struphy 2.4.1__tar.gz → 2.4.2__tar.gz

{struphy-2.4.1/src/struphy.egg-info → struphy-2.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: struphy
-Version: 2.4.1
+Version: 2.4.2
 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
@@ -32,7 +32,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pyccel>=1.11.1
-Requires-Dist: mpi4py<4
+Requires-Dist: mpi4py
 Requires-Dist: scipy
 Requires-Dist: h5py
 Requires-Dist: matplotlib
@@ -67,12 +67,53 @@ Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: mistune; extra == "doc"
 Requires-Dist: docutils; extra == "doc"
 Requires-Dist: ipyparallel; extra == "doc"
+Dynamic: license-file
 
 # Struphy - Structure-preserving hybrid codes
 
 A Python package for plasma physics PDEs.
 
-See the [Struphy documentation](https://struphy.pages.mpcdf.de/struphy/index.html) for details.
+Join the [Struphy mailing list](https://listserv.gwdg.de/mailman/listinfo/struphy) and stay informed on updates.
+
+## Documentation
+See the [Struphy pages](https://struphy.pages.mpcdf.de/struphy/index.html) for details regarding installation, tutorials, use and development.
+
+## Quick install
+
+Use a virtual environment:
+
+    python3 -m pip install -U virtualenv
+    python3 -m venv struphy_env
+    source struphy_env/bin/activate
+
+Install latest release (with test packages):
+
+    pip install --no-cache-dir -U struphy[test]
+
+Compile kernels:
+
+    struphy compile
+
+Quick help:
+
+    struphy -h
+
+In case of problems visit [Trouble shooting](https://struphy.pages.mpcdf.de/struphy/sections/install.html#trouble-shooting).
+
+## Run tests from the command-line
+
+Run available verification tests for [Struphy models](https://struphy.pages.mpcdf.de/struphy/sections/models.html):
+
+    struphy test models --verification --fast --show-plots 
+
+The corresponding parameter files are in [struphy/io/inp/verification/](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/tree/devel/src/struphy/io/inp/verification).
+The corresponding diagnostics functions are in [struphy/models/tests/verification.py](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/src/struphy/models/tests/verification.py). You can repeat the verification run of a single `<model_name>` by typing
+
+    struphy test <model_name> --verification --fast --show-plots 
+
+## Tutorial notebooks
+
+Struphy tutorials are available in the form of [Jupyter notebooks](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/tree/devel/doc/tutorials).  
 
 ## Reference paper
 

struphy-2.4.2/README.md

@@ -0,0 +1,55 @@
+# Struphy - Structure-preserving hybrid codes
+
+A Python package for plasma physics PDEs.
+
+Join the [Struphy mailing list](https://listserv.gwdg.de/mailman/listinfo/struphy) and stay informed on updates.
+
+## Documentation
+See the [Struphy pages](https://struphy.pages.mpcdf.de/struphy/index.html) for details regarding installation, tutorials, use and development.
+
+## Quick install
+
+Use a virtual environment:
+
+    python3 -m pip install -U virtualenv
+    python3 -m venv struphy_env
+    source struphy_env/bin/activate
+
+Install latest release (with test packages):
+
+    pip install --no-cache-dir -U struphy[test]
+
+Compile kernels:
+
+    struphy compile
+
+Quick help:
+
+    struphy -h
+
+In case of problems visit [Trouble shooting](https://struphy.pages.mpcdf.de/struphy/sections/install.html#trouble-shooting).
+
+## Run tests from the command-line
+
+Run available verification tests for [Struphy models](https://struphy.pages.mpcdf.de/struphy/sections/models.html):
+
+    struphy test models --verification --fast --show-plots 
+
+The corresponding parameter files are in [struphy/io/inp/verification/](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/tree/devel/src/struphy/io/inp/verification).
+The corresponding diagnostics functions are in [struphy/models/tests/verification.py](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/src/struphy/models/tests/verification.py). You can repeat the verification run of a single `<model_name>` by typing
+
+    struphy test <model_name> --verification --fast --show-plots 
+
+## Tutorial notebooks
+
+Struphy tutorials are available in the form of [Jupyter notebooks](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/tree/devel/doc/tutorials).  
+
+## Reference paper
+
+* S. Possanner, F. Holderied, Y. Li, B.-K. Na, D. Bell, S. Hadjout and Y. Güçlü, [**High-Order Structure-Preserving Algorithms for Plasma Hybrid Models**](https://link.springer.com/chapter/10.1007/978-3-031-38299-4_28), International Conference on Geometric Science of Information 2023, 263-271, Springer Nature Switzerland.
+
+## Contact
+
+* Stefan Possanner [stefan.possanner@ipp.mpg.de](mailto:spossann@ipp.mpg.de)
+* Eric Sonnendrücker [eric.sonnendruecker@ipp.mpg.de](mailto:eric.sonnendruecker@ipp.mpg.de)
+* Xin Wang [xin.wang@ipp.mpg.de](mailto:xin.wang@ipp.mpg.de)

{struphy-2.4.1 → struphy-2.4.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.4.1"
+version = "2.4.2"
 readme = "README.md"
 requires-python = ">=3.10"
 license = {file = "LICENSE"}
@@ -21,7 +21,7 @@ classifiers = [
 dependencies = [
     'numpy',
     'pyccel>=1.11.1',
-    'mpi4py<4',
+    'mpi4py',
     'scipy',
     'h5py',
     'matplotlib',
@@ -99,7 +99,7 @@ kinetic-diagnostics = "struphy.diagnostics.console_diagn:main"
                     ]
                     
 struphy = ['compile_struphy.mk',
-           'psydac-2.4.1-py3-none-any.whl',]
+           'psydac-2.4.2.dev0-py3-none-any.whl',]
 
 [tool.autopep8]
 # Add specific settings for autopep8

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/conftest.py

@@ -4,6 +4,7 @@ def pytest_addoption(parser):
     parser.addoption("--vrbose", action="store_true")
     parser.addoption("--verification", action="store_true")
     parser.addoption("--show-plots", action="store_true")
+    parser.addoption("--nclones", type=int, default=1)
 
 
 def pytest_generate_tests(metafunc):
@@ -25,6 +26,10 @@ def pytest_generate_tests(metafunc):
     if "verification" in metafunc.fixturenames and option_value is not None:
         metafunc.parametrize("verification", [option_value])
 
+    option_value = metafunc.config.option.nclones
+    if "nclones" in metafunc.fixturenames and option_value is not None:
+        metafunc.parametrize("nclones", [option_value])
+
     option_value = metafunc.config.option.show_plots
     if "show_plots" in metafunc.fixturenames and option_value is not None:
         metafunc.parametrize("show_plots", [option_value])

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/compile.py

@@ -40,6 +40,7 @@ def struphy_compile(language, compiler, omp_pic, omp_feec, delete, status, verbo
 
     import importlib.metadata
     import os
+    import re
     import sysconfig
 
     import pyccel
@@ -255,14 +256,17 @@ def struphy_compile(language, compiler, omp_pic, omp_feec, delete, status, verbo
             install_psydac = False
             if psydac_installed:
                 # only install (from .whl) if psydac not up-to-date
-                if psydac_ver != struphy_ver:
+                if ".".join(psydac_ver.split(".")[:3]) != ".".join(struphy_ver.split(".")[:3]):
                     print(f"You have psydac version {psydac_ver}, but version {struphy_ver} is required.\n")
                     install_psydac = True
             else:
                 install_psydac = True
 
             if install_psydac:
-                psydac_file = "psydac-" + struphy_ver + "-py3-none-any.whl"
+                for filename in os.listdir(libpath):
+                    if re.match("psydac-", filename):
+                        psydac_file = filename
+
                 cmd = ["pip", "uninstall", "-y", "psydac"]
                 subp_run(cmd)
                 print("\nInstalling Psydac ...")

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/format.py

@@ -99,8 +99,7 @@ PASS_GREEN = f"{GREEN_COLOR}PASS{BLACK_COLOR}"
 
 
 def check_omp_flags(file_path, verbose=False):
-    """
-    Checks if a file contains incorrect OpenMP-like flags (`# $`).
+    """Checks if a file contains incorrect OpenMP-like flags (`# $`).
 
     Parameters:
     -----------
@@ -124,8 +123,7 @@ def check_omp_flags(file_path, verbose=False):
 
 
 def check_ruff(file_path, verbose=False):
-    """
-    Check if a file passes Ruff linting.
+    """Check if a file passes Ruff linting.
 
     Parameters
     ----------
@@ -175,8 +173,7 @@ def check_ruff(file_path, verbose=False):
 
 
 def check_isort(file_path, verbose=False):
-    """
-    Check if a file is sorted according to isort.
+    """Check if a file is sorted according to isort.
 
     Parameters
     ----------
@@ -204,8 +201,7 @@ def check_isort(file_path, verbose=False):
 
 
 def check_autopep8(file_path, verbose=False):
-    """
-    Check if a file is formatted according to autopep8.
+    """Check if a file is formatted according to autopep8.
 
     Parameters
     ----------
@@ -235,8 +231,7 @@ def check_autopep8(file_path, verbose=False):
 
 
 def check_flake8(file_path, verbose=False):
-    """
-    Check if a file is formatted according to flake8.
+    """Check if a file is formatted according to flake8.
 
     Parameters
     ----------
@@ -265,8 +260,7 @@ def check_flake8(file_path, verbose=False):
 
 
 def get_pylint_score(file_path, verbose=False, pass_score=8.0):
-    """
-    Get pylint score for a file and determine if it passes.
+    """Get pylint score for a file and determine if it passes.
 
     Parameters
     ----------
@@ -320,8 +314,7 @@ def get_pylint_score(file_path, verbose=False, pass_score=8.0):
 
 
 def check_trailing_commas(file_path, verbose=False):
-    """
-    Check if a file contains trailing commas as required by add-trailing-commas.
+    """Check if a file contains trailing commas as required by add-trailing-commas.
 
     Parameters
     ----------
@@ -367,8 +360,7 @@ def check_trailing_commas(file_path, verbose=False):
 
 
 def parse_path(directory):
-    """
-    Traverse a directory to find Python files, excluding '__XYZ__.py'.
+    """Traverse a directory to find Python files, excluding '__XYZ__.py'.
 
     Parameters
     ----------
@@ -391,8 +383,7 @@ def parse_path(directory):
 
 
 def get_python_files(input_type, path=None):
-    """
-    Retrieve Python files based on the specified input type
+    """Retrieve Python files based on the specified input type.
 
     Parameters
     ----------
@@ -480,8 +471,7 @@ def get_python_files(input_type, path=None):
 
 
 def struphy_lint(config, verbose):
-    """
-    Lint Python files based on the given configuration and specified linters.
+    """Lint Python files based on the given configuration and specified linters.
 
     Parameters
     ----------
@@ -614,8 +604,7 @@ def confirm_formatting(python_files, linters, yes):
 
 
 def files_require_formatting(python_files, linters):
-    """
-    Check if any of the specified files still require formatting based on the specified linters.
+    """Check if any of the specified files still require formatting based on the specified linters.
 
     Parameters
     ----------
@@ -674,8 +663,7 @@ def run_linters_on_files(linters, python_files, flags, verbose):
 
 
 def struphy_format(config, verbose, yes=False):
-    """
-    Format Python files with specified linters, optionally iterating multiple times.
+    """Format Python files with specified linters, optionally iterating multiple times.
 
     Parameters
     ----------
@@ -755,8 +743,7 @@ def struphy_format(config, verbose, yes=False):
 
 
 def print_stats_plain(stats, linters, ci_linters=["ruff"]):
-    """
-    Print statistics for a single file in plain text format.
+    """Print statistics for a single file in plain text format.
 
     Parameters
     ----------
@@ -789,8 +776,7 @@ def print_stats_plain(stats, linters, ci_linters=["ruff"]):
 
 
 def print_stats_table(stats_list, linters, print_header=True, pathlen=0, ci_linters=["ruff"]):
-    """
-    Print statistics for Python files in a tabular format.
+    """Print statistics for Python files in a tabular format.
 
     Parameters
     ----------
@@ -850,8 +836,7 @@ def print_stats_table(stats_list, linters, print_header=True, pathlen=0, ci_lint
 
 
 def analyze_file(file_path, linters=None, verbose=False):
-    """
-    Analyze a Python file with list of linters
+    """Analyze a Python file with list of linters.
 
     Parameters
     ----------
@@ -936,8 +921,7 @@ def analyze_file(file_path, linters=None, verbose=False):
 
 
 def replace_backticks_with_code_tags(text):
-    """
-    Recursively replaces inline backticks with <code> tags.
+    """Recursively replaces inline backticks with <code> tags.
     Handles multiple or nested occurrences.
 
     Args:
@@ -971,7 +955,7 @@ def generate_html_table_from_combined_data(combined_data, sort_descending=True):
 
 
 def parse_json_file_to_html(json_file_path, html_output_path):
-    """
+    """Parses a JSON file containing code issues and writes an HTML report.
     Parses a JSON file containing code issues, groups them by filename,
     reads the source code to extract context, and writes an HTML report.
     Each file's section is foldable using <details> and <summary> tags.
@@ -1288,7 +1272,7 @@ document.addEventListener('DOMContentLoaded', (event) => {
                         html_content.append("</div>")
                 else:
                     html_content.append(
-                        f"<p>Cannot read file <code>{filename}</code> or invalid row " f"<code>{row}</code>.</p>"
+                        f"<p>Cannot read file <code>{filename}</code> or invalid row <code>{row}</code>.</p>"
                     )
 
                 html_content.append("</div>")

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/main.py

@@ -13,9 +13,7 @@ __version__ = importlib.metadata.version("struphy")
 
 
 def struphy():
-    """
-    Struphy main executable. Performs argument parsing and sub-command call.
-    """
+    """Struphy main executable. Performs argument parsing and sub-command call."""
 
     import argparse
     import pickle
@@ -622,6 +620,12 @@ def struphy():
         action="store_true",
     )
 
+    parser_pproc.add_argument(
+        "--no-vtk",
+        help="whether vtk files creation should be skipped",
+        action="store_true",
+    )
+
     # 7. "test" sub-command
     try:
         import pytest_mpi
@@ -693,6 +697,14 @@ def struphy():
             action="store_true",
         )
 
+        parser_test.add_argument(
+            "--nclones",
+            type=int,
+            metavar="N",
+            help="number of domain clones (default=1)",
+            default=1,
+        )
+
         parser_test.add_argument(
             "--show-plots",
             help="show plots of tests",

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/params.py

@@ -1,11 +1,11 @@
 def struphy_params(model, file, yes=False, options=False):
-    '''Create a model's default parameter file and save in current input path.
+    """Create a model's default parameter file and save in current input path.
 
     Parameters
     ----------
     model : str
         The name of the Struphy model.
-        
+
     yes : bool
         If true, say yes on prompt to overwrite .yml FILE
 
@@ -14,9 +14,9 @@ def struphy_params(model, file, yes=False, options=False):
 
     show_options : bool
         Whether to print to screen all possible options for the model.
-    '''
+    """
 
-    from struphy.models import fluid, kinetic, hybrid, toy
+    from struphy.models import fluid, hybrid, kinetic, toy
 
     # load model class
     objs = [fluid, kinetic, hybrid, toy]

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/pproc.py

@@ -1,9 +1,17 @@
 from struphy.console.run import subp_run
 
 
-def struphy_pproc(dirr, dir_abs=None, step=1, celldivide=1, physical=False, guiding_center=False, classify=False):
-    """
-    Post process data from finished Struphy runs.
+def struphy_pproc(
+    dirr,
+    dir_abs=None,
+    step=1,
+    celldivide=1,
+    physical=False,
+    guiding_center=False,
+    classify=False,
+    no_vtk=False,
+):
+    """Post process data from finished Struphy runs.
 
     Parameters
     ----------
@@ -56,4 +64,8 @@ def struphy_pproc(dirr, dir_abs=None, step=1, celldivide=1, physical=False, guid
     if classify:
         command += ["--classify"]
 
+    # Whether vtk files should be created
+    if no_vtk:
+        command += ["--no-vtk"]
+
     subp_run(command)

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/console/test.py

@@ -11,6 +11,7 @@ def struphy_test(
     vrbose: bool = False,
     verification: bool = False,
     show_plots: bool = False,
+    nclones: int = 1,
 ):
     """
     Run Struphy unit and/or model tests.
@@ -92,6 +93,8 @@ def struphy_test(
             cmd += ["--vrbose"]
         if verification:
             cmd += ["--verification"]
+        if nclones > 1:
+            cmd += ["--nclones", f"{nclones}"]
         if show_plots:
             cmd += ["--show-plots"]
         subp_run(cmd)
@@ -123,6 +126,8 @@ def struphy_test(
             cmd += ["--vrbose"]
         if verification:
             cmd += ["--verification"]
+        if nclones > 1:
+            cmd += ["--nclones", f"{nclones}"]
         if show_plots:
             cmd += ["--show-plots"]
         subp_run(cmd)
@@ -146,17 +151,17 @@ def struphy_test(
             )
 
         if group in toy_message:
-            test_mod = "test_toy_models.py"
+            mtype = "toy"
         elif group in fluid_message:
-            test_mod = "test_fluid_models.py"
+            mtype = "fluid"
         elif group in kinetic_message:
-            test_mod = "test_kinetic_models.py"
+            mtype = "kinetic"
         elif group in hybrid_message:
-            test_mod = "test_hybrid_models.py"
+            mtype = "hybrid"
         else:
             raise ValueError(f"{group} is not a valid model name.")
 
-        py_file = os.path.join(libpath, "models", "tests", test_mod)
+        py_file = os.path.join(libpath, "models", "tests", "util.py")
 
         cmd = [
             "mpirun",
@@ -164,11 +169,13 @@ def struphy_test(
             str(mpi),
             "python3",
             py_file,
+            mtype,
             group,
             str(Tend),
             str(fast),
             str(vrbose),
             str(verification),
+            str(nclones),
             str(show_plots),
         ]
         subp_run(cmd)

{struphy-2.4.1 → struphy-2.4.2}/src/struphy/eigenvalue_solvers/kernels_2d.py

@@ -3,7 +3,6 @@
 from pyccel.decorators import pure
 
 
-@pure
 def kernel_mass(
     nel: "int[:]",
     p: "int[:]",
@@ -23,7 +22,7 @@ def kernel_mass(
 ):
     mat[:, :, :, :] = 0.0
 
-    #$ omp parallel private(ie1, ie2, il1, il2, jl1, jl2, value, q1, q2, wvol, bi, bj) shared(mat)
+    #$ omp parallel private(ie1, ie2, il1, il2, jl1, jl2, value1, q1, q2, wvol, bi, bj) shared(mat)
     #$ omp for reduction ( + : mat)
     for ie1 in range(nel[0]):
         for ie2 in range(nel[1]):
@@ -31,7 +30,7 @@ def kernel_mass(
                 for il2 in range(p[1] + 1 - ni[1]):
                     for jl1 in range(p[0] + 1 - nj[0]):
                         for jl2 in range(p[1] + 1 - nj[1]):
-                            value = 0.0
+                            value1 = 0.0
 
                             for q1 in range(nq[0]):
                                 for q2 in range(nq[1]):
@@ -39,15 +38,14 @@ def kernel_mass(
                                     bi = bi1[ie1, il1, 0, q1] * bi2[ie2, il2, 0, q2]
                                     bj = bj1[ie1, jl1, 0, q1] * bj2[ie2, jl2, 0, q2]
 
-                                    value += wvol * bi * bj
+                                    value1 += wvol * bi * bj
 
-                            mat[ind_base1[ie1, il1], ind_base2[ie2, il2], p[0] + jl1 - il1, p[1] + jl2 - il2] += value
+                            mat[ind_base1[ie1, il1], ind_base2[ie2, il2], p[0] + jl1 - il1, p[1] + jl2 - il2] += value1
     #$ omp end parallel
 
     ierr = 0
 
 
-@pure
 def kernel_inner(
     nel: "int[:]",
     n3: "int",
@@ -65,29 +63,28 @@ def kernel_inner(
 ):
     mat[:, :, :] = 0.0
 
-    #$ omp parallel private(ie1, ie2, ie3, il1, il2, value, q1, q2, wvol, bi) shared(mat)
+    #$ omp parallel private(ie1, ie2, ie3, il1, il2, value1, q1, q2, wvol, bi) shared(mat)
     #$ omp for reduction ( + : mat)
     for ie1 in range(nel[0]):
         for ie2 in range(nel[1]):
             for ie3 in range(n3):
                 for il1 in range(p[0] + 1 - ni[0]):
                     for il2 in range(p[1] + 1 - ni[1]):
-                        value = 0.0
+                        value1 = 0.0
 
                         for q1 in range(nq[0]):
                             for q2 in range(nq[1]):
                                 wvol = w1[ie1, q1] * w2[ie2, q2] * mat_fun[ie1, q1, ie2, q2, ie3]
                                 bi = bi1[ie1, il1, 0, q1] * bi2[ie2, il2, 0, q2]
 
-                                value += wvol * bi
+                                value1 += wvol * bi
 
-                        mat[ind_base1[ie1, il1], ind_base2[ie2, il2], ie3] += value
+                        mat[ind_base1[ie1, il1], ind_base2[ie2, il2], ie3] += value1
     #$ omp end parallel
 
     ierr = 0
 
 
-@pure
 def kernel_l2error(
     nel: "int[:]",
     p: "int[:]",
@@ -147,7 +144,6 @@ def kernel_l2error(
     ierr = 0
 
 
-@pure
 def kernel_evaluate_2form(
     nel: "int[:]",
     n3: "int",