Switch to Ruff for formatting and linting (#544)

* configure ruff and settings

* update pre-commit to use ruff

* Refactor MDIO accessor for type hints, style, and clarity

* Remove unnecessary blank lines in __init__.py files

* Set line-length to 100 in Ruff configuration

* Refactor CLI code for improved type hinting and formatting

* Remove unnecessary blank line in constants.py

* Remove redundant `pass` statements from exception classes

* Refactor tuple comprehensions and exception raising

* Refactor SEG-Y utility functions

* Refactor SEG-Y workers for readability

* Refactor SEGY parser for clarity and type consistency

* Refactor SEG-Y geometry logic and improve logging formatting

* Add type annotations to exception class constructors

* Refactor file handling to use `Path` objects consistently

* Refactor and reformat compat.py

* Refactor SEG-Y blocked I/O

* Refactor type annotations in utils_write.py

* Refactor error handling and simplify conditional branches

* Refactor ChunkIterator and added examples.

* Refactor Grid class and enhanced type annotations

* Refactor `Dimension` class and typing improvements

* Refactor SEG-Y to MDIO converter for readability

* Refactor `numpy_to_mdio`

* Refactor MDIO to SEG-Y conversion with minor improvements

* Refactor exception constructors with type annotations.

* Refactor SEG-Y command for formatting

* Simplify and clean up `info.py` code formatting.

* Refactor MDIO copy function docstring

* Refactor `copy` function docstring and suppress linter warning

* Refactor type hints and optimize imports in io_utils.py

* Improve error messages for unsupported serialization formats

* Refactor serialization tests with type hints and stricter checks

* Add return type annotation to test_create_empty_like

* Refactor test functions to add type annotations.

* Add explicit return type annotations to test functions

* Refactor code and type annotations in tests

* Refactor test_accessor.py to improve type annotations

* Refactor unit test fixtures for clarity and typing support

* Enable E501 ignore for specific integration test file

* Refactor imports and type hints in SEG-Y test module

* Fix function call in unsupported format serializer test

* Update typing annotations and cleanup formatting in tests

* Update segy_to_mdio to support Path objects

* Enable per-file linting ignore for notebook tutorials

* Update linting tools and clarify CVE comment in noxfile

* Remove unnecessary blank line in helpers_segy.py

* Use `datetime.UTC` instead of `timezone.utc`.

* Refactor tests to use `Path` over `os.path` for file handling

* Fix comment for query size validation in accessor.py

* Remove .flake8 configuration file

* Add flake8-future-annotations

* lint and format notebooks

* Update docstyle dependencies and tooling configurations

* lint docs and add more details

* Update `setup-uv` action to v6 and adjust parameters

* Update bump-my-version to 1.1.2

* Fix SEG-Y sparsity check bug I introduced.

* Fix environment variable check for ignoring grid sparsity

* Refactor grid sparsity checks and environment variable handling.

* Update environment variable names for grid sparsity checks

* fix sparsity exception bug

* Update test CLI argument handling for consistent type usage

* revert unintended python version matrix change

Author: tasansal

.flake8

@@ -1,2 +1,2 @@
-bump-my-version==1.1.1
+bump-my-version==1.1.2
 nox==2025.2.9

.github/workflows/constraints.txt

@@ -17,10 +17,10 @@ jobs:
           fetch-depth: 2
 
       - name: Install the pinned version of uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: 3.13
-          pyproject-file: "${{ github.workspace }}/pyproject.toml"
+          working-directory: ${{ github.workspace }}
 
       - name: Install bumpversion
         run: |

.github/workflows/release.yml

@@ -43,10 +43,10 @@ jobs:
           python-version: ${{ matrix.python }}
 
       - name: Install the pinned version of uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python }}
-          pyproject-file: ${{ github.workspace }}/pyproject.toml
+          working-directory: ${{ github.workspace }}
 
       - name: Install Nox
         run: |
@@ -105,10 +105,10 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install the pinned version of uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: 3.13
-          pyproject-file: "${{ github.workspace }}/pyproject.toml"
+          working-directory: ${{ github.workspace }}
 
       - name: Install Nox
         run: |

.github/workflows/tests.yml

@@ -1,12 +1,22 @@
 repos:
+  # should be replaced in the future ref https://github.com/astral-sh/ruff/issues/458
+  - repo: https://github.com/jsh9/pydoclint
+    rev: 0.6.6
+    hooks:
+      - id: pydoclint
   - repo: local
     hooks:
-      - id: black
-        name: black
-        entry: black
+      - id: ruff-format
+        name: Format code with Ruff
+        entry: ruff format
+        language: system
+        types_or: [python, pyi, jupyter]
+      - id: ruff
+        name: Lint code with Ruff
+        entry: ruff check
         language: system
-        types: [python]
-        require_serial: true
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
       - id: check-added-large-files
         name: Check for added large files
         entry: check-added-large-files
@@ -22,39 +32,12 @@ repos:
         entry: check-yaml
         language: system
         types: [yaml]
-      - id: darglint
-        name: darglint
-        entry: darglint
-        language: system
-        types: [python]
-        stages: [manual]
       - id: end-of-file-fixer
         name: Fix End of Files
         entry: end-of-file-fixer
         language: system
         types: [text]
         stages: [pre-commit, pre-push, manual]
-      - id: flake8
-        name: flake8
-        entry: flake8
-        language: system
-        types: [python]
-        require_serial: true
-        args: [--darglint-ignore-regex, .*]
-      - id: isort
-        name: isort
-        entry: isort
-        require_serial: true
-        language: system
-        types_or: [cython, pyi, python]
-        args: ["--filter-files"]
-      - id: pyupgrade
-        name: pyupgrade
-        description: Automatically upgrade syntax for newer versions.
-        entry: pyupgrade
-        language: system
-        types: [python]
-        args: [--py38-plus]
       - id: trailing-whitespace
         name: Trim Trailing Whitespace
         entry: trailing-whitespace-fixer
@@ -63,6 +46,6 @@ repos:
         stages: [pre-commit, pre-push, manual]
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.0
+    rev: v2.7.1
     hooks:
       - id: prettier

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 
 project = "MDIO"
 author = "TGS"
-copyright = "2023, TGS"
+copyright = "2023, TGS"  # noqa: A001
 
 # -- General configuration ---------------------------------------------------
 

docs/conf.py

@@ -44,7 +44,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdio import segy_to_mdio, MDIOReader"
+    "from mdio import MDIOReader\n",
+    "from mdio import segy_to_mdio"
    ]
   },
   {
@@ -263,7 +264,7 @@
        "ascii": false,
        "bar_format": null,
        "colour": null,
-       "elapsed": 0.014499902725219727,
+       "elapsed": 0.014499902725219728,
        "initial": 0,
        "n": 0,
        "ncols": null,
@@ -366,28 +367,27 @@
     }
    ],
    "source": [
-    "import os\n",
+    "from pathlib import Path\n",
     "\n",
     "\n",
-    "def get_dir_size(path: str) -> int:\n",
+    "def get_dir_size(path: Path) -> int:\n",
     "    \"\"\"Get size of a directory recursively.\"\"\"\n",
     "    total = 0\n",
-    "    with os.scandir(path) as it:\n",
-    "        for entry in it:\n",
-    "            if entry.is_file():\n",
-    "                total += entry.stat().st_size\n",
-    "            elif entry.is_dir():\n",
-    "                total += get_dir_size(entry.path)\n",
+    "    for entry in path.iterdir():\n",
+    "        if entry.is_file():\n",
+    "            total += entry.stat().st_size\n",
+    "        elif entry.is_dir():\n",
+    "            total += get_dir_size(entry)\n",
     "    return total\n",
     "\n",
     "\n",
-    "def get_size(path: str) -> int:\n",
+    "def get_size(path: Path) -> int:\n",
     "    \"\"\"Get size of a folder or a file.\"\"\"\n",
-    "    if os.path.isfile(path):\n",
-    "        return os.path.getsize(path)\n",
-    "\n",
-    "    elif os.path.isdir(path):\n",
+    "    if path.is_file():\n",
+    "        return path.stat().st_size\n",
+    "    if path.is_dir():\n",
     "        return get_dir_size(path)\n",
+    "    return 0  # Handle case where path is neither file nor directory\n",
     "\n",
     "\n",
     "print(f\"SEG-Y:\\t{get_size('volve.segy') / 1024 / 1024:.2f} MB\")\n",
@@ -466,29 +466,35 @@
    ],
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "from matplotlib.axes import Axes\n",
+    "from matplotlib.image import AxesImage\n",
     "from mpl_toolkits.axes_grid1 import make_axes_locatable\n",
+    "from numpy.typing import NDArray\n",
     "\n",
     "vmin = -3 * std\n",
     "vmax = 3 * std\n",
     "\n",
-    "imshow_kw = dict(vmin=vmin, vmax=vmax, cmap=\"gray_r\", interpolation=\"bilinear\")\n",
+    "imshow_kw = {\"vmin\": -3 * std, \"vmax\": 3 * std, \"cmap\": \"gray_r\", \"interpolation\": \"bilinear\"}\n",
     "\n",
     "\n",
-    "def attach_colorbar(image, axis):\n",
+    "def attach_colorbar(image: AxesImage, axis: Axes) -> None:\n",
+    "    \"\"\"Attach a colorbar to an axis.\"\"\"\n",
     "    divider = make_axes_locatable(axis)\n",
     "    cax = divider.append_axes(\"top\", size=\"2%\", pad=0.05)\n",
     "    plt.colorbar(image, cax=cax, orientation=\"horizontal\")\n",
     "    cax.xaxis.set_ticks_position(\"top\")\n",
     "    cax.tick_params(labelsize=8)\n",
     "\n",
     "\n",
-    "def plot_image_and_cbar(data, axis, title):\n",
+    "def plot_image_and_cbar(data: NDArray, axis: Axes, title: str) -> None:\n",
+    "    \"\"\"Plot an image with a colorbar.\"\"\"\n",
     "    image = axis.imshow(data.T, **imshow_kw)\n",
     "    attach_colorbar(image, axis)\n",
     "    axis.set_title(title, y=-0.15)\n",
     "\n",
     "\n",
-    "def plot_inlines_with_diff(orig, compressed, title):\n",
+    "def plot_inlines_with_diff(orig: NDArray, compressed: NDArray, title: str) -> None:\n",
+    "    \"\"\"Plot lossless and lossy inline with their differences.\"\"\"\n",
     "    fig, ax = plt.subplots(1, 4, sharey=\"all\", sharex=\"all\", figsize=(12, 5))\n",
     "\n",
     "    diff = orig[200] - compressed[200]\n",
@@ -545,19 +551,19 @@
     }
    ],
    "source": [
-    "import skimage\n",
-    "\n",
-    "\n",
-    "def get_metrics(image_true, image_test):\n",
-    "    \"\"\"Get four metrics\"\"\"\n",
-    "    psnr = skimage.metrics.peak_signal_noise_ratio(\n",
-    "        image_true[200], image_test[200], data_range=max_ - min_\n",
-    "    )\n",
-    "    ssim = skimage.metrics.structural_similarity(\n",
-    "        image_true[200], image_test[200], data_range=max_ - min_\n",
-    "    )\n",
-    "    mse = skimage.metrics.mean_squared_error(image_true[200], image_test[200])\n",
-    "    nrmse = skimage.metrics.normalized_root_mse(image_true[200], image_test[200])\n",
+    "from numpy.typing import NDArray\n",
+    "from skimage.metrics import mean_squared_error\n",
+    "from skimage.metrics import normalized_root_mse\n",
+    "from skimage.metrics import peak_signal_noise_ratio\n",
+    "from skimage.metrics import structural_similarity\n",
+    "\n",
+    "\n",
+    "def get_metrics(image_true: NDArray, image_test: NDArray) -> tuple[float, float, float, float]:\n",
+    "    \"\"\"Get four image quality metrics.\"\"\"\n",
+    "    psnr = peak_signal_noise_ratio(image_true[200], image_test[200], data_range=max_ - min_)\n",
+    "    ssim = structural_similarity(image_true[200], image_test[200], data_range=max_ - min_)\n",
+    "    mse = mean_squared_error(image_true[200], image_test[200])\n",
+    "    nrmse = normalized_root_mse(image_true[200], image_test[200])\n",
     "\n",
     "    return psnr, ssim, mse, nrmse\n",
     "\n",