Add computation and visualization of kinetic energy spectrum and spectrograms

.github/workflows/check_and_test_package.yml

@@ -17,20 +17,20 @@ jobs:
   check-code:
     name: Check code
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.10'
 
-      - name: Install dependencies and VaMPy
+      - name: Install dependencies and project
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install types-paramiko .[test]
+          python -m pip install --upgrade pip setuptools types-paramiko
+          python -m pip install '.[test]'
 
-      - run: python -m flake8
-      - run: python -m mypy
+      - name: Run linting and checks
+        run: |
+          bash linting.sh
 
   test-code:
     needs: check-code
@@ -46,8 +46,8 @@ jobs:
     name: Test VaMPy on ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
     defaults:
-      run: # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
-        shell: bash -l {0}
+      run:
+        shell: bash -el {0}
 
     steps:
       - uses: actions/checkout@v3

linting.sh

@@ -0,0 +1,9 @@
+#! /usr/bin/env bash
+
+flake8 src tests
+
+isort src tests
+
+black src tests
+
+mypy src tests

src/vampy/__init__.py

@@ -1,42 +1,45 @@
 """Top-level package for VaMPy."""
+
 from importlib.metadata import metadata
 
 # Imports from post-processing
-from .automatedPostprocessing import compute_flow_and_simulation_metrics
-from .automatedPostprocessing import compute_hemodynamic_indices
-from .automatedPostprocessing import compute_velocity_and_pressure
-from .automatedPostprocessing import postprocessing_common
-from .automatedPostprocessing import visualize_probes
+from .automatedPostprocessing import (
+    compute_flow_and_simulation_metrics,
+    compute_hemodynamic_indices,
+    compute_velocity_and_pressure,
+    postprocessing_common,
+    visualize_probes,
+)
+
 # Imports from pre-processing
 try:
-    from .automatedPreprocessing import DisplayData
-    from .automatedPreprocessing import ImportData
-    from .automatedPreprocessing import NetworkBoundaryConditions
-    from .automatedPreprocessing import repair_tools
-    from .automatedPreprocessing import automated_preprocessing
-    from .automatedPreprocessing import preprocessing_common
-    from .automatedPreprocessing import simulate
-    from .automatedPreprocessing import visualize
-    from .automatedPreprocessing import vmtk_pointselector
+    from .automatedPreprocessing import (
+        DisplayData,
+        ImportData,
+        NetworkBoundaryConditions,
+        automated_preprocessing,
+        preprocessing_common,
+        repair_tools,
+        simulate,
+        visualize,
+        vmtk_pointselector,
+    )
 except ModuleNotFoundError:
-    print("WARNING: morphMan is not installed, automated preprocessing is not available")
+    print(
+        "WARNING: morphMan is not installed, automated preprocessing is not available"
+    )
 # Imports from simulation scripts
 try:
-    from .simulation import Artery
-    from .simulation import Atrium
-    from .simulation import Probe
-    from .simulation import Womersley
-    from .simulation import simulation_common
+    from .simulation import Artery, Atrium, Probe, Womersley, simulation_common
 except ModuleNotFoundError:
     print("WARNING: Oasis is not installed, running CFD is not available")
 
 try:
-    from .simulation import Probe
-    from .simulation import Womersley
-    from .simulation import simulation_common
-    from .simulation import MovingAtrium
+    from .simulation import MovingAtrium, Probe, Womersley, simulation_common
 except ModuleNotFoundError:
-    print("WARNING: OasisMove is not installed, running moving domain simulations (MovingAtrium) is not available")
+    print(
+        "WARNING: OasisMove is not installed, running moving domain simulations (MovingAtrium) is not available"
+    )
 
 
 meta = metadata("vampy")
@@ -66,5 +69,5 @@
     "simulation_common",
     "Probe",
     "Womersley",
-    'MovingAtrium'
+    "MovingAtrium",
 ]

src/vampy/automatedPostprocessing/__init__.py

@@ -1,5 +1,7 @@
-from . import compute_flow_and_simulation_metrics
-from . import compute_hemodynamic_indices
-from . import compute_velocity_and_pressure
-from . import postprocessing_common
-from . import visualize_probes
+from . import (
+    compute_flow_and_simulation_metrics,
+    compute_hemodynamic_indices,
+    compute_velocity_and_pressure,
+    postprocessing_common,
+    visualize_probes,
+)