chore: Adjust dependencies and increase version (#122)

.github/workflows/publish.yml

@@ -0,0 +1,156 @@
+name: Publish Package
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+          - runner: ubuntu-latest
+            target: s390x
+          - runner: ubuntu-latest
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: "true"
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: "true"
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-12
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    needs: [linux, musllinux, windows, macos, sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

Cargo.toml

@@ -3,7 +3,7 @@ members = ["crates/*", "rustmodels"]
 resolver = "2"
 
 [workspace.package]
-version = "0.0.1-a1"
+version = "0.1.0"
 edition = "2021"
 repository = "https://github.com/limebit/medmodels"
 license = "BSD-3-Clause"
@@ -18,6 +18,6 @@ pyo3 = "0.21.2"
 polars = { version = "0.40.0", features = ["polars-io"] }
 pyo3-polars = "0.14.0"
 
-medmodels = { version = "0.0.1-a1", path = "crates/medmodels" }
-medmodels-core = { version = "0.0.1-a1", path = "crates/medmodels-core" }
-medmodels-utils = { version = "0.0.1-a1", path = "crates/medmodels-utils" }
+medmodels = { version = "0.1.0", path = "crates/medmodels" }
+medmodels-core = { version = "0.1.0", path = "crates/medmodels-core" }
+medmodels-utils = { version = "0.1.0", path = "crates/medmodels-utils" }

README.md

@@ -67,4 +67,4 @@ We recommend to use `pip` to install the latest version of MedModels:
 pip install medmodels
 ```
 
-For detailed information on how to use MedModels, please read the [MedModels documentation](https://www.medmodels.de/documentation).
+For detailed information on how to use MedModels, please read the [MedModels documentation](https://www.medmodels.de/api-reference/latest).

medmodels/matching/algorithms/classic_distance_models.py

@@ -84,7 +84,9 @@ def nearest_neighbor(
 
         for neighbor_index in neighbor_indices:
             new_row = pl.DataFrame(
-                [control_array_full[neighbor_index]], schema=treated_set.columns
+                [control_array_full[neighbor_index]],
+                schema=treated_set.columns,
+                orient="row",
             )
             matched_control.append(new_row)
 

medmodels/matching/tests/test_classic_distance_models.py

@@ -23,21 +23,21 @@ def test_nearest_neighbor(self):
         cols = ["a", "b", "c"]
         array = np.array([[1, 3, 5], [5, 2, 1], [1, 4, 10]])
         c_set = pl.DataFrame(array, schema=cols)
-        t_set = pl.DataFrame([[1, 4, 2]], schema=cols)
+        t_set = pl.DataFrame([[1, 4, 2]], schema=cols, orient="row")
         covs = ["a", "c"]
 
         # absolute metric
-        expected_abs = pl.DataFrame([[1.0, 3.0, 5.0]], schema=cols)
+        expected_abs = pl.DataFrame([[1.0, 3.0, 5.0]], schema=cols, orient="row")
         result_abs = cdm.nearest_neighbor(t_set, c_set, "absolute", covariates=covs)
         self.assertTrue(result_abs.equals(expected_abs))
 
         # mahalanobis metric
-        expected_mah = pl.DataFrame([[1.0, 3.0, 5.0]], schema=cols)
+        expected_mah = pl.DataFrame([[1.0, 3.0, 5.0]], schema=cols, orient="row")
         result_mah = cdm.nearest_neighbor(t_set, c_set, "mahalanobis", covariates=covs)
         self.assertTrue(result_mah.equals(expected_mah))
 
         expected_abs_2nn = pl.DataFrame(
-            [[1.0, 3.0, 5.0], [1.0, 4.0, 10.0]], schema=cols
+            [[1.0, 3.0, 5.0], [1.0, 4.0, 10.0]], schema=cols, orient="row"
         )
         result_abs_2nn = cdm.nearest_neighbor(
             t_set, c_set, "absolute", covariates=covs, number_of_neighbors=2

pyproject.toml

@@ -1,28 +1,50 @@
 [project]
 name = "medmodels"
-version = "0.0.1"
+version = "0.1.0"
 description = "Limebit Medmodels Package"
 readme = "README.md"
 requires-python = ">=3.9"
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Healthcare Industry',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: BSD License',
+    'Operating System :: MacOS :: MacOS X',
+    'Operating System :: Microsoft :: Windows',
+    'Operating System :: POSIX',
+    'Operating System :: Unix',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Rust',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Software Development',
+    'Typing :: Typed',
+]
 dependencies = [
-    "numpy==2.0.0",
-    "pandas==2.2.2",
-    "polars[pandas]==0.20.31",
-    "scikit-learn==1.5.0",
+    "numpy>=2.0.0",
+    "pandas>=2.2.2",
+    "polars[pandas]>=0.20.31",
+    "scikit-learn>=1.5.0",
 ]
 
 [project.optional-dependencies]
 dev = [
-    "maturin==1.6.0",
-    "ruff==0.4.9",
-    "py-spy==0.3.14",
-    "pyright==1.1.370",
-    "pandas-stubs==2.2.2.240603",
+    "maturin>=1.6.0",
+    "ruff>=0.4.9",
+    "py-spy",
+    "pyright>=1.1.370",
+    "pandas-stubs>=2.2.2.240603",
 ]
-tests = ["pytest==8.2.2"]
+tests = ["pytest>=8.2.2"]
 
 [build-system]
-requires = ["maturin==1.6.0", "setuptools"]
+requires = ["maturin>=1.6.0", "setuptools"]
 build-backend = "maturin"
 
 [tool.maturin]