oehrpy 0.1.0__tar.gz

oehrpy-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Run ruff lint
+        run: ruff check .
+
+      - name: Run ruff format check
+        run: ruff format --check .
+
+  type-check:
+    name: Type Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run mypy
+        run: mypy src/openehr_sdk
+
+  test:
+    name: Unit Tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+          pip install pytest-cov
+
+      - name: Run unit tests with coverage
+        run: pytest tests/ -m "not integration" -v --tb=short --cov=src/openehr_sdk --cov-report=term-missing --cov-report=xml
+
+      - name: Upload coverage reports
+        if: env.CODECOV_TOKEN != ''
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        continue-on-error: true
+
+  integration-test:
+    name: Integration Tests
+    runs-on: ubuntu-latest
+    # Only run on main/develop or PRs with 'integration' label
+    if: |
+      github.ref == 'refs/heads/main' ||
+      github.ref == 'refs/heads/develop' ||
+      contains(github.event.pull_request.labels.*.name, 'integration')
+
+    services:
+      postgres:
+        image: ehrbase/ehrbase-v2-postgres:16.2
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          EHRBASE_USER: ehrbase
+          EHRBASE_PASSWORD: ehrbase
+          EHRBASE_USER_ADMIN: ehrbase_admin
+          EHRBASE_PASSWORD_ADMIN: ehrbase_admin
+        options: >-
+          --health-cmd "pg_isready -U postgres"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Start EHRBase
+        run: |
+          docker run -d \
+            --name ehrbase \
+            --network host \
+            -e DB_URL=jdbc:postgresql://localhost:5432/ehrbase \
+            -e DB_USER=ehrbase \
+            -e DB_PASS=ehrbase \
+            -e DB_USER_ADMIN=ehrbase_admin \
+            -e DB_PASS_ADMIN=ehrbase_admin \
+            -e SECURITY_AUTHTYPE=BASIC \
+            -e SECURITY_AUTHUSER=ehrbase-user \
+            -e SECURITY_AUTHPASSWORD=SuperSecretPassword \
+            -e SECURITY_AUTHADMINUSER=ehrbase-admin \
+            -e SECURITY_AUTHADMINPASSWORD=EvenMoreSecretPassword \
+            ehrbase/ehrbase:2.26.0
+
+      - name: Wait for EHRBase
+        run: |
+          timeout 120 bash -c 'until curl -f -u ehrbase-user:SuperSecretPassword http://localhost:8080/ehrbase/rest/status; do echo "Waiting for EHRBase..."; sleep 5; done'
+          echo "EHRBase is ready!"
+
+      - name: Fetch Web Template for debugging
+        if: always()
+        continue-on-error: true
+        run: |
+          # Upload the template first (conftest.py does this in tests, but let's ensure it's there)
+          echo "Uploading template..."
+          curl -v -X POST -u ehrbase-user:SuperSecretPassword \
+            -H "Content-Type: application/xml" \
+            -H "Accept: */*" \
+            --data @tests/fixtures/vital_signs.opt \
+            http://localhost:8080/ehrbase/rest/openehr/v1/definition/template/adl1.4 || echo "Template upload may have failed or template already exists"
+
+          echo "Fetching Web Template (JSON format)..."
+          # Fetch the Web Template using the /webtemplate endpoint
+          curl -v -u ehrbase-user:SuperSecretPassword \
+            "http://localhost:8080/ehrbase/rest/definition/template/adl1.4/IDCR%20-%20Vital%20Signs%20Encounter.v1/webtemplate" \
+            -o web_template.json
+
+          # Check if file has content
+          if [ -s web_template.json ]; then
+            echo "Web Template file size: $(wc -c < web_template.json) bytes"
+            echo "First 100 chars:"
+            head -c 100 web_template.json
+            echo ""
+
+            # Try to pretty print (may fail if not JSON)
+            python3 -m json.tool web_template.json > web_template_formatted.json 2>&1 || \
+              cp web_template.json web_template_formatted.json
+          else
+            echo "Error: web_template.json is empty"
+            echo "ERROR: Failed to fetch web template" > web_template_formatted.json
+          fi
+
+      - name: Upload Web Template artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: web-template
+          path: web_template*.json
+
+      - name: Run integration tests
+        run: pytest tests/ -m integration -v --tb=short
+        env:
+          EHRBASE_URL: http://localhost:8080/ehrbase
+          EHRBASE_USER: ehrbase-user
+          EHRBASE_PASSWORD: SuperSecretPassword
+
+      - name: Show EHRBase logs on failure
+        if: failure()
+        run: docker logs ehrbase

oehrpy-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  # Allow manual trigger for testing
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Target repository'
+        required: true
+        default: 'testpypi'
+        type: choice
+        options:
+          - testpypi
+          - pypi
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check package
+        run: python -m twine check dist/*
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'testpypi'
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/oehrpy/
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'pypi')
+    environment:
+      name: pypi
+      url: https://pypi.org/project/oehrpy/
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

oehrpy-0.1.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  release:
+    name: Semantic Release
+    runs-on: ubuntu-latest
+    if: github.repository == 'platzhersh/oehrpy'
+    concurrency:
+      group: release
+      cancel-in-progress: false
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_TOKEN }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install python-semantic-release build
+
+      - name: Python Semantic Release
+        id: release
+        uses: python-semantic-release/python-semantic-release@v9
+        with:
+          github_token: ${{ secrets.GH_TOKEN }}
+          git_committer_name: "github-actions[bot]"
+          git_committer_email: "github-actions[bot]@users.noreply.github.com"

oehrpy-0.1.0/.github/workflows-temp/fetch-webtemplate.yml

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+name: Fetch Web Template
+
+on:
+  push:
+    branches:
+      - feat/integration-testing-with-ehrbase
+
+jobs:
+  fetch:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: ehrbase/ehrbase-v2-postgres:16.2
+        env:
+          POSTGRES_DB: ehrbase
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          EHRBASE_USER: ehrbase
+          EHRBASE_PASSWORD: ehrbase
+        options: >-
+          --health-cmd "pg_isready -U postgres"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    steps:
+      - name: Start EHRBase
+        run: |
+          docker run -d --name ehrbase --network host \
+            -e DB_URL=jdbc:postgresql://localhost:5432/ehrbase \
+            -e DB_USER=ehrbase \
+            -e DB_PASS=ehrbase \
+            -e DB_USER_ADMIN=ehrbase \
+            -e DB_PASS_ADMIN=ehrbase \
+            -e SECURITY_AUTHTYPE=BASIC \
+            -e SECURITY_AUTHUSER=ehrbase-user \
+            -e SECURITY_AUTHPASSWORD=SuperSecretPassword \
+            -e SECURITY_AUTHADMINUSER=ehrbase-admin \
+            -e SECURITY_AUTHADMINPASSWORD=EvenMoreSecretPassword \
+            ehrbase/ehrbase:2.0.0
+
+      - name: Wait for EHRBase
+        run: |
+          for i in {1..30}; do
+            sleep 3
+            curl -sf -u ehrbase-user:SuperSecretPassword \
+              http://localhost:8080/ehrbase/rest/status && break || echo "Waiting..."
+          done
+
+      - name: Upload template
+        run: |
+          curl -X POST -u ehrbase-user:SuperSecretPassword \
+            -H "Content-Type: application/xml" \
+            -H "Accept: */*" \
+            --data @tests/fixtures/vital_signs.opt \
+            http://localhost:8080/ehrbase/rest/openehr/v1/definition/template/adl1.4 || true
+
+      - name: Fetch Web Template
+        run: |
+          curl -u ehrbase-user:SuperSecretPassword \
+            "http://localhost:8080/ehrbase/rest/openehr/v1/definition/template/adl1.4/IDCR%20-%20Vital%20Signs%20Encounter.v1" \
+            | python3 -m json.tool > web_template.json
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: web-template
+          path: web_template.json

oehrpy-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+*.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/
+
+# Translations
+*.mo
+*.pot
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre
+.pyre/
+
+# pytype
+.pytype/
+
+# ruff
+.ruff_cache/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# BMM repository clone (downloaded during generation)
+generator/bmm/specifications-ITS-BMM/
+generator/bmm-repo/
+
+# JSON Schema repository clone (downloaded for RM 1.1.0 generation)
+generator/specifications-ITS-JSON/

oehrpy-0.1.0/CHANGELOG.md

@@ -0,0 +1,52 @@
+# CHANGELOG
+
+
+## v0.1.0 (2026-01-31)
+
+### Bug Fixes
+
+- Install build module inside semantic-release Docker container (#17)
+  ([#17](https://github.com/platzhersh/oehrpy/pull/17),
+  [`23ced62`](https://github.com/platzhersh/oehrpy/commit/23ced6206b6f18ad8e55576c3201b0afdb60685a))
+
+- Update FLAT format paths based on EHRBase 2.26.0 web template (#11)
+  ([#11](https://github.com/platzhersh/oehrpy/pull/11),
+  [`1a4d0aa`](https://github.com/platzhersh/oehrpy/commit/1a4d0aaca0640711ceef771e00ba5e16560ee523))
+
+### Documentation
+
+- Add contribution guidelines (#14) ([#14](https://github.com/platzhersh/oehrpy/pull/14),
+  [`8b12373`](https://github.com/platzhersh/oehrpy/commit/8b123738235b96e226e356ff9a0484a056f639c8))
+
+- Add OPT Parser documentation to GitHub Pages (#9)
+  ([#9](https://github.com/platzhersh/oehrpy/pull/9),
+  [`7ed27de`](https://github.com/platzhersh/oehrpy/commit/7ed27de53baaddc53c50e23cc4d4613495f339bf))
+
+### Features
+
+- Add automated release workflow with python-semantic-release (#16)
+  ([#16](https://github.com/platzhersh/oehrpy/pull/16),
+  [`8201f6a`](https://github.com/platzhersh/oehrpy/commit/8201f6aadc9b7e008bcaf5d4a12c0880222852e1))
+
+- Add complete OPT (Operational Template) support with builder generation (#8)
+  ([#8](https://github.com/platzhersh/oehrpy/pull/8),
+  [`f938e23`](https://github.com/platzhersh/oehrpy/commit/f938e23293db86c613b041e8301403367325b82c))
+
+- Add GitHub Actions CI/CD workflow (#3) ([#3](https://github.com/platzhersh/oehrpy/pull/3),
+  [`ad43fdd`](https://github.com/platzhersh/oehrpy/commit/ad43fdd104dea399efdc013f718ee94f9df01ad5))
+
+- Add PyPI publishing support (#13) ([#13](https://github.com/platzhersh/oehrpy/pull/13),
+  [`052e447`](https://github.com/platzhersh/oehrpy/commit/052e44759657f036114e7eab8a652b0cb0883aae))
+
+- Implement features from PRD-0000 (#2) ([#2](https://github.com/platzhersh/oehrpy/pull/2),
+  [`829ea0b`](https://github.com/platzhersh/oehrpy/commit/829ea0bde75e20d1b72c4c2409c0ed0cb3084cfa))
+
+- Set up GitHub Pages with landing page and brand kit (#4)
+  ([#4](https://github.com/platzhersh/oehrpy/pull/4),
+  [`aa65777`](https://github.com/platzhersh/oehrpy/commit/aa657770be4a2da13898c83b3bc21abe475f3ac3))
+
+### Testing
+
+- Add integration test setup with ehrbase (#10)
+  ([#10](https://github.com/platzhersh/oehrpy/pull/10),
+  [`f1a2aa0`](https://github.com/platzhersh/oehrpy/commit/f1a2aa00669cf46b265a8209c9a012436de9a980))