[pull] master from SMTorg:master

.coveragerc

@@ -11,4 +11,4 @@ omit =
 	*/tests/*
 	*/examples/*
 	*/__init__.py
-	*/setup.py
+	*/setup.py

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/build_release.yml

@@ -0,0 +1,60 @@
+name: Build and upload to PyPI
+
+on:
+  workflow_dispatch:
+  push:
+    tags: ['v*']
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp39-* cp310-* cp311-* cp312-*
+          CIBW_SKIP: cp*_i686
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: smt-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: smt-src
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: smt-*
+          merge-multiple: true
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+

.github/workflows/tests.yml

@@ -10,14 +10,20 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9']
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.12"]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.11"
+          - os: ubuntu-latest
+            python-version: "3.10"
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -27,11 +33,10 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install numpy scipy cython scikit-learn pytest
-        pip install git+https://github.com/hwangjt/sphinx_auto_embed.git
+        pip install -r requirements.txt
         pip install -e .
 
     - name: Test with pytest
-      run: pytest
+      run: pytest -v --durations=0 smt
 
 

.github/workflows/tests_coverage.yml

@@ -12,12 +12,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.6']
+        python-version: ['3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -27,15 +27,19 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install numpy scipy cython scikit-learn pytest
-        pip install git+https://github.com/hwangjt/sphinx_auto_embed.git
+        pip install -r requirements.txt numpy==1.26.4 
         pip list
         pip install -e .
 
+    - name: Check with ruff
+      run: |
+        ruff --version
+        ruff check .
+        ruff format --check
+
     - name: Test with pytest and coverage
       run: |
-        pip install coverage
-        coverage run --source=smt -m pytest
+        RUN_SLOW_TESTS=1 pytest -v --durations=0 --cov=smt
 
     - name: Coveralls
       uses: AndreMiras/coveralls-python-action@develop

.github/workflows/tests_minimal.yml

@@ -0,0 +1,30 @@
+name: Tests Minimal
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.9"
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install numpy cython
+        pip install -e .
+
+    - name: Test with pytest
+      run: |
+        pip install pytest
+        pytest smt
+
+

.gitignore

@@ -1,7 +1,7 @@
 *.pyd
 *.pyc
 *~
-*build*
+**/*build
 *.egg-info
 *.so
 *.so.*
@@ -25,3 +25,4 @@ smt/src/rmts/rmtsclib.cpp
 /venv
 /pip-wheel-metadata
 **/.ipynb_checkpoints
+**/.ruff_cache

.readthedocs.yaml

@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the doc/ directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: doc/requirements.txt
+    - method: pip
+      path: .
+

AUTHORS.md

@@ -1,28 +1,50 @@
-## Authors
+# Authors
 
 SMT is developed by:
-* Mohamed Amine Bouhlel 
-* John Hwang 
-* Nathalie Bartoli 
-* Rémi Lafage 
-* Joseph Morlier 
-* Joaquim Martins 
+
+* Mohamed Amine Bouhlel
+* John Hwang
+* Nathalie Bartoli
+* Rémi Lafage
+* Joseph Morlier
+* Joaquim Martins
 
 SMT has been developed thanks to contributions from:
+
+* Alexandre Thouvenot
 * Andres Lopez Lopera
+* Antoine Averland
 * Emile Roux
+* Enrico Stragiotti
+* Ewout ter Hoeven
 * Florent Vergnes
 * Frederick Zahle
+* Heine Røstum
+* Hugo Reimeringer
+* Hugo Valayer
 * Jasper Bussemaker
 * Julien Schueller
+* Laurent Wilkens
+* Lisa Pretsch
 * Lucas Alber
+* Maël Tremouille
+* Mauricio Castano Aguirre
+* Maxime Lalande
 * Mostafa Meliani
+* Neal Kesterton
+* Nick Thompson
+* Nicolas Gonel
 * Nina Moëllo
 * Paul Saves
 * Raul Carreira Rufato
 * Reino Ruusu
 * Rémi Vauclin
+* Rémy Charayron
 * Rémy Priem
+* Robert Wenink
 * Ruben Conde
 * Steven Berguin
+* Sylvain Dubreuil
 * Vincent Drouet
+* Yingqian Liao
+* Zhou Tianxun

README.md

@@ -1,10 +1,12 @@
+![SMT Logo](./doc/smt_logo.png)
+
+# Surrogate Modeling Toolbox
+
 [![Tests](https://github.com/SMTOrg/smt/workflows/Tests/badge.svg)](https://github.com/SMTorg/smt/actions?query=workflow%3ATests)
-[![Coverage Status](https://coveralls.io/repos/github/SMTorg/smt/badge.svg?branch=master)](https://coveralls.io/github/SMTorg/smt?branch=master) 
+[![Coverage Status](https://coveralls.io/repos/github/SMTorg/smt/badge.svg?branch=master)](https://coveralls.io/github/SMTorg/smt?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/smt/badge/?version=latest)](https://smt.readthedocs.io/en/latest/?badge=latest)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
-
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-# Surrogate Modeling Toolbox
 The surrogate modeling toolbox (SMT) is a Python package that contains a collection of surrogate modeling methods, sampling techniques, and benchmarking functions. This package provides a library of surrogate models that is simple to use and facilitates the implementation of additional methods.
 
 SMT is different from existing surrogate modeling libraries because of its emphasis on derivatives, including training derivatives used for gradient-enhanced modeling, prediction derivatives, and derivatives with respect to the training data.
@@ -14,41 +16,58 @@ SMT is documented using custom tools for embedding automatically-tested code and
 
 SMT is distributed under the New BSD license.
 
-To cite SMT: M. A. Bouhlel and J. T. Hwang and N. Bartoli and R. Lafage and J. Morlier and J. R. R. A. Martins. A Python surrogate modeling framework with derivatives. Advances in Engineering Software, 2019.
+To cite SMT 2.0: P. Saves and R. Lafage and N. Bartoli and Y. Diouane and J. H. Bussemaker and T. Lefebvre and J. T. Hwang and J. Morlier and J. R. R. A. Martins. SMT 2.0: A Surrogate Modeling Toolbox with a focus on Hierarchical and Mixed Variables Gaussian Processes. Advances in Engineering Software, 2024.
 
+```latex
+@article{saves2024smt,
+         author = {P. Saves and R. Lafage and N. Bartoli and Y. Diouane and J. Bussemaker and T. Lefebvre and J. T. Hwang and J. Morlier and J. R. R. A. Martins},
+         title = {{SMT 2.0: A} Surrogate Modeling Toolbox with a focus on Hierarchical and Mixed Variables Gaussian Processes},
+         journal = {Advances in Engineering Sofware},
+         year = {2024},
+         volume = {188}, 
+         pages = {103571},
+         doi = {https://doi.org/10.1016/j.advengsoft.2023.103571}}
 ```
+
+To cite SMT legacy: M. A. Bouhlel and J. T. Hwang and N. Bartoli and R. Lafage and J. Morlier and J. R. R. A. Martins. A Python surrogate modeling framework with derivatives. Advances in Engineering Software, 2019.
+
+```latex
 @article{SMT2019,
-	Author = {Mohamed Amine Bouhlel and John T. Hwang and Nathalie Bartoli and Rémi Lafage and Joseph Morlier and Joaquim R. R. A. Martins},
-	Journal = {Advances in Engineering Software},
-	Title = {A Python surrogate modeling framework with derivatives},
-	pages = {102662},
-	year = {2019},
-	issn = {0965-9978},
-	doi = {https://doi.org/10.1016/j.advengsoft.2019.03.005},
-	Year = {2019}}
+        Author = {Mohamed Amine Bouhlel and John T. Hwang and Nathalie Bartoli and Rémi Lafage and Joseph Morlier and Joaquim R. R. A. Martins},
+        Journal = {Advances in Engineering Software},
+        Title = {A Python surrogate modeling framework with derivatives},
+        pages = {102662},
+        issn = {0965-9978},
+        doi = {https://doi.org/10.1016/j.advengsoft.2019.03.005},
+        Year = {2019}}
 ```
 
 # Required packages
-SMT depends on the following modules: numpy, scipy, scikit-learn, pyDOE2 and Cython. 
+
+SMT depends on the following modules: numpy, scipy, scikit-learn, pyDOE3 and Cython.
 
 # Installation
+
 If you want to install the latest release
 
-```
+```bash
 pip install smt
 ```
 
 or else if you want to install from the current master branch
 
-```
+```bash
 pip install git+https://github.com/SMTOrg/smt.git@master
 ```
 
 # Usage
-For examples demonstrating how to use SMT, you can take a look at the [tutorial notebook](tutorial/SMT_Tutorial.ipynb) or go to the 'smt/examples' folder.
+
+For examples demonstrating how to use SMT, you can take a look at the [tutorial notebooks](https://github.com/SMTorg/smt/tree/master/tutorial#readme) or go to the 'smt/examples' folder.
 
 # Documentation
+
 [Documentation of Surrogate Modeling Toolbox](http://smt.readthedocs.io/en/stable).
 
 # Contributing
+
 To contribute to SMT refer to the [contributing section](https://smt.readthedocs.io/en/latest/_src_docs/dev_docs.html#contributing-to-smt)  of the documentation.