Bump Version to 0.0.1

Author: simonprovost

.github/workflows/publish.yaml

@@ -1,29 +1,84 @@
-#name: Publish (PyPI)
-#
-#on:
-#  release:
-#    types: [published]
-#  workflow_dispatch:
-#
-#jobs:
-#  build-publish:
-#    runs-on: ubuntu-latest
-#    permissions:
-#      id-token: write
-#      contents: read
-#    steps:
-#      - uses: actions/checkout@v4
-#      - uses: astral-sh/setup-uv@v5
-#        with:
-#          version: "latest"
-#          python-version: "3.11"
-#      - run: uv venv
-#      - run: uv pip install -e .[dev]
-#      - run: uv run pytest -q
-#      - run: uv build
-#      - name: Verify package
-#        run: uv run --with twine twine check dist/*
-#      - name: Publish to PyPI
-#        uses: pypa/gh-action-pypi-publish@release/v1
-#        with:
-#          print-hash: true
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:  # Allow manual triggering
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mcpstack_mimic
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: read
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        version: "latest"
+        python-version: "3.11"
+
+    - name: Resolve version
+      id: get_version
+      run: |
+        set -euo pipefail
+        if [[ "${GITHUB_REF:-}" == refs/tags/* ]]; then
+          VERSION="${GITHUB_REF#refs/tags/}"
+          VERSION="${VERSION#v}"
+          FROM=tag
+        else
+          VERSION=$(python -c "import re,pathlib; p=pathlib.Path('src/mcpstack_mimic/__init__.py'); m=re.search(r'__version__\\s*=\\s*\"([^\"]+)\"', p.read_text()); print(m.group(1) if m else '')")
+          FROM=init
+          if [[ -z "$VERSION" ]]; then
+            echo "::error ::Could not determine version from src/mcpstack_mimic/__init__.py"; exit 1
+          fi
+        fi
+        echo "from=$FROM" >> "$GITHUB_OUTPUT"
+        echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+        echo "Publishing version: $VERSION (source: $FROM)"
+
+    - name: Verify version consistency
+      run: |
+        set -euo pipefail
+        INIT_VER=$(grep -Po '__version__\s*=\s*"\K[^"]+' src/mcpstack_mimic/__init__.py)
+        echo "__init__ version: $INIT_VER"
+        echo "resolved version: ${{ steps.get_version.outputs.version }}"
+        if [[ "${GITHUB_REF:-}" == refs/tags/* ]]; then
+          # If triggered by a tag/release, require that the tag matches the version in __init__.py
+          if [[ "$INIT_VER" != "${{ steps.get_version.outputs.version }}" ]]; then
+            echo "::error ::Version mismatch: tag ${{ steps.get_version.outputs.version }} != src/mcpstack_mimic/__init__.py $INIT_VER";
+            exit 1
+          fi
+        fi
+
+    - name: Lock dependencies
+      run: uv lock --locked
+
+    - name: Sync dependencies including dev
+      run: uv sync --all-groups
+
+    - name: Run quick tests
+      run: |
+        uv add pytest==7.4.3
+        uv add pytest-asyncio
+        uv run pytest tests/ -v --tb=short
+
+    - name: Build package
+      run: uv build
+
+    - name: Verify package
+      run: uv run --with twine twine check dist/*
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        print-hash: true

README.md

@@ -27,24 +27,24 @@
 
 ## <a id="about-the-project"></a>💡 About The MCPStack MIMIC Tool
 
-`MCPStack MIMIC` is an MCP tool that connects the **MIMIC-IV clinical database** (with either SQLite or BigQuery backends) 
+`MCPStack MIMIC` is an MCP tool that connects the **MIMIC-IV clinical database** (with either SQLite or BigQuery backends)
 into your **MCPStack pipelines**.
 
 In layman's terms:
-* MIMIC-IV is a large, de-identified database of ICU patient records, commonly used for healthcare research.  
-* This tool makes that dataset accessible to an LLM in a controlled way.  
+* MIMIC-IV is a large, de-identified database of ICU patient records, commonly used for healthcare research.
+* This tool makes that dataset accessible to an LLM in a controlled way.
 * It provides actions like *listing available tables*, *showing table structure with sample data*, and *running queries*; all exposed through MCP so your model can reason with healthcare data securely.
 
 ### What is MCPStack, in layman's terms?
 
-The **Model Context Protocol (MCP)** standardises how tools talk to large language models.  
-`MCPStack` is the orchestrator: it lets you **stack multiple MCP tools together** into a pipeline and then expose them 
-inside an LLM environment (like Claude Desktop).  
+The **Model Context Protocol (MCP)** standardises how tools talk to large language models.
+`MCPStack` is the orchestrator: it lets you **stack multiple MCP tools together** into a pipeline and then expose them
+inside an LLM environment (like Claude Desktop).
 
 Think of it like **scikit-learn pipelines, but for LLMs**:
 
-* In scikit-learn: you chain `preprocessors`, `transformers`, `estimators`.  
-* In MCPStack: you chain MCP tools (like MIMIC, Jupyter Notebook MCP, etc).  
+* In scikit-learn: you chain `preprocessors`, `transformers`, `estimators`.
+* In MCPStack: you chain MCP tools (like MIMIC, Jupyter Notebook MCP, etc).
 
 
 >[!IMPORTANT]
@@ -58,7 +58,7 @@ Think of it like **scikit-learn pipelines, but for LLMs**:
 
 ## Installation
 
-You can install the MIMIC tool as a standalone package. Thanks to `pyproject.toml` entry points, MCPStack 
+You can install the MIMIC tool as a standalone package. Thanks to `pyproject.toml` entry points, MCPStack
 will auto-discover it.
 
 ### PyPI Installation Via `UV`
@@ -75,10 +75,10 @@ pip install mcpstack-mimic
 
 ### Install pre-commit hooks (optional, for development)
 
-```bash 
+```bash
 uv run pre-commit install
 # or pip install pre-commit
-``` 
+```
 
 ### Run Unit Tests (optional, for development)
 
@@ -183,7 +183,7 @@ pipeline = (
         backends=[
             SQLiteBackend("<path_to_your_mimic.db>")  # SQLite backend with local MIMIC-IV database
         ])
-    # Here you can add as many as new `.with_tool(.)` of interest to play with.    
+    # Here you can add as many as new `.with_tool(.)` of interest to play with.
     ).build(
         type="fastmcp",
         save_path="my_mimic_pipeline.json",
@@ -204,4 +204,3 @@ pipeline = (
 🔐 License
 
 MIT — see **[LICENSE](LICENSE)**.
-

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "pdm.backend"
 
 [project]
 name = "mcpstack-mimic"
-version = "0.1.0"
+dynamic = ["version"]
 description = "MIMIC-IV MCPStack tool (standalone package) with pluggable SQLite/BigQuery backends."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -33,7 +33,7 @@ dependencies = [
   "thefuzz>=0.22.1",
   "rich-pyfiglet>=0.1.4",
   "click==8.1.8",
-  "mcpstack",
+  "mcpstack>=0.0.2",
 ]
 
 [dependency-groups]
@@ -55,6 +55,10 @@ mimic = "mcpstack_mimic.tools.mimic.mimic:MIMIC"
 [project.entry-points."mcpstack.tool_clis"]
 mimic = "mcpstack_mimic.tools.mimic.cli:MimicCLI.get_app"
 
+[tool.pdm.version]
+source = "file"
+path = "src/mcpstack_mimic/__init__.py"
+
 [tool.ruff]
 line-length = 88
 target-version = "py310"
@@ -67,6 +71,3 @@ ignore = ["E501"]
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
-
-[tool.uv.sources]
-mcpstack = { path = "../MCPStack" }

src/mcpstack_mimic/__init__.py

@@ -0,0 +1,2 @@
+__version__ = "0.0.1"
+__all__ = ["__version__"]