polarstate 0.1.0__tar.gz

polarstate-0.1.0/.github/workflows/python-package.yml

@@ -0,0 +1,49 @@
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Create virtual environment
+        run: uv venv
+
+      - name: Run tests using uv
+        run: uv run pytest tests
+
+  publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Create virtual environment
+        run: uv venv
+
+      - name: Build package using uv
+        run: uv build
+
+      - name: Publish package using uv
+        run: uv publish

polarstate-0.1.0/.gitignore

@@ -0,0 +1,10 @@
+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv

polarstate-0.1.0/.python-version

@@ -0,0 +1 @@
+3.13

polarstate-0.1.0/PKG-INFO

@@ -0,0 +1,7 @@
+Metadata-Version: 2.4
+Name: polarstate
+Version: 0.1.0
+Summary: Add your description here
+Author-email: Uriah Finkel <Ufinkel@gmail.com>
+Requires-Python: >=3.13
+Requires-Dist: polars>=1.29.0

polarstate-0.1.0/pyproject.toml

@@ -0,0 +1,30 @@
+[project]
+name = "polarstate"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+authors = [
+    { name = "Uriah Finkel", email = "Ufinkel@gmail.com" }
+]
+requires-python = ">=3.13"
+dependencies = [
+    "polars>=1.29.0",
+]
+
+[project.scripts]
+polarstate = "polarstate:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "polars>=1.29.0",
+    "pytest>=8.3.5",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = "test_*.py"
+python_functions = "test_*"

polarstate-0.1.0/src/polarstate/__init__.py

@@ -0,0 +1,6 @@
+from .aj import aalen_johansen
+
+__all__ = ["aalen_johansen"]
+
+def main() -> None:
+    print("Hello from polarstate!")

polarstate-0.1.0/src/polarstate/aj.py

@@ -0,0 +1,20 @@
+import polars as pl
+
+def aalen_johansen(times: pl.Series, reals: pl.Series, event_of_interest: int = 1, competing_events: list[int] = [2]) -> pl.DataFrame:
+    df = pl.DataFrame({"times": times, "reals": reals})
+    df = df.sort("times")
+
+    event_times = df.filter(pl.col("reals") != 0)["times"].unique().sort()
+    result = []
+    cum_hazard = 0.0
+
+    for t in event_times:
+        n_at_risk = df.filter(pl.col("times") >= t).height
+        n_event = df.filter((pl.col("times") == t) & (pl.col("reals") == event_of_interest)).height
+
+        if n_at_risk > 0:
+            hazard = n_event / n_at_risk
+            cum_hazard += hazard
+            result.append({"time": t, "cuminc": cum_hazard})
+
+    return pl.DataFrame(result)

polarstate-0.1.0/tests/test_polarstate.py

@@ -0,0 +1,29 @@
+import polars as pl
+from polarstate.aj import aalen_johansen
+
+def test_aalen_johansen() -> None:
+    # Test data
+    times = pl.Series([1, 2, 3, 4, 5])
+    reals = pl.Series([1, 0, 2, 1, 0])
+
+    # Expected output
+    expected_output = pl.DataFrame({
+        "time": [1, 2, 3],
+        "cuminc": [0.5, 0.5, 0.6666666666666666]
+    })
+
+    # Call the function
+    result = aalen_johansen(times, reals)
+
+    # Check if the result is a DataFrame
+    assert isinstance(result, pl.DataFrame), "Result is not a DataFrame"
+    # Check if the result has the correct columns
+    assert set(result.columns) == {"time", "cuminc"}, f"Expected columns {'time', 'cuminc'} but got {result.columns}"
+    # Check if the result has the correct number of rows
+    assert len(result) == 3, f"Expected 3 rows but got {len(result)}"
+    # Check if the result is sorted by time
+    assert result["time"].is_sorted(), "Result is not sorted by time"
+    # Check if the cumulative incidence is non-decreasing
+    assert all(result["cuminc"].to_list()[i] <= result["cuminc"].to_list()[i + 1] for i in range(len(result) - 1)), "Cumulative incidence is not non-decreasing"
+    
+    

polarstate-0.1.0/uv.lock

@@ -0,0 +1,91 @@
+version = 1
+revision = 1
+requires-python = ">=3.13"
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d8/53/6f443c9a4a8358a93a6792e2acffb9d9d5cb0a5cfd8802644b7b1c9a02e4/colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44", size = 27697 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6", size = 25335 },
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.1.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/f2/97/ebf4da567aa6827c909642694d71c9fcf53e5b504f2d96afea02718862f3/iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7", size = 4793 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2c/e1/e6716421ea10d38022b952c159d5161ca1193197fb744506875fbb87ea7b/iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760", size = 6050 },
+]
+
+[[package]]
+name = "packaging"
+version = "25.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/a1/d4/1fc4078c65507b51b96ca8f8c3ba19e6a61c8253c72794544580a7b6c24d/packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f", size = 165727 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484", size = 66469 },
+]
+
+[[package]]
+name = "pluggy"
+version = "1.6.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/f9/e2/3e91f31a7d2b083fe6ef3fa267035b518369d9511ffab804f839851d2779/pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3", size = 69412 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746", size = 20538 },
+]
+
+[[package]]
+name = "polars"
+version = "1.29.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/0b/92/8d0e80fef779a392b1a736b554ffba62403026bad7df8a9de8b61dce018f/polars-1.29.0.tar.gz", hash = "sha256:d2acb71fce1ff0ea76db5f648abd91a7a6c460fafabce9a2e8175184efa00d02", size = 4582973 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/e7/5f/b277179cfce1258fecf4ad73cf627f670be41fdf088727090f68ca9c96ff/polars-1.29.0-cp39-abi3-macosx_10_12_x86_64.whl", hash = "sha256:d053ee3217df31468caf2f5ddb9fd0f3a94fd42afdf7d9abe23d9d424adca02b", size = 34206809 },
+    { url = "https://files.pythonhosted.org/packages/34/e7/634e5cb55ce8bef23ac8ad8e3834c9045f4b3cbdff1fb9e7826d864436e6/polars-1.29.0-cp39-abi3-macosx_11_0_arm64.whl", hash = "sha256:14131078e365eae5ccda3e67383cd43c0c0598d7f760bdf1cb4082566c5494ce", size = 31100055 },
+    { url = "https://files.pythonhosted.org/packages/50/15/0e9072e410731980ebc567c60a0a5f02bc2183310e48704ef83682cdd54c/polars-1.29.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:54f6902da333f99208b8d27765d580ba0299b412787c0564275912122c228e40", size = 34828438 },
+    { url = "https://files.pythonhosted.org/packages/69/c0/90fcaac5c95aa225b3899698289c0424d429ef72248b593f15294f95a35e/polars-1.29.0-cp39-abi3-manylinux_2_24_aarch64.whl", hash = "sha256:7a0ac6a11088279af4d715f4b58068835f551fa5368504a53401743006115e78", size = 32073830 },
+    { url = "https://files.pythonhosted.org/packages/17/ed/e5e570e22a03549a3c5397035a006b2c6343856a9fd15cccb5db39bdfa0a/polars-1.29.0-cp39-abi3-win_amd64.whl", hash = "sha256:f5aac4656e58b1e12f9481950981ef68b5b0e53dd4903bd72472efd2d09a74c8", size = 34971841 },
+    { url = "https://files.pythonhosted.org/packages/45/fd/9039f609d76b3ebb13777f289502a00b52709aea5c35aed01d1090ac142f/polars-1.29.0-cp39-abi3-win_arm64.whl", hash = "sha256:0c105b07b980b77fe88c3200b015bf4695e53185385f0f244c13e2d1027c7bbf", size = 31298689 },
+]
+
+[[package]]
+name = "polarstate"
+version = "0.1.0"
+source = { editable = "." }
+dependencies = [
+    { name = "polars" },
+]
+
+[package.dev-dependencies]
+dev = [
+    { name = "polars" },
+    { name = "pytest" },
+]
+
+[package.metadata]
+requires-dist = [{ name = "polars", specifier = ">=1.29.0" }]
+
+[package.metadata.requires-dev]
+dev = [
+    { name = "polars", specifier = ">=1.29.0" },
+    { name = "pytest", specifier = ">=8.3.5" },
+]
+
+[[package]]
+name = "pytest"
+version = "8.3.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "iniconfig" },
+    { name = "packaging" },
+    { name = "pluggy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ae/3c/c9d525a414d506893f0cd8a8d0de7706446213181570cdbd766691164e40/pytest-8.3.5.tar.gz", hash = "sha256:f4efe70cc14e511565ac476b57c279e12a855b11f48f212af1080ef2263d3845", size = 1450891 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/30/3d/64ad57c803f1fa1e963a7946b6e0fea4a70df53c1a7fed304586539c2bac/pytest-8.3.5-py3-none-any.whl", hash = "sha256:c69214aa47deac29fad6c2a4f590b9c4a9fdb16a403176fe154b79c0b4d4d820", size = 343634 },
+]