Initial port from marburg repo

.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/tests.yml'
+      - 'src/obr/**.py'
+      - 'pyproject.toml'
+      - 'uv.lock'
+  pull_request:
+    paths:
+      - '.github/workflows/tests.yml'
+      - 'src/obr/**.py'
+      - 'pyproject.toml'
+      - 'uv.lock'
+jobs:
+  ci:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v5
+      - name: Setup uv
+        run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh
+      - name: Install the project
+        run: uv sync --all-extras --dev
+      - name: Run tests
+        run: uv run pytest

pyproject.toml

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+[project]
+name = "obr"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "chevron>=0.14.0",
+    "pandas>=2.2.2",
+    "python-dateutil>=2.9.0.post0",
+    "plotly>=5.23.0",
+    "boto3>=1.35.8",
+]
+scripts = { obr = "obr:main" }
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.uv]
+dev-dependencies = [
+    "pytest>=8.3.2",
+]

src/obr/__init__.py

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+import sys
+import argparse
+from .util import build
+from .outbreaks import OUTBREAKS
+
+
+def abort(msg):
+    print(msg)
+    sys.exit(1)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Global.health outbreak report creator"
+    )
+    parser.add_argument("outbreak", help="Outbreak name")
+    parser.add_argument("url", help="Data URL")
+    parser.add_argument("-b", "--bucket", help="S3 bucket to write outbreak report to")
+    parser.add_argument(
+        "--cloudfront", help="Cloudfront distribution which should be invalidated"
+    )
+
+    args = parser.parse_args()
+    if args.outbreak not in OUTBREAKS:
+        abort(f"Outbreak not supported: {args.outbreak}")
+
+    build(
+        args.outbreak,
+        args.url,
+        OUTBREAKS[args.outbreak],
+        output_bucket=args.bucket,
+        cloudfront_distribution=args.cloudfront,
+    )
+
+
+if __name__ == "__main__":
+    main()

src/obr/outbreaks/__init__.py

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+"""
+Outbreak configurations
+"""
+
+from ..plots import (
+    get_counts,
+    plot_epicurve,
+    plot_timeseries_location_status,
+    plot_age_gender,
+    plot_delay_distribution,
+)
+
+outbreak_marburg = [
+    ("data", get_counts),
+    ("figure/epicurve", plot_epicurve),
+    (
+        "figure/epicurve_location_status",
+        plot_timeseries_location_status,
+        dict(admin_column="Location_District"),
+    ),
+    ("figure/age_gender", plot_age_gender),
+    (
+        "figure/delay_distribution_consult",
+        plot_delay_distribution,
+        dict(
+            col="Date_of_first_consult",
+            title="Delay to consultation from onset",
+            index="A",
+            max_delay_days=20,
+        ),
+    ),
+    (
+        "figure/delay_distribution_death",
+        plot_delay_distribution,
+        dict(
+            col="Date_death",
+            title="Delay to death from onset",
+            index="B",
+            max_delay_days=20,
+        ),
+    ),
+]
+
+OUTBREAKS = {"marburg": outbreak_marburg}
+__all__ = ["OUTBREAKS"]