Merge branch 'main' into pre-commit-ci-update-config

.github/workflows/benchmarks.yml

@@ -26,7 +26,7 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Miniconda
-        uses: conda-incubator/[email protected].2
+        uses: conda-incubator/[email protected].3
         with:
           # installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
           installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

.github/workflows/ci.yaml

@@ -33,7 +33,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up conda
-        uses: conda-incubator/[email protected].2
+        uses: conda-incubator/[email protected].3
         with:
           auto-update-conda: false
           channels: conda-forge
@@ -60,7 +60,7 @@ jobs:
         shell: 'bash -l {0}'
     steps:
       - uses: actions/[email protected]
-      - uses: conda-incubator/[email protected].2
+      - uses: conda-incubator/[email protected].3
         with:
           channels: conda-forge
           miniforge-variant: Mambaforge
@@ -91,7 +91,7 @@ jobs:
     steps:
       - uses: actions/[email protected]
       - name: Set up conda
-        uses: conda-incubator/[email protected].2
+        uses: conda-incubator/[email protected].3
         with:
           auto-update-conda: false
           channels: conda-forge
@@ -134,7 +134,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Setup python
-        uses: actions/setup-python@v5.0.0
+        uses: actions/setup-python@v5.1.0
         with:
           python-version: '3.11'
       - name: Set up Julia

.github/workflows/pypi.yml

@@ -16,7 +16,7 @@ jobs:
     - uses: actions/[email protected]
 
     - name: Set up Python
-      uses: actions/setup-python@v5.0.0
+      uses: actions/setup-python@v5.1.0
       with:
         python-version: "3.10"
 
@@ -45,7 +45,7 @@ jobs:
 
     - name: Publish a Python distribution to PyPI
       if: success() && github.event_name == 'release'
-      uses: pypa/[email protected].11
+      uses: pypa/[email protected].14
       with:
         user: __token__
         password: ${{ secrets.PYPI_PASSWORD }}

.pre-commit-config.yaml

@@ -2,7 +2,6 @@ ci:
     autoupdate_schedule: quarterly
 
 
-# https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -12,52 +11,21 @@ repos:
       - id: check-yaml
       - id: debug-statements
       - id: mixed-line-ending
-    # This wants to go before isort & flake8
-  - repo: https://github.com/PyCQA/autoflake
-    rev: "v2.3.1"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.2
     hooks:
-      - id: autoflake # isort should run before black as black sometimes tweaks the isort output
-        args: ["--in-place", "--ignore-init-module-imports"]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        args: ["--profile", "black"]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
-    hooks:
-      - id: pyupgrade
-        args:
-          - "--py38-plus"
-  # https://github.com/python/black#version-control-integration
+      # run the linter
+      - id: ruff
+        args: [--fix, --ignore-noqa]
+
   - repo: https://github.com/psf/black
     rev: 24.3.0
     hooks:
       - id: black
       - id: black-jupyter
+
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
         exclude: docs/index.rst
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
-    hooks:
-      - id: mypy
-        exclude: "properties|asv_bench"
-        # This is slow and so we take it out of the fast-path; requires passing
-        # `--hook-stage manual` to pre-commit
-        stages: [manual]
-        additional_dependencies: [
-            # Type stubs
-            types-python-dateutil,
-            types-pkg_resources,
-            types-PyYAML,
-            types-pytz,
-            typing-extensions,
-            numpy,
-          ]

pyproject.toml

@@ -0,0 +1,110 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "pip"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest]
+addopts = "--ignore=setup.py"
+
+[tool.pytest.ini_options]
+norecursedirs = [
+    ".git",
+    ".github",
+    "docs",
+]
+
+[tool.ruff]
+line-length = 120
+target-version = "py38"
+exclude = [".git", "asv_bench", "docs", "conftest.py"]
+
+
+[tool.ruff.lint]
+select = [
+    # https://pypi.org/project/pycodestyle
+    "E",
+    "W",
+    # https://pypi.org/project/pyflakes
+    "F",
+    # https://pypi.org/project/flake8-bandit
+    "S",
+    # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "UP",
+    "I002",    # Missing required imports
+    "UP008",   # Super calls with redundant arguments passed.
+    "G010",    # Deprecated log warn.
+    "PLR1722", # Use sys.exit() instead of exit() and quit().
+    "PT014",   # pytest-duplicate-parametrize-test-cases.
+    "PT006",   # Checks for the type of parameter names passed to pytest.mark.parametrize.
+    "PT007",   # Checks for the type of parameter values passed to pytest.mark.parametrize.
+    "PT018",   # Checks for assertions that combine multiple independent conditions.
+]
+
+extend-select = [
+    "I",      # isort
+    "C4",     # https://pypi.org/project/flake8-comprehensions
+]
+
+ignore = [
+    "S101",  # Use of `assert` detected
+    "E203", # Whitespace-before-punctuation.
+    "E402", # Module-import-not-at-top-of-file.
+    "E731", # Do not assign a lambda expression, use a def.
+    "D100", # Missing docstring in public module.
+    "D101", # Missing docstring in public class.
+    "D102", # Missing docstring in public method.
+    "D103", # Missing docstring in public function.
+    "D104", # Missing docstring in public package.
+    "D105", # Missing docstring in magic method.
+    "D106", # Missing docstring in public nested class.
+    "D107", # Missing docstring in `__init__`.
+    "RET504", # Unnecessary variable assignment before `return` statement.
+    "S101", # Use of `assert` detected.
+    "S108",
+    "D203", # 1 blank line required before class docstring.
+    "D205", # 1 blank line required between summary line and description.
+    "D212", # Multi-line docstring summary should start at the first line.
+    "D213", # Multi-line docstring summary should start at the second line.
+    "D209", # Multi-line docstring closing quotes should be on a separate line.
+    "D400", # First line should end with a period.
+    "D413", # Missing blank line after last section of docstrings.
+    "D401", # First line of docstring should be in imperative mood.
+    "D415", # First line should end with a period, question mark, or exclamation point.
+    "D416", # Section name should end with a colon ("Attributes").
+    "D417", # Missing argument description in the docstring for argument "X".
+    "RUF100", # https://docs.astral.sh/ruff/rules/unused-noqa/
+    "C408",
+    "SIM118",
+    "RET506",
+    "TRY004",
+    "RET505",
+    "RET507",
+    "SIM108",
+    "SIM102",
+    "E501", # line too long
+    "E266",
+    "F403",
+    "F401",
+    "F841",
+    "RET",
+    "SIM",
+    "PT",
+]
+ignore-init-module-imports = true
+
+[tool.ruff.lint.per-file-ignores]
+
+"setup.py" = ["S101"]
+"**/__init__.py" = ["F401", "F403", "F405", "F811", "F821", "E501", "SIM102"]
+"tests/**" = [
+    "S605",  # Starting a process with a shell: seems safe, but may be changed in the future; consider rewriting without `shell`
+    "S607",  # Starting a process with a partial executable path
+    "RET504",  # todo:Unnecessary variable assignment before `return` statement
+    "PT004",  # Fixture `tmpdir_unittest_fixture` does not return anything, add leading underscore
+    "PT011",  # `pytest.raises(ValueError)` is too broad, set the `match` parameter or use a more specific exception
+    "PT012",  # `pytest.raises()` block should contain a single simple statement
+    "PT019",  # Fixture `_` without value is injected as parameter, use `@pytest.mark.usefixtures` instead
+    "PT006" # Checks for the type of parameter names passed to pytest.mark.parametrize.
+]
+
+[tool.blackdoc]
+exclude = "docs/index.rst"

tests/test_bitround.py

@@ -86,26 +86,26 @@ def test_bitround_along_dim(air_temperature):
         ds, info_per_bit, dim="lon", inflevels=[1.0, 0.9999, 0.99, 0.975]
     )
 
-    assert ds_bitrounded_along_lon.air.dtype == "float32"
+    assert ds_bitrounded_along_lon.air.dtype == "float64"
     assert ds_bitrounded_along_lon.lon.size == ds.lon.size
     assert ds_bitrounded_along_lon.lat.size == ds.lat.size
     assert ds_bitrounded_along_lon.time.size == ds.time.size
     assert ds.air.values.dtype == ds_bitrounded_along_lon.air.values.dtype
 
-    assert (ds - ds_bitrounded_along_lon).air.mean() < 0.001
+    assert (ds - ds_bitrounded_along_lon).air.mean() < 0.01
 
     # test for keepbits
     ds_bitrounded_along_lon = bi.bitround_along_dim(
         ds, info_per_bit, dim="lon", inflevels=None, keepbits=2
     )
 
-    assert ds_bitrounded_along_lon.air.dtype == "float32"
+    assert ds_bitrounded_along_lon.air.dtype == "float64"
     assert ds_bitrounded_along_lon.lon.size == ds.lon.size
     assert ds_bitrounded_along_lon.lat.size == ds.lat.size
     assert ds_bitrounded_along_lon.time.size == ds.time.size
     assert ds.air.values.dtype == ds_bitrounded_along_lon.air.values.dtype
 
-    assert (ds - ds_bitrounded_along_lon).air.mean() < 0.001
+    assert (ds - ds_bitrounded_along_lon).air.mean() < 0.01
 
     # Test error when both keepbits and inflevels are provided
     with pytest.raises(ValueError):

xbitinfo/xbitinfo.py

@@ -152,13 +152,13 @@ def get_bitinformation(  # noqa: C901
     -------
     >>> ds = xr.tutorial.load_dataset("air_temperature")
     >>> xb.get_bitinformation(ds, dim="lon")  # doctest: +ELLIPSIS
-    <xarray.Dataset> Size: 652B
-    Dimensions:     (bitfloat32: 32)
+    <xarray.Dataset> Size: 1kB
+    Dimensions:     (bitfloat64: 64)
     Coordinates:
-      * bitfloat32  (bitfloat32) <U3 384B '±' 'e1' 'e2' 'e3' ... 'm21' 'm22' 'm23'
+      * bitfloat64  (bitfloat64) <U3 768B '±' 'e1' 'e2' 'e3' ... 'm50' 'm51' 'm52'
         dim         <U3 12B 'lon'
     Data variables:
-        air         (bitfloat32) float64 256B 0.0 0.0 0.0 ... 3.953e-05 0.0006889
+        air         (bitfloat64) float64 512B 0.0 0.0 0.0 ... 0.002847 0.0 0.0005092
     Attributes:
         xbitinfo_description:       bitinformation calculated by xbitinfo.get_bit...
         python_repository:          https://github.com/observingClouds/xbitinfo
@@ -167,13 +167,13 @@ def get_bitinformation(  # noqa: C901
         xbitinfo_version:           ...
         BitInformation.jl_version:  ...
     >>> xb.get_bitinformation(ds)
-    <xarray.Dataset> Size: 1kB
-    Dimensions:     (bitfloat32: 32, dim: 3)
+    <xarray.Dataset> Size: 2kB
+    Dimensions:     (bitfloat64: 64, dim: 3)
     Coordinates:
-      * bitfloat32  (bitfloat32) <U3 384B '±' 'e1' 'e2' 'e3' ... 'm21' 'm22' 'm23'
+      * bitfloat64  (bitfloat64) <U3 768B '±' 'e1' 'e2' 'e3' ... 'm50' 'm51' 'm52'
       * dim         (dim) <U4 48B 'lat' 'lon' 'time'
     Data variables:
-        air         (dim, bitfloat32) float64 768B 0.0 0.0 ... 6.327e-06 0.0004285
+        air         (dim, bitfloat64) float64 2kB 0.0 0.0 0.0 ... 0.0 0.0004498
     Attributes:
         xbitinfo_description:       bitinformation calculated by xbitinfo.get_bit...
         python_repository:          https://github.com/observingClouds/xbitinfo
@@ -411,23 +411,23 @@ def get_keepbits(info_per_bit, inflevel=0.99):
         dim       <U3 12B 'lon'
       * inflevel  (inflevel) float64 8B 0.99
     Data variables:
-        air       (inflevel) int64 8B 7
+        air       (inflevel) int64 8B 6
     >>> xb.get_keepbits(info_per_bit, inflevel=0.99999999)
     <xarray.Dataset> Size: 28B
     Dimensions:   (inflevel: 1)
     Coordinates:
         dim       <U3 12B 'lon'
       * inflevel  (inflevel) float64 8B 1.0
     Data variables:
-        air       (inflevel) int64 8B 14
+        air       (inflevel) int64 8B 7
     >>> xb.get_keepbits(info_per_bit, inflevel=1.0)
     <xarray.Dataset> Size: 28B
     Dimensions:   (inflevel: 1)
     Coordinates:
         dim       <U3 12B 'lon'
       * inflevel  (inflevel) float64 8B 1.0
     Data variables:
-        air       (inflevel) int64 8B 23
+        air       (inflevel) int64 8B 52
     >>> info_per_bit = xb.get_bitinformation(ds)
     >>> xb.get_keepbits(info_per_bit)
     <xarray.Dataset> Size: 80B
@@ -436,7 +436,7 @@ def get_keepbits(info_per_bit, inflevel=0.99):
       * dim       (dim) <U4 48B 'lat' 'lon' 'time'
       * inflevel  (inflevel) float64 8B 0.99
     Data variables:
-        air       (dim, inflevel) int64 24B 5 7 6
+        air       (dim, inflevel) int64 24B 5 6 6
     """
     if not isinstance(inflevel, list):
         inflevel = [inflevel]