Feature/jupyter gui improvements

.coveragerc

@@ -0,0 +1,8 @@
+[run]
+source = 
+    ms_mint
+omit = 
+    */_version.py
+    */__init__.py
+    ms_mint/filelock.py
+    tests/*

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+per-file-ignores = 
+    **/MintPlotter.py:F821
+    **/TargetOptimizer.py:F821 
+    **/io.py:F821
+    **/pca.py:F821

.gitattributes

@@ -0,0 +1,3 @@
+notebooks/* linguist-documentation=false
+*.py linguist-language=python
+ms_mint/_version.py export-subst

.github/workflows/codeql-analysis.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ develop ]
+    paths-ignore:
+      - '**/*.md'
+      - '**/*.txt'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # 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
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

.github/workflows/documentation.yml

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+name: Create Documentation
+on:
+  push:
+    branches:
+      - develop
+      - docs/mkdocs
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Install your package to ensure autodoc works
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install package with docs dependencies
+        run: python -m pip install -e ".[docs]"
+
+      # Build the MkDocs documentation
+      - name: Build Documentation
+        run: |
+          mkdocs build --clean
+
+      # Deploy the built documentation to the gh-pages branch
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: site  # MkDocs builds to the 'site' directory by default

.github/workflows/pythonpackage.yml

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+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Upgrade pip
+      run: python -m pip install --upgrade pip    
+    - name: Install package with docs dependencies
+      run: python -m pip install -e ".[dev]"
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        PYTHONPATH=. pytest

.github/workflows/pythonpublish.yml

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+name: Publish Python Package to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: |
+        python -m build
+        ls -l dist  # List files in dist directory for debugging
+
+    - name: Publish package
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        twine upload dist/*

.gitignore

@@ -1,3 +1,24 @@
 .localhistory
-*.csv
-
+.ipynb_checkpoints
+.*.ipynb
+.pytest_cache
+*egg-info*
+__pycache__
+.*
+devel
+output
+build
+dist
+site
+htmlcov
+Untitled*.ipynb
+"nohup.out" 
+nohup.out
+InnoSetup/Output
+*lock
+ChEBI.tsv
+data.sqlite
+app.db
+docs/_*
+HILICNeg15_StdH1.feather
+*_version.py