Test Polish

.github/workflows/ci.yml

@@ -0,0 +1,121 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Cache OFT
+        uses: actions/cache@v4
+        with:
+          path: submodules/OpenFUSIONToolkit
+          key: oft-v1.0.0-beta6-ubuntu-22.04
+
+      - name: Install
+        run: ./install.sh
+
+      - name: Ruff format check
+        run: uv run ruff format --check synthwave/
+
+      - name: Ruff lint
+        run: uv run ruff check synthwave/
+
+      - name: Isort
+        run: uv run isort synthwave/
+
+  test:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        test-file:
+          - test_utils.py
+          - test_equilibrium_field.py
+          - test_filaments.py
+    name: test (${{ matrix.test-file }})
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Cache OFT
+        uses: actions/cache@v4
+        with:
+          path: submodules/OpenFUSIONToolkit
+          key: oft-v1.0.0-beta6-ubuntu-22.04
+
+      - name: Install
+        run: ./install.sh
+
+      - name: Run tests
+        run: uv run pytest synthwave/tests/${{ matrix.test-file }}
+
+  test-thincurr-other:
+    runs-on: ubuntu-22.04
+    name: test (test_thincurr.py - other)
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Cache OFT
+        uses: actions/cache@v4
+        with:
+          path: submodules/OpenFUSIONToolkit
+          key: oft-v1.0.0-beta6-ubuntu-22.04
+
+      - name: Install
+        run: ./install.sh
+
+      - name: Run tests
+        run: uv run pytest synthwave/tests/test_thincurr.py --deselect synthwave/tests/test_thincurr.py::test_toroidal_angles
+
+  test-thincurr-toroidal-angles:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        mode: ["m2n1", "m3n2", "m-3n2", "m3n1", "m4n3"]
+        major_radius: [1, 10]
+    name: test (test_toroidal_angles[${{ matrix.major_radius }}-${{ matrix.mode }}])
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Cache OFT
+        uses: actions/cache@v4
+        with:
+          path: submodules/OpenFUSIONToolkit
+          key: oft-v1.0.0-beta6-ubuntu-22.04
+
+      - name: Install
+        run: ./install.sh
+
+      - name: Run tests
+        run: uv run pytest "synthwave/tests/test_thincurr.py::test_toroidal_angles[${{ matrix.major_radius }}-${{ matrix.mode }}]"
+
+  notebooks:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Cache OFT
+        uses: actions/cache@v4
+        with:
+          path: submodules/OpenFUSIONToolkit
+          key: oft-v1.0.0-beta6-ubuntu-22.04
+
+      - name: Install
+        run: ./install.sh
+
+      - name: Run notebooks
+        run: uv run pytest --nbmake examples/

.gitignore

@@ -208,6 +208,7 @@ __marimo__/
 
 # VSCode
 .vscode/
+CLAUDE.md
 
 # Install
 submodules/OpenFUSIONToolkit
@@ -216,8 +217,14 @@ setup_env.sh
 # Tests
 synthwave/tests/figures/*.png
 synthwave/tests/figures/**/*.png
+synthwave/tests/**/*.h5
+synthwave/tests/**/*.save
+
+# Examples
+examples/freq_response/
+examples/mesh_plot/
 
 # scratch
 thincurr_scratch/
-synthwave/input_data
+scratch/
 synthwave/vessel_caches

.pre-commit-config.yaml

@@ -10,14 +10,19 @@ repos:
         entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
       - id: ruff_format
         name: ruff_format 
-        entry: poetry run ruff format
+        entry: uv run ruff format
         language: system
         types: [python]
         files: "^synthwave/"
       - id: ruff_check
         name: ruff_check
-        entry: poetry run ruff check --fix
+        entry: uv run ruff check --fix
         language: system
         types: [python]
         files: "^synthwave/"
-        exclude: "^synthwave/tests/"
+      - id: isort
+        name: isort
+        entry: uv run isort
+        language: system
+        types: [python]
+        files: "^synthwave/"

README.md

@@ -37,3 +37,7 @@ Given the provided input files, the magnitude of the output signal across the se
 
 ![Basic sensor signal response output](https://github.com/MIT-PSFC/SynthWave/blob/main/synthwave/mirnov/input_data/Sensor_Signals_m04_n02_f1.0e%2B01kHz_CMod.svg)
 
+## Generative AI Disclosure
+
+Github Copilot and Claude Code were used for code completion, snippet generation, and code review.
+However, the results of this were carefully vetted. A human has read and understands every line in this repo.

examples/freq_response.ipynb

@@ -0,0 +1,154 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "2dc6a9e2",
+   "metadata": {},
+   "source": [
+    "# Frequency Response Example\n",
+    "\n",
+    "Quick demonstration of vessel response changing measured probe angle."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0d2855e5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
+    "import os\n",
+    "import shutil\n",
+    "import xarray as xr\n",
+    "import numpy as np\n",
+    "from OpenFUSIONToolkit._core import OFT_env\n",
+    "from synthwave import PACKAGE_ROOT\n",
+    "from synthwave.magnetic_geometry.utils import create_torus_mesh\n",
+    "from synthwave.magnetic_geometry.filaments import ToroidalFilamentTracer\n",
+    "from synthwave.mirnov.prep_thincurr_input import (\n",
+    "    gen_OFT_filament_and_eta_file,\n",
+    "    gen_OFT_sensors_file,\n",
+    ")\n",
+    "from synthwave.mirnov.run_thincurr_model import calc_frequency_response\n",
+    "\n",
+    "EXAMPLE_DIR = os.path.join(PACKAGE_ROOT, \"..\", \"examples\", \"freq_response\")\n",
+    "\n",
+    "MAJOR_RADIUS = 1\n",
+    "MINOR_RADIUS = 0.5\n",
+    "\n",
+    "os.makedirs(EXAMPLE_DIR, exist_ok=True)\n",
+    "\n",
+    "torus_mesh_file = os.path.join(EXAMPLE_DIR, \"thincurr_torus_mesh.h5\")\n",
+    "if not os.path.exists(torus_mesh_file):\n",
+    "    torus_mesh = create_torus_mesh(MAJOR_RADIUS, MINOR_RADIUS)\n",
+    "    torus_mesh.write_to_file(torus_mesh_file)\n",
+    "\n",
+    "# Create 'oft_in.xml' file with icoil definitions\n",
+    "toroidal_tracer = ToroidalFilamentTracer(2, 1, MAJOR_RADIUS, 0, MINOR_RADIUS - 0.1)\n",
+    "filament_list, _ = toroidal_tracer.get_filament_list(num_filaments=10)\n",
+    "\n",
+    "gen_OFT_filament_and_eta_file(\n",
+    "    working_directory=EXAMPLE_DIR,\n",
+    "    filament_list=filament_list,\n",
+    "    resistivity_list=[1e-6],\n",
+    ")\n",
+    "\n",
+    "sensor_details = xr.Dataset(\n",
+    "    data_vars={\n",
+    "        \"position\": (\n",
+    "            (\"sensor\", \"coord\"),\n",
+    "            np.array(\n",
+    "                [\n",
+    "                    [MAJOR_RADIUS + MINOR_RADIUS, 0.0, 0.0],  # sensor on x axis\n",
+    "                    [0, MAJOR_RADIUS + MINOR_RADIUS, 0.0],  # sensor on y axis\n",
+    "                    [MAJOR_RADIUS, 0, MINOR_RADIUS],  # sensor on z axis\n",
+    "                ]\n",
+    "            ),\n",
+    "        ),\n",
+    "        \"normal\": (\n",
+    "            (\"sensor\", \"coord\"),\n",
+    "            np.array(\n",
+    "                [\n",
+    "                    [1.0, 0.0, 0.0],\n",
+    "                    [0.0, 1.0, 0.0],\n",
+    "                    [0.0, 0.0, 1.0],\n",
+    "                ]\n",
+    "            ),\n",
+    "        ),\n",
+    "        \"radius\": (\"sensor\", np.array([0.01, 0.01, 0.01])),\n",
+    "    },\n",
+    "    coords={\n",
+    "        \"sensor\": np.array([\"sensor_x\", \"sensor_y\", \"sensor_z\"]),\n",
+    "    },\n",
+    "    attrs={\n",
+    "        \"sensor_set_name\": \"test_sensors\",\n",
+    "    },\n",
+    ")\n",
+    "sensor_file_path = gen_OFT_sensors_file(\n",
+    "    sensor_details=sensor_details,\n",
+    "    working_directory=EXAMPLE_DIR,\n",
+    ")\n",
+    "\n",
+    "oft_tmpdir = os.path.join(\"tmp\", f\"oft_{os.getpid()}\")\n",
+    "if os.path.exists(oft_tmpdir):\n",
+    "    shutil.rmtree(oft_tmpdir)\n",
+    "\n",
+    "oft_env = OFT_env(nthreads=min(4, os.cpu_count()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "72474b42",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "total_response, direct_response, vessel_response = calc_frequency_response(\n",
+    "    oft_env=oft_env,\n",
+    "    tracer=toroidal_tracer,\n",
+    "    freq=10e3,\n",
+    "    working_directory=EXAMPLE_DIR,\n",
+    "    mesh_file=torus_mesh_file,\n",
+    "    sensor_file_path=sensor_file_path,\n",
+    "    sensor_details=sensor_details,\n",
+    ")\n",
+    "\n",
+    "# Get the angle of each response\n",
+    "total_response_angle = np.angle(total_response)\n",
+    "vessel_response_angle = np.angle(vessel_response)\n",
+    "direct_response_angle = np.angle(direct_response)\n",
+    "\n",
+    "# Print the results\n",
+    "for i, sensor in enumerate(sensor_details.sensor.values):\n",
+    "    print(f\"Sensor: {sensor}\")\n",
+    "    print(f\"  Total Response Angle: {total_response_angle[i]:.2f} rad\")\n",
+    "    print(f\"  Vessel Response Angle: {vessel_response_angle[i]:.2f} rad\")\n",
+    "    print(f\"  Direct Response Angle: {direct_response_angle[i]:.2f} rad\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}