struphy 2.3.2__tar.gz → 2.4.0__tar.gz

{struphy-2.3.2 → struphy-2.4.0}/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2019-2024, Struphy developers, Max Planck Institute for Plasma Physics
+Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
 associated documentation files (the "Software"), to deal in the Software without restriction, 

{struphy-2.3.2/src/struphy.egg-info → struphy-2.4.0}/PKG-INFO

@@ -1,10 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: struphy
-Version: 2.3.2
+Version: 2.4.0
 Summary: Multi-model plasma physics package
 Author: Max Planck Institute for Plasma Physics
 Author-email: stefan.possanner@ipp.mpg.de, eric.sonnendruecker@ipp.mpg.de
-License: Copyright (c) 2019-2024, Struphy developers, Max Planck Institute for Plasma Physics
+License: Copyright (c) 2019-2025, Struphy developers, Max Planck Institute for Plasma Physics
         
         Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
         associated documentation files (the "Software"), to deal in the Software without restriction, 
@@ -27,37 +27,47 @@ Project-URL: changelog, https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel
 Project-URL: Bug Tracker, https://gitlab.mpcdf.mpg.de/struphy/struphy/-/issues
 Keywords: plasma physics, fusion, numerical modeling, partial differential equations, energetic particles
 Classifier: Programming Language :: Python :: 3
-Requires-Python: <3.12,>=3.10
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: PyYAML==6.0.1
-Requires-Dist: argcomplete==3.4.0
-Requires-Dist: desc-opt==0.12.0
-Requires-Dist: docutils==0.21.2
-Requires-Dist: gvec-to-python==1.2.2
-Requires-Dist: h5py==3.11.0
-Requires-Dist: ipyparallel==8.8.0
-Requires-Dist: lxml_html_clean==0.1.1
-Requires-Dist: m2r2==0.3.3.post2
-Requires-Dist: matplotlib==3.9.0
-Requires-Dist: mistune==0.8.4
-Requires-Dist: mpi4py==3.1.6
-Requires-Dist: myst-parser==3.0.1
-Requires-Dist: nbsphinx==0.9.4
-Requires-Dist: netCDF4==1.6.5
-Requires-Dist: notebook==7.2.1
-Requires-Dist: numpy==1.24.4
-Requires-Dist: pyccel==1.12.1
-Requires-Dist: pydata-sphinx-theme==0.15.3
-Requires-Dist: pytest==8.2.2
-Requires-Dist: pytest-monitor==1.6.6
-Requires-Dist: pytest-mpi==0.6
-Requires-Dist: scipy==1.13.1
-Requires-Dist: Sphinx==7.3.7
-Requires-Dist: sphinxcontrib-napoleon==0.7
-Requires-Dist: tqdm==4.66.4
-Requires-Dist: vtk==9.3.0
-Requires-Dist: wheel==0.43.0
+Requires-Dist: numpy
+Requires-Dist: pyccel>=1.11.1
+Requires-Dist: mpi4py<4
+Requires-Dist: scipy
+Requires-Dist: h5py
+Requires-Dist: matplotlib
+Requires-Dist: pyyaml
+Requires-Dist: vtk
+Requires-Dist: tqdm
+Requires-Dist: argcomplete
+Requires-Dist: gvec-to-python
+Requires-Dist: desc-opt
+Requires-Dist: netcdf4<1.7
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-mpi; extra == "test"
+Provides-Extra: dev
+Requires-Dist: struphy[test]; extra == "dev"
+Requires-Dist: notebook; extra == "dev"
+Requires-Dist: autopep8; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: add-trailing-comma; extra == "dev"
+Requires-Dist: ruff>=0.9.1; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: lxml_html_clean; extra == "doc"
+Requires-Dist: sphinxcontrib-napoleon; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: m2r2; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: mistune; extra == "doc"
+Requires-Dist: docutils; extra == "doc"
+Requires-Dist: ipyparallel; extra == "doc"
 
 # Struphy - Structure-preserving hybrid codes
 

struphy-2.4.0/pyproject.toml

@@ -0,0 +1,158 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "struphy"
+version = "2.4.0"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+authors = [
+  { name = "Max Planck Institute for Plasma Physics"},
+  { email = "stefan.possanner@ipp.mpg.de"},
+  { email = "eric.sonnendruecker@ipp.mpg.de"}
+]
+description = "Multi-model plasma physics package"
+keywords = ["plasma physics, fusion, numerical modeling, partial differential equations, energetic particles"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    ]
+dependencies = [
+    'numpy',
+    'pyccel>=1.11.1',
+    'mpi4py<4',
+    'scipy',
+    'h5py',
+    'matplotlib',
+    'pyyaml',
+    'vtk',
+    'tqdm',
+    'argcomplete',
+    'gvec-to-python',
+    'desc-opt',
+    'netcdf4<1.7',
+]
+
+[project.optional-dependencies]
+test = [
+    'pytest',
+    'pytest-mpi',
+]
+dev = [
+    'struphy[test]',
+    'notebook',
+    'autopep8',
+    'isort',
+    'flake8',
+    'pylint',
+    'add-trailing-comma',
+    'ruff>=0.9.1',
+    'pre-commit',
+]
+doc = [
+    'sphinx',
+    'sphinx-design',
+    'lxml_html_clean',
+    'sphinxcontrib-napoleon',
+    'pydata-sphinx-theme',
+    'nbsphinx',
+    'm2r2',
+    'myst-parser',
+    'mistune',
+    'docutils',
+    'ipyparallel',
+]
+
+
+[project.urls]
+homepage = "https://struphy.pages.mpcdf.de/struphy/"
+documentation = "https://struphy.pages.mpcdf.de/struphy/"
+repository = "https://gitlab.mpcdf.mpg.de/struphy/struphy"
+changelog = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/CHANGELOG.md"
+"Bug Tracker" = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/issues"
+
+[project.scripts]
+struphy = "struphy.console.main:struphy"
+
+[tool.setuptools.package-data]
+'struphy.fields_background.mhd_equil.eqdsk' = [
+            'data/*.high',
+        ]
+
+'struphy.fields_background.mhd_equil.gvec' = [
+            'ellipstell_v2/newBC_E1D6_M6N6/*.dat',
+            'ellipstell_v2/newBC_E1D6_M6N6/*.ini',
+            'ellipstell_v2/newBC_E4D6_M6N6/*.dat',
+            'ellipstell_v2/newBC_E4D6_M6N6/*.ini',
+            'ellipstell_v2/oldBC_E40D5M6N6/*.dat',
+            'ellipstell_v2/oldBC_E40D5M6N6/*.ini',
+        ]
+
+'struphy.io' = ['batch/*.sh']
+
+'struphy.io.inp' = ['parameters.yml',
+                    'tests/*.yml',
+                    'tutorials/*.yml',
+                    'longer_examples/*.yml',
+                    ]
+                    
+struphy = ['compile_struphy.mk',
+           'psydac-2.4.0-py3-none-any.whl',]
+
+[tool.autopep8]
+# Add specific settings for autopep8
+max_line_length = 120
+ignore = ["E221,E226,E203,E265,E731,E711"]
+# Descriptions of error codes: https://www.flake8rules.com/
+# E201 – Whitespace after  (, [ or {
+# E202 – Whitespace before (, [ or {
+# E221 – Multiple spaces before operator
+# E226 – Missing whitespace around arithmetic operators
+# E265 - Block comment should start with '# '
+# E266 – Too many leading # for block comment
+# E731 – Do not assign a lambda expression
+# E203 – Whitespace before : (used in slicing)
+# E711 - Ignore enforcing 'is not None' over '!= None'
+
+[tool.isort]
+# Configuration for isort
+profile = "black"  # Using the Black profile to match formatting styles
+line_length = 120
+multi_line_output = 3  # Control how isort wraps imports
+include_trailing_comma = true
+force_grid_wrap = 0
+combine_as_imports = true
+
+[tool.pylint]
+max-line-length=120
+quote-style = "single"
+
+[tool.ruff]
+line-length=120
+lint.ignore = [
+    "E265",  # Checks for block comments that lack a single space after the leading # character.
+    "E402",  # Module-level imports should be placed at the top of the file (before any other code)
+    "E701",  # Multiple statements on one line (colon)
+    # "E711",  # Comparison to `None` should be `cond is None`
+    # "E712",  # Comparison to True, False, or None should be avoided (e.g., use `if variable:` instead of `if variable == True:`)
+    # "E713",  # Convert to `not in`
+    # "E721",  # Avoid comparing types directly with `type()` (e.g., use `isinstance()` instead of `type(variable) == list`)
+    "E722",  # Do not use bare 'except'
+    "E731",  # Do not assign a lambda expression, use a def
+    "E741",  # Do not use variables named 'l', 'O', or 'I'
+    "E742",  # Do not define classes named 'l', 'O', or 'I'
+    "E743",  # Do not define functions named 'l', 'O', or 'I'
+    "E902",  # IOError
+    # "E999",  # SyntaxError
+    "F401",  # Module imported but unused
+    "F403",  # 'from module import *' used; unable to detect undefined names
+    "F405",  # Name may be undefined, or defined from star imports: module
+    # "F811",  # Redefinition of a variable that might cause ambiguity (e.g., reusing a variable name in a conflicting scope)
+    # "F821",  # Undefined name
+    # "F822",  # Undefined name in __all__
+    # "F823",  # Local variable name referenced before assignment
+    # "F841",  # Local variable name assigned to but never used
+    "D211",  # Checks for docstrings on class definitions that are preceded by a blank line
+    "D213",  # Checks for docstring summary lines that are not positioned on the second physical line of the docstring
+]

{struphy-2.3.2 → struphy-2.4.0}/setup.cfg

@@ -4,6 +4,9 @@ source-dir = doc/
 build-dir = doc/
 warning_is_error = 1
 
+[flake8]
+max-line-length = 120
+
 [egg_info]
 tag_build = 
 tag_date = 0

{struphy-2.3.2 → struphy-2.4.0}/src/struphy/bsplines/bsplines_kernels.py

@@ -3,9 +3,8 @@
 """
 Basic functions for point-wise B-spline evaluation
 """
-from pyccel.decorators import pure, stack_array
-
 from numpy import empty, zeros
+from pyccel.decorators import pure, stack_array
 
 
 @pure
@@ -256,8 +255,9 @@ def basis_funs_all_ders(knots: 'float[:]', degree: int, eta: float, span: int, l
                 d = a[s2, 0] * ndu[rk, pk]
             j1 = 1 if (rk > -1) else -rk
             j2 = k-1 if (r-1 <= pk) else degree-r
-            a[s2, j1:j2+1] = (a[s1, j1:j2+1] - a[s1, j1-1:j2]
-                              ) * ndu[pk+1, rk+j1:rk+j2+1]
+            a[s2, j1:j2+1] = (
+                a[s1, j1:j2+1] - a[s1, j1-1:j2]
+            ) * ndu[pk+1, rk+j1:rk+j2+1]
             for l in range(j2 + 1 - j1):
                 d += a[s2, j1 + l] * ndu[rk + j1 + l, pk]
             #d += dot(a[s2, j1:j2+1], ndu[rk+j1:rk+j2+1, pk])
@@ -375,8 +375,10 @@ def d_splines_slim(tn: 'float[:]', pn: 'int', eta: 'float', span: 'int', values:
 
     # compute D-splines values by scaling
     for il in range(pd + 1):
-        values[pd - il] = pn/(tn[span - il + pn] -
-                              tn[span - il]) * b_values[pd - il]
+        values[pd - il] = pn/(
+            tn[span - il + pn] -
+            tn[span - il]
+        ) * b_values[pd - il]
 
 
 @pure
@@ -427,8 +429,10 @@ def b_d_splines_slim(tn: 'float[:]', pn: 'int', eta: 'float', span: 'int', bn: '
         if j == pn-1:
             # compute D-splines values by scaling B-splines of degree pn-1
             for il in range(pd + 1):
-                bd[pd - il] = pn/(tn[span - il + pn] -
-                                  tn[span - il]) * bn[pd - il]
+                bd[pd - il] = pn/(
+                    tn[span - il + pn] -
+                    tn[span - il]
+                ) * bn[pd - il]
 
         for r in range(j + 1):
             temp = bn[r]/(right[r] + left[j - r])
@@ -656,7 +660,7 @@ def b_spl_1st_der_slim(t: 'float[:]', p: 'int', eta: 'float', span: 'int', value
 def piecewise(p: 'int', delta: 'float', eta: 'float') -> 'float':
     r"""
     evaluate a hat function (B-spline) centered at eta0 (the center of the support) at eta1, i.e. 
-    
+
     .. math::
         1.0 / delta * S((eta1 - eta0)/ delta)
 
@@ -753,7 +757,7 @@ def piecewise_der(p: 'int', delta: 'float', eta: 'float') -> 'float':
 def convolution(p: 'int', grids: 'float[:]', eta: 'float') -> 'float':
     r"""
     evaluate a hat function (B-spline) at eta, i.e. 
-    
+
     .. math::
         1.0 / delta * S(eta/ delta)
 
@@ -808,7 +812,7 @@ def convolution(p: 'int', grids: 'float[:]', eta: 'float') -> 'float':
 def convolution_der(p: 'int', grids: 'float[:]', eta: 'float') -> 'float':
     r"""
     evaluate the derivative of a hat function (B-spline) at eta, i.e. 
-    
+
     .. math::
         1.0 / delta^2 * S'(eta/ delta)
 

{struphy-2.3.2 → struphy-2.4.0}/src/struphy/bsplines/tests/test_bsplines_kernels.py

@@ -1,7 +1,8 @@
-import pytest
+import time
+
 import numpy as np
+import pytest
 from mpi4py import MPI
-import time
 
 
 @pytest.mark.mpi(min_size=2)
@@ -14,11 +15,11 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     Print timings.
     '''
 
-    from struphy.feec.psydac_derham import Derham
+    import psydac.core.bsplines_kernels as bsp_psy
 
-    from struphy.feec.utilities import create_equal_random_arrays as cera
     import struphy.bsplines.bsplines_kernels as bsp
-    import psydac.core.bsplines_pyccel as bsp_psy
+    from struphy.feec.psydac_derham import Derham
+    from struphy.feec.utilities import create_equal_random_arrays as cera
 
     comm = MPI.COMM_WORLD
     assert comm.size >= 2
@@ -48,7 +49,7 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'struphy find_span  : {t1 - t0}')
-        
+
     # psydac find_span_p
     t0 = time.time()
     span1s_psy, span2s_psy, span3s_psy = [], [], []
@@ -59,20 +60,20 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'psydac find_span_p : {t1 - t0}')
-        
+
     assert np.allclose(span1s, span1s_psy)
     assert np.allclose(span2s, span2s_psy)
     assert np.allclose(span3s, span3s_psy)
-    
+
     # allocate tmps
     bn1 = np.empty(derham.p[0] + 1, dtype=float)
     bn2 = np.empty(derham.p[1] + 1, dtype=float)
     bn3 = np.empty(derham.p[2] + 1, dtype=float)
-    
+
     bd1 = np.empty(derham.p[0], dtype=float)
     bd2 = np.empty(derham.p[1], dtype=float)
     bd3 = np.empty(derham.p[2], dtype=float)
-    
+
     # struphy b_splines_slim
     val1s, val2s, val3s = [], [], []
     t0 = time.time()
@@ -86,7 +87,7 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'bsp.b_splines_slim        : {t1 - t0}')
-        
+
     # psydac basis_funs_p
     val1s_psy, val2s_psy, val3s_psy = [], [], []
     t0 = time.time()
@@ -100,17 +101,17 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'bsp_psy.basis_funs_p for N: {t1 - t0}')
-    
+
     # compare
     for val1, val1_psy in zip(val1s, val1s_psy):
         assert np.allclose(val1, val1_psy)
-        
+
     for val2, val2_psy in zip(val2s, val2s_psy):
         assert np.allclose(val2, val2_psy)
-        
+
     for val3, val3_psy in zip(val3s, val3s_psy):
         assert np.allclose(val3, val3_psy)
-        
+
     # struphy b_d_splines_slim
     val1s_n, val2s_n, val3s_n = [], [], []
     val1s_d, val2s_d, val3s_d = [], [], []
@@ -128,24 +129,24 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'bsp.b_d_splines_slim      : {t1 - t0}')
-        
+
     # compare
     for val1, val1_psy in zip(val1s_n, val1s_psy):
         assert np.allclose(val1, val1_psy)
-        
+
     for val2, val2_psy in zip(val2s_n, val2s_psy):
         assert np.allclose(val2, val2_psy)
-        
+
     for val3, val3_psy in zip(val3s_n, val3s_psy):
         assert np.allclose(val3, val3_psy)
-        
+
     # struphy d_splines_slim
     span1s, span2s, span3s = [], [], []
     for eta1, eta2, eta3 in zip(eta1s, eta2s, eta3s):
         span1s += [bsp.find_span(td1, derham.p[0] - 1, eta1)]
         span2s += [bsp.find_span(td2, derham.p[1] - 1, eta2)]
         span3s += [bsp.find_span(td3, derham.p[2] - 1, eta3)]
-    
+
     val1s, val2s, val3s = [], [], []
     t0 = time.time()
     for eta1, eta2, eta3, span1, span2, span3 in zip(eta1s, eta2s, eta3s, span1s, span2s, span3s):
@@ -158,7 +159,7 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'bsp.d_splines_slim        : {t1 - t0}')
-        
+
     # psydac basis_funs_p for D-splines
     val1s_psy, val2s_psy, val3s_psy = [], [], []
     t0 = time.time()
@@ -172,26 +173,26 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     t1 = time.time()
     if rank == 0:
         print(f'bsp_psy.basis_funs_p for D: {t1 - t0}')
-    
+
     # compare
     for val1, val1_psy in zip(val1s, val1s_psy):
         assert np.allclose(val1, val1_psy)
-        
+
     for val2, val2_psy in zip(val2s, val2s_psy):
         assert np.allclose(val2, val2_psy)
-        
+
     for val3, val3_psy in zip(val3s, val3s_psy):
         assert np.allclose(val3, val3_psy)
-        
+
     for val1, val1_psy in zip(val1s_d, val1s_psy):
         assert np.allclose(val1, val1_psy)
-        
+
     for val2, val2_psy in zip(val2s_d, val2s_psy):
         assert np.allclose(val2, val2_psy)
-        
+
     for val3, val3_psy in zip(val3s_d, val3s_psy):
         assert np.allclose(val3, val3_psy)
-    
-    
+
+
 if __name__ == '__main__':
     test_bsplines_span_and_basis([8, 9, 10], [3, 4, 3], [False, False, True])

{struphy-2.3.2 → struphy-2.4.0}/src/struphy/compile_struphy.mk

@@ -5,7 +5,6 @@
 PYTHON  := python3
 SO_EXT  := $(shell $(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))")
 LIBDIR  := $(shell $(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
-psydac_path := $(shell $(PYTHON) -c "import psydac as _; print(_.__path__[0])")
 struphy_path := $(shell $(PYTHON) -c "import struphy as _; print(_.__path__[0])")
 
 # Arguments to this script are: 
@@ -18,13 +17,7 @@ FLAGS_openmp_mhd := $(flags_openmp_mhd)
 # SOURCE FILES 
 #--------------------------------------
 
-PSY0  := $(psydac_path)/core/arrays
-PSY1  := $(psydac_path)/core/kernels
-PSY2  := $(psydac_path)/core/bsplines_pyccel
-PSY3  := $(psydac_path)/linalg/kernels
-PSY4  := $(psydac_path)/feec/dof_kernels
-
-SOURCES := $(PSY0).py $(PSY1).py $(PSY2).py $(PSY3).py $(PSY4).py $(STRUPHY_SOURCES)
+SOURCES := $(STRUPHY_SOURCES)
 
 OUTPUTS := $(SOURCES:.py=$(SO_EXT))
 
@@ -52,11 +45,6 @@ all: $(OUTPUTS)
 .PHONY: clean
 clean:
 	rm -rf $(OUTPUTS)
-
-	rm -rf $(psydac_path)/__pyccel__ $(psydac_path)/__pycache__
-	rm -rf $(psydac_path)/core/__pyccel__ $(psydac_path)/core/__pycache__ $(psydac_path)/core/.lock_acquisition.lock
-	rm -rf $(psydac_path)/linalg/__pyccel__ $(psydac_path)/linalg/__pycache__ $(psydac_path)/linalg/.lock_acquisition.lock
-	rm -rf $(psydac_path)/feec/__pyccel__ $(psydac_path)/feec/__pycache__ $(psydac_path)/feec/.lock_acquisition.lock
     
 	find $(struphy_path)/ -type d -name '__pyccel__' -prune -exec rm -rf {} \;
 	find $(struphy_path)/ -type d -name '__pycache__' -prune -exec rm -rf {} \;

{struphy-2.3.2 → struphy-2.4.0}/src/struphy/conftest.py

@@ -1,15 +1,20 @@
 def pytest_addoption(parser):
     parser.addoption("--fast", action="store_true")
     parser.addoption("--with-desc", action="store_true")
+    parser.addoption("--vrbose", action="store_true")
 
 
 def pytest_generate_tests(metafunc):
     # This is called for every test. Only get/set command line arguments
     # if the argument is specified in the list of test "fixturenames".
     option_value = metafunc.config.option.fast
-    if 'fast' in metafunc.fixturenames and option_value is not None:
+    if "fast" in metafunc.fixturenames and option_value is not None:
         metafunc.parametrize("fast", [option_value])
-        
+
     option_value = metafunc.config.option.with_desc
-    if 'with_desc' in metafunc.fixturenames and option_value is not None:
+    if "with_desc" in metafunc.fixturenames and option_value is not None:
         metafunc.parametrize("with_desc", [option_value])
+
+    option_value = metafunc.config.option.vrbose
+    if "vrbose" in metafunc.fixturenames and option_value is not None:
+        metafunc.parametrize("vrbose", [option_value])