Merge pull request #202 from PrincetonUniversity/numpy2_fix

forcing this merge as the current state fails in the simsopt docker container build (py_spec.math not added in install)

.github/workflows/build.yml

@@ -8,7 +8,6 @@ jobs:
       fail-fast: false
     env:
       SPEC_PATH: ${{ github.workspace }}
-      PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
     steps:
@@ -22,6 +21,8 @@ jobs:
         sudo apt-get update
         sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-103 libhdf5-dev libfftw3-bin libfftw3-dev libopenblas0-openmp libopenblas-dev 
         pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib
+        cd ${{ github.workspace }}/Utilities/pythontools
+        pip3 install -v .
     - name: compile_xspec
       run: |
         cd ${SPEC_PATH}
@@ -33,14 +34,12 @@ jobs:
     - name: run_fast_cartesian
       run: |
         cd ${SPEC_PATH}/ci/G1V03L2Fi
-        echo ${PYTHONPATH}
         export OMP_NUM_THREADS=1
         mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G1V03L2Fi.001.sp
         python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 
     - name: run_fast_cylinder
       run: |
         cd ${SPEC_PATH}/ci/G2V32L1Fi
-        echo ${PYTHONPATH}
         export OMP_NUM_THREADS=1
         mpiexec -n 2 --allow-run-as-root ${SPEC_PATH}/xspec G2V32L1Fi.001.sp
         python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 

.github/workflows/build_cmake.yml

@@ -8,7 +8,6 @@ jobs:
       fail-fast: false
     env:
       SPEC_PATH: ${{ github.workspace }}
-      PYTHONPATH: ${{ github.workspace }}/Utilities/pythontools
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
     steps:
@@ -20,6 +19,8 @@ jobs:
         pip3 install --upgrade pip
         pip3 install --user ninja cmake scipy
         pip3 install --user numpy f90nml scikit-build scipy h5py matplotlib
+        cd ${{ github.workspace }}/Utilities/pythontools
+        pip3 install -v .
     - name: Build & Test
       uses: ashutoshvarma/action-cmake-build@master
       with:
@@ -39,14 +40,12 @@ jobs:
     - name: run_fast_cartesian
       run: |
         cd ${SPEC_PATH}/ci/G1V03L2Fi
-        echo ${PYTHONPATH}
         export OMP_NUM_THREADS=1
         mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G1V03L2Fi.001.sp
         python3 -m py_spec.ci.test compare.h5 G1V03L2Fi.001.sp.h5 
     - name: run_fast_cylinder
       run: |
         cd ${SPEC_PATH}/ci/G2V32L1Fi
-        echo ${PYTHONPATH}
         export OMP_NUM_THREADS=1
         mpiexec -n 2 --allow-run-as-root $SPEC_PATH/install/bin/xspec G2V32L1Fi.001.sp
         python3 -m py_spec.ci.test compare.h5 G2V32L1Fi.001.sp.h5 

.github/workflows/py_spec.yml

@@ -19,7 +19,6 @@ jobs:
       working-directory: ${{ env.PY_SPEC_DIR }}
       run: |
         pip install --upgrade pip
-        pip3 install -r requirements.txt
         pip3 install setuptools wheel twine
 
     - name: Build py_spec

.github/workflows/python_wrapper.yml

@@ -19,7 +19,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install gfortran mpi-default-bin mpi-default-dev libhdf5-dev libfftw3-bin libfftw3-dev  libopenblas-dev cmake ninja-build
         pip install  numpy f90nml scikit-build scipy meson meson-python
-        pip install  git+https://github.com/zhucaoxiang/f90wrap@main_off
+        pip install f90wrap
 
     - name: Build python_wrapper
       run: |

Utilities/pythontools/py_spec/__init__.py

@@ -1,5 +1,10 @@
-# import of all SPEC-related python scripts.
-__version__ = "3.3.4"
+try:
+    from importlib import metadata
+except ImportError:
+    # Running on pre-3.8 Python; use importlib-metadata package
+    import importlib_metadata as metadata
+
+__version__ = metadata.version(__package__ or __name__)
 
 from .ci import test
 from .input.spec_namelist import SPECNamelist

Utilities/pythontools/pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name="py_spec"
+version="3.3.5"
+dependencies = ["numpy>=1.21.1", 
+            "f90nml",
+            "h5py", 
+            "matplotlib",
+            "coilpy; python_version<'3.12'",
+            "scipy>=1.7.0"]
+description="SPEC(Stepped-Pressure Equilibrium Code) python utilities"
+readme="README.md"
+authors = [
+    { name = "Christopher Berg Smiet", email = "[email protected]" },
+    { name = "Caoxiang Zhu", email = "[email protected]" },
+    { name = "SPEC developers"}
+]
+maintainers = [
+    { name = "Christopher Berg Smiet", email = "[email protected]" },
+]
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+]
+license = {text = "GNU 3.0"}

Utilities/pythontools/setup.py

@@ -1,26 +1,6 @@
 import setuptools
-from py_spec import __version__
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
 
 setuptools.setup(
     name="py_spec",
-    version=__version__,
-    setup_requires=["numpy>=2.0.0; python_version > '3.8'",
-                    "oldest-supported-numpy; python_version <= '3.8'"],
-    install_requires=["numpy>=1.21.1"],
-    description="SPEC(Stepped-Pressure Equilibrium Code) python utilities",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
-        "Programming Language :: Python :: 3",
-        "Topic :: Scientific/Engineering",
-    ],
-    url="https://princetonuniversity.github.io/SPEC/",
-    author="SPEC developers",
-    license="GNU 3.0",
-    packages=['py_spec', 'py_spec.input', 'py_spec.output', 'py_spec.ci']
+    packages=['py_spec', 'py_spec.input', 'py_spec.output', 'py_spec.ci', 'py_spec.math']
 )