Quality and Linting (#1010)

- Applied advanced linting to code base
- Fixed small bugs relating to use of methods on incorrect types.
- Updated `pyproject.toml` dependencies.
- Updated CI action versions.

Author: kzscisoft

.github/workflows/citation.yml

@@ -2,9 +2,9 @@ name: Citation File Validation
 
 on:
   push:
-    branches: [ "main", "dev", "hotfix/update-ci" ]
+    branches: ["main", "dev", "hotfix/update-ci"]
   pull_request:
-    branches: [ "main", "dev", "hotfix/update-ci" ]
+    branches: ["main", "dev", "hotfix/update-ci"]
 
 permissions:
   contents: read
@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
-    - name: Set up Python
-      uses: actions/setup-python@v6
-    - name: Install Checker
-      run: python3 -m pip install cffconvert
-    - name: Check Citation File
-      run: cffconvert --validate
+      - uses: actions/checkout@v7
+      - name: Set up Python
+        uses: actions/setup-python@v7
+      - name: Install Checker
+        run: python3 -m pip install cffconvert
+      - name: Check Citation File
+        run: cffconvert --validate

.github/workflows/examples.yml

@@ -50,7 +50,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Install Simvue
@@ -66,7 +66,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Install Simvue
@@ -86,7 +86,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Install Simvue
@@ -106,7 +106,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Download SU2
@@ -128,7 +128,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Install Simvue
@@ -150,7 +150,7 @@ jobs:
         with:
           submodules: recursive
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
       - name: Install Simvue

.github/workflows/prek.yml

@@ -21,8 +21,8 @@ jobs:
     timeout-minutes: 30
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: Run Prek
-        uses: j178/prek-action@v2
+        uses: j178/prek-action@v3.0.0
         with:
-          extra-args: '--all-files --skip no-commit-to-branch'
+          extra-args: "--all-files --skip no-commit-to-branch"

.github/workflows/test_client_macos_nightlies.yml

@@ -17,9 +17,9 @@ jobs:
     runs-on: macos-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -42,9 +42,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -67,9 +67,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -91,9 +91,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -116,9 +116,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -141,9 +141,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -165,9 +165,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.14
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.14"
     - name: Install dependencies
@@ -189,9 +189,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -213,9 +213,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies
@@ -237,9 +237,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v7
     - name: Set up Python 3.13
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: "3.13"
     - name: Install dependencies

.github/workflows/test_client_ubuntu.yml

@@ -22,9 +22,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -46,9 +46,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -70,9 +70,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -93,9 +93,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -117,9 +117,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -141,9 +141,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -164,9 +164,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -187,9 +187,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -210,9 +210,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies
@@ -233,9 +233,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
       - name: Set up Python 3.14
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: "3.14"
       - name: Install dependencies