Initial commit

.github/workflows/REGX_test_import_libraries.sh

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+# Install nbcommands if not already installed. More info: https://github.com/vinayak-mehta/nbcommands
+if ! command -v nbgrep &> /dev/null; then
+    echo "nbcommands is not installed. Installing..."
+    pip install nbcommands
+fi
+
+# Specify the path for the output Python file
+mkdir -p ./.github/workflows/testing
+touch ./.github/workflows/testing/test_import_libraries.py
+PYTHON_FILE="./.github/workflows/testing/test_import_libraries.py"
+
+# Remove the output file if it already exists
+rm -f "$PYTHON_FILE"
+
+# Search for *.ipynb files recursively in all folders
+find . -type f -name '*.ipynb' -print0 |
+    while IFS= read -r -d '' file; do
+        # Extract import statements from Jupyter notebooks               
+        # new one catch the import xx.x as y and removing the space
+        # nbgrep "(?:from\s+(\w+(?:\.\w+)*)\s+import\s+(\*|\w+)(?:\s+as\s+\w+)?(?:,s*\w+(?:\\s+as\s+\w+)?)*|import\s+(\w+(?:\.\w+)*)\s+as\s+\w+(?:,\s*\w+(?:\s+as\s+\w+)?)*)" "$file" | grep -v 'nbgrep:' | awk -F ':' '{sub(/^[^:]*:[^:]*:line [0-9]+:/, " ", $0)}1'| sed 's/^[[:space:]]*//'
+        nbgrep "(?:from\s+(\w+(?:\.\w+)*)\s+import\s+(\*|\w+)(?:\s+as\s+\w+)?(?:,\s*\w+(?:\s+as\s+\w+)?)*|import\s+(\w+(?:\.\w+)*)\s+as\s+\w+(?:,\s*\w+(?:\s+as\s+\w+)?)*)|(?:^|\n)import\s+(\w+(?:\.\w+)*)\s+" "$file" | grep -v 'nbgrep:' | awk -F ':' '{sub(/^[^:]*:[^:]*:line [0-9]+:/, " ", $0)}1'| sed 's/^[[:space:]]*//'
+
+
+    done | sort -u > "$PYTHON_FILE"
+echo "<<<<<<< All extract import statements from Jupyter notebooks >>>>>>"
+cat  "$PYTHON_FILE"
+
+
+# Generate test function in test.py
+echo "#!/usr/bin/env python" > "$PYTHON_FILE.tmp"
+echo "" >> "$PYTHON_FILE.tmp"
+echo "def test_import_libraries():" >> "$PYTHON_FILE.tmp"
+echo "    try:" >> "$PYTHON_FILE.tmp"
+grep -v "^import" "$PYTHON_FILE" | sed 's/^/        /' >> "$PYTHON_FILE.tmp"
+echo "    except ImportError as e:" >> "$PYTHON_FILE.tmp"
+echo "        # If any of the libraries cannot be imported, the test will fail" >> "$PYTHON_FILE.tmp"
+echo "        assert False, f\"Failed to import library: {e}\"" >> "$PYTHON_FILE.tmp"
+echo "" >> "$PYTHON_FILE.tmp"
+echo "    # If all libraries are imported successfully, the test passes" >> "$PYTHON_FILE.tmp"
+echo "    assert True" >> "$PYTHON_FILE.tmp"
+
+# Move the temporary file to the final location
+mv "$PYTHON_FILE.tmp" "$PYTHON_FILE"

.github/workflows/workflow-02.yml

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+name: Test in different OS
+## The events
+on:
+  workflow_dispatch:
+    inputs:
+      include-MacOS-M1-M2:
+        description: 'Include macOS-(M1-M2)variations'
+        required: true
+        default: 'false'
+        type: choice
+        options:
+        - 'true'
+        - 'false'
+  # push:
+  #   branches:
+  #     - main
+    # paths:
+    #   - requirements.txt
+
+jobs:
+
+  Test_under_ubuntu:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-22.04, ubuntu-20.04] 
+        python-version: [3.11.3] 
+
+## The actions
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Create import_libraries_test.py from Notebooks 
+        run: |    
+          echo "<<<<<<< Search for *.ipynb files recursively in all folders >>>>>>"
+          chmod +x .github/workflows/REGX_test_import_libraries.sh
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo  "<<<<<<< Create import libraries from the Notebook run successfully  >>>>>>"
+
+      - name:  Install dependencies 
+        run: |
+          python --version
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip list
+          pip install -r requirements.txt
+          echo "<<<<<<< Install dependencies run successfully >>>>>>"
+
+      - name:  Test the import libraries
+        run: |
+          source .venv/bin/activate
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo "<<<<<<< Test the dependencies in the import libraries from the Notebook >>>>>>"
+          pip install pytest
+          pytest ./.github/workflows/testing/test_import_libraries.py
+          echo  "<<<<<<< Test_under_ubuntuOS run successfully  >>>>>>"
+
+
+  Test_under_windows:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-2022, windows-2019]
+        python-version: [3.11.3]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Create import_libraries_test.py from Notebooks 
+        shell: bash   
+        run: |    
+          echo "<<<<<<< Search for *.ipynb files recursively in all folders >>>>>>"
+          chmod +x .github/workflows/REGX_test_import_libraries.sh
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo  "<<<<<<< Create import libraries from the Notebook run successfully  >>>>>>"
+
+      - name:  Install dependencies 
+        shell: bash  
+        run: |
+          echo "Note: This code is intended to run under the Bash CLI, not PowerShell."
+          python --version
+          python -m venv .venv
+          source .venv/Scripts/activate
+          python -m pip install --upgrade pip
+          pip list
+          pip install -r requirements.txt
+          echo "<<<<<<< Install dependencies run successfully >>>>>>"
+
+      - name:  Test the import libraries
+        shell: bash  
+        run: |
+          echo "Note: This code is intended to run under the Bash CLI, not PowerShell."
+          source .venv/Scripts/activate
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo "<<<<<<< Test the dependencies in the import libraries from the Notebook >>>>>>"
+          pip install pytest
+          pytest ./.github/workflows/testing/test_import_libraries.py
+          echo  "<<<<<<< Test_under_ubuntuOS run successfully  >>>>>>"
+
+      
+
+  Test_under_macos:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest,macos-13]
+        python-version: [3.11.3] 
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Create import_libraries_test.py from Notebooks 
+        run: |    
+            echo "<<<<<<< Search for *.ipynb files recursively in all folders >>>>>>"
+            chmod +x .github/workflows/REGX_test_import_libraries.sh
+            ./.github/workflows/REGX_test_import_libraries.sh
+            echo  "<<<<<<< Create import libraries from the Notebook run successfully  >>>>>>"
+
+      - name:  Install dependencies 
+        run: |
+          python --version
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip list
+          pip install -r requirements.txt
+          echo "<<<<<<< Install dependencies run successfully >>>>>>"
+
+      - name:  Test the import libraries
+        run: |
+          source .venv/bin/activate
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo "<<<<<<< Test the dependencies in the import libraries from the Notebook >>>>>>"
+          pip install pytest
+          pytest ./.github/workflows/testing/test_import_libraries.py
+          echo  "<<<<<<< Test_under_ubuntuOS run successfully  >>>>>>"
+          
+
+  Test_under_macos_M1-M2:
+    runs-on: ${{ matrix.os }}
+    if: github.event.inputs.include-MacOS-M1-M2 == 'true'
+    strategy:
+      matrix:
+        os: [macos-14] #[flyci-macos-large-latest-m1,flyci-macos-large-latest-m2] # Price on FlyC (https://github.com/apps/flyci-prod) (https://github.com/actions/runner-images)
+        python-version: [3.11.3]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Create import_libraries_test.py from Notebooks 
+        run: |    
+            echo "<<<<<<< Search for *.ipynb files recursively in all folders >>>>>>"
+            chmod +x .github/workflows/REGX_test_import_libraries.sh
+            ./.github/workflows/REGX_test_import_libraries.sh 
+            echo  "<<<<<<< Create import libraries from the Notebook run successfully  >>>>>>"
+
+      - name:  Install dependencies 
+        run: |
+          python --version
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip list
+          pip install -r requirements.txt
+          echo "<<<<<<< Install dependencies run successfully >>>>>>"
+
+      - name:  Test the import libraries
+        run: |
+          source .venv/bin/activate
+          ./.github/workflows/REGX_test_import_libraries.sh
+          echo "<<<<<<< Test the dependencies in the import libraries from the Notebook >>>>>>"
+          pip install pytest
+          pytest ./.github/workflows/testing/test_import_libraries.py
+          echo  "<<<<<<< Test_under_ubuntuOS run successfully  >>>>>>"

.gitignore

@@ -0,0 +1,139 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+# Mac Stuff
+.DS_Store
+
+# vscode Stuff
+.vscode
+
+# Data 
+data/