Merge branch 'main' of github.com:Sm00thix/IKPLS

.github/actions/build/action.yml

@@ -0,0 +1,50 @@
+name: Build
+description: Test
+
+runs:
+    # strategy:
+    #   fail-fast: false
+    #   matrix:
+    #     # os: [ubuntu-latest, windows-latest, macos-latest]
+    #     os: [ubuntu-latest]
+    #     # python-version: ["3.9", "3.10", "3.11", "3.12"]
+    #     python-version: ["3.10"]
+    #     include:
+    #       - os: ubuntu-latest
+    #         path: ~/.cache/pip
+
+    # runs-on: ${{ matrix.os }}
+   using: "composite"
+   steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python #${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install build --user
+        pip install -U "jax[cpu]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+      shell: bash  
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      shell: bash
+
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+      shell: bash
+
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/

.github/actions/publish/action.yml

@@ -0,0 +1,13 @@
+name: Publish
+
+runs:
+    using: "composite"
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/actions/test/action.yml

@@ -0,0 +1,24 @@
+name: Test
+description: Test
+
+inputs:
+  PYTHON_VERSION:
+    description: test
+    required: true
+
+runs:
+    using: "composite"
+    steps:
+    - name: Test
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --upgrade pandas
+        python -m pip install --upgrade numpy
+        python -m pip install --upgrade tqdm
+        python -m pip install --upgrade scikit-learn
+        python -m pip install flake8 pytest
+        python -m pip install build --user
+        pip install -U "jax[cpu]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+        pip install pytest pytest-cov
+        python3 -m pytest tests --doctest-modules --junitxml=junit/test-results.xml --cov=ikpls/ --cov-report=xml --cov-report=html
+      shell: bash 

.github/workflows/pull_request.yml

@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  test_package:
+    runs-on: ${{ matrix.os }}  
+    strategy:  
+      fail-fast: false  
+      matrix:  
+        os: [ubuntu-latest]  # os: [ubuntu-latest, windows-latest, macos-latest] 
+        python-version: ["3.10"] # python-version: ["3.9", "3.10", "3.11", "3.12"]  
+    env:  
+      JAX_ENABLE_X64: True  
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/test
+
+  build_package:
+    runs-on: ubuntu-latest  
+    env:
+      JAX_ENABLE_X64: True
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/build

.github/workflows/workflow.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+
+jobs:
+  test_package:
+    runs-on: ${{ matrix.os }}  
+    strategy:  
+      fail-fast: false  
+      matrix:  
+        os: [ubuntu-latest]  # os: [ubuntu-latest, windows-latest, macos-latest] 
+        python-version: ["3.10"] # python-version: ["3.9", "3.10", "3.11", "3.12"]  
+    env:  
+      JAX_ENABLE_X64: True  
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/test
+
+  build_package:
+    runs-on: ubuntu-latest  
+    env:
+      JAX_ENABLE_X64: True
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/build
+
+  publish_package:
+    needs: [build_package, test_package]
+    runs-on: ubuntu-latest
+    steps:  
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/publish
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ikpls

.gitignore

@@ -161,3 +161,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+!.github/*

algorithms/jax_ikpls_alg_1.py → ikpls/jax_ikpls_alg_1.py

@@ -1,4 +1,4 @@
-from algorithms.jax_ikpls_base import PLSBase
+from ikpls.jax_ikpls_base import PLSBase
 import jax
 from jax.experimental import host_callback
 import jax.numpy as jnp

algorithms/jax_ikpls_alg_2.py → ikpls/jax_ikpls_alg_2.py

@@ -1,4 +1,4 @@
-from algorithms.jax_ikpls_base import PLSBase
+from ikpls.jax_ikpls_base import PLSBase
 import jax
 from jax.experimental import host_callback
 import jax.numpy as jnp

pyproject.toml

@@ -0,0 +1,19 @@
+[tool.poetry]
+name = "ikpls"
+version = "0.1.1"
+description = ""
+authors = ["Sm00thix <[email protected]>"]
+license = "Apache-2.0"
+readme = "README.md"
+repository = "https://github.com/Sm00thix/IKPLS"
+
+[tool.poetry.dependencies]
+python = ">=3.9, <3.13"
+numpy = "^1.26.1"
+jax = "^0.4.19"
+scikit-learn = "^1.3.2"
+tqdm = "^4.66.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

tests/__init__.py

@@ -1,3 +1,3 @@
-from . import load_data, test_consistency
+from . import load_data, test_ikpls
 
-__all__ = ["load_data", "test_consistency"]
+__all__ = ["load_data", "test_ikpls"]

tests/test_consistency.py → tests/test_ikpls.py

@@ -6,9 +6,9 @@
 from jax import numpy as jnp
 from typing import Tuple, Callable
 from sklearn.cross_decomposition import PLSRegression as SkPLS
-from algorithms.jax_ikpls_alg_1 import PLS as JAX_Alg_1
-from algorithms.jax_ikpls_alg_2 import PLS as JAX_Alg_2
-from algorithms.numpy_ikpls import PLS as NpPLS
+from ikpls.jax_ikpls_alg_1 import PLS as JAX_Alg_1
+from ikpls.jax_ikpls_alg_2 import PLS as JAX_Alg_2
+from ikpls.numpy_ikpls import PLS as NpPLS
 from . import load_data
 
 
@@ -2234,7 +2234,7 @@ def jax_rmse_per_component(
             ] + sk_models[i].intercept_
             sk_preds[i] = sk_pred
             assert_allclose(
-                sk_pred[-1], sk_models[i].predict(X), atol=0, rtol=1e-14
+                sk_pred[-1], sk_models[i].predict(X), atol=0, rtol=1e-13
             )  # Sanity check. SkPLS also uses the maximum number of components in its predict method.
 
         # Compute RMSE on the validation predictions

time_pls.py

@@ -7,9 +7,9 @@
     gen_random_data,
     SK_PLS_All_Components,
 )
-from algorithms.numpy_ikpls import PLS as NP_PLS
-from algorithms.jax_ikpls_alg_1 import PLS as JAX_PLS_Alg_1
-from algorithms.jax_ikpls_alg_2 import PLS as JAX_PLS_Alg_2
+from ikpls.numpy_ikpls import PLS as NP_PLS
+from ikpls.jax_ikpls_alg_1 import PLS as JAX_PLS_Alg_1
+from ikpls.jax_ikpls_alg_2 import PLS as JAX_PLS_Alg_2
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()