Merge pull request #870 from ScilifelabDataCentre/dev

New release: 2.14.0

Author: valyo

.github/workflows/codeql-cli.yml

@@ -55,7 +55,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -66,7 +66,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v4
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 https://git.io/JvXDl
@@ -80,4 +80,4 @@ jobs:
       #   make release
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v4

.github/workflows/gui-executable.yml

@@ -12,7 +12,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        # If new Python versions are added, update pylint accordingly
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -23,7 +24,11 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-          pip install pylint==2.17.3
+          pip install setuptools wheel
+          pip install pylint==3.3.0
       - name: Analysing the code with pylint
+        # Disable rule that limits to 5 the number of positional arguments
         run: |
-          pylint --rcfile=.pylintrc $(git ls-files '*.py')
+          pylint --rcfile=.pylintrc \
+            --disable=too-many-positional-arguments \
+            -- $(git ls-files '*.py')

.github/workflows/lint-pylint.yml

@@ -46,7 +46,7 @@ jobs:
           files: ./coverage/report.xml
 
   build-on-windows:
-    runs-on: windows-latest
+    runs-on: windows-2022
 
     steps:
       - uses: actions/checkout@v3
@@ -65,6 +65,7 @@ jobs:
           SET COVERAGE_FILE=./coverage/.coverage
           pytest --color=yes --cov=./dds_cli --cov-report=xml:coverage/report-windows.xml
 
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v5
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage/report-windows.xml

.github/workflows/pytest-cli.yml

@@ -100,10 +100,10 @@ jobs:
             ASSET_MIME: application/x-elf
     steps:
       - uses: actions/checkout@v4
-      - name: Python 3.9 setup
+      - name: Python 3.12 setup
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.12
           # architecture: 'x64'
       - name: Install dependencies
         run: |
@@ -146,7 +146,12 @@ jobs:
         uses: matthiaszepper/sphinx-action-v4@pdflatex
         with:
           container: pdflatex
-          pre-build-command: "apt-get update && apt-get install -y librsvg2-bin && apt-get -y install build-essential"
+          pre-build-command: |
+            apt-get update && \
+            apt-get install -y librsvg2-bin && \
+            apt-get -y install build-essential && \
+            apt-get install -y fonts-noto-color-emoji && \
+            apt-get install -y texlive-luatex
           build-command: "make latexpdf"
           docs-folder: "docs/"
       - name: Create an artifact of the previously built HTML

.github/workflows/release-cli.yml

@@ -13,10 +13,10 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v2
         with:
-          python-version: 3.10.8
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/rich-codex-cli.yml

@@ -42,7 +42,7 @@ jobs:
           command: code test
           args: --sarif-file-output=snyk.sarif
       - name: Upload result to GitHub Code Scanning
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v4
         with:
           sarif_file: snyk.sarif
           category: snyk

.github/workflows/snyk-scan-cli.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/test-pypi-cli.yml

@@ -33,6 +33,6 @@ jobs:
           severity: "CRITICAL,HIGH"
 
       - name: Upload Trivy scan results to GitHub Security tab
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v4
         with:
           sarif_file: "trivy-results.sarif"

.github/workflows/trivy-cli.yml

@@ -48,8 +48,3 @@ timings
 .DS_Store
 *test-venv*
 test-directory*
-gui_build/dist
-gui_build/build
-gui_build/dds_gui_standalone.spec
-gui_build/dds_gui_standalone.spec.py
-gui_build/dds_gui_standalone.spec.pyc