Feat/medcat-den CU-869an5f00 Add medcat den

.github/workflows/medcat-den_main.yml

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+name: medcat-den - Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    paths:
+      - 'medcat-den/**'
+      - '.github/workflows/medcat-den**'
+
+permissions:
+  id-token: write
+
+defaults:
+  run:
+    working-directory: ./medcat-den
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+      max-parallel: 4
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv for Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+      - name: Install the project
+        run: |
+          uv sync --all-extras --dev
+          uv run python -m ensurepip
+          uv run python -m pip install --upgrade pip
+      - name: Check types
+        run: |
+          uv run python -m mypy --follow-imports=normal src/medcat_den
+      - name: Ruff linting
+        run: |
+          uv run ruff check src/medcat_den --preview
+      - name: Test
+        run: |
+          uv run pytest tests
+
+  publish-to-test-PyPI:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.9'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade build
+
+      - name: Install package in development mode
+        run: |
+          pip install -e .
+
+      - name: Bump version for TestPyPI
+        run: sed -i "s/^version = .*/version = \"1.0.0.dev$(date +%s)\"/" pyproject.toml
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Publish distribution to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository_url: https://test.pypi.org/legacy/
+          packages_dir: medcat-den/dist

.github/workflows/medcat-den_release.yml

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+name: medcat-den release-build
+
+on:
+  push:
+    tags:
+      - 'medcat-den/v*.*.*'  
+
+permissions:
+  id-token: write
+
+defaults:
+  run:
+    working-directory: ./medcat-den
+
+jobs:
+  test-and-publish-to-PyPI:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v5
+
+      - name: Release Tag
+        # If GITHUB_REF=refs/tags/medcat-den/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt
+        run: echo "RELEASE_VERSION=${GITHUB_REF##refs/*/}" >> $GITHUB_ENV
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.9'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+
+      - name: Install client package in development mode
+        run: |
+          pip install -e .
+
+      - name: Test
+        run: |
+          pytest tests
+
+      - name: Build client package
+        run: |
+          python -m build
+
+      - name: Publish production distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages_dir: medcat-den/dist

medcat-den/.gitignore

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+
+# Python gitignore https://github.com/github/gitignore/blob/main/Python.gitignore
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml