New build system based on scikit-build-core

.coveragerc

@@ -1,9 +1,12 @@
 [run]
 parallel = true
 source = simsopt
+relative_files = true
 
 [paths]
 sources = 
-    /opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages
-    /opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages
-    /opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages
+    src/
+    /**/lib/python3.8/site-packages
+    /**/lib/python3.9/site-packages
+    /**/lib/python3.10/site-packages
+    /**/lib/python3.11/site-packages

.github/workflows/conda.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest,  macos-11]
-        python-version: ["3.8"]
+        python-version: ["3.9"]
 
     runs-on: ${{ matrix.platform }}
 
@@ -41,7 +41,7 @@ jobs:
           channel-priority: strict
 
       - name: Prepare
-        run: conda install -y conda-build conda-verify setuptools_scm anaconda-client
+        run: conda install -y conda-build conda-verify setuptools_scm anaconda-client scikit-build-core
 
       - name: Build and upload
         if: github.event_name == 'release' && github.event.action == 'published'

.github/workflows/extensive_ci.yml → .github/workflows/extensive_test.yml

@@ -29,12 +29,12 @@ jobs:
       matrix:
         test-type: [unit, integrated]
         packages: [all, vmec, spec, none]
-        python-version: [3.8.17, 3.9.17, 3.10.12] # To sync with coveragerc use 3 levels with python version
+        python-version: [3.8, 3.9, "3.10"]
         include:
-            - python-version: 3.9.17
+            - python-version: 3.9
               test-type: unit
               packages: none
-            - python-version: 3.9.17
+            - python-version: 3.9
               test-type: integrated
               packages: none
 
@@ -165,15 +165,19 @@ jobs:
 
     - name: Install simsopt package
       if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
-      run: pip install -v .[MPI,SPEC]
+      run: |
+        pip install -v .
+        pip install mpi4py py_spec pyoculus h5py
 
     - name: Install simsopt package
       if: contains(matrix.packages, 'none')
       run: pip install -v .
 
     - name: Install simsopt package
       if: contains(matrix.packages, 'vmec')
-      run: pip install -v .[MPI]
+      run: |
+        pip install -v .
+        pip install mpi4py
 
     - name: Run serial examples as part of integrated tests
       if: contains(matrix.test-type, 'integrated') && (contains(matrix.packages, 'none') || contains(matrix.packages, 'all'))
@@ -247,7 +251,7 @@ jobs:
     - name: Set up Python 
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8.17
+        python-version: 3.9
 
     - name: Install coverage
       run: pip install coverage

.github/workflows/linting.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/non_simd_tests.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8.15] # To sync with coveragerc use 3 level
+        python-version: [3.9]
 
     steps:
     # First print out lots of information. We do this in separate 

.github/workflows/ci.yml → .github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8.17] # To sync with coveragerc use 3 level
+        python-version: [3.9]
         test-type: [unit, integrated]
 
     steps:
@@ -49,6 +49,11 @@ jobs:
         set -ex
         ls -l
 
+    - name: Print python location
+      run: |
+        set -ex
+        which python
+
     - name: apt-get stuff needed for libstell and vmec
       run: |
         sudo apt-get update
@@ -88,7 +93,7 @@ jobs:
     - name: Install python dependencies
       run: |
         sudo apt-get install graphviz graphviz-dev
-        pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz
+        pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py  py_spec pyoculus h5py
 
     - name: Install booz_xform
       run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform
@@ -130,8 +135,6 @@ jobs:
       run: |
         cd SPEC
         pip install .
-        # python setup.py bdist_wheel
-        # pip install dist/*.whl
 
     - name: Try import spec
       run: python -c "import spec.spec_f90wrapped as spec; print(spec.constants.version)"
@@ -159,7 +162,8 @@ jobs:
       run: python -c "print(dir()); import vmec; print(dir()); print(dir(vmec)); print('package:', vmec.__package__); print('spec:', vmec.__spec__); print('doc:', vmec.__doc__); print('file:', vmec.__file__); print('path:', vmec.__path__)"
 
     - name: Install simsopt package
-      run: env CMAKE_BUILD_TYPE=Debug pip install -v .[MPI,SPEC]
+      # run: env CMAKE_BUILD_TYPE=Debug pip install -v .[MPI,SPEC]
+      run: pip install -v ".[MPI,SPEC,VIS]"
 
     - name: Verify that importing simsopt does not automatically initialize MPI
       run: ./tests/verify_MPI_not_initialized.py

.github/workflows/wheel.yml

@@ -45,7 +45,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Download all submodules
         run: git submodule update --init

CMakeLists.txt

@@ -1,12 +1,13 @@
 cmake_minimum_required(VERSION 3.15)
-project(simsoptpp)
+project(simsoptpp LANGUAGES CXX)
 #set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})
 
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 set(Python_FIND_STRATEGY LOCATION)
-find_package(Python 3 COMPONENTS Interpreter Development.Module NumPy)
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module NumPy)
+find_package(pybind11 CONFIG REQUIRED)
 
 message(status "Python executable is ${Python_EXECUTABLE}")
 message(status "Python Development Module found value is ${Python_Development.Module_FOUND}")
@@ -40,8 +41,12 @@ include_directories(${CMAKE_CURRENT_BINARY_DIR})
 
 include(CheckCXXCompilerFlag)
 IF(DEFINED ENV{CI})
-    message(STATUS "CI environment detected. Set compilation flags targetting Westmere microarch.")
-    set(CMAKE_CXX_FLAGS "-O3 -march=westmere")
+    if (APPLE)
+    	set(CMAKE_CXX_FLAGS "-O3")
+    else()
+        message(STATUS "CI environment detected. Set compilation flags targetting Westmere microarch.")
+        set(CMAKE_CXX_FLAGS "-O3 -march=westmere")
+    endif()
 elseif(DEFINED ENV{CONDA_BUILD})
     message(STATUS "conda build environment detected. Let conda set compilation flags accordingly.")
     # set(CMAKE_CXX_FLAGS "-O3 -march=ivybridge -mfma -ffp-contract=fast")
@@ -106,7 +111,7 @@ else()
     message(STATUS "Boost include dirs are ${Boost_INCLUDE_DIRS}")
 endif()
 
-add_subdirectory(thirdparty/pybind11)
+# add_subdirectory(thirdparty/pybind11)
 add_subdirectory(thirdparty/fmt EXCLUDE_FROM_ALL)
 set(XTENSOR_USE_OPENMP 0)
 set(XTENSOR_USE_TBB 0)
@@ -164,4 +169,4 @@ target_link_libraries(profiling PRIVATE fmt::fmt-header-only)
 #install(TARGETS ${PROJECT_NAME}
 #        #LIBRARY
 #        DESTINATION src/${PROJECT_NAME})
-#install(TARGETS ${PROJECT_NAME} LIBRARY DESTINATION ${PROJECT_NAME})
+install(TARGETS ${PROJECT_NAME} LIBRARY DESTINATION .)

conda.recipe/meta.yaml

@@ -1,9 +1,6 @@
-{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %}
-{% set version = data.get('version') %}
-
 package:
   name: simsopt
-  version: {{ version }}
+  version: {{ GIT_DESCRIBE_TAG }}+{{ GIT_BUILD_STR }}
 
 source:
   path: ..
@@ -24,14 +21,17 @@ requirements:
     - libgomp      # [linux]
     - "setuptools_scm[toml]"
     - boost
+    - pybind11
+    - scikit-build-core
 
   host:
     - pip
     - wheel
-    - setuptools
     - numpy {{ numpy }}
     - "setuptools_scm[toml]"
+    - scikit-build-core
     - python {{ python }}
+    - pybind11
 
   run:
     - python
@@ -49,13 +49,13 @@ requirements:
     - pyevtk
 
 about:
-  home: {{ data.get('url') }}
+  home: https://github.com/hiddenSymmetries/simsopt
   summary: simplified framework for stellarator optimization
   license: MIT
   license_file: "LICENSE"
   description:
   doc_url: https://simsopt.readthedocs.io/
-  dev_url: {{ data.get('url') }}
+  dev_url: https://github.com/hiddenSymmetries/simsopt
 
 extra:
   recipe-maintainers:

pyproject.toml

@@ -1,8 +1,95 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "oldest-supported-numpy", "cmake", "ninja", "setuptools_scm[toml]>=6.0"]
-build-backend = "setuptools.build_meta"
+requires = [
+  "scikit-build-core>=0.3.3",
+  "pybind11",
+  "oldest-supported-numpy",
+  "setuptools_scm>=8.0",
+  'tomli; python_version < "3.11"',]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "simsopt"
+license = {text = "MIT License"}
+description="Framework for optimizing stellarators"
+readme = "README.md"
+# long_description = file: README.md
+# long_description_content_type = text/markdown
+requires-python = ">=3.8"
+authors = [
+  {name = "Matt Landreman", email = "[email protected]"},
+  {name = "Bharat Medasani", email = "[email protected]"},
+  {name = "Florian Wechsung", email = "[email protected]"}
+]
+maintainers = [
+  {name = "Bharat Medasani", email = "[email protected]"},
+  {name = "Matt Landreman", email = "[email protected]"},
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Environment :: Console",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10"
+]
+keywords = [
+    "plasma physics",
+    "plasma",
+    "magnetohydrodynamics",
+    "mhd",
+    "nuclear fusion reactor",
+    "fusion",
+    "stellarator",
+    "vmec",
+    "spec",
+    "optimization",
+    "Biot-Savart",
+    "magnetostatics"
+]
+dependencies = [
+    "numpy>=1.21",
+    "jax>=0.2.5",
+    "jaxlib>=0.1.56",
+    "scipy>=1.5.4",
+    "Deprecated>=1.2.10",
+    "nptyping>=1.3.0",
+    "monty>=2021.6.10",
+    "ruamel.yaml",
+    "sympy",
+    "f90nml",
+    "randomgen",
+    "pyevtk",
+    "matplotlib"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+SPEC = ["py_spec>=3.0.1", "pyoculus>=0.1.1", "h5py>=3.1.0"]
+MPI = ["mpi4py>=3.0.3"]
+VIS = ["vtk >= 8.1.2", "PyQt5", "mayavi", "plotly", "networkx"]
+DOCS = ["sphinx", "sphinx-rtd-theme"]
+
+[project.urls]
+Homepage = "https://github.com/hiddenSymmetries/simsopt"
+Download = "https://pypi.org/project/simsopt"
+Issues = "https://github.com/hiddenSymmetries/simsopt/issues"
+Documentation = "https://simsopt.readthedocs.io"
+Repository = "https://github.com/hiddenSymmetries/simsopt"
+
+[tool.setuptools_scm]
+write_to = "src/simsopt/_version.py"
+local_scheme = "dirty"
+
+[tool.scikit-build]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["src/simsopt/_version.py"]
+build-dir = "build/{wheel_tag}"
 
-[tools.setuptools_scm]
 
 [tool.ruff]
 src = ["src/simsopt"] 
@@ -18,3 +105,14 @@ extend-exclude = ["thirdparty"]
 "tests/geo/test_curve.py" = ["F401"]
 "tests/geo/test_surface.py" = ["F401"]
 "tests/mhd/test_virtual_casing.py" = ["F841"]
+
+[tool.coverage.run]
+parallel = true
+relative_files = true
+source = ["simsopt"]
+
+[tool.coverage.paths]
+source = [
+    "src",
+    "/**/lib*/python*/site-packages"
+]