Merge remote-tracking branch 'origin/titan' into get_atom_data_error

.github/workflows/python-publish.yml

@@ -20,8 +20,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel numpy
-    - name: Build the package
-      run: python setup.py sdist
+    #- name: Build the package
+    #  run: python setup.py sdist
     - name: Publish distribution 📦 to Test PyPI
       if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@master

.github/workflows/tests.yml

@@ -11,11 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        build_command: ["python setup.py develop",
-                        "pip install .",
-                        "pip install --editable .",
-                        "python setup.py install",
-                        # "echo 'no operation'",  # how to test this one?
+        build_command: [
+          "pip install .",
+          "pip install --editable .",
         ]
       fail-fast: false
 
@@ -25,15 +23,15 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: '3.9'
-    - name: Install dependencies
-      run: |
-        python -m pip install -r requirements.txt
     - name: Install Aurora
       run: ${{ matrix.build_command }}
     - name: Move to root and try importing Aurora
       run: |
         cd /
         python -c "import aurora; print(aurora.__version__)"
+    - name: Run test_basic.py
+      run: |
+        python examples/test_basic.py
 #    - name: Test with pytest and coverage
 #      run: |
 #        pip install pytest

CMakeLists.txt

@@ -0,0 +1,43 @@
+cmake_minimum_required(VERSION 3.17.2...3.26)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES C Fortran)
+
+find_package(
+  Python
+  COMPONENTS Interpreter Development.Module NumPy
+  REQUIRED)
+
+# F2PY headers
+execute_process(
+  COMMAND "${PYTHON_EXECUTABLE}" -c
+          "import numpy.f2py; print(numpy.f2py.get_include())"
+  OUTPUT_VARIABLE F2PY_INCLUDE_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+add_library(fortranobject OBJECT "${F2PY_INCLUDE_DIR}/fortranobject.c")
+target_link_libraries(fortranobject PUBLIC Python::NumPy)
+target_include_directories(fortranobject PUBLIC "${F2PY_INCLUDE_DIR}")
+set_property(TARGET fortranobject PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+add_custom_command(
+  OUTPUT _auroramodule.c example-f2pywrappers.f
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/aurora/main.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/impden.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/math.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/grids.f90"
+  VERBATIM
+  COMMAND "${Python_EXECUTABLE}" -m numpy.f2py
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/main.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/impden.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/math.f90"
+          "${CMAKE_CURRENT_SOURCE_DIR}/aurora/grids.f90"
+          -m _aurora --lower)
+
+python_add_library(_aurora MODULE "${CMAKE_CURRENT_BINARY_DIR}/_auroramodule.c"
+                   "${CMAKE_CURRENT_SOURCE_DIR}/aurora/main.f90"
+                   "${CMAKE_CURRENT_SOURCE_DIR}/aurora/impden.f90"
+                   "${CMAKE_CURRENT_SOURCE_DIR}/aurora/math.f90"
+                   "${CMAKE_CURRENT_SOURCE_DIR}/aurora/grids.f90"
+                   WITH_SOABI)
+target_link_libraries(_aurora PRIVATE fortranobject)
+
+install(TARGETS _aurora DESTINATION aurora/)

aurora/adas_files.py

@@ -382,6 +382,11 @@ def adas_files_dict():
     files["Ca"]["brs"] = "brs05360.dat"
     files["Ca"]["pbs"] = ""
     files["Ca"]["prc"] = ""
+    files["Ti"] = {}  # 22
+    files["Ti"]["acd"] = "acd00_ti.dat"
+    files["Ti"]["scd"] = "scd00_ti.dat"
+    files["Ti"]['prb'] = "prb00_ti.dat"
+    files["Ti"]['plt'] = "plt00_ti.dat"
     files["Fe"] = {}  # 26
     files["Fe"]["acd"] = "acd89_fe.dat"
     files["Fe"]["scd"] = "scd89_fe.dat"

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "aurorafusion"
+dynamic = ["version"]
+description = "Aurora package for particle transport, radiation and neutrals in magnetically-confined plasmas"
+authors = [
+    { name = "F. Sciortino", email = "[email protected]" },
+]
+urls = { "Homepage" = "https://github.com/fsciortino/Aurora" }
+keywords = ["particle and impurity transport, neutrals, radiation, magnetic confinement fusion"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+    "matplotlib",
+    "numpy<2.0.0",
+    "omfit_classes",
+    "pandas",
+    "pexpect",
+    "requests",
+    "scipy",
+    # transitive dependencies of omfit_classes
+    # that omfit_classes does not advertise
+    "fortranformat",
+    "netCDF4",
+    "uncertainties",
+    "omas",
+    # omfit_classes will have issues with newer versions
+    # of xarray for two different reasons:
+    # 1. because of a recently-introduced xarray bug that
+    #    will be fixed in the next release after v2024.02.0
+    #    (this commit: https://github.com/pydata/xarray/commit/a241845c0dfcb8a5a0396f5ef7602e9dae6155c0).
+    #    This constrains xarray<=v2023.07.0.
+    # 2. because omfit_classes uses xarray.plot.plot, which has
+    #    been removed/renamed by a commit from October 2022.
+    #    This constrains xarray<=v2022.09.0
+    "xarray==v2022.09.0",
+    # omfit_classes has issues with newer versions of
+    # matplotlib, see https://github.com/gafusion/OMFIT-source/issues/6784
+    "matplotlib<=3.5",
+]
+
+[build-system]
+requires = ["scikit-build-core", "numpy"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+ninja.minimum-version = "1.10"
+cmake.minimum-version = "3.17.2"
+wheel.packages = ["aurora"]
+
+[tool.scikit-build.metadata.version]
+provider = "scikit_build_core.metadata.regex"
+input = "aurora/__init__.py"