struphy 3.0.0__tar.gz → 3.0.1__tar.gz

{struphy-3.0.0/src/struphy.egg-info → struphy-3.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: struphy
-Version: 3.0.0
+Version: 3.0.1
 Summary: Multi-model plasma physics package
 Author: Max Planck Institute for Plasma Physics
 Author-email: stefan.possanner@ipp.mpg.de, max.lindqvist@ipp.mpg.de, eric.sonnendruecker@ipp.mpg.de
@@ -32,7 +32,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<=2.2.6
 Requires-Dist: cunumpy<=0.1
-Requires-Dist: pyccel<=2.0.1,>=2.0
+Requires-Dist: pyccel<=2.1.0,>=2.0
+Requires-Dist: feectools<=0.1.0
 Requires-Dist: scipy<=1.15.3
 Requires-Dist: h5py<=3.14.0
 Requires-Dist: matplotlib<=3.10.5
@@ -40,8 +41,9 @@ Requires-Dist: pyyaml<=6.0.3
 Requires-Dist: vtk<=9.5.2
 Requires-Dist: tqdm<=4.67.1
 Requires-Dist: argcomplete<=3.6.3
-Requires-Dist: pytest<=9.0.1
+Requires-Dist: pytest<=9.0.2
 Requires-Dist: pytest-mpi<=0.6
+Requires-Dist: pytest-testmon<=2.2.0
 Requires-Dist: line_profiler<=5.0.0
 Provides-Extra: phys
 Requires-Dist: gvec<=1.2.0,>=1.1.0; extra == "phys"

{struphy-3.0.0 → struphy-3.0.1}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.0.0"
+version = "3.0.1"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -25,7 +25,8 @@ classifiers = [
 dependencies = [
     "numpy<=2.2.6",
     "cunumpy<=0.1",
-    "pyccel<=2.0.1, >=2.0",
+    "pyccel<=2.1.0, >=2.0",
+    "feectools<=0.1.0",
     "scipy<=1.15.3",
     "h5py<=3.14.0",
     "matplotlib<=3.10.5",
@@ -33,8 +34,9 @@ dependencies = [
     "vtk<=9.5.2",
     "tqdm<=4.67.1",
     "argcomplete<=3.6.3",
-    "pytest<=9.0.1",
+    "pytest<=9.0.2",
     "pytest-mpi<=0.6",
+    "pytest-testmon<=2.2.0",
     "line_profiler<=5.0.0",
 ]
 
@@ -120,19 +122,8 @@ kinetic-diagnostics = "struphy.diagnostics.console_diagn:main"
     "run_03/*.ini",
     "run_03/*.nc",
 ]
-"struphy.io" = [
-    "batch/*.sh",
-]
-"struphy.io.inp" = [
-    "parameters.yml",
-    "tests/*.yml",
-    "tutorials/*.yml",
-    "longer_examples/*.yml",
-    "verification/*.yml",
-]
 struphy = [
     "compile_struphy.mk",
-    "psydac-3.0.0.dev0-py3-none-any.whl",
 ]
 
 [tool.autopep8]

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/bsplines/bsplines.py

@@ -534,7 +534,7 @@ def elements_spans(knots, degree):
     Examples
     --------
     >>> import numpy as np
-    >>> from psydac.core.bsplines import make_knots, elements_spans
+    >>> from feectools.core.bsplines import make_knots, elements_spans
 
     >>> p = 3 ; n = 8
     >>> grid  = xp.arange( n-p+1 )

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/bsplines/tests/test_bsplines_kernels.py

@@ -2,7 +2,7 @@ import time
 
 import cunumpy as xp
 import pytest
-from psydac.ddm.mpi import mpi as MPI
+from feectools.ddm.mpi import mpi as MPI
 
 
 @pytest.mark.parametrize("Nel", [[8, 9, 10]])
@@ -14,7 +14,7 @@ def test_bsplines_span_and_basis(Nel, p, spl_kind):
     Print timings.
     """
 
-    import psydac.core.bsplines_kernels as bsp_psy
+    import feectools.core.bsplines_kernels as bsp_psy
 
     import struphy.bsplines.bsplines_kernels as bsp
     from struphy.feec.psydac_derham import Derham

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/bsplines/tests/test_eval_spline_mpi.py

@@ -3,7 +3,7 @@ from time import sleep
 
 import cunumpy as xp
 import pytest
-from psydac.ddm.mpi import mpi as MPI
+from feectools.ddm.mpi import mpi as MPI
 
 
 @pytest.mark.parametrize("Nel", [[8, 9, 10]])

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/conftest.py

@@ -1,3 +1,11 @@
+import pytest
+
+
+def pytest_unconfigure(config):
+    if hasattr(config, "testmon_data"):
+        config.testmon_data.db.con.close()
+
+
 def pytest_addoption(parser):
     parser.addoption("--with-desc", action="store_true")
     parser.addoption("--vrbose", action="store_true")

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/console/compile.py

@@ -89,7 +89,6 @@ def struphy_compile(
                     and ".py" in file
                     and "_tmp.py" not in file
                     and "test" not in file
-                    and "legacy" not in subdir
                     and "__pycache__" not in subdir
                 ):
                     state["kernels"] += [os.path.join(subdir, file)]

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/console/params.py

@@ -1,7 +1,7 @@
 import sys
 
 import yaml
-from psydac.ddm.mpi import mpi as MPI
+from feectools.ddm.mpi import mpi as MPI
 
 from struphy.models import fluid, hybrid, kinetic, toy
 from struphy.models.base import StruphyModel

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/console/profile.py

@@ -110,7 +110,7 @@ def struphy_profile(dirs, replace, all, n_lines, print_callers, savefig):
     )
     print("-" * 154)
     for position, key in enumerate(dicts[0].keys()):
-        if list_of_funcs == None:
+        if list_of_funcs is None:
             for dict, sim_name, n, dim in zip(dicts, sim_names, nproc, Nel):
                 string = f"{sim_name}".ljust(20) + f"{n}".ljust(7) + f"{position:2d}".ljust(5) + str(key.ljust(70))
                 for value in dict[key].values():

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/console/test.py

@@ -1,5 +1,10 @@
+import os
+
+import struphy
 from struphy.utils.utils import subp_run
 
+LIBPATH = struphy.__path__[0]
+
 
 def struphy_test(
     group: str,
@@ -35,22 +40,36 @@ def struphy_test(
     """
 
     if "unit" in group:
+        list_of_tests = [
+            f"{LIBPATH}/bsplines/tests/",
+            f"{LIBPATH}/console/tests/",
+            f"{LIBPATH}/feec/tests/",
+            f"{LIBPATH}/fields_background/tests/",
+            f"{LIBPATH}/geometry/tests/",
+            f"{LIBPATH}/initial/tests/",
+            f"{LIBPATH}/kinetic_background/tests/",
+            f"{LIBPATH}/linear_algebra/tests/",
+            f"{LIBPATH}/ode/tests/",
+            f"{LIBPATH}/pic/tests/",
+            f"{LIBPATH}/polar/tests/",
+            f"{LIBPATH}/post_processing/tests/",
+            f"{LIBPATH}/propagators/tests/",
+        ]
+
         if mpi > 1:
             cmd = [
                 "mpirun",
                 "-n",
                 str(mpi),
                 "pytest",
-                "-k",
-                "not _models and not _tutorial and not pproc and not _verif_",
+                "--testmon",
                 "--with-mpi",
-            ]
+            ] + list_of_tests
         else:
             cmd = [
                 "pytest",
-                "-k",
-                "not _models and not _tutorial and not pproc and not _verif_",
-            ]
+                "--testmon",
+            ] + list_of_tests
 
         if with_desc:
             cmd += ["--with-desc"]
@@ -62,6 +81,10 @@ def struphy_test(
         subp_run(cmd)
 
     elif group in {"models", "fluid", "kinetic", "hybrid", "toy"}:
+        list_of_tests = [
+            f"{LIBPATH}/models/tests/default_params/",
+        ]
+
         if mpi > 1:
             cmd = [
                 "mpirun",
@@ -69,22 +92,18 @@ def struphy_test(
                 "-n",
                 str(mpi),
                 "pytest",
-                "-k",
-                "_models",
                 "-m",
                 group,
-                "-s",
+                "--testmon-forceselect",
                 "--with-mpi",
-            ]
+            ] + list_of_tests
         else:
             cmd = [
                 "pytest",
-                "-k",
-                "_models",
                 "-m",
                 group,
-                "-s",
-            ]
+                "--testmon-forceselect",
+            ] + list_of_tests
 
         if vrbose:
             cmd += ["--vrbose"]
@@ -92,9 +111,14 @@ def struphy_test(
             cmd += ["--nclones", f"{nclones}"]
         if show_plots:
             cmd += ["--show-plots"]
+
         subp_run(cmd)
 
     elif "verification" in group:
+        list_of_tests = [
+            f"{LIBPATH}/models/tests/verification/",
+        ]
+
         if mpi > 1:
             cmd = [
                 "mpirun",
@@ -102,18 +126,14 @@ def struphy_test(
                 "-n",
                 str(mpi),
                 "pytest",
-                "-k",
-                "_verif_",
-                "-s",
+                "--testmon",
                 "--with-mpi",
-            ]
+            ] + list_of_tests
         else:
             cmd = [
                 "pytest",
-                "-k",
-                "_verif_",
-                "-s",
-            ]
+                "--testmon",
+            ] + list_of_tests
 
         if vrbose:
             cmd += ["--vrbose"]
@@ -121,6 +141,7 @@ def struphy_test(
             cmd += ["--nclones", f"{nclones}"]
         if show_plots:
             cmd += ["--show-plots"]
+
         subp_run(cmd)
 
     else:
@@ -130,10 +151,9 @@ def struphy_test(
             "-n",
             str(mpi),
             "pytest",
-            "-k",
-            "_models",
             "-m",
             "single",
+            "--testmon-forceselect",
             "-s",
             "--with-mpi",
             "--model-name",
@@ -145,4 +165,5 @@ def struphy_test(
             cmd += ["--nclones", f"{nclones}"]
         if show_plots:
             cmd += ["--show-plots"]
+
         subp_run(cmd)

struphy-3.0.1/src/struphy/console/tests/test_console.py

@@ -0,0 +1,158 @@
+import os
+import pickle
+import sys
+from unittest import mock
+from unittest.mock import patch
+
+import pytest
+
+import struphy as struphy_lib
+from struphy.console.compile import struphy_compile
+from struphy.console.main import struphy
+from struphy.console.params import struphy_params
+from struphy.utils.utils import read_state, subp_run
+
+libpath = struphy_lib.__path__[0]
+state = read_state()
+
+# Create models_list if it doesn't exist
+if not os.path.isfile(os.path.join(libpath, "models", "models_list")):
+    cmd = ["struphy", "--refresh-models"]
+    subp_run(cmd)
+
+with open(os.path.join(libpath, "models", "models_list"), "rb") as fp:
+    struphy_models = pickle.load(fp)
+
+
+def is_sublist(main_list, sub_list):
+    """
+    Check if sub_list is a sublist of main_list.
+    """
+    sub_len = len(sub_list)
+    return any(main_list[i : i + sub_len] == sub_list for i in range(len(main_list) - sub_len + 1))
+
+
+def split_command(command):
+    """
+    Split a command string into a list of arguments.
+    """
+    # only works if there are no real spaces in the element.
+    # Could be improved by not splitting if the space is '\ ' with regex
+    spl = []
+    for element in command:
+        spl.extend(element.split())
+    return spl
+
+
+@pytest.mark.mpi_skip
+@pytest.mark.parametrize(
+    "args",
+    [
+        # Test cases for 'compile' sub-command with options
+        ["compile"],
+        ["compile", "-y"],
+        ["compile", "--language", "fortran"],
+        ["compile", "--compiler", "intel"],
+        ["compile", "--omp-pic"],
+        ["compile", "--verbose"],
+        ["compile", "--delete"],
+        # Test cases for 'params' sub-command
+        ["params", "Maxwell"],
+        ["params", "Vlasov"],
+        # ["params", "Maxwell", "-f", "params_Maxwell.yml"],
+        # Test cases for 'profile' sub-command
+        ["profile", "sim_1"],
+        ["profile", "sim_2", "--replace"],
+        ["profile", "sim_3", "--n-lines", "10"],
+        ["profile", "sim_1", "--savefig", "profile_output.png"],
+        # Test cases for 'test' sub-command
+        ["test", "models"],
+        ["test", "unit"],
+        ["test", "Maxwell"],
+        ["test", "hybrid", "--mpi", "8"],
+    ],
+)
+def test_main(args):
+    # Mock the func call (don't execute it)
+    with (
+        patch("struphy.console.compile.struphy_compile") as mock_compile,
+        patch("struphy.console.params.struphy_params") as mock_params,
+        patch("struphy.console.profile.struphy_profile") as mock_profile,
+        patch("struphy.console.test.struphy_test") as mock_test,
+    ):
+        funcs = {
+            "compile": mock_compile,
+            "params": mock_params,
+            "profile": mock_profile,
+            "test": mock_test,
+        }
+
+        # Set sys args
+        sys.argv = ["struphy"] + args
+
+        # Call struphy
+        try:
+            struphy()
+        except SystemExit:
+            pass  # Ignore the exit in tests
+
+        for func_name, func in funcs.items():
+            if args[0] == func_name:
+                func.assert_called_once()
+            else:
+                func.assert_not_called()
+
+
+def run_struphy(args):
+    with mock.patch.object(sys, "argv", ["struphy"] + args):
+        struphy()
+
+
+@pytest.mark.mpi_skip
+@pytest.mark.parametrize(
+    "args_expected",
+    [
+        [["--version"], [""]],
+        [["--short-help"], ["available commands"]],
+        [["--fluid"], ["Fluid models"]],
+        [["--kinetic"], ["Kinetic models"]],
+        [["--hybrid"], ["Hybrid models"]],
+        [["--toy"], ["Toy models"]],
+        [["--refresh-models"], ["Collecting available models"]],
+    ],
+)
+def test_main_options(args_expected, capsys):
+    args = args_expected[0]
+
+    with pytest.raises(SystemExit):
+        run_struphy(args)
+
+    # Capture the output
+    captured = capsys.readouterr()
+
+    # Assert that output was printed
+    assert captured.out != ""
+
+    for expected in args_expected[1]:
+        assert expected in captured.out
+
+
+@pytest.mark.mpi_skip
+@pytest.mark.parametrize("model", ["Maxwell"])
+@pytest.mark.parametrize("yes", [True])
+def test_struphy_params(model, yes):
+    struphy_params(model, yes=yes)
+
+
+if __name__ == "__main__":
+    # Set test parameters
+    model = "Maxwell"
+    input_abs = os.path.join(libpath, "io/inp/parameters.yml")
+    output_abs = os.path.join(libpath, "io/out/sim_1")
+    batch_abs = os.path.join(libpath, "io/batch/batch_cobra.sh")
+    runtime = 300
+    save_step = 300
+    restart = True
+    cprofile = False
+    likwid = False
+    mpi = 2

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/diagnostics/diagn_tools.py

@@ -120,19 +120,19 @@ def power_spectrum_2d(
         temp[n, :, :, :] = snapshot[component]
 
     # Extract 2d data (t, eta) for fft
-    if slice_at[0] == None:
+    if slice_at[0] is None:
         data = temp[:, :, slice_at[1], slice_at[2]]
         grid = grids[0]
         if grids_mapped is not None:
             grid = grids_mapped[0][:, slice_at[1], slice_at[2]]
 
-    elif slice_at[1] == None:
+    elif slice_at[1] is None:
         data = temp[:, slice_at[0], :, slice_at[2]]
         grid = grids[1]
         if grids_mapped is not None:
             grid = grids_mapped[1][slice_at[0], :, slice_at[2]]
 
-    elif slice_at[2] == None:
+    elif slice_at[2] is None:
         data = temp[:, slice_at[0], slice_at[1], :]
         grid = grids[2].flatten()
         if grids_mapped is not None:

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/examples/_draw_parallel.py

@@ -1,5 +1,5 @@
 import cunumpy as xp
-from psydac.ddm.mpi import mpi as MPI
+from feectools.ddm.mpi import mpi as MPI
 
 from struphy.feec.psydac_derham import Derham
 from struphy.geometry import domains

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/feec/basis_projection_ops.py

@@ -1,11 +1,11 @@
 import cunumpy as xp
-from psydac.api.settings import PSYDAC_BACKEND_GPYCCEL
-from psydac.ddm.mpi import mpi as MPI
-from psydac.fem.basic import FemSpace
-from psydac.fem.tensor import TensorFemSpace
-from psydac.linalg.basic import IdentityOperator, LinearOperator, Vector
-from psydac.linalg.block import BlockLinearOperator, BlockVector, BlockVectorSpace
-from psydac.linalg.stencil import StencilMatrix, StencilVector, StencilVectorSpace
+from feectools.api.settings import PSYDAC_BACKEND_GPYCCEL
+from feectools.ddm.mpi import mpi as MPI
+from feectools.fem.basic import FemSpace
+from feectools.fem.tensor import TensorFemSpace
+from feectools.linalg.basic import IdentityOperator, LinearOperator, Vector
+from feectools.linalg.block import BlockLinearOperator, BlockVector, BlockVectorSpace
+from feectools.linalg.stencil import StencilMatrix, StencilVector, StencilVectorSpace
 
 from struphy.feec import basis_projection_kernels
 from struphy.feec.linear_operators import BoundaryOperator, LinOpWithTransp
@@ -950,7 +950,7 @@ class BasisProjectionOperatorLocal(LinOpWithTransp):
     P : struphy.feec.projectors.CommutingProjectorLocal
         Local commuting projector mapping into TensorFemSpace/VectorFemSpace W = P.space (codomain of operator).
 
-    V : psydac.fem.basic.FemSpace
+    V : feectools.fem.basic.FemSpace
         Finite element spline space (domain, input space).
 
     weights : list
@@ -1158,15 +1158,15 @@ class BasisProjectionOperatorLocal(LinOpWithTransp):
 
         Parameters
         ----------
-        v : psydac.linalg.basic.Vector
+        v : feectools.linalg.basic.Vector
             Vector the operator shall be applied to.
 
-        out : psydac.linalg.basic.Vector, optional
+        out : feectools.linalg.basic.Vector, optional
             If given, the output will be written in-place into this vector.
 
         Returns
         -------
-         out : psydac.linalg.basic.Vector
+         out : feectools.linalg.basic.Vector
             The output (codomain) vector.
         """
 
@@ -1609,7 +1609,7 @@ class BasisProjectionOperator(LinOpWithTransp):
     P : struphy.feec.projectors.Projector
         Global commuting projector mapping into TensorFemSpace/VectorFemSpace W = P.space (codomain of operator).
 
-    V : psydac.fem.basic.FemSpace
+    V : feectools.fem.basic.FemSpace
         Finite element spline space (domain, input space).
 
     weights : list
@@ -1804,10 +1804,10 @@ class BasisProjectionOperator(LinOpWithTransp):
 
         Parameters
         ----------
-        v : psydac.linalg.basic.Vector
+        v : feectools.linalg.basic.Vector
             Vector the operator shall be applied to.
 
-        out : psydac.linalg.basic.Vector, optional
+        out : feectools.linalg.basic.Vector, optional
             If given, the output will be written in-place into this vector.
 
         tol : float, optional
@@ -1821,7 +1821,7 @@ class BasisProjectionOperator(LinOpWithTransp):
 
         Returns
         -------
-         out : psydac.linalg.basic.Vector
+         out : feectools.linalg.basic.Vector
             The output (codomain) vector.
         """
 
@@ -2161,7 +2161,7 @@ def prepare_projection_of_basis(V1d, W1d, starts_out, ends_out, n_quad=None, pol
 
 class CoordinateProjector(LinearOperator):
     r"""
-    Class of projectors on one component of a :class:`~psydac.linalg.block.BlockVectorSpace`.
+    Class of projectors on one component of a :class:`~feectools.linalg.block.BlockVectorSpace`.
     Represent the projection on the :math:`\mu`-th component :
 
     .. math::
@@ -2265,7 +2265,7 @@ class CoordinateProjector(LinearOperator):
 
 class CoordinateInclusion(LinearOperator):
     r"""
-    Class of inclusion operator from one component of a :class:`~psydac.linalg.block.BlockVectorSpace`.
+    Class of inclusion operator from one component of a :class:`~feectools.linalg.block.BlockVectorSpace`.
     Represent the canonical inclusion on the :math:`\mu`-th component :
 
     .. math::

{struphy-3.0.0 → struphy-3.0.1}/src/struphy/feec/linear_operators.py

@@ -2,11 +2,11 @@ import itertools
 from abc import abstractmethod
 
 import cunumpy as xp
-from psydac.ddm.mpi import MockComm
-from psydac.ddm.mpi import mpi as MPI
-from psydac.linalg.basic import LinearOperator, Vector, VectorSpace
-from psydac.linalg.block import BlockVectorSpace
-from psydac.linalg.stencil import StencilVectorSpace
+from feectools.ddm.mpi import MockComm
+from feectools.ddm.mpi import mpi as MPI
+from feectools.linalg.basic import LinearOperator, Vector, VectorSpace
+from feectools.linalg.block import BlockVectorSpace
+from feectools.linalg.stencil import StencilVectorSpace
 from scipy import sparse
 
 from struphy.feec.utilities import apply_essential_bc_to_array
@@ -303,7 +303,7 @@ class BoundaryOperator(LinOpWithTransp):
 
     Parameters
     ----------
-    vector_space : psydac.linalg.basic.VectorSpace
+    vector_space : feectools.linalg.basic.VectorSpace
         The vector space associated to the operator.
 
     space_id : str
@@ -476,15 +476,15 @@ class BoundaryOperator(LinOpWithTransp):
 
         Parameters
         ----------
-        v : psydac.linalg.basic.Vector
+        v : feectools.linalg.basic.Vector
             The input (domain) vector.
 
-        out : psydac.linalg.basic.Vector, optional
+        out : feectools.linalg.basic.Vector, optional
             If given, the output will be written in-place into this vector.
 
         Returns
         -------
-        out : psydac.linalg.basic.Vector
+        out : feectools.linalg.basic.Vector
             The output (codomain) vector.
         """