GEMScienceTools · mouayed-nafeh · Mar 6, 2025 · Mar 5, 2025 · Mar 5, 2025 · Mar 5, 2025
diff --git a/.github/workflows/linux_test.yml b/.github/workflows/linux_test.yml
@@ -45,4 +45,4 @@ jobs:
         run: |
           source ~/openquake/bin/activate
           cd openquake/vmtk
-          pytest --doctest-modules -x --color=yes --durations=10 tests/
+          pytest -v --doctest-modules -x --color=yes --durations=10 tests/
diff --git a/.github/workflows/windows_test.yml b/.github/workflows/windows_test.yml
@@ -0,0 +1,45 @@
+name: Windows tests
+on:
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      git-ref:
+        description: Git Ref
+        default: master
+        required: true
+      debug_enabled:
+        type: boolean
+        description: 'tmate debug enabled'
+        required: false
+        default: false
+  schedule:
+    - cron: "0 2 * * 0"
+
+jobs:
+  vulnerability_test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-2022]
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python  ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies of OpenQuake engine
+        run: |
+          curl.exe -LO https://github.com/gem/oq-engine/raw/master/install.py
+          python install.py user --version=master
+      - name: Install vmtk Package
+        run: |
+          Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
+          C:\Users\runneradmin\openquake\Scripts\activate.ps1
+          pip install -e .
+      - name: Run tests
+        run: |
+          C:\Users\runneradmin\openquake\Scripts\activate.ps1
+          cd openquake\vmtk
+          pytest -v --doctest-modules -x --color=yes --durations=10 tests/
diff --git a/demos/notebooks/example_1.ipynb → demos/example_1.ipynb b/demos/notebooks/example_1.ipynb → demos/example_1.ipynb
@@ -59,13 +59,7 @@
     "\n",
     "# Import the IMCalculator class\n",
     "from openquake.vmtk.im_calculator import IMCalculator \n",
-    "from openquake.vmtk.utilities     import sorted_alphanumeric, export_to_pkl\n",
-    "\n",
-    "# Change the working directory to the folder containing your notebook\n",
-    "os.chdir('/Users/mnafeh/Documents/GitHub/vulnerability-toolkit/demos/notebooks')  # Replace this with your desired directory\n",
-    "\n",
-    "# Verify the current directory\n",
-    "print(\"Current working directory:\", os.getcwd())"
+    "from openquake.vmtk.utilities     import sorted_alphanumeric, export_to_pkl"
    ]
   },
   {
@@ -123,7 +117,7 @@
     "IMT = ['PGA','PGV','PGD','SA(0.3s)','SA(0.6s)','SA(1.0s)','AvgSA','AvgSA(0.3s)','AvgSA(0.6s)','AvgSA(1.0s)','AI','D595']\n",
     "\n",
     "# Load the records directory which contains two folders where the time and acceleration arrays of each ground-motion record are stored\n",
-    "gm_directory = os.path.join(os.getcwd(), 'in', 'records') \n",
+    "gm_directory = './in/records' \n",
     "\n",
     "# Fetch the acceleration files\n",
     "gmrs = sorted_alphanumeric(os.listdir(os.path.join(gm_directory, 'acc')))\n",
@@ -281,11 +275,16 @@
     "            imls[current_imt].append(t595) \n",
     "\n",
     "# Export to pickle format \n",
-    "export_to_pkl(os.path.join(gm_directory,'imls_esrm20.pkl'), imls)\n",
-    "\n",
-    "# Visualise the dictionary\n",
-    "print(imls)"
+    "export_to_pkl(os.path.join(gm_directory,'imls_esrm20.pkl'), imls)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26a56310-fcf6-4a7a-ae71-22eb85a87bf7",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -304,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/demos/notebooks/example_2.ipynb → demos/example_2.ipynb b/demos/notebooks/example_2.ipynb → demos/example_2.ipynb
@@ -48,39 +48,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "0d7fbfbf-e29a-4403-983f-932d528c6a18",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'vmtk'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[1], line 8\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpyplot\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mplt\u001b[39;00m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;66;03m# Import the classes necessary for structural analysis\u001b[39;00m\n\u001b[0;32m----> 8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mvmtk\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcalibration\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m calibrate_model\n\u001b[1;32m      9\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mvmtk\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodeller\u001b[39;00m    \u001b[38;5;28;01mimport\u001b[39;00m modeller\n\u001b[1;32m     10\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mvmtk\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutilities\u001b[39;00m   \u001b[38;5;28;01mimport\u001b[39;00m sorted_alphanumeric, import_from_pkl, export_to_pkl\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'vmtk'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "import sys\n",
+    "import shutil\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# Import the classes necessary for structural analysis\n",
+    "from openquake.vmtk.units       import units\n",
     "from openquake.vmtk.calibration import calibrate_model\n",
     "from openquake.vmtk.modeller    import modeller\n",
-    "from openquake.vmtk.utilities   import sorted_alphanumeric, import_from_pkl, export_to_pkl\n",
-    "\n",
-    "# Change the working directory to the folder containing your notebook\n",
-    "os.chdir('/Users/mnafeh/Documents/GitHub/vulnerability-toolkit/demos/notebooks')  # Replace this with your desired directory\n",
-    "\n",
-    "# Verify the current directory\n",
-    "print(\"Current working directory:\", os.getcwd())"
+    "from openquake.vmtk.utilities   import sorted_alphanumeric, import_from_pkl, export_to_pkl"
    ]
   },
   {
@@ -131,15 +115,14 @@
    "outputs": [],
    "source": [
     "# Define the directory of the capacities\n",
-    "capacity_directory = f'{vmtk}/demos/in/capacity'          \n",
+    "capacity_directory = './in/capacity'          \n",
     "\n",
     "# Define the directory of the ground-motion records\n",
-    "gm_directory  = f'{vmtk}/demos/in/records'            \n",
+    "gm_directory  = './in/records'            \n",
     "\n",
     "# Define the main output directory\n",
-    "nltha_directory = f'{vmtk}/demos/out/nltha'  \n",
-    "if not os.path.exists(f'{nltha_directory}'):\n",
-    "    os.makedirs(f'{nltha_directory}')"
+    "nrha_directory = './out/nltha'  \n",
+    "os.makedirs(nrha_directory, exist_ok=True)"
    ]
   },
   {
@@ -273,10 +256,9 @@
     "mdof_max_peak_accel_dir_list = []       # List for maximum peak floor acceleration directions \n",
     "mdof_max_peak_accel_loc_list = []       # List for maximum peak floor acceleration locations \n",
     "\n",
-    "# Define directory for temporary analysis outputs\n",
-    "temp_nrha_outdir = f'{nltha_directory}/temp'\n",
-    "if not os.path.exists(f'{temp_nrha_outdir}'):\n",
-    "    os.makedirs(f'{temp_nrha_outdir}')"
+    "# Define directory for temporary analysis outputs: it is used to store temporary .txt files used as accelerations recorders\n",
+    "temp_nrha_directory = os.path.join(nrha_directory,'temp')\n",
+    "os.makedirs(temp_nrha_directory, exist_ok=True)"
    ]
   },
   {
@@ -287,8 +269,8 @@
    "outputs": [],
    "source": [
     "# Loop over ground-motion records, compile MDOF model and run NLTHA\n",
-    "gmrs = sorted_alphanumeric(os.listdir(f'{gm_directory}/acc'))                         # Sort the ground-motion records alphanumerically\n",
-    "dts  = sorted_alphanumeric(os.listdir(f'{gm_directory}/dts'))                         # Sort the ground-motion time-step files alphanumerically\n",
+    "gmrs = sorted_alphanumeric(os.listdir(os.path.join(gm_directory,'acc')))                         # Sort the ground-motion records alphanumerically\n",
+    "dts  = sorted_alphanumeric(os.listdir(os.path.join(gm_directory,'dts')))                         # Sort the ground-motion time-step files alphanumerically\n",
     "\n",
     "for i in range(len(gmrs)):\n",
     "    ### Print post-processing iteration\n",
@@ -307,19 +289,18 @@
     "    model.compile_model()                                                                             # Compile the MDOF model\n",
     "    \n",
     "    if i==0:\n",
-    "        model.plot_model()                                                                            # Visualise the model (only on first iteration)\n",
-    "        \n",
+    "        model.plot_model()                                                                            # Visualise the model (only on first iteration)        \n",
     "    model.do_gravity_analysis()                                                                       # Do gravity analysis\n",
     "\n",
     "    if number_storeys == 1:\n",
     "        num_modes = 1\n",
     "    else:\n",
     "        num_modes = 3\n",
-    "    T, _ = model.do_modal_analysis(num_modes = num_modes)                                             # Do modal analysis and get period of vibration\n",
+    "    T, phi = model.do_modal_analysis(num_modes = num_modes)                                           # Do modal analysis and get period of vibration (Essential step for running NLTHA)\n",
     "\n",
     "    ### Define ground motion objects\n",
-    "    fnames = [f'{gm_directory}/acc/{gmrs[i]}']                                                        # Ground-motion record names\n",
-    "    fdts   =  f'{gm_directory}/dts/{dts[i]}'                                                          # Ground-motion time-step names \n",
+    "    fnames = [os.path.join(gm_directory,'acc',f'{gmrs[i]}')]                                          # Ground-motion record names\n",
+    "    fdts   =  os.path.join(gm_directory,'dts',f'{dts[i]}')                                            # Ground-motion time-step names \n",
     "    dt_gm = pd.read_csv(fdts, header=None)[pd.read_csv(fdts,header=None).columns[0]].loc[1]-\\\n",
     "            pd.read_csv(fdts, header=None)[pd.read_csv(fdts,header=None).columns[0]].loc[0]           # Ground-motion time-step\n",
     "    t_max = pd.read_csv(fdts)[pd.read_csv(fdts).columns[0]].iloc[-1]                                  # Ground-motion duration\n",
@@ -348,6 +329,9 @@
     "    mdof_max_peak_accel_dir_list.append(max_peak_accel_dir)\n",
     "    mdof_max_peak_accel_loc_list.append(max_peak_accel_loc)\n",
     "\n",
+    "# Remove the temporary directory\n",
+    "shutil.rmtree(f'{temp_nrha_directory}')\n",
+    "\n",
     "print('ANALYSIS COMPLETED')"
    ]
   },
@@ -377,27 +361,8 @@
     "for i, label in enumerate(labels):\n",
     "    ansys_dict[label] = vars()[f'{label}']\n",
     "# Export the analysis output variable to a pickle file using the \"export_to_pkl\" function from \"utilities\"\n",
-    "export_to_pkl(f'{nltha_directory}/ansys_out.pkl', ansys_dict) "
+    "export_to_pkl(os.path.join(nrha_directory,'ansys_out.pkl'), ansys_dict) "
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c597d643-c4a5-4794-85e7-f3bc29094f79",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "end = time.time()\n",
-    "print('Elapsed Time:', (end - start)/60, 'minutes')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6ca99f93-fd56-4abc-9b17-3a378b258f03",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -416,7 +381,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/demos/notebooks/example_3.ipynb → demos/example_3.ipynb b/demos/notebooks/example_3.ipynb → demos/example_3.ipynb
@@ -40,22 +40,14 @@
    "source": [
     "import os\n",
     "import sys\n",
-    "import time\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "start = time.time()\n",
-    "\n",
-    "# Set paths\n",
-    "vmtk = os.path.abspath(os.path.join(\"..\",\"..\"))\n",
-    "sys.path.append(vmtk)\n",
-    "os.chdir(os.path.join(vmtk,'src'))\n",
-    "\n",
     "# Import the classes necessary for postprocessing and visualising structural analysis results\n",
-    "from src.postprocessor import postprocessor\n",
-    "from src.plotter       import plotter\n",
-    "from src.utilities     import import_from_pkl\n",
+    "from openquake.vmtk.postprocessor import postprocessor\n",
+    "from openquake.vmtk.plotter       import plotter\n",
+    "from openquake.vmtk.utilities     import import_from_pkl\n",
     "\n",
     "# Initialise the postprocessor and plotter classes\n",
     "pp = postprocessor()\n",
@@ -141,12 +133,14 @@
    "outputs": [],
    "source": [
     "# Define the directory of the ground-motion records and import the intensity measure pickle file containing all IMs (processed from example 1)\n",
-    "gm_directory  = f'{vmtk}/demos/in/records'            \n",
-    "ims           = import_from_pkl(f'{gm_directory}/imls_esrm20.pkl')     \n",
+    "gm_directory  = './in/records'            \n",
+    "\n",
+    "# Import the intensity measure dictionary (output from example 1)\n",
+    "ims           = import_from_pkl(os.path.join(gm_directory, 'imls_esrm20.pkl'))  \n",
     "\n",
     "# Define the main output directory and import the analysis output from a pickle file using the \"import_from_pkl\" function from \"utilities\"\n",
-    "nltha_directory = f'{vmtk}/demos/out/nltha' \n",
-    "ansys_dict      = import_from_pkl(f'{nltha_directory}/ansys_out.pkl') # processed from example 2"
+    "nrha_directory = './out/nltha' \n",
+    "ansys_dict      = import_from_pkl(os.path.join(nrha_directory, 'ansys_out.pkl')) # processed from example 2"
    ]
   },
   {
@@ -196,9 +190,8 @@
     "                                      censored_limit) \n",
     "    \n",
     "    ## Create a figures directory for each building class\n",
-    "    figures_directory = f'{vmtk}/demos/out/nltha/figures'    \n",
-    "    if not os.path.exists(f'{figures_directory}'):\n",
-    "        os.makedirs(f'{figures_directory}')\n",
+    "    figures_directory = './out/figures' \n",
+    "    os.makedirs(figures_directory, exist_ok=True)\n",
     "    \n",
     "    ## Visualise the cloud analysis results\n",
     "    pl.plot_cloud_analysis(cloud_dict, \n",
@@ -250,35 +243,33 @@
     "# To do so, we can use the \"get_vulnerability_function\" method from the \"postprocessor\" class.\n",
     "# Setting the uncertainty to True will additionally calculate the coefficient of variation to explicitly\n",
     "# consider the uncertainty in the Loss|IM as per Silva et al. (2019)\n",
+    "\n",
     "structural_vulnerability = pp.get_vulnerability_function(cloud_dict['poes'],\n",
     "                                                         consequence_model,\n",
     "                                                         uncertainty=True)\n",
     "\n",
     "\n",
-    "# The output is a DataFrame with three keys: IMLs (i.e., intensity measure levels), Loss and COV\n",
-    "print(structural_vulnerability)\n",
+    "# Plot the structural vulnerability function\n",
+    "pl.plot_vulnerability_analysis(structural_vulnerability['IMLs'],\n",
+    "                               structural_vulnerability['Loss'],\n",
+    "                               structural_vulnerability['COV'],\n",
+    "                               'SA(1.0s)',\n",
+    "                               'Structural Loss Ratio',\n",
+    "                               figures_directory,\n",
+    "                               'Structural Vulnerability')\n",
+    "\n",
     "\n",
-    "# Plot the vulnerability function to visualise\n",
-    "plt.plot(structural_vulnerability['IMLs'], structural_vulnerability['Loss'], label = 'Structural Loss', color = COLOR, lw=LINEWIDTH_1)\n",
-    "plt.xlabel('Spectral Acceleration, Sa(T=1.0s) [g]', fontsize= FONTSIZE_1) # This is because the latest cloud_dict variable is associated with SA(1.0s)\n",
-    "plt.ylabel('Expected Loss Ratio', fontsize = FONTSIZE_1)\n",
-    "plt.legend(loc = 'lower right')\n",
-    "plt.grid(visible=True, which='major')\n",
-    "plt.grid(visible=True, which='minor')\n",
-    "plt.xlim([0.00, 5.00])\n",
-    "plt.show()"
+    "# The output is a DataFrame with three keys: IMLs (i.e., intensity measure levels), Loss and COV\n",
+    "print(structural_vulnerability)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39c357a7-e6b1-43b3-a58b-f9cee926cdc9",
+   "id": "a587cb59-faa8-4f1f-bb5a-445322cfff51",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "end = time.time()\n",
-    "print('Elapsed Time:', (end - start)/60, 'minutes')"
-   ]
+   "source": []
   }
  ],
  "metadata": {
@@ -297,7 +288,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/demos/in/records/imls_esrm20.pkl b/demos/in/records/imls_esrm20.pkl