: ruff check --fix
         types: [python]
-
-      - id: flake8
-        name: flake8
+      - id: xdoctest
+        name: xdoctest
         stages: [commit]
         language: system
-        entry: poetry run flake8 src
+        entry: poetry run xdoctest
         types: [python]
-        exclude: setup.py
-
       - id: mypy
         name: mypy
         stages: [commit]
         language: system
         entry: poetry run mypy
         types: [python]
         require_serial: true
-
-      - id: darglint
-        name: darglint
+      - id: pydoclint
+        name: pydoclint
         stages: [commit]
         language: system
-        entry: poetry run darglint src
+        entry: poetry run pydoclint # src tests
         types: [python]
         require_serial: true
-
-      - id: pyupgrade
-        name: pyupgrade
-        stages: [commit]
-        language: system
-        entry: poetry run pyupgrade
-        types: [python]
-        require_serial: true
-
       - id: pytest
         name: pytest
         stages: [commit]
         language: system
         entry: poetry run pytest tests
         types: [python]
         pass_filenames: false
+      - id: pydocstringformatter
+        name: pydocstringformatter
+        stages: [commit]
+        language: system
+        entry: rye run pydocstringformatter src tests
+        types: [python]
diff --git a/examples/custom_generator.py b/examples/custom_generator.py
@@ -3,35 +3,36 @@
 from itertools import cycle
 
 import numpy as np
-
-import volcano_cooking.modules.convert as convert
-import volcano_cooking.modules.create as create
+from volcano_cooking.modules import convert, create
 
 # We first need to create a generator class. This inherits from Generate. Let us just
 # create the regular intervals generator again.
 
 
 class GenerateRegularIntervals2(create.Generate):
+    """Create a custom generator class."""
+
     def gen_dates_totalemission_vei(self) -> None:
+        """Implement necessary methods."""
         self.yoes, self.moes, self.does, self.tes = regular_intervals2()
         self.veis = convert.totalemission_to_vei(self.tes)
 
 
-def regular_intervals2():
+def regular_intervals2() -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
     """Create dates with regular intervals.
 
     This function creates dates with regular intervals and a pre-defined magnitude as
     VEI.
 
     Returns
     -------
-    yoes: np.ndarray
+    yoes : np.ndarray
         Array of length 'size' with the year of a date
-    moes: np.ndarray
+    moes : np.ndarray
         Array of length 'size' with the month of a date
-    does: np.ndarray
+    does : np.ndarray
         Array of length 'size' with the day of a date
-    veis: np.ndarray
+    veis : np.ndarray
         Array of length 'size' with the VEI
     """
     year_sep = 2
@@ -51,6 +52,7 @@ def regular_intervals2():
 
 
 def create_synthetic_file() -> None:
+    """Run example."""
     # CREATE DATA -------------------------------------------------------------------- #
     size, init_year = 100, 1850
     g = GenerateRegularIntervals2(size, init_year)

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "volcano-cooking"
-version = "0.12.2"
+version = "1.0.0"
 description = "Make some volcanoes and simulate them in CESM2"
 authors = ["engeir <[email protected]>"]
 license = "GPL-3.0-or-later"
@@ -29,18 +29,18 @@ xarray = ">=2023.12,<2025.0"
 
 [tool.poetry.dev-dependencies]
 coverage = "^7.5"
-black = "^24.4"
-isort = "^5.13.2"
-flake8 = "^7.1.0"
 pre-commit = "^3.7.1"
 pre-commit-hooks = "^4.6.0"
 pyupgrade = "^3.16.0"
-darglint = "^1.8.0"
 pytest = "^8.2.2"
 pytest-cov = "^5.0.0"
 mypy = "^1.10"
 xdoctest = "^1.1.5"
-Pygments = "^2.18.0"
+
+[tool.poetry.group.dev.dependencies]
+ruff = "^0.4.9"
+pydoclint = "^0.4.1"
+pydocstringformatter = "^0.7.3"
 
 [tool.coverage.paths]
 source = ["src", "*/site-packages"]
@@ -55,3 +55,134 @@ show_missing = true
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.mypy]
+files = ["src"]
+ignore_missing_imports = true
+allow_redefinition = false
+check_untyped_defs = true
+ignore_errors = false
+implicit_reexport = false
+local_partial_types = true
+no_implicit_optional = true
+strict_equality = true
+strict_optional = true
+warn_no_return = true
+warn_redundant_casts = true
+warn_unreachable = true
+warn_unused_configs = true
+warn_unused_ignores = true
+
+[tool.ruff]
+# Same as Black.
+line-length = 88
+
+# Files that were downloaded
+extend-exclude = []
+
+# Allow unused variables when underscore-prefixed.
+
+# Assume Python 3.9
+target-version = "py39"
+
+[tool.ruff.lint]
+per-file-ignores = {}
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+select = [ # https://docs.astral.sh/ruff/rules/
+  "B", # flake8-bugbear
+  "D", # pydocstyle
+  "E", # pycodestyle
+  "F", # pyflakes
+  "I", # isort
+  "NPY201",
+  "PL", # pylint
+  "Q", # flake8-quotes
+  "UP", # pyupgrade
+]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+# select = ["E4", "E7", "E9", "F"]  # These are the default
+# https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+ignore = [
+  # "COM812", # Since we don't select COM, this is already ignored
+  # "COM819", # Since we don't select COM, this is already ignored
+  "D206",
+  "D300",
+  "E111",
+  "E114",
+  "E117",
+  "E266",
+  "E501",
+  # "ISC001", # Since we don't select ISC, this is already ignored
+  # "ISC002", # Since we don't select ISC, this is already ignored
+  "PLR0913", # Sometimes we want a lot of function signatures (6 not enough)
+  "Q000",
+  "Q001",
+  "Q002",
+  "Q003",
+  # "W191",  # Since we don't select W, this is already ignored
+]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+  ".bzr",
+  ".direnv",
+  ".eggs",
+  ".git",
+  ".git-rewrite",
+  ".hg",
+  ".mypy_cache",
+  ".nox",
+  ".pants.d",
+  ".pytype",
+  ".ruff_cache",
+  ".svn",
+  ".tox",
+  ".venv",
+  "__pypackages__",
+  "_build",
+  "buck-out",
+  "build",
+  "dist",
+  "node_modules",
+  "venv",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+ignore-decorators = ["typing.overload"]
+
+[tool.ruff.lint.flake8-quotes]
+docstring-quotes = "double"
+
+[tool.ruff.lint.flake8-import-conventions.aliases]
+# Declare the default aliases.
+"matplotlib.pyplot" = "plt"
+numpy = "np"
+scipy = "sp"
+xarray = "xr"
+
+[tool.ruff.lint.isort]
+case-sensitive = true
+known-local-folder = ["src", "de_verify"]
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 88
+profile = "black"
+combine_as_imports = true
+
+[tool.pydocstringformatter]
+write = true
+strip-whitespaces = true
+split-summary-body = false
+numpydoc-section-hyphen-length = false
+style = ["pep257", "numpydoc"]
diff --git a/setup.cfg b/setup.cfg
diff --git a/src/volcano_cooking/__main__.py b/src/volcano_cooking/__main__.py
@@ -4,14 +4,14 @@
 import ssl
 import subprocess
 import sys
-from typing import List, Optional
+from typing import Optional
 
 import click
 import wget
 
-import volcano_cooking.configurations.shift_eruption_to_date as shift_eruption_to_date
 import volcano_cooking.synthetic_volcanoes as sv
 from volcano_cooking import __version__
+from volcano_cooking.configurations import shift_eruption_to_date
 
 
 @click.command()
@@ -97,7 +97,7 @@
 )
 def main(
     frc: int,
-    init_year: List[int],
+    init_year: list[int],
     size: int,
     lst: bool,
     option: int,
@@ -106,6 +106,7 @@ def main(
     package_last: bool,
     file: Optional[str],
 ) -> None:
+    """Volcano cooking."""
     # First handle list, run ncl and package commands which overrides all other.
     if lst:
         for cl in sv.__GENERATORS__:
@@ -163,11 +164,11 @@ def get_forcing_file(
 
     Parameters
     ----------
-    file: str
+    file : str
         The filename the file to download will be saved as.
-    url: str, optional
+    url : Optional[str]
         Provide the full url for where to download the file.
-    not_forcing: bool
+    not_forcing : bool
         If some other file is downloaded, use generic text without file size warning.
     """
     here = os.path.join(os.getcwd(), "data", "originals")