Silence all other warnings

Commands used:
```
ruff format
ruff check --add-noqa
ruff format  # 331 files left unchanged
ruff check  # All checks passed!
```

build.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python  # noqa: EXE001, D100
 
 from bincrafters import build_template_default
 

conanfile.py

@@ -1,30 +1,30 @@
-import os
+import os  # noqa: D100
 
 from conans import CMake, ConanFile
 
 
-class simCenterBackendApps(ConanFile):
+class simCenterBackendApps(ConanFile):  # noqa: D101
     name = 'SimCenterBackendApplications'
     version = '1.2.2'
     description = 'Backend applications for SimCenter software'
     license = 'BSD 3-Clause'
     author = 'Michael Gardner [email protected]'
     url = 'https://github.com/NHERI-SimCenter/SimCenterBackendApplications'
-    settings = {
+    settings = {  # noqa: RUF012
         'os': None,
         'build_type': None,
         'compiler': None,
         'arch': ['x86_64', 'armv8'],
     }
-    options = {'shared': [True, False]}
-    default_options = {
+    options = {'shared': [True, False]}  # noqa: RUF012
+    default_options = {  # noqa: RUF012
         'mkl-static:threaded': False,
         'ipp-static:simcenter_backend': True,
         'libcurl:with_ssl': 'openssl',
     }
     generators = 'cmake'
     build_policy = 'missing'
-    requires = [
+    requires = [  # noqa: RUF012
         'jansson/2.13.1',
         'zlib/1.2.11',
         'libcurl/8.1.1',
@@ -40,30 +40,30 @@ class simCenterBackendApps(ConanFile):
     _build_subfolder = 'build_subfolder'
     # Set short paths for Windows
     short_paths = True
-    scm = {
+    scm = {  # noqa: RUF012
         'type': 'git',  # Use "type": "svn", if local repo is managed using SVN
         'subfolder': _source_subfolder,
         'url': 'auto',
         'revision': 'auto',
     }
 
-    def configure(self):
+    def configure(self):  # noqa: D102
         self.options.shared = False
 
-    def configure_cmake(self):
+    def configure_cmake(self):  # noqa: D102
         cmake = CMake(self)
         cmake.configure(source_folder=self._source_subfolder)
         return cmake
 
-    def build(self):
+    def build(self):  # noqa: D102
         cmake = self.configure_cmake()
         cmake.build()
 
-    def package(self):
+    def package(self):  # noqa: D102
         self.copy(pattern='LICENSE', dst='licenses', src=self._source_subfolder)
         cmake = self.configure_cmake()
         cmake.install()
         self.copy('*', dst='bin', src=self._source_subfolder + '/applications')
 
-    def package_info(self):
-        self.env_info.PATH.append(os.path.join(self.package_folder, 'bin'))
+    def package_info(self):  # noqa: D102
+        self.env_info.PATH.append(os.path.join(self.package_folder, 'bin'))  # noqa: PTH118

modules/Workflow/AggregateResults.py

@@ -1,4 +1,4 @@
-#
+#  # noqa: INP001, D100
 # Copyright (c) 2018 Leland Stanford Junior University
 # Copyright (c) 2018 The Regents of the University of California
 #
@@ -46,14 +46,14 @@
 import pandas as pd
 
 
-def log_msg(msg):
-    print(
-        '{} {}'.format(datetime.utcnow().strftime('%Y-%m-%dT%H:%M:%S:%fZ')[:-4], msg)
+def log_msg(msg):  # noqa: D103
+    print(  # noqa: T201
+        '{} {}'.format(datetime.utcnow().strftime('%Y-%m-%dT%H:%M:%S:%fZ')[:-4], msg)  # noqa: DTZ003
     )
 
 
-def main(threads=1):
-    headers = dict(
+def main(threads=1):  # noqa: C901, D103
+    headers = dict(  # noqa: C408
         IM=[0, 1, 2, 3],
         BIM=[
             0,
@@ -85,13 +85,13 @@ def read_csv_np(file, header):
             data[data == ''] = np.nan
 
             tuples = [tuple(h) for h in res[:first_row].T[1:]]
-            MI = pd.MultiIndex.from_tuples(tuples, names=res[:first_row].T[0])
+            MI = pd.MultiIndex.from_tuples(tuples, names=res[:first_row].T[0])  # noqa: N806
 
-            df = pd.DataFrame(
+            df = pd.DataFrame(  # noqa: PD901
                 data, columns=MI, index=res[first_row:].T[0], dtype=float
             )
 
-            return df
+            return df  # noqa: RET504
 
         @delayed
         def read_csv_files_np(file_list, header):
@@ -106,7 +106,7 @@ def read_csv_files_np(file_list, header):
     for res_type in ['IM', 'BIM', 'EDP', 'DM', 'DV']:
         log_msg(f'Loading {res_type} files...')
 
-        files = glob.glob(f'./results/{res_type}/*/{res_type}_*.csv')
+        files = glob.glob(f'./results/{res_type}/*/{res_type}_*.csv')  # noqa: PTH207
         # files = files[:1000]
 
         if len(files) > 0:
@@ -115,7 +115,7 @@ def read_csv_files_np(file_list, header):
                 chunk = math.ceil(file_count / threads)
                 df_list = []
 
-                print(f'Creating threads for {file_count} files...')
+                print(f'Creating threads for {file_count} files...')  # noqa: T201
 
                 for t_i in range(threads):
                     # print(t_i)
@@ -152,7 +152,7 @@ def read_csv_files_np(file_list, header):
                 log_msg('Concatenating all files')
                 df_all = pd.concat(df_list, axis=0, sort=False)
 
-            df_all.sort_index(axis=0, inplace=True)
+            df_all.sort_index(axis=0, inplace=True)  # noqa: PD002
 
             # save the results
             log_msg('Saving results')
@@ -168,7 +168,7 @@ def read_csv_files_np(file_list, header):
             # df_all.to_csv('{}.csv'.format(res_type))
 
         else:
-            print(f'No {res_type} files found')
+            print(f'No {res_type} files found')  # noqa: T201
 
     if use_dask:
         log_msg('Closing cluster...')
@@ -178,7 +178,7 @@ def read_csv_files_np(file_list, header):
     # aggregate the realizations files
     log_msg('Aggregating individual realizations...')
 
-    files = glob.glob(
+    files = glob.glob(  # noqa: PTH207
         './results/{}/*/{}_*.hdf'.format('realizations', 'realizations')
     )
 
@@ -199,7 +199,7 @@ def read_csv_files_np(file_list, header):
 
             df_all.index = df_all.index.astype(np.int32)
 
-            df_all.sort_index(axis=0, inplace=True)
+            df_all.sort_index(axis=0, inplace=True)  # noqa: PD002
 
             try:
                 df_all.astype(np.float32).to_hdf(
@@ -210,7 +210,7 @@ def read_csv_files_np(file_list, header):
                     complevel=1,
                     complib='blosc:blosclz',
                 )
-            except:
+            except:  # noqa: E722
                 df_all.to_hdf(
                     'realizations.hdf',
                     key,
@@ -228,7 +228,7 @@ def read_csv_files_np(file_list, header):
 if __name__ == '__main__':
     # Defining the command line arguments
 
-    workflowArgParser = argparse.ArgumentParser('Aggregate the results from rWHALE.')
+    workflowArgParser = argparse.ArgumentParser('Aggregate the results from rWHALE.')  # noqa: N816
 
     workflowArgParser.add_argument(
         '-threads',