Use reusable test workflow

.github/workflows/test_suite.yml

@@ -1,63 +1,30 @@
-name: Install and test UM2N
+name: 'Run UM2N Test Suite'
 
 on:
+  # Run test suite whenever main is updated
   push:
     branches:
       - main
 
+  # Run test suite whenever commits are pushed to an open PR
   pull_request:
 
-jobs:
-  test-warpmesh:
-    name: Test UM2N
-    runs-on: ubuntu-latest
-    container:
-      image: firedrakeproject/firedrake:latest
-      options: --user root
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Cleanup
-        if: ${{ always() }}
-        run: |
-          cd ..
-          rm -rf build
-
-      - name: Setup Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Lint check
-        if: ${{ always() }}
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python3 -m pip install ruff
-          ruff check
-
-      - name: Install Movement
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          git clone https://github.com/mesh-adaptation/movement.git
-          cd movement
-          python3 -m pip install -e .
+  # Run test suite every Sunday at 1AM
+  schedule:
+    - cron: '0 1 * * 0'
 
-      - name: Install PyTorch
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python3 -m pip install torch --index-url https://download.pytorch.org/whl/cpu
-
-      - name: Install PyTorch3d
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python3 -m pip install 'git+https://github.com/facebookresearch/pytorch3d.git'
-
-      - name: Install UM2N
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python3 -m pip install -e .
-
-      - name: Run UM2N test suite
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python3 -m pytest tests/test* -v
+jobs:
+  test_suite:
+    uses: mesh-adaptation/mesh-adaptation-docs/.github/workflows/reusable_test_suite.yml@main
+    with:
+      install-command: 'python -m pip uninstall -y UM2N && python -m pip install -e .'
+      test-command: |
+        export GITHUB_ACTIONS_TEST_RUN=1
+        python $(which firedrake-clean)
+        python -m coverage erase
+        python -m coverage run -a --source=UM2N -m pytest -v --durations=20 test
+        python -m coverage report
+      changed-files-patterns: |
+        **/*.py
+        **/*.msh
+        **/*.geo

test/dataset_integrity_check.ipynb

@@ -0,0 +1,228 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
+    "import warnings\n",
+    "\n",
+    "# import glob\n",
+    "import torch\n",
+    "from torch_geometric.utils import index_to_mask\n",
+    "\n",
+    "import UM2N\n",
+    "\n",
+    "warnings.filterwarnings('ignore')\n",
+    "device = torch.device('cuda' if torch.cuda.is_available()\n",
+    "else 'cpu')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def check_phi_attached(data_path):\n",
+    "    data_set = UM2N.MeshDataset(data_path)\n",
+    "    for i in range(len(data_set)):\n",
+    "        try:\n",
+    "            assert hasattr(data_set[i], 'phi')\n",
+    "        except AttributeError:\n",
+    "            raise ValueError(\"[NO PHI]: \", data_path)\n",
+    "    return\n",
+    "\n",
+    "data_type = [\n",
+    "    \"iso_full\",\n",
+    "    \"iso_pad\",\n",
+    "    \"aniso_full\",\n",
+    "    \"aniso_pad\",\n",
+    "]\n",
+    "\n",
+    "subset_name = [\n",
+    "    \"data\",\n",
+    "]\n",
+    "\n",
+    "\n",
+    "n_grid_start = 15\n",
+    "n_grid_end = 35\n",
+    "\n",
+    "data_type = [\n",
+    "    \"iso_full\",\n",
+    "    \"iso_pad\",\n",
+    "    \"aniso_full\",\n",
+    "    \"aniso_pad\",\n",
+    "]\n",
+    "\n",
+    "subset_name = [\n",
+    "    \"data\",\n",
+    "]\n",
+    "\n",
+    "\n",
+    "# check for validation set\n",
+    "for n_grid in range(n_grid_start, n_grid_end + 1):\n",
+    "    for data in data_type:\n",
+    "        for subset in subset_name:\n",
+    "            base_path = (\n",
+    "                f\"/Users/cw1722/Documents/warpmesh/data/dataset/helmholtz/z=<0,1>_ndist=None_max_dist=6_<{n_grid}x{n_grid}>_n=100_{data}/{subset}\"\n",
+    "            )\n",
+    "            try:\n",
+    "                check_phi_attached(base_path)\n",
+    "                print(f\"suceess: check for {base_path}\")\n",
+    "            except ValueError:\n",
+    "                print(f\"failed: check for {base_path}\")\n",
+    "            print()\n",
+    "\n",
+    "\n",
+    "n_grid_start = 15\n",
+    "n_grid_end = 20\n",
+    "\n",
+    "data_type = [\n",
+    "    \"iso_pad\",\n",
+    "    \"aniso_full\",\n",
+    "]\n",
+    "\n",
+    "subset_name = [\n",
+    "    \"data\",\n",
+    "]\n",
+    "\n",
+    "# check for training set\n",
+    "for n_grid in range(n_grid_start, n_grid_end + 1, 5):\n",
+    "    for data in data_type:\n",
+    "        for subset in subset_name:\n",
+    "            base_path = (\n",
+    "                f\"/Users/cw1722/Documents/warpmesh/data/dataset/helmholtz/z=<0,1>_ndist=None_max_dist=6_<{n_grid}x{n_grid}>_n=100_{data}/{subset}\"\n",
+    "            )\n",
+    "            try:\n",
+    "                check_phi_attached(base_path)\n",
+    "            except ValueError:\n",
+    "                print(f\"failed: check for {base_path}\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def check_neighbour(data_path, source_idx=3):\n",
+    "    # file_pattern = os.path.join(data_path, 'data_*.npy')\n",
+    "    # files = glob.glob(file_pattern)\n",
+    "    # for file in files:\n",
+    "    data_set = UM2N.MeshDataset(data_path)\n",
+    "    for i in range(len(data_set)):\n",
+    "        coords = data_set[i].x[:, :2]\n",
+    "        num_nodes = coords.shape[0]\n",
+    "        source_mask = index_to_mask(\n",
+    "            torch.tensor([source_idx]), num_nodes\n",
+    "        )\n",
+    "        nei = UM2N.get_neighbors(source_mask, data_set[i].edge_index)\n",
+    "        if (nei.sum() == 6):\n",
+    "            pass\n",
+    "        else:\n",
+    "            raise ValueError(f\"In dataset {data_path} The number of neighbors is not 6\")\n",
+    "    return\n",
+    "\n",
+    "\n",
+    "check_neighbour(\"/Users/cw1722/Documents/warpmesh/data/helmholtz/z=<0,1>_ndist=None_max_dist=6_<16x16>_n=100_iso_full/data\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "n_grid_start = 15\n",
+    "n_grid_end = 35\n",
+    "\n",
+    "data_type = [\n",
+    "    \"iso_full\",\n",
+    "    \"iso_pad\",\n",
+    "    \"aniso_full\",\n",
+    "    \"aniso_pad\",\n",
+    "]\n",
+    "\n",
+    "subset_name = [\n",
+    "    \"data\",\n",
+    "]\n",
+    "\n",
+    "\n",
+    "# check for validation set\n",
+    "for n_grid in range(n_grid_start, n_grid_end + 1):\n",
+    "    for data in data_type:\n",
+    "        for subset in subset_name:\n",
+    "            base_path = (\n",
+    "                f\"/Users/cw1722/Documents/warpmesh/data/dataset/helmholtz/z=<0,1>_ndist=None_max_dist=6_<{n_grid}x{n_grid}>_n=100_{data}/{subset}\"\n",
+    "            )\n",
+    "            print(f\"passed: check for {base_path}\")\n",
+    "            check_neighbour(base_path)\n",
+    "\n",
+    "\n",
+    "n_grid_start = 15\n",
+    "n_grid_end = 20\n",
+    "\n",
+    "data_type = [\n",
+    "    \"iso_pad\",\n",
+    "    \"aniso_full\",\n",
+    "]\n",
+    "\n",
+    "subset_name = [\n",
+    "    \"data\",\n",
+    "]\n",
+    "\n",
+    "# check for training set\n",
+    "for n_grid in range(n_grid_start, n_grid_end + 1, 5):\n",
+    "    for data in data_type:\n",
+    "        for subset in subset_name:\n",
+    "            base_path = (\n",
+    "                f\"/Users/cw1722/Documents/warpmesh/data/dataset/helmholtz/z=<0,1>_ndist=None_max_dist=6_<{n_grid}x{n_grid}>_n=100_{data}/{subset}\"\n",
+    "            )\n",
+    "            print(f\"passed: check for {base_path}\")\n",
+    "            check_neighbour(base_path)\n",
+    "\n",
+    "print(\"All checks passed!\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

test/test_import.py

@@ -0,0 +1,31 @@
+# Author: Chunyang Wang
+# GitHub Username: acse-cw1722
+
+from pytest import fixture
+
+
+@fixture(scope="module")
+def UM2N():
+    import UM2N
+
+    return UM2N
+
+
+@fixture(scope="module")
+def firedrake():
+    import firedrake
+
+    return firedrake
+
+
+@fixture(scope="module")
+def movement():
+    import movement
+
+    return movement
+
+
+def test_import(UM2N, firedrake, movement):
+    assert UM2N
+    assert firedrake
+    assert movement