Merge remote-tracking branch 'upstream/master'

NHERI-SimCenter · Sep 30, 2024 · ca4878c · ca4878c
2 parents 63d4294 + da3e5bc
commit ca4878c
Show file tree

Hide file tree

Showing 345 changed files with 4,202,434 additions and 46,715 deletions.
diff --git a/.github/workflows/.wordlist.txt b/.github/workflows/.wordlist.txt
@@ -0,0 +1,25 @@
+theRes
+nd
+ned
+pres
+writeT
+sOrD
+responseD
+WORKD
+workd
+oT
+WriteT
+Suh
+WLL
+VIE
+Momento
+lamda
+dum
+numer
+reord
+fro
+Equil
+ot
+repID
+BROWER
+PEASE
diff --git a/.gitignore b/.gitignore
@@ -96,5 +96,6 @@ fmkTest.sh
 #Remove .vscode
 .vscode
 
+.coverage
 
-
+applications.*
diff --git a/.wordlist.txt b/.wordlist.txt
@@ -0,0 +1,25 @@
+theRes
+nd
+ned
+pres
+writeT
+sOrD
+responseD
+WORKD
+workd
+oT
+WriteT
+Suh
+WLL
+VIE
+Momento
+lamda
+dum
+numer
+reord
+fro
+Equil
+ot
+repID
+BROWER
+PEASE
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # SimCenterBackendApplications
 
-[![Build status](https://ci.appveyor.com/api/projects/status/2fitp6tm5sj00qwr?svg=true)](https://ci.appveyor.com/project/fmckenna/simcenterbackendapplications)
+[![Build status](https://ci.appveyor.com/api/projects/status/2fitp6tm5sj00qwr?svg=true)](https://ci.appveyor.com/project/JustinBonus/simcenterbackendapplications)
 
 This repo contains the backend applications that make up SimCeA (SimCenter Aquarium). SimCeA is a collection of applications developed by SimCenter that are utilized when the research applications (quoFEM, EE-UQ, WE-UQ, PBE, and RDT) perform the numerical computations. These computations are performed using scientific workflows; the software that runs the workflows are found in the modules/Workflow directory. The applications these workflows invoke when running are found in the other directories under modules. 
 

diff --git a/appveyor.yml b/appveyor.yml
@@ -1,11 +1,11 @@
-version: 1.0.{build}
+version: 24.09.{build}
 
 image:
+  - Visual Studio 2019
   - macOS
   - Ubuntu1804
-  - Visual Studio 2019
 
-stack: python 3.7
+stack: python 3.9
 
 for:
   # macOS 
@@ -18,14 +18,15 @@ for:
 
     init:
        - export PATH="$HOME/Qt/5.15.2/clang_64/bin:$HOME/venv3.9/bin:$PATH"
-       - python -m pip install --upgrade pip
-       - pip install conan
+       - python3 -m pip install --upgrade pip
+       - pip install conan==1.60.1
        - conan user
        - conan remote add simcenter https://nherisimcenter.jfrog.io/artifactory/api/conan/simcenter
 
     install:
        - uname
-       - git clone https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git       
+       - rm -rf SimCenterBackendApplications
+       - git clone https://github.com/JustinBonus/SimCenterBackendApplications.git       
 
     build_script:
 
@@ -39,6 +40,7 @@ for:
        - qmake --version
        - gcc --version
        - python --version
+       - python3 --version
 
   # Ubuntu1804 
   -
@@ -49,18 +51,19 @@ for:
     clone_folder: ~/SimCenter
 
     init:
-       - export PATH="$HOME/Qt/5.15.2/gcc_64/bin:$HOME/venv3.8.6/bin:$PATH"
+       - export PATH="$HOME/Qt/5.15.2/gcc_64/bin:$HOME/venv3.9/bin:$PATH"
        - export PATH="/home/appveyor/.local/bin:$PATH"
 
     install:
        - uname
        - sudo update-alternatives --set gcc /usr/bin/gcc-9
        - sudo apt-get -y install libglu1-mesa-dev freeglut3-dev mesa-common-dev libblas-dev liblapack-dev
-       - python -m pip install --upgrade pip
-       - pip install conan
+       - python3 -m pip install --upgrade pip
+       - pip install conan==1.60.1
        - conan user
        - conan remote add simcenter https://nherisimcenter.jfrog.io/artifactory/api/conan/simcenter
-       - git clone https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git
+       - rm -rf SimCenterBackendApplications
+       - git clone https://github.com/JustinBonus/SimCenterBackendApplications.git
 
     build_script:
        # build SimCenterBackendApplications
@@ -73,6 +76,7 @@ for:
        - qmake --version
        - gcc --version
        - python --version
+       - python3 --version
 
   # Visual Studio 2019
   -
@@ -85,11 +89,11 @@ for:
 
     init:
        - cmd: set PYTHON=C:\PYTHON38-x64
-       - cmd: set PYTHONNET_PYDLL=%PYTHON%\python3.8.dll
+       - cmd: set PYTHONNET_PYDLL=%PYTHON%\python3.9.dll
        - cmd: set QT=C:\Qt\5.15.2\msvc2019_64\bin
        - cmd: set PATH=%PYTHON%;%PYTHON%\Scripts;%QT%;%PATH%
        - cmd: call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat"
-       - cmd: pip.exe install conan
+       - cmd: pip.exe install conan==1.60.1
        - cmd: conan user
        - cmd: conan profile new default --detect
        - cmd: conan profile show default
@@ -99,7 +103,8 @@ for:
        - cmd: echo %PATH%
 
     install:
-       - cmd: git clone https://github.com/NHERI-SimCenter/SimCenterBackendApplications.git
+       - cmd: rm -rf SimCenterBackendApplications
+       - cmd: git clone https://github.com/JustinBonus/SimCenterBackendApplications.git
        - cmd: dir
 
     build_script:

diff --git a/conanfile.py b/conanfile.py
@@ -2,6 +2,7 @@
 
 from conans import CMake, ConanFile
 
+
 class simCenterBackendApps(ConanFile):  # noqa: D101
     name = 'SimCenterBackendApplications'
     version = '1.2.2'
@@ -30,8 +31,8 @@ class simCenterBackendApps(ConanFile):  # noqa: D101
         'jsonformoderncpp/3.7.0',
         'nanoflann/1.3.2',
         'nlopt/2.7.1',
-        "boost/1.71.0",
-        'kissfft/131.1.0'
+        'boost/1.71.0',
+        'kissfft/131.1.0',
     ]
 
     # Custom attributes for Bincrafters recipe conventions

diff --git a/ignore_words.txt b/ignore_words.txt
@@ -21,3 +21,5 @@ fro
 Equil
 ot
 repID
+BROWER
+PEASE
diff --git a/makeEXE.sh b/makeEXE.sh
@@ -1,11 +1,11 @@
 #!/bin/bash
 
-echo "Building SimCenterBackendApplicationss ..."
+echo "Building SimCenterBackendApplications ..."
 mkdir -p build
 cd build
 conan install .. --build missing
 status=$?; if [[ $status != 0 ]]; then echo "conan failed"; exit $status; fi
-cmake ..
+cmake -DCMAKE_CXX_STANDARD=17 -DCMAKE_CXX_STANDARD_REQUIRED=ON -DCMAKE_CXX_EXTENSIONS=OFF ..
 status=$?; if [[ $status != 0 ]]; then echo "cmake failed"; exit $status; fi
 cmake --build . --config Release
 status=$?; if [[ $status != 0 ]]; then echo "make failed"; exit $status; fi

diff --git a/modules/Workflow/WorkflowApplications.json b/modules/Workflow/WorkflowApplications.json
@@ -544,6 +544,11 @@
         "ExecutablePath": "applications/createEVENT/stochasticWave/StochasticWave.py",
         "ApplicationSpecificInputs":[]
       },  
+      {
+        "Name": "TaichiEvent",
+        "ExecutablePath": "applications/createEVENT/TaichiEvent/TaichiEvent.py",
+        "ApplicationSpecificInputs":[]
+      },  
       {
         "Name": "GeoClawOpenFOAM",
         "ExecutablePath": "applications/createEVENT/GeoClawOpenFOAM/GeoClawOpenFOAM.py",
@@ -974,6 +979,10 @@
         "Name": "IMasEDP",
         "ExecutablePath": "applications/performSIMULATION/IMasEDP/IMasEDP.py"
       },
+      {
+        "Name": "CapacitySpectrumMethod",
+        "ExecutablePath": "applications/performSIMULATION/capacitySpectrum/runCMS.py"
+      },
       {
         "Name": "SurrogateSimulation",
         "ExecutablePath": "applications/performSIMULATION/surrogateSimulation/SurrogateSimulation.py"

diff --git a/modules/Workflow/whale/main.py b/modules/Workflow/whale/main.py
@@ -1507,27 +1507,33 @@ def augment_asset_files(self):  # noqa: C901
         return assetFilesList  # noqa: DOC201, RUF100
 
     def perform_system_performance_assessment(self, asset_type):
-        """For an asset type run the system level performance assessment application
+        """Run the system level performance assessment application.
 
-        Longer description
+        For an asset type run the system level performance assessment
+        application.
 
         Parameters
         ----------
         asset_type: string
            Asset type to run perform system assessment of
 
-        """  # noqa: D400
-        if 'SystemPerformance' in self.workflow_apps.keys():  # noqa: SIM118
+        """
+        # Make sure that we are in the run directory before we run REWET
+        # Every other path will be relative to the Run Directory (result dir)
+        os.chdir(self.run_dir)
+
+        # Check if system performance is requested
+        if 'SystemPerformance' in self.workflow_apps:
             performance_app = self.workflow_apps['SystemPerformance'][asset_type]
         else:
             log_msg(
                 f'No Performance application to run for asset type: {asset_type}.',
                 prepend_timestamp=False,
             )
             log_div()
-            return False  # noqa: DOC201, RUF100
+            return False
 
-        if performance_app.rel_path == None:  # noqa: E711
+        if performance_app.rel_path is None:
             log_msg(
                 f'No Performance application to run for asset type: {asset_type}.',
                 prepend_timestamp=False,
@@ -1536,8 +1542,7 @@ def perform_system_performance_assessment(self, asset_type):
             return False
 
         log_msg(
-            'Performing System Performance Application for asset type: '
-            + asset_type,
+            f'Performing System Performance Application for asset type: {asset_type}',
             prepend_timestamp=False,
         )
         log_div()
@@ -1550,18 +1555,13 @@ def perform_system_performance_assessment(self, asset_type):
         # defaults added to a system performance app are asset_type, input_dir and running_parallel (default False)
         #
 
-        # app_command_list.append('--asset_type')
-        # app_command_list.append(asset_type)
         app_command_list.append('--input')
         app_command_list.append(self.input_file)
-        # app_command_list.append('--working_dir')
-        # app_command_list.append(self.working_dir)
 
         # Sina added this part for parallel run in REWET
         if self.parType == 'parSETUP':
             log_msg(
-                '\nParallel settings for System Performance for asset type:'
-                + asset_type,
+                f'\nParallel settings for System Performance for asset type:{asset_type}',
                 prepend_timestamp=False,
             )
             app_command_list.append('--par')
@@ -1583,34 +1583,10 @@ def perform_system_performance_assessment(self, asset_type):
         )
 
         log_msg(
-            'System Performance Application Completed for asset type: ' + asset_type,
+            f'System Performance Application Completed for asset type: {asset_type}',
             prepend_timestamp=False,
         )
 
-        #  end of Sina's odifications for parallel run
-
-        # if (self.parType == 'parSETUP'):
-
-        #     log_msg('\nWriting System Performance application for asset type:' + asset_type, prepend_timestamp=False)
-        #     self.parCommandFile.write("\n# Writing System Performance application for asset type:" + asset_type +"\n")
-
-        #     if performance_app.runsParallel == False:
-        #         self.parCommandFile.write(command + "\n")
-        #     else:
-        #         self.parCommandFile.write(self.mpiExec + " -n " + str(self.numProc) + " " + command + " --running_parallel True\n")
-
-        # else:
-
-        #     log_msg('\n{}\n'.format(command), prepend_timestamp=False,
-        #             prepend_blank_space=False)
-
-        #     result, returncode = run_command(command)
-
-        #     log_msg('Output: ', prepend_timestamp=False, prepend_blank_space=False)
-        #     log_msg('\n{}\n'.format(result), prepend_timestamp=False, prepend_blank_space=False)
-
-        #     log_msg('System Performance Application Completed for asset type: ' + asset_type, prepend_timestamp=False)
-
         log_div()
         return True
 
@@ -2870,7 +2846,7 @@ def aggregate_results(  # noqa: C901, PLR0912, PLR0915
                 bldg_dir = Path(os.path.dirname(asst_data[a_i]['file'])).resolve()  # noqa: PTH120
                 main_dir = bldg_dir
                 assetTypeHierarchy = [bldg_dir.name]  # noqa: N806
-                while main_dir.parent.name != self.run_dir.name:
+                while main_dir.parent.name != 'Results':
                     main_dir = bldg_dir.parent
                     assetTypeHierarchy = [main_dir.name] + assetTypeHierarchy  # noqa: N806, RUF005
 

diff --git a/modules/createAIM/GeoJSON_to_ASSET/GeoJSON_to_ASSET.py b/modules/createAIM/GeoJSON_to_ASSET/GeoJSON_to_ASSET.py
@@ -1,4 +1,4 @@
-import argparse  # noqa: INP001, D100
+import argparse  # noqa: D100, INP001
 import importlib
 import json
 import os
@@ -8,7 +8,8 @@
 import warnings
 
 import geopandas as gpd
-import momepy
+
+# import momepy
 import numpy as np
 import pandas as pd
 import shapely
@@ -179,10 +180,10 @@ def defineConnectivities(  # noqa: N802, D102
         # Convert find connectivity and add start_node, end_node attributes
         edges = self.gdf
         datacrs = edges.crs
-        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')
+        graph = momepy.gdf_to_nx(edges.to_crs('epsg:6500'), approach='primal')  # noqa: F821
         with warnings.catch_warnings():  # Suppress the warning of disconnected components in the graph
             warnings.simplefilter('ignore')
-            nodes, edges, sw = momepy.nx_to_gdf(
+            nodes, edges, sw = momepy.nx_to_gdf(  # noqa: F821
                 graph, points=True, lines=True, spatial_weights=True
             )
         # edges = edges.set_index('ind')
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,3 +21,5 @@ fro @@
     Equil
     ot
     repID
+    BROWER
+    PEASE