Merge pull request #6 from NHERI-SimCenter/master

abs - merging updates from upstream

.github/workflows/format_check.yml

@@ -1,25 +1,10 @@
-name: Format Check
-
+name: Ruff format
 on: [push, pull_request]
-
 jobs:
-  format-check:
+  ruff:
     runs-on: ubuntu-latest
-
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install ruff
-
-    - name: Check code formatting
-      run: |
-        ruff check . --diff
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: 'format --check'

.github/workflows/lint.yml

@@ -1,25 +1,8 @@
-name: Lint
-
+name: Ruff check
 on: [push, pull_request]
-
 jobs:
-  lint:
+  ruff:
     runs-on: ubuntu-latest
-
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install ruff
-
-    - name: Run linter
-      run: |
-        ruff check .
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

modules/Workflow/CMakeLists.txt

@@ -4,6 +4,7 @@ simcenter_add_python_script(SCRIPT changeJSON.py)
 simcenter_add_python_script(SCRIPT "sWHALE.py")
 simcenter_add_python_script(SCRIPT "qWHALE.py")
 simcenter_add_python_script(SCRIPT "rWHALE.py")
+simcenter_add_python_script(SCRIPT "createResponseCSV.py")
 simcenter_add_python_script(SCRIPT "siteResponseWHALE.py")
 simcenter_add_python_script(SCRIPT "createGM4BIM.py")
 simcenter_add_python_script(SCRIPT "computeResponseSpectrum.py")
@@ -19,4 +20,4 @@ simcenter_add_python_script(SCRIPT R2DTool_workflow.py)
 simcenter_add_python_script(SCRIPT CreateWorkflowJobs.py)
 
 simcenter_add_executable(NAME runMultiModelDriver
-                         FILES runMultiModelDriver.cpp)
+                         FILES runMultiModelDriver.cpp)

modules/Workflow/MultiModelDriver.py

@@ -162,14 +162,16 @@ def main(inputFile, driverFile, appKey, registryFile, appDir, runType, osType):
                     'UTF-8',
                 )
             )
-    elif osType == 'Windows' and runType == 'runningRemote':
+    elif runType == 'runningRemote':
         with open(driverFile, 'wb') as f:  # noqa: PTH123
             f.write(
-                appDir
-                + '/applications/Workflow/'
-                + exeFileName
-                + f' {paramsFileName} {driverFile} {multiModelString}',
-                'UTF-8',
+                bytes(
+                    appDir
+                    + '/applications/Workflow/'
+                    + exeFileName
+                    + f' {paramsFileName} {driverFile} {multiModelString}',
+                    'UTF-8',
+                )
             )
     else:
         with open(driverFile, 'wb') as f:  # noqa: PTH123

modules/Workflow/computeResponseSpectrum.py

@@ -23,7 +23,7 @@ def convert_accel_units(acceleration, from_, to_='cm/s/s'):  # noqa: C901
     acceleration = np.asarray(acceleration)
     if from_ == 'g':
         if to_ == 'g':
-            return acceleration
+            return acceleration  # noqa: DOC201, RUF100
         if to_ in m_sec_square:
             return acceleration * g
         if to_ in cm_sec_square:
@@ -70,7 +70,7 @@ def get_velocity_displacement(
         velocity = time_step * cumtrapz(acceleration, initial=0.0)
     if displacement is None:
         displacement = time_step * cumtrapz(velocity, initial=0.0)
-    return velocity, displacement
+    return velocity, displacement  # noqa: DOC201, RUF100
 
 
 class NewmarkBeta:
@@ -160,7 +160,7 @@ def run(self):
             'PGV': np.max(np.fabs(self.velocity)),
             'PGD': np.max(np.fabs(self.displacement)),
         }
-        return self.response_spectrum, time_series, accel, vel, disp
+        return self.response_spectrum, time_series, accel, vel, disp  # noqa: DOC201, RUF100
 
     def _newmark_beta(self, omega, cval, kval):  # noqa: ARG002
         """Newmark-beta integral
@@ -216,4 +216,4 @@ def _newmark_beta(self, omega, cval, kval):  # noqa: ARG002
             disp[j, :] = delta_u + disp[j - 1, :]
             a_t[j, :] = ground_acc[j] + accel[j, :]
 
-        return accel, vel, disp, a_t
+        return accel, vel, disp, a_t  # noqa: DOC201, RUF100

modules/Workflow/createGM4BIM.py

@@ -120,7 +120,7 @@ def get_scale_factors(input_units, output_units):  # noqa: C901
 
             scale_factors.update({input_name: f_scale})
 
-    return scale_factors
+    return scale_factors  # noqa: DOC201, RUF100
 
 
 def createFilesForEventGrid(inputDir, outputDir, removeInputDir):  # noqa: C901, N802, N803, D103, PLR0915
@@ -410,28 +410,28 @@ def createFilesForEventGrid(inputDir, outputDir, removeInputDir):  # noqa: C901,
                 m_pgd_y = 0.0
                 s_pgd_y = 0.0
             # add to dictionary
-            dict_im[('type', 'loc', 'dir', 'stat')].append(int(siteID))
+            dict_im[('type', 'loc', 'dir', 'stat')].append(int(siteID))  # noqa: RUF031, RUF100
             # pga
-            dict_im[('PGA', 0, 1, 'median')].append(m_pga_x)
-            dict_im[('PGA', 0, 1, 'beta')].append(s_pga_x)
-            dict_im[('PGA', 0, 2, 'median')].append(m_pga_y)
-            dict_im[('PGA', 0, 2, 'beta')].append(s_pga_y)
+            dict_im[('PGA', 0, 1, 'median')].append(m_pga_x)  # noqa: RUF031, RUF100
+            dict_im[('PGA', 0, 1, 'beta')].append(s_pga_x)  # noqa: RUF031, RUF100
+            dict_im[('PGA', 0, 2, 'median')].append(m_pga_y)  # noqa: RUF031, RUF100
+            dict_im[('PGA', 0, 2, 'beta')].append(s_pga_y)  # noqa: RUF031, RUF100
             # pgv
-            dict_im[('PGV', 0, 1, 'median')].append(m_pgv_x)
-            dict_im[('PGV', 0, 1, 'beta')].append(s_pgv_x)
-            dict_im[('PGV', 0, 2, 'median')].append(m_pgv_y)
-            dict_im[('PGV', 0, 2, 'beta')].append(s_pgv_y)
+            dict_im[('PGV', 0, 1, 'median')].append(m_pgv_x)  # noqa: RUF031, RUF100
+            dict_im[('PGV', 0, 1, 'beta')].append(s_pgv_x)  # noqa: RUF031, RUF100
+            dict_im[('PGV', 0, 2, 'median')].append(m_pgv_y)  # noqa: RUF031, RUF100
+            dict_im[('PGV', 0, 2, 'beta')].append(s_pgv_y)  # noqa: RUF031, RUF100
             # pgd
-            dict_im[('PGD', 0, 1, 'median')].append(m_pgd_x)
-            dict_im[('PGD', 0, 1, 'beta')].append(s_pgd_x)
-            dict_im[('PGD', 0, 2, 'median')].append(m_pgd_y)
-            dict_im[('PGD', 0, 2, 'beta')].append(s_pgd_y)
+            dict_im[('PGD', 0, 1, 'median')].append(m_pgd_x)  # noqa: RUF031, RUF100
+            dict_im[('PGD', 0, 1, 'beta')].append(s_pgd_x)  # noqa: RUF031, RUF100
+            dict_im[('PGD', 0, 2, 'median')].append(m_pgd_y)  # noqa: RUF031, RUF100
+            dict_im[('PGD', 0, 2, 'beta')].append(s_pgd_y)  # noqa: RUF031, RUF100
             for jj, Ti in enumerate(periods):  # noqa: N806
                 cur_sa = f'SA({Ti}s)'
-                dict_im[(cur_sa, 0, 1, 'median')].append(m_psa_x[jj])
-                dict_im[(cur_sa, 0, 1, 'beta')].append(s_psa_x[jj])
-                dict_im[(cur_sa, 0, 2, 'median')].append(m_psa_y[jj])
-                dict_im[(cur_sa, 0, 2, 'beta')].append(s_psa_y[jj])
+                dict_im[(cur_sa, 0, 1, 'median')].append(m_psa_x[jj])  # noqa: RUF031, RUF100
+                dict_im[(cur_sa, 0, 1, 'beta')].append(s_psa_x[jj])  # noqa: RUF031, RUF100
+                dict_im[(cur_sa, 0, 2, 'median')].append(m_psa_y[jj])  # noqa: RUF031, RUF100
+                dict_im[(cur_sa, 0, 2, 'beta')].append(s_psa_y[jj])  # noqa: RUF031, RUF100
 
             # aggregate
             for cur_key, cur_value in dict_im.items():

modules/Workflow/createResponseCSV.py

@@ -0,0 +1,89 @@
+# noqa: D100
+
+#
+# Code to write response.csv file given input and dakotaTab.out files
+#
+
+# Written fmk, important code copied from whale/main.py
+# date: 08/24
+
+import argparse
+import json
+import os
+
+import numpy as np
+import pandas as pd
+
+def main(input_file, dakota_tab_file): # noqa: D103
+
+    directory_inputs = os.path.dirname(input_file) # noqa: PTH120
+    os.chdir(directory_inputs)
+
+    try:
+        # Attempt to open the file
+        with open(input_file) as file:  # noqa: PTH123
+            data = json.load(file)
+
+    except FileNotFoundError:
+        # Handle the error if the file is not found
+        print(f"Error createResponseCSV.py: The file '{input_file}' was not found.") # noqa: T201
+        return
+    except OSError:
+        # Handle other I/O errors
+        print(f"Error createResponseCSV.py: Error reading the file '{input_file}'.") # noqa: T201
+        return
+
+    app_data = data.get('Applications', None)
+    if app_data is not None:
+        dl_data = app_data.get('DL', None)
+
+        if dl_data is not None:
+            dl_app_data = dl_data.get('ApplicationData', None)
+
+            if dl_app_data is not None:
+                is_coupled = dl_app_data.get('coupled_EDP', None)
+
+    try:
+        # sy, abs - added try-statement because dakota-reliability does not write DakotaTab.out
+        dakota_out = pd.read_csv(dakota_tab_file, sep=r'\s+', header=0, index_col=0)
+
+        if is_coupled:
+            if 'eventID' in dakota_out.columns:
+                events = dakota_out['eventID'].values  # noqa: PD011
+                events = [int(e.split('x')[-1]) for e in events]
+                sorter = np.argsort(events)
+                dakota_out = dakota_out.iloc[sorter, :]
+                dakota_out.index = np.arange(dakota_out.shape[0])
+
+        dakota_out.to_csv('response.csv')
+
+    except FileNotFoundError:
+        # Handle the error if the file is not found
+        print(f"Error createResponseCSV.py: The file '{dakota_tab_file}' not found.") # noqa: T201
+        return
+
+    except OSError:
+        # Handle other I/O errors
+        print(f"Error createResponseCSV.py: Error reading '{dakota_tab_file}'.") # noqa: T201
+        return
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    # Add arguments with default values
+    parser.add_argument(
+        '--inputFile', type=str, default='AIM.json', help='Path to the input file)'
+    )
+    parser.add_argument(
+        '--dakotaTab',
+        type=str,
+        default='dakotaTab.out',
+        help='Path to the dakotaTab file)',
+    )
+
+    # Parse the arguments
+    args = parser.parse_args()
+
+    # Use the arguments
+    main(args.inputFile, args.dakotaTab)

modules/Workflow/whale/main.py

@@ -310,7 +310,7 @@ def create_command(command_list, enforced_python=None):
         for command_arg in command_list[1:]:
             command += f'"{command_arg}" '
 
-    return command
+    return command  # noqa: DOC201, RUF100
 
 
 def run_command(command):
@@ -357,7 +357,7 @@ def run_command(command):
 
         py_script.main(arg_list)
 
-        return '', ''
+        return '', ''  # noqa: DOC201, RUF100
 
     else:  # noqa: RET505
         # fmk with Shell=True not working on older windows machines, new approach needed for quoted command .. turn into a list
@@ -668,7 +668,7 @@ def get_command_list(self, app_path, force_posix=False):  # noqa: FBT002, C901
 
         # pp.pprint(arg_list)
 
-        return arg_list
+        return arg_list  # noqa: DOC201, RUF100
 
 
 class Workflow:
@@ -1316,7 +1316,7 @@ def create_asset_files(self):
 
         log_div()
 
-        return assetFilesList
+        return assetFilesList  # noqa: DOC201, RUF100
 
     def augment_asset_files(self):  # noqa: C901
         """Short description
@@ -1504,7 +1504,7 @@ def augment_asset_files(self):  # noqa: C901
         )
         log_div()
 
-        return assetFilesList
+        return assetFilesList  # noqa: DOC201, RUF100
 
     def perform_system_performance_assessment(self, asset_type):
         """For an asset type run the system level performance assessment application
@@ -1525,7 +1525,7 @@ def perform_system_performance_assessment(self, asset_type):
                 prepend_timestamp=False,
             )
             log_div()
-            return False
+            return False  # noqa: DOC201, RUF100
 
         if performance_app.rel_path == None:  # noqa: E711
             log_msg(
@@ -1909,7 +1909,7 @@ def init_simdir(self, asst_id=None, AIM_file_path='AIM.json'):  # noqa: C901, N8
             prepend_timestamp=False,
         )
         log_div()
-        return dst
+        return dst  # noqa: DOC201, RUF100
 
     def cleanup_simdir(self, asst_id):
         """Short description
@@ -2734,7 +2734,7 @@ def estimate_losses(  # noqa: C901
                     ],
                 )
                 if ('PID', '0') in df_res.columns:
-                    del df_res[('PID', '0')]
+                    del df_res[('PID', '0')]  # noqa: RUF031, RUF100
 
                 # store the EDP statistics in the output DF
                 for col in np.transpose(col_info):

modules/common/simcenter_common.py

@@ -283,7 +283,7 @@ def get_scale_factors(input_units, output_units):  # noqa: C901
 
             scale_factors.update({input_name: f_scale})
 
-    return scale_factors
+    return scale_factors  # noqa: DOC201, RUF100
 
 
 def get_unit_bases(input_units):
@@ -306,4 +306,4 @@ def get_unit_bases(input_units):
                 input_unit_bases = cur_unit_bases
                 break
 
-    return input_unit_bases
+    return input_unit_bases  # noqa: DOC201, RUF100

modules/createEVENT/CFDEvent/CFDEvent.py

@@ -13,7 +13,7 @@ def directionToDof(direction):  # noqa: N802
     """Converts direction to degree of freedom"""  # noqa: D400, D401
     directioMap = {'X': 1, 'Y': 2, 'Z': 3}  # noqa: N806
 
-    return directioMap[direction]
+    return directioMap[direction]  # noqa: DOC201, RUF100
 
 
 def addFloorForceToEvent(patternsArray, force, direction, floor):  # noqa: ARG001, N802, N803

modules/createEVENT/EmptyDomainCFD/EmptyDomainCFD.py

@@ -13,7 +13,7 @@ def directionToDof(direction):  # noqa: N802
     """Converts direction to degree of freedom"""  # noqa: D400, D401
     directioMap = {'X': 1, 'Y': 2, 'Z': 3}  # noqa: N806
 
-    return directioMap[direction]
+    return directioMap[direction]  # noqa: DOC201, RUF100
 
 
 def addFloorForceToEvent(patternsArray, force, direction, floor):  # noqa: ARG001, N802, N803