Nanobind

.github/workflows/doctest.yml

@@ -6,22 +6,19 @@ jobs:
     env:
       OS: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
+      - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.13"
       - name: Build myfm
         run: |
-          pip install --upgrade pip
-          pip install numpy scipy pandas scikit-learn
+          pip install --upgrade pip scikit-build setuptools-scm nanobind
           pip install .
           curl http://files.grouplens.org/datasets/movielens/ml-100k.zip -o ~/.ml-100k.zip
-      - name: Run pytest
+      - name: install pytest
         run: |
-          pip install pytest phmdoctest sphinx==4.4.0 sphinx_rtd_theme
+          pip install pytest phmdoctest sphinx==8.2.3 sphinx_rtd_theme scikit-learn
       - name: Test Readme.md
         run: |
           GEN_TEST_FILE=phmdoctest_out.py

.github/workflows/pre-commit.yml

@@ -8,6 +8,6 @@ jobs:
     env:
       SKIP: no-commit-to-branch
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/action@v3.0.0
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.0

.github/workflows/run-test.yml

@@ -2,37 +2,35 @@ name: Test & Upload coverage
 on: [push]
 jobs:
   run_pytest_upload_coverage:
+    permissions:
+      id-token: write
     runs-on: ubuntu-latest
     env:
       OS: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
-      - name: Build myfm
+          python-version: '3.13'
+      - name: Build myfm & test
         run: |
-          pip install --upgrade pip
-          pip install numpy scipy pandas
           sudo apt-get install lcov
-          FLAGS="-fprofile-arcs -ftest-coverage"
-          CFLAGS="$FLAGS" CXXFLAGS="$FLAGS" pip install -e .
-      - name: Run pytest
-        run: |
-          pip install pytest pytest-cov pytest-mock
+          pip install --upgrade pip
+          pip install scikit-build setuptools-scm pytest pytest-cov pytest-mock nanobind
+          FLAGS="-O0 -fprofile-arcs -ftest-coverage -fprofile-update=atomic"
+          CFLAGS="$FLAGS" CXXFLAGS="$FLAGS" pip install --editable .
           pytest --cov=./src/myfm tests/
-      - name: Generate coverage (ubuntu)
-        run: |
           coverage xml
-          lcov -d `pwd` -c -o coverage.info
+          lcov -d `pwd` -c -o coverage.info --ignore-errors source
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v5
         with:
+          use_oidc: true
           files: ./coverage.xml,./coverage.info
-          verbose: false
+          verbose: true
           env_vars: OS,PYTHON
           name: codecov-umbrella
           fail_ci_if_error: false

.github/workflows/wheels.yml

@@ -7,160 +7,71 @@ on:
     types:
       - created
 env:
-  cibuildwheel_version: "2.12.2"
+  cibuildwheel_version: '3.0.1'
 jobs:
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: '3.13'
       - name: Build sdist
-        run: pip install pybind11 && python setup.py sdist
-      - uses: actions/upload-artifact@v2
+        run: pip install build && python -m build --sdist
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    env:
-      MACOSX_DEPLOYMENT_TARGET: "10.9"
-      CIBW_BUILD_VERBOSITY: "1"
-      CIBW_BUILD: "${{ matrix.cibw.build || '*' }}"
-      CIBW_SKIP: "${{ matrix.cibw.skip || '' }}"
-      CIBW_ENVIRONMENT: "${{ matrix.cibw.env || '' }}"
-      CIBW_TEST_COMMAND: "pytest {project}/tests"
-      CIBW_TEST_REQUIRES: pytest pytest-mock
-      CIBW_MANYLINUX_X86_64_IMAGE: "${{ matrix.cibw.manylinux_image }}"
-      CIBW_MANYLINUX_I686_IMAGE: "${{ matrix.cibw.manylinux_image }}"
-      CIBW_MANYLINUX_AARCH64_IMAGE: "${{ matrix.cibw.manylinux_image }}"
-      CIBW_ARCHS_LINUX: "${{ matrix.cibw.arch || 'auto' }}"
-      CIBW_ARCHS_MACOS: "${{ matrix.cibw.arch || 'auto' }}"
+    runs-on: ${{ matrix.runs-on }}
     strategy:
       matrix:
         include:
-          - os: macos-10.15
-            name: mac
-            cibw:
-              arch: x86_64
-              build: "cp37* cp38*"
-
-          - os: macos-10.15
-            name: mac-arm
-            cibw:
-              arch: universal2
-              build: "cp39* cp310* cp311*"
-
-          - os: ubuntu-20.04
-            name: manylinux1
-            cibw:
-              build: "cp37*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2010
-              arch: auto64
-
-          - os: ubuntu-20.04
-            name: manylinux2014
-            cibw:
-              build: "cp38* cp39* cp310* cp311*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: auto64
-
-          - os: ubuntu-20.04
-            name: manylinux_aarch64_cp37
-            cibw:
-              build: "cp37*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: aarch64
-
-          - os: ubuntu-20.04
-            name: manylinux_aarch64_cp38
-            cibw:
-              build: "cp38*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: aarch64
-
-          - os: ubuntu-20.04
-            name: manylinux_aarch64_cp39
-            cibw:
-              build: "cp39*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: aarch64
-
-          - os: ubuntu-20.04
-            name: manylinux_aarch64_cp310
-            cibw:
-              build: "cp310*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: aarch64
-
-          - os: ubuntu-20.04
-            name: manylinux_aarch64_cp311
-            cibw:
-              build: "cp311*"
-              skip: "*musllinux*"
-              manylinux_image: manylinux2014
-              arch: aarch64
-
-          - os: windows-2019
-            name: win_amd64
-            architecture: x64
-            cibw:
-              skip: "cp36*"
-              build: "cp*win_amd64"
-
+          - os: linux-intel
+            runs-on: ubuntu-latest
+          - os: linux-arm
+            runs-on: ubuntu-24.04-arm
+          - os: windows-intel
+            runs-on: windows-latest
+          - os: macos-intel
+            runs-on: macos-13
+          - os: macos-arm
+            runs-on: macos-latest
     steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v2
-        name: Install Python
-      - name: register qemu
-        if: contains(matrix.cibw.arch, 'aarch64')
-        run: |
-          docker run --rm --privileged hypriot/qemu-register:v4.2.0
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel=="${{env.cibuildwheel_version}}"
+      - uses: actions/checkout@v4
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-
-      - uses: actions/upload-artifact@v2
+        uses: pypa/cibuildwheel@v3.0.1
+        env:
+          CIBW_PLATFORM: ${{ matrix.platform || 'auto' }}
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
-
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: cibw-*
           path: dist
+          merge-multiple: true
       - name: Publish package to TestPyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_APITOKEN }}
-          packages_dir: dist/
-          repository_url: https://test.pypi.org/legacy/
+          packages-dir: dist/
+          repository-url: https://test.pypi.org/legacy/
           verbose: true
-          skip_existing: true
+          skip-existing: true
+          attestations: false
       - name: Publish package to PyPI
         if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_APITOKEN }}
-          packages_dir: dist/
+          packages-dir: dist/
           verbose: true
-          skip_existing: true
+          skip-existing: true

.gitignore

@@ -23,3 +23,8 @@ stubs/*
 
 doc/source/api_reference/*.rst
 .cache
+src/myfm/_version.py
+
+mise.toml
+
+.venv

.pre-commit-config.yaml

@@ -2,28 +2,21 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.6.0
     hooks:
       - id: check-merge-conflict
       - id: check-yaml
       - id: end-of-file-fixer
       - id: no-commit-to-branch
         args: [--branch, main]
       - id: trailing-whitespace
-      - id: end-of-file-fixer
       - id: check-added-large-files
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
-        language_version: python3 # Should be a command that runs python3.6+
-  - repo: https://github.com/hadialqattan/pycln
-    rev: v1.1.0
-    hooks:
-      - id: pycln
-        args: [--config=pyproject.toml]

CMakeLists.txt

@@ -1,16 +1,42 @@
-set(CMAKE_C_COMPILER gcc)
-set(CMAKE_CXX_COMPILER g++)
+cmake_minimum_required(VERSION 3.15...3.27)
+project(myFM VERSION 0.1.0)
 
-cmake_minimum_required(VERSION 3.0.0)
-project(myfm)
+if (CMAKE_VERSION VERSION_LESS 3.18)
+  set(DEV_MODULE Development)
+else()
+  set(DEV_MODULE Development.Module)
+endif()
 
-set(CMAKE_BUILD_TYPE Release)
-set(CMAKE_CXX_FLAGS                " ${CMAKE_CXX_FLAGS_INIT} -std=c++11 -fPIC")
 
-add_subdirectory(pybind11)
-include_directories(include eigen-3.3.7)
-pybind11_add_module(_myfm src/bind.cpp src/Faddeeva.cc)
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
 
+if (NOT EXISTS "${CMAKE_CURRENT_BINARY_DIR}/eigen-3.4.0")
+  file(DOWNLOAD https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.zip "${CMAKE_CURRENT_BINARY_DIR}/eigen-3.4.0.zip")
+  file(ARCHIVE_EXTRACT INPUT "${CMAKE_CURRENT_BINARY_DIR}/eigen-3.4.0.zip")
+endif()
+
+find_package(Threads REQUIRED)
+
+
+include_directories("${CMAKE_BINARY_DIR}/eigen-3.4.0" cpp_source)
+include_directories("${CMAKE_SOURCE_DIR}/include" cpp_source)
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+include(CPack)
+
+
+# Detect the installed nanobind package and import it into CMake
+find_package(Python 3.8 COMPONENTS Interpreter ${DEV_MODULE} REQUIRED)
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+  OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE nanobind_ROOT)
+find_package(nanobind CONFIG REQUIRED)
+
+nanobind_add_module(_myfm cpp_source/bind.cpp cpp_source/Faddeeva.cc)
+
+install(TARGETS _myfm LIBRARY DESTINATION myfm/)

README.md

@@ -169,7 +169,7 @@ X_movie = movie_ohe.transform(
 block_user = RelationBlock(user_indices, X_user)
 block_movie = RelationBlock(movie_indices, X_movie)
 
-fm = MyFMRegressor(rank=2).fit(None, ratings.rating, X_rel=[block_user, block_movie])
+fm = MyFMRegressor(rank=2).fit(None, ratings.rating.values, X_rel=[block_user, block_movie])
 
 prediction_df = pd.DataFrame([
     dict(user_id=user_id,movie_id=movie_id,

cpp_source/bind.cpp

@@ -1,5 +1,7 @@
 #include "declare_module.hpp"
+#include <nanobind/nanobind.h>
+#include <nanobind/nb_defs.h>
 
-PYBIND11_MODULE(_myfm, m) {
+NB_MODULE(_myfm, m) {
   declare_functional<double>(m);
 }