update python tests and python module to work with new pybind11 bindings

.github/workflows/ci.yml

@@ -53,10 +53,17 @@ jobs:
         env:
           SETUPTOOLS_SCM_SUBPROCESS_TIMEOUT: "120"
 
-      - name: Run tests
+      - name: Run unmarked tests
         # Disable MacOS for now - we do not yet officially support it and we need to invest a bit
         # more efforts into investigating broken LAZ files written by Helios on MacOS.
         if: runner.os != 'macOS' 
         run: |
           python -m pytest
 
+      - name: Run marked tests
+        if: runner.os != 'macOS' 
+        run: |
+          python -m pytest -m exe
+          python -m pytest -m pyh
+
+

CMakeLists.txt

@@ -153,7 +153,7 @@ target_link_libraries(helios++ PRIVATE helios)
 
 if(BUILD_PYTHON)
   include_directories(${Python_INCLUDE_DIRS})
-  include_directories(${CMAKE_SOURCE_DIR}/src/binds)
+  include_directories(${CMAKE_SOURCE_DIR}/src/python)
   pybind11_add_module(_helios MODULE python/helios/helios_python.cpp)
   target_link_libraries(_helios PUBLIC helios pybind11::module)
   install(TARGETS _helios DESTINATION .)
@@ -175,7 +175,7 @@ endif()
 install(
   TARGETS
     helios++
-  DESTINATION helios/bin
+  DESTINATION pyhelios/bin
 )
 
 include(FeatureSummary)

environment-dev.yml

@@ -28,3 +28,11 @@ dependencies:
   - pytest
   - laspy
   - lazrs-python
+  - scipy
+  - polyscope
+  - tqdm
+  - pandas
+  - pdal
+  - ipywidgets
+variables:
+  PYTHONPATH: "python"

example_notebooks/I-getting-started.ipynb

@@ -36,18 +36,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "190276b5",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "2.0.0a3.dev10+g9e1844ae.d20240528\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import pyhelios\n",
     "\n",
@@ -56,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "0d4d3428",
    "metadata": {},
    "outputs": [],
@@ -75,19 +67,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "5411a736",
    "metadata": {},
    "outputs": [],
    "source": [
     "# pyhelios.loggingQuiet()\n",
     "# pyhelios.loggingSilent()\n",
-    "pyhelios.loggingDefault()\n",
+    "pyhelios.logging_default()\n",
     "# pyhelios.loggingVerbose()\n",
     "# pyhelios.loggingVerbose2()\n",
     "\n",
     "# Set seed for default random number generator.\n",
-    "pyhelios.setDefaultRandomnessGeneratorSeed(\"123\")"
+    "pyhelios.default_rand_generator_seed(\"123\")"
    ]
   },
   {
@@ -100,19 +92,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "5e5fd46a",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "SimulationBuilder is building simulation ...\n",
-      "SimulationBuilder built simulation in 0.06853010000486393 seconds\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "simBuilder = pyhelios.SimulationBuilder(\n",
     "    \"data/surveys/toyblocks/als_toyblocks.xml\", [\"assets/\"], \"output/\"\n",
@@ -161,27 +144,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "b744c735",
    "metadata": {
     "pycharm": {
      "is_executing": true
     }
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Simulation is started!\n",
-      "Simulation is paused!\n",
-      "Simulation is not running.\n",
-      "Simulation is resumed!\n",
-      "Simulation is running since 0 min and 3 sec. Please wait.\n",
-      "Simulation has finished.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import time\n",
     "\n",
@@ -235,40 +205,31 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "26589610",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Trajectory starting point : (-30.0, -50.0, 100.0)\n",
-      "Trajectory end point : (69.9, 50.0, 100.0)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Create instance of PyHeliosOutputWrapper class using sim.join().\n",
     "# Contains attributes 'measurements' and 'trajectories' which are Python wrappers\n",
     "# of classes that contain the output vectors.\n",
     "output = sim.join()\n",
     "\n",
     "# Create instances of vector classes by accessing 'measurements' and 'trajectories' attributes of output wrapper.\n",
-    "measurements = output.measurements\n",
-    "trajectories = output.trajectories\n",
+    "measurements = output[0]\n",
+    "trajectories = output[1]\n",
     "\n",
     "# Each element of vectors contains a measurement point or point in trajectory respectively.\n",
     "# Access through getPosition().\n",
-    "starting_point = trajectories[0].getPosition()\n",
-    "end_point = trajectories[len(trajectories) - 1].getPosition()\n",
+    "starting_point = trajectories[0].position\n",
+    "end_point = trajectories[len(trajectories) - 1].position\n",
     "\n",
     "# Access individual x, y and z vals.\n",
     "print(\n",
-    "    f\"Trajectory starting point : ({starting_point.x}, {starting_point.y}, {starting_point.z})\"\n",
+    "    f\"Trajectory starting point : ({starting_point[0]}, {starting_point[1]}, {starting_point[2]})\"\n",
     ")\n",
     "print(\n",
-    "    f\"Trajectory end point : ({end_point.x:.1f}, {end_point.y:.1f}, {end_point.z:.1f})\"\n",
+    "    f\"Trajectory end point : ({end_point[0]:.1f}, {end_point[1]:.1f}, {end_point[2]:.1f})\"\n",
     ")"
    ]
   },
@@ -282,7 +243,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "cf678697",
    "metadata": {},
    "outputs": [],
@@ -292,33 +253,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "41887ac9",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "First three rows of measurement array:\n",
-      "\n",
-      "[[-29.846 -13.246 0.012 -50.000 -49.915 89.871 0.001 0.342 -0.940 4.339\n",
-      "  0.000 1.000 1.000 1.000 0.000 0.000 -2147483648.000]\n",
-      " [-24.944 -13.595 0.012 -49.997 -49.915 89.871 0.047 0.339 -0.940 4.970\n",
-      "  0.000 1.000 1.000 33.000 0.000 0.000 -2147483648.000]\n",
-      " [-29.693 -13.259 0.046 -50.000 -49.915 89.871 0.003 0.342 -0.940 5.601\n",
-      "  0.000 1.000 1.000 2.000 0.000 0.000 -2147483648.000]]\n",
-      "\n",
-      "First three rows of trajectory array:\n",
-      "\n",
-      "[[-30.000 -50.000 100.000 -2147483648.000 0.000 0.000 4.712]\n",
-      " [-29.700 -50.000 100.000 -2147483648.000 0.000 0.000 4.712]\n",
-      " [-29.400 -50.000 100.000 -2147483648.000 0.000 0.000 4.712]]\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "\n",
@@ -373,7 +311,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.12.5"
   }
  },
  "nbformat": 4,