Merge branch 'master' of https://github.com/hiddenSymmetries/simsopt …

…into I_current_profiles

.coveragerc

@@ -6,7 +6,6 @@ relative_files = true
 [paths]
 sources = 
     src/
-    /**/lib/python3.8/site-packages
     /**/lib/python3.9/site-packages
     /**/lib/python3.10/site-packages
     /**/lib/python3.11/site-packages

.github/workflows/extensive_test.yml

@@ -98,7 +98,7 @@ jobs:
     - name: Install python dependencies
       run: |
            sudo apt-get install graphviz graphviz-dev
-           pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann f90wrap
+           pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann f90wrap
 
     - name: Install booz_xform
       if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
@@ -290,7 +290,7 @@ jobs:
     - name: Upload coverage to Codecov
       # The next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error
       if: github.repository_owner == 'hiddenSymmetries'
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

.github/workflows/linting.yml

@@ -20,5 +20,5 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Run ruff
-      uses: chartboost/ruff-action@v1
+      uses: astral-sh/ruff-action@v1
 

.github/workflows/non_simd_tests.yml

@@ -84,7 +84,7 @@ jobs:
     - name: Install python dependencies
       run: |
         sudo apt-get install graphviz graphviz-dev
-        pip install wheel "numpy<2.0.0" scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann
+        pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz ground bentley_ottmann
 
     - name: Install booz_xform
       run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform

.github/workflows/tests.yml

@@ -93,7 +93,7 @@ jobs:
     - name: Install python dependencies
       run: |
         sudo apt-get install graphviz graphviz-dev
-        pip install "numpy<2.0.0" cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec h5py ground bentley_ottmann f90wrap
+        pip install numpy cmake scikit-build f90nml ninja wheel setuptools sympy qsc pyevtk matplotlib plotly networkx pygraphviz mpi4py py_spec h5py ground bentley_ottmann f90wrap
 
     - name: Install pyoculus
       run: pip install -v git+https://github.com/zhisong/pyoculus

.github/workflows/wheel.yml

@@ -17,15 +17,15 @@ jobs:
         run: git fetch --prune --unshallow
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.4
+        uses: pypa/cibuildwheel@v2.21.3
         # To supply options, put them in 'env'
         env:
-          # Only build for python 3.{8,9,10,11}
-          CIBW_BUILD : cp38-* cp39-* cp310-* cp311-*
+          # Only build for python 3.{9,10,11,12}
+          CIBW_BUILD : cp39-* cp310-* cp311-* cp312-*
           # Supports only x86_64 arch for linux
           CIBW_ARCHS_LINUX: x86_64
           CIBW_ARCHS_MACOS: "x86_64 arm64"
-          CIBW_SKIP: cp27-* cp36-* cp37-*
+          CIBW_SKIP: cp27-* cp36-* cp37-* cp38-*
           CIBW_DEPENDENCY_VERSIONS: latest
 
       - uses: actions/upload-artifact@v3
@@ -68,7 +68,7 @@ jobs:
     # alternatively, to publish when a GitHub Release is created, use the following rule:
     # if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v4.1.7
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist

ci/Dockerfile.ubuntu

@@ -40,7 +40,10 @@ RUN python3 -m pip install wheel
 RUN python3 -m venv /venv/
 
 RUN /venv/bin/pip install -U pip
-RUN /venv/bin/python -m pip install numpy scipy jax jaxlib f90nml mpi4py jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake f90wrap h5py
+# 2024-11-12 MJL: mpi4py < 4.0 in the next line is due to
+# https://github.com/hiddenSymmetries/simsopt/issues/455
+# Once NERSC gets Shifter working with mpi4py >= 4 we can remove this inequality
+RUN /venv/bin/python -m pip install numpy scipy jax jaxlib f90nml "mpi4py<4.0" jupyter notebook ipython qsc sympy scikit-build ninja "pybind11[global]" cmake f90wrap h5py
 ENV PATH="/venv/bin:${PATH}"
 
 RUN git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git /src/SPEC && \

ci/singularity.def

@@ -50,15 +50,17 @@ Stage: devel
 
     git clone --depth 1 https://github.com/mpi4py/mpi4py.git && \
     cd mpi4py && \
-    /venv/bin/python setup.py build --mpicc=mpicc --mpicxx=mpicxx --mpifort=mpifort --mpif90=mpif90 --mpif77=mpif77 --mpild=mpicc  && \
-    /venv/bin/python setup.py install  && \
+    # /venv/bin/python setup.py build --mpicc=mpicc --mpicxx=mpicxx --mpifort=mpifort --mpif90=mpif90 --mpif77=mpif77 --mpild=mpicc  && \
+    # /venv/bin/python setup.py install  && \
+    /venv/bin/pip install . && \
     cd .. && \
     rm -rf mpi4py
 
     git clone --depth 1 https://github.com/PrincetonUniversity/SPEC.git && \
     cd SPEC   &&  \
-    /venv/bin/python setup.py bdist_wheel && \
-    /venv/bin/pip install -v dist/*.whl &&  \
+    # /venv/bin/python setup.py bdist_wheel && \
+    # /venv/bin/pip install -v dist/*.whl &&  \
+    /venv/bin/pip install -v . 
     cd Utilities/pythontools && \
     /venv/bin/pip install -r requirements.txt && \
     /venv/bin/pip install . && \

conda.recipe/conda_build_config.yaml

@@ -2,7 +2,6 @@ numpy:
   - 1.23
   - 1.24
 python:
-  - 3.8
   - 3.9
   - 3.10
   - 3.11

docs/source/example_islands.rst

@@ -109,10 +109,10 @@ We now combine the four residues into a least-squares objective
 function, by summing the squares of the residues::
 
   # Objective function is \sum_j residue_j ** 2
-  prob = LeastSquaresProblem.from_tuples([(residue1, 0, 1),
-                                          (residue2, 0, 1),
-                                          (residue3, 0, 1),
-                                          (residue4, 0, 1)])
+  prob = LeastSquaresProblem.from_tuples([(residue1.J, 0, 1),
+                                          (residue2.J, 0, 1),
+                                          (residue3.J, 0, 1),
+                                          (residue4.J, 0, 1)])
 
 If you wanted an island to be present instead of absent, which might
 be the case when designing an island divertor, a value other than zero

docs/source/example_quasisymmetry.rst

@@ -268,7 +268,7 @@ axisymmetric::
   # Define objective function
   prob = LeastSquaresProblem.from_tuples([(vmec.aspect, 6, 1),
                                           (vmec.mean_iota, 0.42, 1),
-                                          (qs, 0, 1)])
+                                          (qs.residuals, 0, 1)])
 
 It can be seen here that we are seeking a configuration with aspect
 ratio 6, and average iota of 0.42, slightly above the resonance at 2 /
@@ -387,7 +387,7 @@ at the edge and magnetic axis, in order to prescribe the magnetic shear::
   prob = LeastSquaresProblem.from_tuples([(vmec.aspect, 6, 1),
                                           (vmec.iota_axis, 0.465, 1),
                                           (vmec.iota_edge, 0.495, 1),
-                                          (qs, 0, 1)])
+                                          (qs.residuals, 0, 1)])
 
 It can be seen here that we are seeking a configuration with aspect
 ratio 6, and iota slightly below 0.5.

pyproject.toml

@@ -2,8 +2,7 @@
 requires = [
   "scikit-build-core",
   "pybind11",
-  "numpy >= 2.0.0; python_version > '3.8'",
-  "oldest-supported-numpy; python_version <= '3.8'",
+  "numpy >= 2.0.0",
   "setuptools_scm>=8.0",
   'tomli; python_version < "3.11"',]
 build-backend = "scikit_build_core.build"
@@ -53,7 +52,7 @@ keywords = [
     "magnetostatics"
 ]
 dependencies = [
-    "numpy>=1.21,<2.0.0",
+    "numpy>=1.21",
     "jax>=0.2.5",
     "jaxlib>=0.1.56",
     "scipy>=1.5.4",

requirements.txt

@@ -1,5 +1,5 @@
 setuptools_scm >= 6.0
-numpy >= 1.19.4
+numpy >= 1.21.0
 jax >= 0.2.5
 jaxlib >= 0.1.56
 scipy >= 1.5.4

src/simsopt/_core/optimizable.py

@@ -87,7 +87,7 @@ def __init__(self,
             free: Array of boolean values denoting if the DOFs is are free.
                   False values implies the corresponding DOFs are fixed
             lower_bounds: Lower bounds for the DOFs. Meaningful only if
-                DOF is not fixed. Default is np.NINF
+                DOF is not fixed. Default is -np.inf
             upper_bounds: Upper bounds for the DOFs. Meaningful only if
                 DOF is not fixed. Default is np.inf
         """
@@ -106,7 +106,7 @@ def __init__(self,
             free = np.asarray(free, dtype=np.bool_)
 
         if lower_bounds is None:
-            lower_bounds = np.full(len(x), np.NINF)
+            lower_bounds = np.full(len(x), -np.inf)
         else:
             lower_bounds = np.asarray(lower_bounds, np.double)
 

src/simsopt/mhd/spec.py

@@ -199,7 +199,7 @@ def __init__(self,
                                           mpol=self.mpol, ntor=self.ntor)
         self._boundary.rc[:] = self.array_translator(si.rbc, style='spec').as_simsopt
         self._boundary.zs[:] = self.array_translator(si.zbs, style='spec').as_simsopt 
-        if not self.freebound:
+        if not self.stellsym:
             self._boundary.rs[:] = self.array_translator(si.rbs, style='spec').as_simsopt
             self._boundary.zc[:] = self.array_translator(si.zbc, style='spec').as_simsopt
         self._boundary.local_full_x = self._boundary.get_dofs()

tests/core/test_dofs.py

@@ -168,7 +168,7 @@ def test_lower_bounds(self):
                     names=np.array(['x', 'y', 'z']),
                     free=np.array([True, True, False]))
         self.assertTrue(np.allclose(dofs.free_lower_bounds,
-                                    np.array([np.NINF, np.NINF])))
+                                    np.array([-np.inf, -np.inf])))
 
         with self.assertRaises(DofLengthMismatchError):
             dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.0])
@@ -180,7 +180,7 @@ def test_lower_bounds(self):
 
         dofs.unfix_all()
         self.assertTrue(np.allclose(dofs.free_lower_bounds,
-                                    np.array([-1000.0, -1001.0, np.NINF])))
+                                    np.array([-1000.0, -1001.0, -np.inf])))
 
         dofs.free_lower_bounds = np.array([-1000.0, -1001.0, -1002.])
         self.assertTrue(np.allclose(dofs.free_lower_bounds,