Merge branch 'master' into ag/pr

.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
@@ -19,13 +19,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install python dependencies
-      run: |
-        pip install flake8
+    - name: Run ruff
+      uses: chartboost/ruff-action@v1
 
-    - name: Run linting tests
-      run: |
-        export EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
-        flake8  --ignore $EXCLUDE src/
-        flake8  --ignore $EXCLUDE tests/
-        flake8  --ignore $EXCLUDE examples/

.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

.readthedocs.yaml

@@ -1,6 +1,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/source/conf.py
@@ -11,9 +16,7 @@ sphinx:
 # formats:
 #   - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.8
    install:
    - requirements: docs/requirements.txt
    - requirements: requirements.txt

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")
@@ -58,6 +63,8 @@ else()
     	set(CMAKE_CXX_FLAGS "-O3 -ffp-contract=fast")
     endif()
 endif()
+# Ensure all code used from Eigen does not have LGPL license:
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DEIGEN_MPL2_ONLY")
 message(STATUS "CMAKE_CXX_FLAGS are ${CMAKE_CXX_FLAGS}")
 
 if(DEFINED ENV{CONDA_PREFIX})
@@ -104,7 +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)
@@ -117,7 +124,7 @@ pybind11_add_module(${PROJECT_NAME}
     src/simsoptpp/biot_savart_py.cpp
     src/simsoptpp/biot_savart_vjp_py.cpp
     src/simsoptpp/regular_grid_interpolant_3d_py.cpp
-    src/simsoptpp/curve.cpp src/simsoptpp/curverzfourier.cpp src/simsoptpp/curvexyzfourier.cpp
+    src/simsoptpp/curve.cpp src/simsoptpp/curverzfourier.cpp src/simsoptpp/curvexyzfourier.cpp src/simsoptpp/curveplanarfourier.cpp
     src/simsoptpp/surface.cpp src/simsoptpp/surfacerzfourier.cpp src/simsoptpp/surfacexyzfourier.cpp
     src/simsoptpp/integral_BdotN.cpp
     src/simsoptpp/dipole_field.cpp src/simsoptpp/permanent_magnet_optimization.cpp
@@ -163,4 +170,4 @@ 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 .)