Merge branch 'devel' into Issue1037_rays_touch

Author: Didou09

MANIFEST.in

@@ -7,6 +7,13 @@ include _updateversion.py
 recursive-include tofu/geom *.pxd
 recursive-include tofu/geom/inputs *.txt
 recursive-include tofu/spectro *.txt
+
+# physics
+tofu/physics_tools/runaways/emission/*.csv
+tofu/physics_tools/transmission/inputs_filter/*.txt
+tofu/physics_tools/transmission/inputs_filter/*.csv
+
+# tests data
 recursive-include tofu/tests/tests01_geom/test_data *.txt
 recursive-include tofu/tests/tests01_geom/test_data *.npz
 recursive-include tofu/tests/tests01_geom/test_data *.svg

README.md

@@ -108,6 +108,9 @@ Do you want to use **tofu** on IMAS and don't know where to start?
 
 
 ## Installing tofu
+Tofu installation currently works with Python 3.10 & 3.11.
+
+For Windows installations, make sure that you've installed [Microsoft C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/) prior to proceeding. Select the "Desktop Development with C++" module.
 
 **From source** (compiled on your system using pip, all platforms)
 

pyproject.toml

@@ -0,0 +1,67 @@
+[build-system]
+requires = [
+        "setuptools>=40.8.0, <64",
+	"wheel",
+	"Cython>=0.26",
+	"numpy",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tofu"
+dynamic = ["version"]
+description="A python library for Tomography for Fusion"
+readme = "README.md"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+]
+authors = [
+    { name = "Didier Vezinet", email = "didier.vezinet@gmail.com" }
+]
+requires-python = ">=3.8"
+dependencies = [
+    "setuptools>=40.8.0, <64",
+    "numpy",
+    "scipy",
+    # "scikit-sparse",
+    # "scikit-umfpack",
+    "matplotlib",
+    "contourpy",
+    "requests",
+    "svg.path",
+    "Polygon3",
+    "cython>=0.26",
+    "datastock>=0.0.49",
+    "bsplines2d>=0.0.21",
+    "spectrally>=0.0.9",
+]
+
+[project.optional-dependencies]
+interactive = ["PyQt5", "PySide2"]
+
+[tool.setuptools.packages.find]
+where = ["tofu"]
+
+[tool.setuptools.package-data]
+"*" = ["*.txt", "*.csv", "*.pxd", "*.in", "*.toml", "*.npz", "*.svg", "*.sh", "*.f"]
+
+[tool.coverage.report]
+precision = 2
+fail_under = 85
+
+[tool.pytest.ini_options]
+testpaths = [
+  "tofu.tests",
+]
+
+[project.urls]
+Homepage = "https://tofuproject.github.io/tofu/index.html"
+Documentation = "https://tofuproject.github.io/tofu/index.html"
+Repository = "https://github.com/ToFuProject/tofu"
+"Bug Tracker" = "https://github.com/ToFuProject/tofu/issues"

pyproject_temp.toml

@@ -11,5 +11,7 @@ svg.path
 Polygon3
 
 ######## Requirements with Version Specifier ########
+datastock>=0.0.49
+bsplines2d>=0.0.21
 spectrally>=0.0.9
 Cython>=0.26

requirements.txt

@@ -325,6 +325,8 @@ def get_version_tofu(path=_HERE):
         "svg.path",
         "Polygon3",
         "cython>=0.26",
+        "datastock>=0.0.49",
+        "bsplines2d>=0.0.21",
         "spectrally>=0.0.9",
     ],
     python_requires=">=3.6",
@@ -361,6 +363,8 @@ def get_version_tofu(path=_HERE):
         "tofu.tests.tests06_mesh.test_data": ['*.txt', '*.npz'],
         "tofu.geom.inputs": ["*.txt"],
         "tofu.spectro": ["*.txt"],
+        "tofu.physics_tools.runaways.emission": ['*.csv'],
+        "tofu.physics_tools.transmission.inputs_filter": ['*.txt', '*.csv'],
         "tofu.mag.mag_ripple": ['*.sh', '*.f']
     },
     include_package_data=True,

setup.py

@@ -88,6 +88,8 @@
 import tofu.spectro as spectro
 import tofu.tests as tests
 import tofu.benchmarks as benchmarks
+from . import physics_tools
+from . import omas2tofu
 
 
 # -------------------------------------

tofu/__init__.py

@@ -12,4 +12,4 @@
 from ._class10_Inversion import Inversion as Collection
 from ._spectralunits import *
 from ._saveload import *
-from ._class08_saveload_from_file import load as load_diagnostic_from_file
+from ._class08_saveload_from_file import load as load_diagnostic_from_file

tofu/data/__init__.py

@@ -624,17 +624,6 @@ def _extract(
 
             for k0, v0 in dptsx.items():
 
-                # get kcam
-                kcam, axis = _get_kcam(
-                    coll=coll,
-                    k0=k0,
-                    key=key,
-                    key_cam=key_cam,
-                    key_rays=key_rays,
-                )
-
-                shape_cam = coll.dobj['camera'][kcam]['dgeom']['shape']
-
                 # both ways
                 npts = dptsx[k0].shape[0]
                 sli = tuple(
@@ -662,7 +651,19 @@ def _extract(
                     dptsz[k0] = np.ravel(ptsz, order='F')
 
                 elif chain == 'pixel':
+
+                    # get kcam
+                    kcam = _get_kcam(
+                        coll=coll,
+                        k0=k0,
+                        key=key,
+                        key_cam=key_cam,
+                        key_rays=key_rays,
+                    )[0]
+
+                    shape_cam = coll.dobj['camera'][kcam]['dgeom']['shape']
                     shape = shape_cam + (-1,)
+
                     dptsx[k0] = np.moveaxis(
                         np.moveaxis(ptsx, 0, -1).reshape(shape),
                         -1,

tofu/data/_class02_save2stp.py

@@ -31,7 +31,7 @@
 from . import _class8_plot as _plot
 from . import _class8_plot_vos as _plot_vos
 from . import _class8_plot_coverage as _plot_coverage
-from . import _class08_save2stp as _save2stp
+# from . import _class08_save2stp as _save2stp
 from . import _class08_saveload_from_file as _saveload_from_file
 
 
@@ -395,6 +395,7 @@ def add_rays_from_diagnostic(
         config=None,
         # storing
         store=None,
+        strict=None,
         key_rays=None,
         overwrite=None,
     ):
@@ -410,6 +411,7 @@ def add_rays_from_diagnostic(
             config=config,
             # storing
             store=store,
+            strict=strict,
             key_rays=key_rays,
             overwrite=overwrite,
         )
@@ -1262,6 +1264,9 @@ def plot_diagnostic(
         alpha=None,
         dx0=None,
         dx1=None,
+        # plot vos polygons
+        plot_pcross=None,
+        plot_phor=None,
         # config
         plot_config=None,
         plot_colorbar=None,
@@ -1297,6 +1302,9 @@ def plot_diagnostic(
             alpha=alpha,
             dx0=dx0,
             dx1=dx1,
+            # plot vos polygons
+            plot_pcross=plot_pcross,
+            plot_phor=plot_phor,
             # config
             plot_config=plot_config,
             plot_colorbar=plot_colorbar,
@@ -1334,6 +1342,9 @@ def plot_diagnostic_vos(
         vmax_cam=None,
         dvminmax=None,
         alpha=None,
+        # plot vos polygons
+        plot_pcross=None,
+        plot_phor=None,
         plot_colorbar=None,
         # config
         plot_config=None,
@@ -1368,6 +1379,9 @@ def plot_diagnostic_vos(
             vmax_cam=vmax_cam,
             dvminmax=dvminmax,
             alpha=alpha,
+            # plot vos polygons
+            plot_pcross=plot_pcross,
+            plot_phor=plot_phor,
             plot_colorbar=plot_colorbar,
             # config
             plot_config=plot_config,
@@ -1521,4 +1535,4 @@ def add_diagnostic_from_file(
             coll=self,
             pfe=pfe,
             returnas=returnas,
-        )
+        )