Merge pull request #1 from smart-on-fhir/mikix/initial

Initial skeleton project

.github/workflows/ci.yaml

@@ -0,0 +1,69 @@
+name: CI
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+# The goal here is to cancel older workflows when a PR is updated (because it's pointless work)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+  unittest:
+    name: unit tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[tests]"
+
+      - name: Test with pytest
+        run: |
+          python -m pytest
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install linters
+        # black is synced with the .pre-commit-hooks version
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[dev] bandit[toml] pycodestyle pylint
+
+      - name: Run pycodestyle
+        # E203: pycodestyle is a little too rigid about slices & whitespace
+        #  See https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#slices
+        # W503: a default ignore that we are restoring
+        run: |
+          pycodestyle --max-line-length=100 --ignore=E203,W503 .
+
+      - name: Run pylint
+        if: success() || failure() # still run pylint if above checks fail
+        run: |
+          pylint cumulus_fhir_support tests
+
+      - name: Run bandit
+        if: success() || failure() # still run bandit if above checks fail
+        run: |
+          bandit -c pyproject.toml -r .
+
+      - name: Run black
+        if: success() || failure() # still run black if above checks fails
+        run: |
+          black --check --verbose .

.github/workflows/pypi.yaml

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+name: PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      id-token: write # this permission is required for PyPI "trusted publishing"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build
+
+    - name: Build
+      run: python -m build
+
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

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+/.idea/
+__pycache__/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/psf/black
+    #this version is synced with the black mentioned in .github/workflows/ci.yml
+    rev: 23.10.0
+    hooks:
+      - id: black
+        entry: bash -c 'black "$@"; git add -u' --