Merge babf9b06ff into acdd03d3ed

.github/workflows/test-and-deploy.yml

@@ -30,20 +30,15 @@ jobs:
 
       - name: Install build dependencies
         run: |
-          pip install setuptools
+          pip install poetry
       
       - name: Install lib
         run: |
-          python setup.py develop
+          poetry install
-      
-      - name: Install test dependencies
-        run: |
-          pip install matplotlib
-          pip install pytest
 
       - name: pytest
         run: |
-          pytest GPy/testing
+          poetry run pytest
 
   test-linux:
     strategy:
@@ -62,20 +57,15 @@ jobs:
 
       - name: Install build dependencies
         run: |
-          pip install setuptools
+          pip install poetry
-
+      
       - name: Install lib
         run: |
-          python setup.py develop
+          poetry install
-
-      - name: Install test dependencies
-        run: |
-          pip install matplotlib
-          pip install pytest
 
       - name: pytest
         run: |
-          pytest GPy/testing
+          poetry run pytest
 
   test-macos:
     strategy:
@@ -94,20 +84,15 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install setuptools
+          pip install poetry
       
       - name: Install lib
         run: |
-          python setup.py develop
+          poetry install
-
-      - name: Install test dependencies
-        run: |
-          pip install matplotlib
-          pip install pytest
 
       - name: pytest
         run: |
-          pytest GPy/testing
+          poetry run pytest
 
   build-windows:
     if: github.event_name == 'release'
@@ -127,11 +112,8 @@ jobs:
 
       - name: Build lib
         run: |
-          pip install setuptools
+          pip install poetry
-          pip install wheel
+          poetry build
-          python setup.py develop
-          python setup.py bdist_wheel
-          python setup.py sdist bdist_wheel
 
       - name: List contents of dist
         run: ls -R dist
@@ -160,10 +142,8 @@ jobs:
 
       - name: Build lib
         run: |
-          pip install setuptools
+          pip install poetry
-          pip install wheel
+          poetry build
-          python setup.py develop
-          python setup.py bdist_wheel
 
       - name: List contents of dist
         run: ls -R dist
@@ -183,48 +163,53 @@ jobs:
     container: quay.io/pypa/manylinux2014_x86_64
 
     steps:
-    - uses: actions/checkout@v1
+      - name: Checkout
+        uses: actions/checkout@v1
 
-    - name: Compile c headers
+      - name: Install poetry
-      run: |
+        run: |
-        /opt/python/${{ matrix.python }}/bin/python setup.py develop
+          /opt/python/${{ matrix.python }}/bin/python -m pip install poetry
 
-    - name: Build wheel files
+      - name: Compile c headers
-      run: |
+        run: |
-        /opt/python/${{ matrix.python }}/bin/python setup.py bdist_wheel
+          /opt/python/${{ matrix.python }}/bin/python -m poetry install
 
-    - name: Install auditwheel
+      - name: Build wheel files
-      run: |
+        run: |
-        /opt/python/${{ matrix.python }}/bin/python -m pip install auditwheel
+          /opt/python/${{ matrix.python }}/bin/python -m poetry build
-    
-    - name: Repair wheel files
-      run: |
-        /opt/python/${{ matrix.python }}/bin/python -m auditwheel repair dist/*${{ matrix.python }}-linux_x86_64.whl
 
-    - name: List contents of dist
+      - name: Install auditwheel
-      run: ls -R dist
+        run: |
+          /opt/python/${{ matrix.python }}/bin/python -m pip install auditwheel
+      
+      - name: Repair wheel files
+        run: |
+          /opt/python/${{ matrix.python }}/bin/python -m auditwheel repair dist/*${{ matrix.python }}-linux_x86_64.whl
 
-    - name: List contests of wheelhouse
+      - name: List contents of dist
-      run: ls -R wheelhouse
+        run: ls -R dist
 
-    - name: Move wheelhouse wheel files to dist
+      - name: List contests of wheelhouse
-      run: |
+        run: ls -R wheelhouse
-        rm dist/*
-        mv wheelhouse/* dist/
-        rmdir wheelhouse
 
-    - name: List contents of dist
+      - name: Move wheelhouse wheel files to dist
-      run: ls -R dist
+        run: |
+          rm dist/*
+          mv wheelhouse/* dist/
+          rmdir wheelhouse
 
-    - name: Get the name of the wheel file
+      - name: List contents of dist
-      id: get-wheel-name
+        run: ls -R dist
-      run: echo "::set-output name=wheel-name::$(ls dist/*.whl)"
 
-    - name: Archive build artifacts
+      - name: Get the name of the wheel file
-      uses: actions/upload-artifact@v1
+        id: get-wheel-name
-      with:
+        run: echo "::set-output name=wheel-name::$(ls dist/*.whl)"
-        name: dist-artifacts-manylinux-${{ matrix.python }}
+
-        path: ${{ steps.get-wheel-name.outputs.wheel-name }}
+      - name: Archive build artifacts
+        uses: actions/upload-artifact@v1
+        with:
+          name: dist-artifacts-manylinux-${{ matrix.python }}
+          path: ${{ steps.get-wheel-name.outputs.wheel-name }}
 
   deploy:
     runs-on: ubuntu-latest
@@ -265,8 +250,7 @@ jobs:
         run: |
           ls -R dist
 
-      - name: Upload to PyPI using twine
+      - name: Upload to PyPI
-        run: twine upload --skip-existing dist/*
+        run: |
-        env:
+          poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }}
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          poetry publish
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

GPy/testing/test_gpy_kernels_state_space.py

@@ -4,6 +4,7 @@
 """
 Testing state space related functions.
 """
+import pytest
 import numpy as np
 import GPy
 import GPy.models.state_space_model as SS_model
@@ -620,7 +621,7 @@ class TestStateSpaceKernels:
                 var_compare_decimal=2,
             )
         except AssertionError:
-            raise SkipTest(
+            raise pytest.skip(
                 "Skipping Regular kalman filter for kernel addition, because it is not stable (normal situation) for this data."
             )
 

README.md

@@ -19,9 +19,7 @@ The Gaussian processes framework in Python.
 
 ## What's new:
 
-From now on we keep track of changes in the CHANGELOG.md.
+We switched to [poetry](https://python-poetry.org/). This means that `GPy` has become a `poetry` project. This change won't affect you if you are using `GPy` as a dependency. However, for developers and contributors, this change will make the development process easier and more consistent.
-If you want your changes to show up there follow the [guidelines](#gl).
-In particular tag your commits by the [gitchangelog](https://github.com/vaab/gitchangelog) commit message format.
 
 ## Contributing to GPy
 
@@ -54,24 +52,6 @@ For any further questions/suggestions head over to the issues section in GPy.
 
 Ask questions using the issues section.
 
-## Updated Structure
-
-We have pulled the core parameterization out of GPy. It is a package called [paramz](https://github.com/sods/paramz) and is the pure gradient based model optimization.
-
-If you installed GPy with pip, just upgrade the package using:
-
-    $ pip install --upgrade GPy
-
-If you have the developmental version of GPy (using the develop or -e option) just install the dependencies by running
-
-    $ python setup.py develop
-
-again, in the GPy installation folder.
-
-A warning: This usually works, but sometimes `distutils/setuptools` opens a
-whole can of worms here, specially when compiled extensions are involved.
-If that is the case, it is best to clean the repo and reinstall.
-
 ## Supported Platforms:
 
 [<img src="https://www.python.org/static/community_logos/python-logo-generic.svg" height=40px>](https://www.python.org/)

build_extension.py

@@ -0,0 +1,62 @@
+import sys
+import numpy as np
+from setuptools import setup, Extension
+
+
+def ismac():
+    return sys.platform[:6] == "darwin"
+
+if ismac():
+    compile_flags = ["-O3"]
+    link_args = []
+else:
+    compile_flags = ["-fopenmp", "-O3"]
+    link_args = ["-lgomp"]
+
+extensions = [
+    Extension(
+        name="GPy.kern.src.stationary_cython",
+        sources=[
+            "GPy/kern/src/stationary_cython.pyx",
+            "GPy/kern/src/stationary_utils.c",
+        ],
+        include_dirs=[np.get_include(), "."],
+        extra_compile_args=compile_flags,
+        extra_link_args=link_args,
+    ),
+    Extension(
+        name="GPy.util.choleskies_cython",
+        sources=["GPy/util/choleskies_cython.pyx"],
+        include_dirs=[np.get_include(), "."],
+        extra_link_args=link_args,
+        extra_compile_args=compile_flags,
+    ),
+    Extension(
+        name="GPy.util.linalg_cython",
+        sources=["GPy/util/linalg_cython.pyx"],
+        include_dirs=[np.get_include(), "."],
+        extra_compile_args=compile_flags,
+        extra_link_args=link_args,
+    ),
+    Extension(
+        name="GPy.kern.src.coregionalize_cython",
+        sources=["GPy/kern/src/coregionalize_cython.pyx"],
+        include_dirs=[np.get_include(), "."],
+        extra_compile_args=compile_flags,
+        extra_link_args=link_args,
+    ),
+    Extension(
+        name="GPy.models.state_space_cython",
+        sources=["GPy/models/state_space_cython.pyx"],
+        include_dirs=[np.get_include(), "."],
+        extra_compile_args=compile_flags,
+        extra_link_args=link_args,
+    ),
+]
+
+def build(setup_kwargs):
+    """Needed for the poetry building interface."""
+    setup_kwargs.update({
+        'ext_modules': extensions,
+        # 'include_dirs': [np.get_include()],
+    })

pyproject.toml

@@ -0,0 +1,51 @@
+[tool.poetry]
+name = "GPy"
+version = "1.13.1"
+description = "The Gaussian Process Toolbox"
+authors = ["GPy Authors <gpy.authors@gmail.com>"]
+license = "BSD-3-Clause"
+keywords = ["machine-learning", "gaussian-processes", "kernels"]
+homepage = "https://sheffieldml.github.io/GPy/"
+repository = "https://github.com/SheffieldML/GPy"
+documentation = "https://github.com/SheffieldML/GPy"
+readme = "README.md"
+build = "build_extension.py"
+include = ["build_extension.py"]
+packages = [{ include = "GPy" }]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<4"
+numpy = ">=1.7,<2"  # paramz is not compatible with numpy 2.0
+six = "*"
+paramz = ">=0.9.6"
+cython = "^0.29"
+scipy = [
+    { version = ">=1.3.0,<1.14.0", markers = "python_version == \"3.9\"" },
+    # as off scipy 1.14.0, the minimum python version is 3.10
+    { version = ">=1.3.0", markers = "python_version > \"3.9\"" },
+]
+tables = ">=3.9.0"
+sphinx = { version = "*", optional = true }
+mpi4py = { version = "*", optional = true }
+ipython = { version = ">=4.0.0", optional = true }
+matplotlib = { version = ">=3.3.4", optional = true }
+plotly = { version = ">=1.8.6", optional = true }
+jupyter_client = { version = ">=4.0.6", optional = true }
+ipywidgets = { version = ">=4.0.3", optional = true }
+ipykernel = { version = ">=4.1.0", optional = true }
+notebook = { version = ">=4.0.5", optional = true }
+
+[tool.poetry.extras]
+docs = ["sphinx"]
+optional = ["mpi4py", "ipython"]
+plotting = ["matplotlib", "plotly"]
+notebook = ["jupyter_client", "ipywidgets", "ipykernel", "notebook"]
+
+[tool.poetry.group.dev.dependencies]
+matplotlib = "^3.9.1"
+pytest = "^8.2.2"
+pods = "^0.1.14"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "setuptools", "wheel", "numpy", "cython"]
+build-backend = "poetry.core.masonry.api"