struphy 2.3.3__tar.gz → 2.4.0__tar.gz

{struphy-2.3.3 → 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-2.3.3/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: 2.3.3
+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, 
@@ -27,43 +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: add-trailing-comma==3.1.0
-Requires-Dist: argcomplete==3.4.0
-Requires-Dist: autopep8==2.3.1
-Requires-Dist: desc-opt==0.12.0
-Requires-Dist: docutils==0.21.2
-Requires-Dist: flake8==7.1.1
-Requires-Dist: gvec-to-python==1.2.2
-Requires-Dist: h5py==3.11.0
-Requires-Dist: ipyparallel==8.8.0
-Requires-Dist: isort==5.13.2
-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: pre_commit==4.0.1
-Requires-Dist: pyccel==1.12.1
-Requires-Dist: pydata-sphinx-theme==0.15.3
-Requires-Dist: pylint==3.3.1
-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-2.3.3 → struphy-2.4.0}/pyproject.toml

@@ -4,9 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.3.3"
+version = "2.4.0"
 readme = "README.md"
-requires-python = ">=3.10, <3.12"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
   { name = "Max Planck Institute for Plasma Physics"},
@@ -19,42 +19,52 @@ classifiers = [
     "Programming Language :: Python :: 3",
     ]
 dependencies = [
-    'PyYAML==6.0.1',
-    'add-trailing-comma==3.1.0',
-    'argcomplete==3.4.0',
-    'autopep8==2.3.1',
-    'desc-opt==0.12.0',
-    'docutils==0.21.2',
-    'flake8==7.1.1',
-    'gvec-to-python==1.2.2',
-    'h5py==3.11.0',
-    'ipyparallel==8.8.0',
-    'isort==5.13.2',
-    'lxml_html_clean==0.1.1',
-    'm2r2==0.3.3.post2',
-    'matplotlib==3.9.0',
-    'mistune==0.8.4',
-    'mpi4py==3.1.6',
-    'myst-parser==3.0.1',
-    'nbsphinx==0.9.4',
-    'netCDF4==1.6.5',
-    'notebook==7.2.1',
-    'numpy==1.24.4',
-    'pre_commit==4.0.1',
-    'pyccel==1.12.1',
-    'pydata-sphinx-theme==0.15.3',
-    'pylint==3.3.1',
-    'pytest==8.2.2',
-    'pytest-monitor==1.6.6',
-    'pytest-mpi==0.6',
-    'scipy==1.13.1',
-    'Sphinx==7.3.7',
-    'sphinxcontrib-napoleon==0.7',
-    'tqdm==4.66.4',
-    'vtk==9.3.0',
-    'wheel==0.43.0',
+    '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/"
@@ -88,8 +98,7 @@ struphy = "struphy.console.main:struphy"
                     ]
                     
 struphy = ['compile_struphy.mk',
-           'psydac-0.1.13-py3-none-any.whl',
-           ]
+           'psydac-2.4.0-py3-none-any.whl',]
 
 [tool.autopep8]
 # Add specific settings for autopep8
@@ -116,4 +125,34 @@ force_grid_wrap = 0
 combine_as_imports = true
 
 [tool.pylint]
-max-line-length=120
+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-2.3.3 → 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-2.3.3 → 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-2.3.3 → 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])