style(pre-commit): apply style

Author: jourdain

.github/workflows/package.yml

@@ -1,7 +1,7 @@
 name: "Package"
 
 on:
-  workflow_dispatch:  # manually triggered
+  workflow_dispatch: # manually triggered
   workflow_run:
     workflows: ["Release"]
     types: [completed]
@@ -17,12 +17,12 @@ jobs:
         include:
           - platform: "macos-latest" # for Arm based macs (M1 and above).
             args: "--target aarch64-apple-darwin"
-          - platform: 'macos-latest' # for Intel based macs.
-            args: '--target x86_64-apple-darwin'
-          - platform: 'ubuntu-22.04' # for Tauri v1 you could replace this with ubuntu-20.04.
-            args: ''
-          - platform: 'windows-latest'
-            args: ''
+          - platform: "macos-latest" # for Intel based macs.
+            args: "--target x86_64-apple-darwin"
+          - platform: "ubuntu-22.04" # for Tauri v1 you could replace this with ubuntu-20.04.
+            args: ""
+          - platform: "windows-latest"
+            args: ""
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4

.github/workflows/release.yml

@@ -1,6 +1,6 @@
 name: "Release"
 on:
-  workflow_dispatch:  # manually triggered
+  workflow_dispatch: # manually triggered
 
 env:
   # Many color libraries just need this to be set to any value, but at least

README.md

@@ -7,12 +7,12 @@
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/e3sm-quickview.svg)](https://anaconda.org/conda-forge/e3sm-quickview)
 
 **EAM QuickView** is an open-source, interactive visualization tool
-designed for scientists working with the atmospheric component of the 
-[Energy Exascale Earth System Model (E3SM)](https://e3sm.org/), 
-known as the E3SM Atmosphere Model (EAM). 
-Its Python- and [Trame](https://www.kitware.com/trame/)-based 
+designed for scientists working with the atmospheric component of the
+[Energy Exascale Earth System Model (E3SM)](https://e3sm.org/),
+known as the E3SM Atmosphere Model (EAM).
+Its Python- and [Trame](https://www.kitware.com/trame/)-based
 Graphical User Interface (GUI) provides
-intuitive access to [ParaView](https://www.paraview.org/)'s 
+intuitive access to [ParaView](https://www.paraview.org/)'s
 powerful analysis and visualization capabilities, without the steep learning curve.
 
 ![Application](https://raw.githubusercontent.com/Kitware/QuickView/master/QuickView-app.png)

pyproject.toml

@@ -40,7 +40,13 @@ tauri = [
 jupyter = [
     "jupyter-server-proxy>=4.0.0",
 ]
-
+dev = [
+    "pre-commit",
+    "ruff",
+    "pytest >=6",
+    "pytest-asyncio",
+    "pytest-cov >=3",
+]
 
 [build-system]
 requires = ["hatchling"]
@@ -69,8 +75,8 @@ quickview = "e3sm_quickview.jupyter:setup_quickview"
 
 [tool.ruff.lint.per-file-ignores]
 # Ignore star import issues in ParaView plugins
-"e3sm_quickview/plugins/*.py" = ["F403", "F405"]
-"e3sm_quickview/pipeline.py" = ["F821"]  # Plugin classes loaded dynamically
+"src/e3sm_quickview/plugins/*.py" = ["F403", "F405"]
+"src/e3sm_quickview/pipeline.py" = ["F821"]  # Plugin classes loaded dynamically
 
 [tool.semantic_release]
 version_toml = [

src/e3sm_quickview/plugins/eam_projection.py

@@ -3,7 +3,6 @@
 from vtkmodules.numpy_interface import dataset_adapter as dsa
 from vtkmodules.vtkCommonCore import (
     vtkPoints,
-    vtkIdList,
 )
 from vtkmodules.vtkCommonDataModel import (
     vtkPolyData,
@@ -58,6 +57,7 @@ def ProcessPoint(point, radius):
     z = rho * math.cos(math.radians(phi))
     return [x, y, z]
 
+
 @smproxy.filter()
 @smproperty.input(name="Input")
 @smdomain.datatype(
@@ -412,9 +412,7 @@ def RequestData(self, request, inInfo, outInfo):
 
 @smproxy.filter()
 @smproperty.input(name="Input")
-@smdomain.datatype(
-    dataTypes=["vtkPolyData"], composite_data_supported=False
-)
+@smdomain.datatype(dataTypes=["vtkPolyData"], composite_data_supported=False)
 @smproperty.xml(
     """
                 <DoubleVectorProperty name="Longitude Range"
@@ -475,11 +473,10 @@ def RequestData(self, request, inInfo, outInfo):
         return 1
 
 
-
 @smproxy.filter()
 @smproperty.input(name="Input")
 @smproperty.xml(
-                """
+    """
                 <IntVectorProperty name="Meridian"
                     command="SetMeridian"
                     number_of_elements="1"
@@ -502,11 +499,12 @@ def RequestData(self, request, inInfo, outInfo):
     dataTypes=["vtkPolyData", "vtkUnstructuredGrid"], composite_data_supported=False
 )
 class EAMCenterMeridian(VTKPythonAlgorithmBase):
-    '''Cuts an unstructured grid and re-arranges the pieces such that
+    """Cuts an unstructured grid and re-arranges the pieces such that
     the specified meridian is in the middle.  Note that the mesh is
     specified with bounds [0, 360], but the meridian is specified in the more
     common bounds [-180, 180].
-    '''
+    """
+
     def __init__(self):
         super().__init__(
             nInputPorts=1, nOutputPorts=1, outputType="vtkUnstructuredGrid"
@@ -516,19 +514,23 @@ def __init__(self):
         self._cached_output = None
 
     def SetMeridian(self, meridian_):
-        '''
+        """
         Specifies the central meridian (longitude in the middle of the map)
-        '''
+        """
         if meridian_ < -180 or meridian_ > 180:
-            print_error("SetMeridian called with parameter outside [-180, 180]: {}".format(meridian_))
+            print_error(
+                "SetMeridian called with parameter outside [-180, 180]: {}".format(
+                    meridian_
+                )
+            )
             return
         self._center_meridian = meridian_
         self.Modified()
 
     def GetMeridian(self):
-        '''
+        """
         Returns the central meridian
-        '''
+        """
         return self._center_meridian
 
     def RequestData(self, request, inInfo, outInfo):
@@ -537,8 +539,11 @@ def RequestData(self, request, inInfo, outInfo):
         inCellArray = inData.GetCells()
 
         outData = self.GetOutputData(outInfo, 0)
-        if self._cached_output and self._cached_output.GetMTime() > inPoints.GetMTime() and \
-           self._cached_output.GetMTime() > inCellArray.GetMTime():
+        if (
+            self._cached_output
+            and self._cached_output.GetMTime() > inPoints.GetMTime()
+            and self._cached_output.GetMTime() > inCellArray.GetMTime()
+        ):
             # only scalars have been added or removed
             cached_cell_data = self._cached_output.GetCellData()
 
@@ -564,7 +569,9 @@ def RequestData(self, request, inInfo, outInfo):
                     out_array.SetNumberOfTuples(array0.GetNumberOfTuples())
                     out_array.SetName(in_array.GetName())
                     out_cell_data.AddArray(out_array)
-                    outData.cell_data[out_array.GetName()] = inData.cell_data[i][self._cached_output.cell_data['PedigreeIds']]
+                    outData.cell_data[out_array.GetName()] = inData.cell_data[i][
+                        self._cached_output.cell_data["PedigreeIds"]
+                    ]
         else:
             generate_ids = vtkGenerateIds()
             generate_ids.SetInputData(inData)

src/e3sm_quickview/plugins/eam_reader.py

@@ -463,7 +463,6 @@ def _build_geometry(self, meshdata):
         lat = meshdata[latdim][:].data.flatten()
         lon = meshdata[londim][:].data.flatten()
 
-
         if self._ForceFloatPoints:
             points_type = np.float32
         else:

src/e3sm_quickview/presets/acton_PARAVIEW.xml

@@ -257,4 +257,4 @@
   <Point x="0.996078" o="1" r="0.938996" g="0.915599" b="0.976685"/>
   <Point x="1.000000" o="1" r="0.939858" g="0.919150" b="0.979353"/>
 </ColorMap>
-</ColorMaps>
+</ColorMaps>

src/e3sm_quickview/presets/bam_PARAVIEW.xml

@@ -257,4 +257,4 @@
   <Point x="0.996078" o="1" r="0.060124" g="0.303780" b="0.005140"/>
   <Point x="1.000000" o="1" r="0.049098" g="0.296663" b="0.000000"/>
 </ColorMap>
-</ColorMaps>
+</ColorMaps>

src/e3sm_quickview/presets/batlow_PARAVIEW.xml

@@ -257,4 +257,4 @@
   <Point x="0.996078" o="1" r="0.982048" g="0.797228" b="0.972070"/>
   <Point x="1.000000" o="1" r="0.981354" g="0.800406" b="0.981267"/>
 </ColorMap>
-</ColorMaps>
+</ColorMaps>

src/e3sm_quickview/presets/berlin_PARAVIEW.xml

@@ -257,4 +257,4 @@
   <Point x="0.996078" o="1" r="0.991448" g="0.671939" b="0.670216"/>
   <Point x="1.000000" o="1" r="0.999873" g="0.680072" b="0.679950"/>
 </ColorMap>
-</ColorMaps>
+</ColorMaps>