Set up for package release

.github/workflows/publish.yml

@@ -0,0 +1,70 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+      - name: Build package
+        run: |
+          python -m build
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to TestPyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.TESTPYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.TESTPYPI_PASSWORD }}
+        run: |
+          twine upload --repository testpypi dist/*
+
+      # Updated verification step with basic import test instead of pytest
+      - name: Verify package from TestPyPI
+        run: |
+          # Wait for TestPyPI to process the upload
+          sleep 60
+
+          # Create a new virtual environment for testing
+          python -m venv test_env
+          source test_env/bin/activate
+
+          # Install the package from TestPyPI
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ patientflow
+
+          # Perform a basic import test (more reliable than requiring pytest)
+          python -c "import patientflow; print(f'Successfully installed patientflow version: {patientflow.__version__}')"
+
+          # Deactivate the virtual environment
+          deactivate
+
+      # Add a manual approval step before publishing to PyPI
+      - name: Request approval for PyPI publish
+        uses: trstringer/manual-approval@v1
+        with:
+          secret: ${{ secrets.GITHUB_TOKEN }}
+          approvers: zmek
+          minimum-approvals: 1
+          issue-title: "Approve PyPI Deployment for ${{ github.event.release.tag_name }}"
+          issue-body: "The package has been successfully published to TestPyPI and verified. Please approve to publish to PyPI."
+          exclude-workflow-initiator-as-approver: false
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          twine upload dist/*

README.md

@@ -5,12 +5,8 @@
 [![Linting status][linting-badge]][linting-link]
 [![Documentation status][documentation-badge]][documentation-link]
 [![License][license-badge]](./LICENSE.md)
-
-<!--
 [![PyPI version][pypi-version]][pypi-link]
-[![Conda-Forge][conda-badge]][conda-link]
 [![PyPI platforms][pypi-platforms]][pypi-link]
--->
 
 <!-- prettier-ignore-start -->
 [tests-badge]:              https://github.com/zmek/patientflow/actions/workflows/tests.yml/badge.svg
@@ -19,14 +15,11 @@
 [linting-link]:             https://github.com/zmek/patientflow/actions/workflows/linting.yml
 [documentation-badge]:      https://github.com/zmek/patientflow/actions/workflows/docs.yml/badge.svg
 [documentation-link]:       https://github.com/zmek/patientflow/actions/workflows/docs.yml
-[conda-badge]:              https://img.shields.io/conda/vn/conda-forge/patientflow
-[conda-link]:               https://github.com/conda-forge/patientflow-feedstock
 [license-badge]:            https://img.shields.io/badge/License-MIT-yellow.svg
-[![ORCID](https://img.shields.io/badge/ORCID-0000--0001--7389--1527-green.svg)](https://orcid.org/0000-0001-7389-1527)
-
-<!-- [pypi-link]:                https://pypi.org/project/patientflow/
+[pypi-link]:                https://pypi.org/project/patientflow/
 [pypi-platforms]:           https://img.shields.io/pypi/pyversions/patientflow
-[pypi-version]:             https://img.shields.io/pypi/v/patientflow -->
+[pypi-version]:             https://img.shields.io/pypi/v/patientflow
+[![ORCID](https://img.shields.io/badge/ORCID-0000--0001--7389--1527-green.svg)](https://orcid.org/0000-0001-7389-1527)
 <!-- prettier-ignore-end -->
 
 ## Summary
@@ -90,18 +83,22 @@ This snapshot-based approach to predicting demand generalises to other aspects o
 
 ### Installation
 
-To install the latest development version, clone it first (so that you have access to the synthetic data and the notebooks) and then install it.
+You can install `patientflow` directly from PyPI:
 
 ```sh
-git clone https://github.com/zmek/patientflow.git
-cd patientflow
-pip install -e ".[test]" #this will install the code in test mode
+pip install patientflow
+```
+
+To access the example notebooks and synthetic data, clone the repository:
 
+```sh
+git clone https://github.com/ucl-coru/patientflow.git
+cd patientflow
 ```
 
 ### Development Installation (optional)
 
-If you plan to contribute to the project or run documentation locally, install the development and documentation dependencies:
+If you want to contribute or modify the code, or run documentation locally, install the development and documentation dependencies:
 
 ```sh
 # For development tools (linting, formatting, etc.)
@@ -208,8 +205,8 @@ Thank you for contributing!
 ## Roadmap
 
 - [x] Initial Research
-- [x] Minimum viable product <-- You are Here
-- [ ] Alpha Release
+- [x] Minimum viable product
+- [x] Alpha Release (PyPI Package) <-- You are Here
 - [ ] Feature-Complete Release
 
 ### Project Team

docs/notebooks/0_Set_up_your_environment.md

@@ -24,8 +24,9 @@ try:
    import patientflow
    print(f"✓ patientflow {patientflow.__version__} imported successfully")
 except ImportError:
-   print("❌ patientflow not found - please check installation instructions in README")
-   print("   pip install -e '.[test]'")
+   print("❌ patientflow not found - please install using one of the following methods:")
+   print("   From PyPI: pip install patientflow")
+   print("   For development: pip install -e '.[test]'")
 except Exception as e:
    print(f"❌ Error: {e}")
 ```

docs/notebooks/README.md

@@ -36,7 +36,15 @@ A set of notebooks follow, to show how we have used the functions in `patientflo
 
 ## Preparing your notebook environment
 
-The `PATH_TO_PATIENTFLOW` environment variable needs to be set so notebooks know where the patientflow repository resides on your computer. You have various options:
+### Installation
+
+You can install the `patientflow` package directly from PyPI:
+
+```bash
+pip install patientflow
+```
+
+For development purposes or to run these notebooks with the latest code, you may still want to use the Github repository directly. In that case, the `PATH_TO_PATIENTFLOW` environment variable needs to be set so notebooks know where the patientflow repository resides on your computer. You have various options:
 
 - use a virtual environment and set PATH_TO_PATIENTFLOW up within that
 - set PATH_TO_PATIENTFLOW globally on your computer

notebooks/0_Set_up_your_environment.ipynb

@@ -59,8 +59,9 @@
     "   import patientflow\n",
     "   print(f\"✓ patientflow {patientflow.__version__} imported successfully\")\n",
     "except ImportError:\n",
-    "   print(\"❌ patientflow not found - please check installation instructions in README\")\n",
-    "   print(\"   pip install -e '.[test]'\")\n",
+    "   print(\"❌ patientflow not found - please install using one of the following methods:\")\n",
+    "   print(\"   From PyPI: pip install patientflow\")\n",
+    "   print(\"   For development: pip install -e '.[test]'\")\n",
     "except Exception as e:\n",
     "   print(f\"❌ Error: {e}\")"
    ]

notebooks/README.md

@@ -36,7 +36,15 @@ A set of notebooks follow, to show how we have used the functions in `patientflo
 
 ## Preparing your notebook environment
 
-The `PATH_TO_PATIENTFLOW` environment variable needs to be set so notebooks know where the patientflow repository resides on your computer. You have various options:
+### Installation
+
+You can install the `patientflow` package directly from PyPI:
+
+```bash
+pip install patientflow
+```
+
+For development purposes or to run these notebooks with the latest code, you may still want to use the Github repository directly. In that case, the `PATH_TO_PATIENTFLOW` environment variable needs to be set so notebooks know where the patientflow repository resides on your computer. You have various options:
 
 - use a virtual environment and set PATH_TO_PATIENTFLOW up within that
 - set PATH_TO_PATIENTFLOW globally on your computer

src/patientflow/__init__.py

@@ -5,6 +5,10 @@
 making predictions about emergency demand, elective demand, and hospital discharges.
 """
 
-__version__ = "0.2.0"
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = "0.0.0"  # Fallback for when not installed
+
 __author__ = "Zella King"
 __email__ = "zella.king@ucl.ac.uk"