32 provide installation instructions (#33)

Support dual-mode: powers on-the-fly parsing + testing (MCP) as well as coding (parser bundle)
- Split regular tool wrappers from MCP and async functionalities
- Automate central registration of tools, resources, prompts and other relevant metadata
- Document options for MCP integration and deployment
- Add resources:
-- for calling tools as dependencies
-- extensive list of programmatic support per parser (TODO: test necessity)
- Update schema:
-- add metadata about file type and code that was parsed to the Parsers MCP
-- add `formula_type` to NOMAD MCP

Perform major reconstruction:
- Restructure folders to distinguish MCP servers: parsers, databases, RAG (in the future)
-- Reserve folder for code tests
-- Generate a template folder for different hosts + dedicated README
- Make imports modular + bundle together
- Add tests (with `pytest`) + dedicated README
-- For MCP loading and running
-- For NOMAD API calls
- Add Github workflows

Miscellaneous:
- Fix start-up bug: use relative path instead of absolute
- Decrease request package version for compatibility with NOMAD v1.3.16
- Suppress version warning in `cclib`

---------

Co-authored-by: ndaelman <ndaelman@physik.hu-berlin.de>

Author: ndaelman-hu

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input.gjf

@@ -0,0 +1,46 @@
+name: Code Quality
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install 3.12
+
+    - name: Install dependencies with dev extras
+      run: uv sync --extra dev
+
+    # Linting is available but not enforced yet
+    # Uncomment these steps when ready to enforce code quality
+    
+    # - name: Run ruff linting
+    #   run: uv run ruff check .
+
+    # - name: Run ruff formatting check
+    #   run: uv run ruff format --check .
+
+    # - name: Type checking with mypy (if available)
+    #   run: |
+    #     if uv run python -c "import mypy" 2>/dev/null; then
+    #       uv run mypy src/parse_patrol --ignore-missing-imports
+    #     else
+    #       echo "mypy not available, skipping type checking"
+    #     fi
+    #   continue-on-error: true
+
+    - name: Placeholder for future linting
+      run: echo "Linting workflow ready - uncomment steps above when ready to enforce"

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input_smiles.txt

@@ -0,0 +1,44 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Install dependencies with all extras
+      run: uv sync --extra all
+
+    - name: Run tests
+      run: uv run python -m pytest tests/ -v
+
+    - name: Run tests with coverage
+      run: |
+        uv add --dev coverage[toml] pytest-cov
+        uv run python -m pytest tests/ --cov=parse_patrol --cov-report=xml --cov-report=term-missing
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/molecule.mol

@@ -1,5 +1,8 @@
-# Repo
-.data
+# Project folders
+.pipelines/data
+.pipelines/resources
+.pipelines/scripts
+tests/.data
 
 # VS Code
 .vscode/