Update packaging practices (#83)

* Update packaging practices

* lint

* Updates

* upgrade to ruff for linting

* Use extent for image data spacing calculation

* Bump version

* Fix memory sharing issues from pandas 3.0 copied Index

Author: banesullivan

.flake8

@@ -15,20 +15,20 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' || github.event_name == 'workflow_dispatch' || ( github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository )
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Log into the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: token
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Extract metadata for the Docker image
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: Build and push the Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: Dockerfile

.github/workflows/docker.yml

@@ -6,19 +6,19 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.12"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip install build twine
       - name: Build and Publish to PyPI
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
           twine upload --skip-existing dist/*

.github/workflows/release.yml

@@ -14,11 +14,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9, "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -36,11 +36,11 @@ jobs:
       #   run: |
       #     make doctest
       - name: Stash coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: coverage.xml
+          name: coverage-${{ matrix.python-version }}.xml
           path: coverage.xml
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: coverage.xml

.github/workflows/test.yml

@@ -5,35 +5,22 @@ ci:
     autoupdate_schedule: monthly
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 24.10.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.11.2
   hooks:
-  - id: black
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.9
+  rev: v0.4.6
   hooks:
   - id: blackdoc
     files: '\.py$'
     exclude: pyvista/plotting/charts.py
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-  - id: isort
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.1.1
-  hooks:
-  - id: flake8
-    additional_dependencies: [
-      "flake8-black==0.3.6",
-      "flake8-isort==6.0.0",
-      # "flake8-quotes==3.3.2",
-    ]
-
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.3.0
+  rev: v2.4.1
   hooks:
   - id: codespell
     args: [
@@ -53,7 +40,7 @@ repos:
     exclude: ^pyvista/ext/
 
 - repo: https://github.com/DanielNoord/pydocstringformatter
-  rev: v0.7.3
+  rev: v0.7.5
   hooks:
     - id: pydocstringformatter
       args: [
@@ -62,14 +49,8 @@ repos:
         "--no-capitalize-first-letter",
       ]
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.19.1
-  hooks:
-  - id: pyupgrade
-    args: [--py38-plus, --keep-runtime-typing]
-
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: check-merge-conflict
   - id: debug-statements

.pre-commit-config.yaml

@@ -24,8 +24,9 @@
    "source": [
     "import geovista as gv\n",
     "import pyvista as pv\n",
-    "from pvxarray.vtk_source import PyVistaXarraySource\n",
-    "import xarray as xr"
+    "import xarray as xr\n",
+    "\n",
+    "from pvxarray.vtk_source import PyVistaXarraySource"
    ]
   },
   {

MANIFEST.in

@@ -9,13 +9,8 @@
    },
    "outputs": [],
    "source": [
-    "from siphon.catalog import TDSCatalog\n",
-    "import xarray as xr\n",
     "import pyvista as pv\n",
-    "import pvxarray\n",
-    "import numpy as np\n",
-    "import ipywidgets as widgets\n",
-    "import matplotlib.pyplot as plt\n",
+    "from siphon.catalog import TDSCatalog\n",
     "\n",
     "pv.set_plot_theme(\"document\")\n",
     "pv.set_jupyter_backend(\"server\")  # critical for large data"
@@ -91,7 +86,7 @@
    },
    "outputs": [],
    "source": [
-    "dt = da[dict(time=0)]"
+    "dt = da[{\"time\": 0}]"
    ]
   },
   {

examples/cartographic.ipynb

@@ -15,10 +15,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pvxarray\n",
-    "import xarray as xr\n",
     "import numpy as np\n",
-    "import pyvista as pv"
+    "import pyvista as pv\n",
+    "import xarray as xr"
    ]
   },
   {
@@ -54,7 +53,7 @@
    "outputs": [],
    "source": [
     "ds = xr.tutorial.load_dataset(\"air_temperature\")\n",
-    "da = ds.air[dict(time=0)]  # Select DataArray for a timestep\n",
+    "da = ds.air[{\"time\": 0}]  # Select DataArray for a timestep\n",
     "\n",
     "# Plot in 3D\n",
     "da.pyvista.plot(x=\"lon\", y=\"lat\", cpos=\"xy\")"
@@ -129,7 +128,7 @@
     "da = da.rio.reproject(\"EPSG:3857\")\n",
     "\n",
     "# Grab the mesh object for use with PyVista\n",
-    "mesh = da[dict(band=0)].pyvista.mesh(x=\"x\", y=\"y\")\n",
+    "mesh = da[{\"band\": 0}].pyvista.mesh(x=\"x\", y=\"y\")\n",
     "\n",
     "# plot in 3D\n",
     "mesh.warp_by_scalar().plot(jupyter_backend=\"server\")"

examples/data-cube.ipynb

@@ -72,18 +72,20 @@ def update_time_index(time_index=0, **kwargs):
             style="max-width: 150px",
         )
 
-    with layout.content:
-        with vuetify.VContainer(
+    with (
+        layout.content,
+        vuetify.VContainer(
             fluid=True,
             classes="pa-0 fill-height",
-        ):
-            view = vtk.VtkRemoteView(
-                plotter.ren_win,
-                ref="view",
-                interactive_ratio=1,
-            )
-            ctrl.view_update = view.update
-            ctrl.view_reset_camera = view.reset_camera
+        ),
+    ):
+        view = vtk.VtkRemoteView(
+            plotter.ren_win,
+            ref="view",
+            interactive_ratio=1,
+        )
+        ctrl.view_update = view.update
+        ctrl.view_reset_camera = view.reset_camera
 
     # Uncomment following line to hide footer
     # layout.footer.hide()