Refactor project structure to follow Python module conventions (#5)

* Refactor project structure to follow Python module conventions

* Add pytest-cov in requirements.txt

* Add coverage conf

* Remove code duplication: extension relies on design space base classes from smt

* Update license

* Expose only required symbols to work with smt at module level

* numpy has to be installed for CI tests

* Avoid importing version from main module

* Bump version 0.2.1

* Use smt master in CI tests

* Take into account smt changes (ext dep removal)

* Use smt master in requirements

* Bump 0.2.2

Author: relf

.coveragerc

@@ -0,0 +1,14 @@
+[paths]
+source = 
+   smt_design_space_ext
+
+[html]
+directory = coverage_html_report
+
+[run]
+relative_files = True
+omit =
+	*/tests/*
+	*/examples/*
+	*/__init__.py
+	*/setup.py

.github/workflows/build_release.yml

@@ -6,26 +6,6 @@ on:
     tags: ['v*']
 
 jobs:
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.3
-        env:
-          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
-          CIBW_SKIP: cp*_i686
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: smt-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
@@ -38,20 +18,18 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: smt-src
+          name: smt-design-space-ext-src
           path: dist/*.tar.gz
 
   upload_pypi:
-    needs: [build_wheels, build_sdist]
+    needs: [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

README.md

@@ -1,67 +1,3 @@
-![SMT Logo](./doc/smt_logo.png)
-# Surrogate Modeling Toolbox
+# SMT Design Space Extension
 
-[![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) 
-[![Documentation Status](https://readthedocs.org/projects/smt/badge/?version=latest)](https://smt.readthedocs.io/en/latest/?badge=latest)
-[![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)
-
-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.
-
-It also includes new surrogate models that are not available elsewhere: kriging by partial-least squares reduction and energy-minimizing spline interpolation.
-SMT is documented using custom tools for embedding automatically-tested code and dynamically-generated plots to produce high-quality user guides with minimal effort from contributors.
-
-SMT is distributed under the New BSD license.
-
-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.
-
-```
-@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.
-
-```
-@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},
-	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, pyDOE3 and Cython. 
-
-# Installation
-If you want to install the latest release
-
-```
-pip install smt
-```
-
-or else if you want to install from the current master branch
-
-```
-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 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.
+This module allows to use advanced design space implementation for hierachical variables handling.

__version__.py

@@ -1,16 +1,6 @@
-Cython
-numpy
-scipy
-scikit-learn
-pyDOE3
-numba           # JIT compiler
-matplotlib      # used in examples and tests
-pytest          # tests runner
-pytest-xdist    # allows running parallel testing with pytest -n <num_workers>
-pytest-cov      # allows to get coverage report
-ruff            # format and lint code
-smt
-jenn >= 1.0.2, <2.0
-egobox ~= 0.20.0
+smt @ git+https://github.com/SMTorg/smt@master
 ConfigSpace==0.6.1 
-adsg-core==1.1.1
+adsg-core==1.1.1
+pytest     # tests runner
+pytest-cov # allows to get coverage report
+ruff       # format and lint code

requirements.txt

@@ -8,34 +8,29 @@
 
 from setuptools import setup
 
-version = {}
-with open("./__version__.py") as fp:
-    exec(fp.read(), version)
-
+# Import __version__ without importing the module in setup
+exec(open("./smt_design_space_ext/version.py").read())
 
 setup(
-    name="smt_design_space",
+    name="smt_design_space_ext",
+    version=__version__,  # noqa
     author="Paul Saves et al.",
     author_email="paul.saves@onera.fr",
     keywords=["SMT, DesignSpace, Graph"],
-    license="ONERA",
-    description="SMT Design Space",
+    license="BSD-3",
+    description="SMT design space extension for hierarchical variables handling",
     install_requires=[
-        "scipy",
         "numpy",
-        "scikit-learn",
+        "smt",
         "ConfigSpace==0.6.1",
         "adsg-core==1.1.1",
     ],
     maintainer="Paul Saves",
     maintainer_email="paul.saves@onera.fr",
     packages=[
-        "smt_design_space",
+        "smt_design_space_ext",
     ],
-    include_package_data=True,
-    python_requires=">=3.8",
-    version=version["__version__"],
-    zip_safe=False,
+    python_requires=">=3.9",
     url="https://github.com/SMTorg/smt-design-space",  # use the URL to the github repo
     download_url="https://github.com/SMTorg/smt-design-space/releases",
 )

setup.py

@@ -0,0 +1,9 @@
+from .version import __version__
+
+# Symbols imported in smt to handle hierarchical variables
+from smt_design_space_ext.design_space import (
+    DesignSpace,
+    ensure_design_space,
+)
+
+__all__ = ["__version__", "DesignSpace", "ensure_design_space"]