struphy 3.2.0__tar.gz → 3.4.0__tar.gz

{struphy-3.2.0/src/struphy.egg-info → struphy-3.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: struphy
-Version: 3.2.0
+Version: 3.4.0
 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
@@ -30,38 +30,45 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<=2.4.3
-Requires-Dist: cunumpy<=0.1.1
+Requires-Dist: numpy<=2.5.0
+Requires-Dist: cunumpy<=0.2.0,>=0.2.0
 Requires-Dist: pyccel<=2.2.3,>=2.2.0
-Requires-Dist: feectools<=0.1.3
-Requires-Dist: scipy<=1.17.1
+Requires-Dist: feectools<=0.1.11,>=0.1.11
+Requires-Dist: scipy<=1.18.0
 Requires-Dist: h5py<=3.16.0
-Requires-Dist: matplotlib<=3.10.8
+Requires-Dist: h5netcdf<=1.8.1
+Requires-Dist: xarray<=2026.2.0
+Requires-Dist: matplotlib<=3.11.0
 Requires-Dist: pyyaml<=6.0.3
-Requires-Dist: vtk<=9.6.1
-Requires-Dist: tqdm<=4.68.1
-Requires-Dist: argcomplete<=3.6.3
+Requires-Dist: vtk<=9.7.0
+Requires-Dist: tqdm<=4.70.0
+Requires-Dist: argcomplete<=3.7.0
 Requires-Dist: ipywidgets<=8.1.8
-Requires-Dist: plotly<=6.8.0
-Requires-Dist: pyvista<=0.48.0
-Requires-Dist: trame<=3.13.0
+Requires-Dist: plotly<=7.1.0
+Requires-Dist: pyvista<=0.49.0
+Requires-Dist: trame<=4.0.0
 Requires-Dist: trame-vtk<=2.11.8
 Requires-Dist: trame-vuetify<=3.2.2
 Requires-Dist: nest_asyncio2<=1.7.2
-Requires-Dist: vtk<=9.6.1
-Requires-Dist: pytest<=9.0.3
+Requires-Dist: vtk<=9.7.0
+Requires-Dist: pytest<=9.1.0
 Requires-Dist: pytest-mpi<=0.6
 Requires-Dist: pytest-testmon<=2.2.0
-Requires-Dist: ruff<=0.15.12,>=0.15.0
+Requires-Dist: ruff<=0.16.0,==0.15.0
 Requires-Dist: line_profiler<=5.0.2
-Requires-Dist: scope-profiler<=0.1.9,>=0.1.7
+Requires-Dist: scope-profiler<=0.7.2,>=0.5.0
 Provides-Extra: mpi
 Requires-Dist: mpi4py<=4.1.1; extra == "mpi"
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda12x; extra == "gpu"
 Provides-Extra: phys
-Requires-Dist: gvec<=1.4.1,>=1.1.0; extra == "phys"
+Requires-Dist: gvec<=1.5.0,>=1.1.0; extra == "phys"
 Requires-Dist: desc-opt<=0.17.1; extra == "phys"
+Provides-Extra: pproc
+Requires-Dist: plasma-plots>=0.1.0; extra == "pproc"
 Provides-Extra: dev
 Requires-Dist: struphy[mpi]; extra == "dev"
+Requires-Dist: struphy[pproc]; extra == "dev"
 Requires-Dist: notebook; extra == "dev"
 Requires-Dist: autopep8; extra == "dev"
 Requires-Dist: isort; extra == "dev"
@@ -75,8 +82,11 @@ Requires-Dist: tabulate; extra == "dev"
 Requires-Dist: tomli-w; extra == "dev"
 Requires-Dist: kaleido; extra == "dev"
 Requires-Dist: pandas; extra == "dev"
+Requires-Dist: scope-profiler[pproc]; extra == "dev"
+Requires-Dist: slurm-script-generator>=0.3.6; extra == "dev"
 Provides-Extra: doc
 Requires-Dist: struphy[phys]; extra == "doc"
+Requires-Dist: struphy[pproc]; extra == "doc"
 Requires-Dist: jupyter; extra == "doc"
 Requires-Dist: nbconvert; extra == "doc"
 Requires-Dist: ipykernel; extra == "doc"
@@ -92,11 +102,13 @@ Requires-Dist: m2r2; extra == "doc"
 Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: docutils; extra == "doc"
 Requires-Dist: ipyparallel; extra == "doc"
+Requires-Dist: scope-profiler[pproc]; extra == "doc"
 Provides-Extra: likwid
 Requires-Dist: struphy[dev]; extra == "likwid"
 Requires-Dist: pylikwid; extra == "likwid"
 Provides-Extra: all
 Requires-Dist: struphy[phys]; extra == "all"
+Requires-Dist: struphy[pproc]; extra == "all"
 Requires-Dist: struphy[dev]; extra == "all"
 Requires-Dist: struphy[mpi]; extra == "all"
 Requires-Dist: struphy[doc]; extra == "all"
@@ -155,6 +167,8 @@ This will create `params_Maxwell.py` in your current working directory (cwd). Yo
 
 The default output is in `sim_1/` in your cwd. You can change the output path via the class `EnvironmentOptions` in the parameter file.
 
+For plots and diagnostics of the output, install [plasma-plots](https://struphy-hub.github.io/plasma-plots) with `pip install "struphy[pproc]"`; `Output` loads it automatically, adding `out.plot`, `out.analysis` and `.plasma.plot` on every product.
+
 Parallel simulations are run for example with
 
     pip install -U mpi4py

{struphy-3.2.0 → struphy-3.4.0}/README.md

@@ -50,6 +50,8 @@ This will create `params_Maxwell.py` in your current working directory (cwd). Yo
 
 The default output is in `sim_1/` in your cwd. You can change the output path via the class `EnvironmentOptions` in the parameter file.
 
+For plots and diagnostics of the output, install [plasma-plots](https://struphy-hub.github.io/plasma-plots) with `pip install "struphy[pproc]"`; `Output` loads it automatically, adding `out.plot`, `out.analysis` and `.plasma.plot` on every product.
+
 Parallel simulations are run for example with
 
     pip install -U mpi4py

{struphy-3.2.0 → struphy-3.4.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "3.2.0"
+version = "3.4.0"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
@@ -23,31 +23,33 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dependencies = [
-    "numpy<=2.4.3",
-    "cunumpy<=0.1.1",
+    "numpy<=2.5.0",
+    "cunumpy>=0.2.0, <=0.2.0",
     "pyccel>=2.2.0, <=2.2.3",
-    "feectools<=0.1.3",
-    "scipy<=1.17.1",
+    "feectools >= 0.1.11, <=0.1.11",
+    "scipy<=1.18.0",
     "h5py<=3.16.0",
-    "matplotlib<=3.10.8",
+    "h5netcdf<=1.8.1",
+    "xarray<=2026.2.0",
+    "matplotlib<=3.11.0",
     "pyyaml<=6.0.3",
-    "vtk<=9.6.1",
-    "tqdm<=4.68.1",
-    "argcomplete<=3.6.3",
+    "vtk<=9.7.0",
+    "tqdm<=4.70.0",
+    "argcomplete<=3.7.0",
     "ipywidgets<=8.1.8",
-    "plotly<=6.8.0",
-    "pyvista<=0.48.0",
-    "trame<=3.13.0",
+    "plotly<=7.1.0",
+    "pyvista<=0.49.0",
+    "trame<=4.0.0",
     "trame-vtk<=2.11.8",
     "trame-vuetify<=3.2.2",
     "nest_asyncio2<=1.7.2",
-    "vtk<=9.6.1",
-    "pytest<=9.0.3",
+    "vtk<=9.7.0",
+    "pytest<=9.1.0",
     "pytest-mpi<=0.6",
     "pytest-testmon<=2.2.0",
-    "ruff>=0.15.0, <=0.15.12",
+    "ruff==0.15.0, <=0.16.0",
     "line_profiler<=5.0.2",
-    "scope-profiler>=0.1.7, <=0.1.9",
+    "scope-profiler>=0.5.0, <=0.7.2",
 ]
 
 [project.license]
@@ -57,12 +59,19 @@ file = "LICENSE"
 mpi = [
     "mpi4py<=4.1.1",
 ]
+gpu = [
+    "cupy-cuda12x",
+]
 phys = [
-    "gvec>=1.1.0, <=1.4.1",
+    "gvec>=1.1.0, <=1.5.0",
     "desc-opt<=0.17.1",
 ]
+pproc = [
+    "plasma-plots>=0.1.0",
+]
 dev = [
     "struphy[mpi]",
+    "struphy[pproc]",
     "notebook",
     "autopep8",
     "isort",
@@ -76,9 +85,12 @@ dev = [
     "tomli-w",
     "kaleido",
     "pandas",
+    "scope-profiler[pproc]",
+    "slurm-script-generator>=0.3.6",
 ]
 doc = [
     "struphy[phys]",
+    "struphy[pproc]",
     "jupyter",
     "nbconvert",
     "ipykernel",
@@ -94,6 +106,7 @@ doc = [
     "myst-parser",
     "docutils",
     "ipyparallel",
+    "scope-profiler[pproc]",
 ]
 likwid = [
     "struphy[dev]",
@@ -101,6 +114,7 @@ likwid = [
 ]
 all = [
     "struphy[phys]",
+    "struphy[pproc]",
     "struphy[dev]",
     "struphy[mpi]",
     "struphy[doc]",
@@ -116,7 +130,6 @@ changelog = "https://github.com/struphy-hub/struphy/blob/devel/CHANGELOG.md"
 
 [project.scripts]
 struphy = "struphy.console.main:struphy"
-kinetic-diagnostics = "struphy.diagnostics.console_diagn:main"
 
 [tool.setuptools.package-data]
 "struphy.fields_background.mhd_equil.eqdsk" = [
@@ -133,6 +146,8 @@ kinetic-diagnostics = "struphy.diagnostics.console_diagn:main"
 ]
 struphy = [
     "compile_struphy.mk",
+    "**/*.cu",
+    "**/*.cuh",
 ]
 
 [tool.autopep8]
@@ -176,5 +191,7 @@ markers = [
     "fluid",
     "kinetic",
     "hybrid",
+    "toy",
     "single",
+    "mpi_pic",
 ]

struphy-3.4.0/src/struphy/__init__.py

@@ -0,0 +1,253 @@
+# Logging parameters and filters
+import atexit
+import logging
+import logging.config
+import os
+from typing import TYPE_CHECKING
+
+from feectools.ddm.mpi import launched_under_mpi
+
+
+class RankZeroFilter(logging.Filter):
+    def __init__(self, rank: int):
+        super().__init__()
+        self.rank = rank
+
+    def filter(self, record):
+        return self.rank == 0
+
+
+class BelowWarningFilter(logging.Filter):
+    """Let only DEBUG and INFO records pass (WARNING and above go to stderr)."""
+
+    def filter(self, record):
+        return record.levelno < logging.WARNING
+
+
+# logger configuration
+config = {
+    "version": 1,
+    "disable_existing_loggers": False,
+    "formatters": {
+        "simple": {"format": "%(message)s"},
+        "detailed": {
+            "format": "[%(levelname)s|%(module)s|L%(lineno)d] %(asctime)s: %(message)s",
+            "datefmt": "%Y-%m-%dT%H:%M:%S%z",
+        },
+    },
+    "filters": {
+        "below_warning": {"()": BelowWarningFilter},
+    },
+    "handlers": {
+        "stdout": {
+            "class": "logging.StreamHandler",
+            "level": "DEBUG",
+            "formatter": "simple",
+            "filters": ["below_warning"],
+            "stream": "ext://sys.stdout",
+        },
+        "stderr": {
+            "class": "logging.StreamHandler",
+            "level": "WARNING",
+            "formatter": "simple",
+            "stream": "ext://sys.stderr",
+        },
+        "file": {
+            "class": "logging.handlers.RotatingFileHandler",
+            "level": "DEBUG",
+            "formatter": "detailed",
+            # Overridable via STRUPHY_LOG_FILE so processes sharing a cwd (e.g. several
+            # profiling jobs launched from the same case directory) don't rotate the
+            # same file concurrently -- RotatingFileHandler's rollover isn't safe across
+            # separate OS processes and races with FileNotFoundError when they collide.
+            "filename": os.environ.get("STRUPHY_LOG_FILE", "struphy.log"),
+            "maxBytes": 10000,
+            "backupCount": 3,
+        },
+    },
+    "loggers": {"struphy": {"level": "WARNING", "handlers": ["stdout", "stderr", "file"]}},
+}
+
+
+def set_logging_level(level: int = logging.WARNING):
+    """Set logging level for struphy logger and its handlers.
+
+    Useful levels are:
+    * logging.DEBUG: for detailed debugging information.
+    * logging.INFO: for general informational messages about the simulation setup and progress, plus key events.
+    * logging.WARNING: for warnings about potential issues that do not stop the simulation.
+    * logging.ERROR: for errors that occur during the simulation, which may affect results but do not necessarily stop the simulation.
+    * logging.CRITICAL: for critical errors that likely cause the simulation to stop or produce invalid results.
+
+    Which handler a record ends up in is fixed by the configuration and not changed here:
+    DEBUG/INFO go to stdout, WARNING and above to stderr; records that pass the logger level are also written to the log file.
+    """
+    logger = logging.getLogger("struphy")
+    logger.setLevel(level)
+
+    logger.debug(
+        f"\nNew logger level: {logger.level}, effective: {logger.getEffectiveLevel()}, propagate: {logger.propagate}"
+    )
+    for h in logger.handlers:
+        logger.debug(f"{type(h).__name__}: handler level: {h.level}")
+
+
+def setup_logging(logging_level: int = logging.WARNING):
+    """Setup logging configuration for struphy."""
+    logger = logging.getLogger("struphy")
+
+    log_path = config["handlers"]["file"]["filename"]
+    os.makedirs(os.path.dirname(log_path) or ".", exist_ok=True)
+
+    logging.config.dictConfig(config)
+
+    set_logging_level(logging_level)
+
+    # Add RankZeroFilter to all handlers
+    # This helper function figures out whether
+    # the current process is launched with mpirun
+    # or not without importing mpi4py, which would initialize MPI
+    # and cause issues if imported prematurely.
+    # Instead, it checks for the presence of certain environment
+    # variables that are typically set by MPI launchers (like mpirun or mpiexec).
+    if not launched_under_mpi():
+        rank = 0
+        # Serial run: tell feectools not to import mpi4py (which initializes MPI and takes
+        # ~1 s) and use its MockMPI instead. This is an in-process flag, deliberately not an
+        # environment variable, so that it is not inherited by ``mpirun`` subprocesses.
+        # It only has an effect if feectools.ddm.mpi has not been imported yet.
+        import feectools
+
+        feectools.use_mpi = False
+    else:
+        # deferred: importing feectools (and thereby mpi4py) is expensive
+        from feectools.ddm.mpi import mpi as MPI
+
+        rank = MPI.COMM_WORLD.Get_rank()
+    rank_filter = RankZeroFilter(rank)
+
+    # Apply filter to struphy logger handlers
+    for handler in logger.handlers:
+        handler.addFilter(rank_filter)
+
+    # Apply filter to root logger handlers
+    root_logger = logging.getLogger()
+    for handler in root_logger.handlers:
+        handler.addFilter(rank_filter)
+
+    # Start queue handler listener if present
+    queue_handler = None
+    for handler in logger.handlers:
+        if hasattr(handler, "listener"):
+            queue_handler = handler
+            break
+    if queue_handler is not None:
+        queue_handler.listener.start()
+        atexit.register(queue_handler.listener.stop)
+
+
+# Default logging setup
+logger = logging.getLogger("struphy")
+setup_logging(logging_level=logging.WARNING)
+logger.info(f"Logging setup complete, log-file at {config['handlers']['file']['filename']}")
+
+# Public API components.
+#
+# They are resolved lazily (PEP 562): ``import struphy`` stays cheap, and
+# ``from struphy import X`` only imports the module that actually provides ``X``.
+# Importing everything eagerly pulled in the whole package (geometry, models,
+# post-processing, feectools, ...), costing several seconds.
+_LAZY_API = {
+    "Compiler": "struphy.api.compiler",
+    "domains": "struphy.api.domains",
+    "equils": "struphy.api.equils",
+    "grids": "struphy.api.grids",
+    "maxwellians": "struphy.api.maxwellians",
+    "ButcherTableau": "struphy.api.ode",
+    "BaseUnits": "struphy.api.options",
+    "DerhamOptions": "struphy.api.options",
+    "EnvironmentOptions": "struphy.api.options",
+    "FieldsBackground": "struphy.api.options",
+    "ProfilingOptions": "struphy.api.options",
+    "Time": "struphy.api.options",
+    "BinningPlot": "struphy.api.particles",
+    "BoundaryParameters": "struphy.api.particles",
+    "KernelDensityPlot": "struphy.api.particles",
+    "LoadingParameters": "struphy.api.particles",
+    "SavingParameters": "struphy.api.particles",
+    "SortingParameters": "struphy.api.particles",
+    "WeightsParameters": "struphy.api.particles",
+    "perturbations": "struphy.api.perturbations",
+    "Output": "struphy.api.post_processing",
+    "open_output": "struphy.api.post_processing",
+    "Simulation": "struphy.api.simulation",
+}
+
+if TYPE_CHECKING:  # static analysis and IDEs see the eager imports
+    from struphy.api.compiler import Compiler
+    from struphy.api.domains import domains
+    from struphy.api.equils import equils
+    from struphy.api.grids import grids
+    from struphy.api.maxwellians import maxwellians
+    from struphy.api.ode import ButcherTableau
+    from struphy.api.options import (
+        BaseUnits,
+        DerhamOptions,
+        EnvironmentOptions,
+        FieldsBackground,
+        ProfilingOptions,
+        Time,
+    )
+    from struphy.api.particles import (
+        BinningPlot,
+        BoundaryParameters,
+        KernelDensityPlot,
+        LoadingParameters,
+        SavingParameters,
+        SortingParameters,
+        WeightsParameters,
+    )
+    from struphy.api.perturbations import perturbations
+    from struphy.api.post_processing import Output, open_output
+    from struphy.api.simulation import Simulation
+
+__all__ = [
+    "Compiler",
+    "domains",
+    "equils",
+    "grids",
+    "maxwellians",
+    "EnvironmentOptions",
+    "BaseUnits",
+    "Time",
+    "ProfilingOptions",
+    "perturbations",
+    "LoadingParameters",
+    "WeightsParameters",
+    "BoundaryParameters",
+    "SortingParameters",
+    "SavingParameters",
+    "BinningPlot",
+    "KernelDensityPlot",
+    "DerhamOptions",
+    "FieldsBackground",
+    "ButcherTableau",
+    "Output",
+    "open_output",
+    "Simulation",
+]
+
+
+def __getattr__(name: str):
+    module_name = _LAZY_API.get(name)
+    if module_name is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    import importlib
+
+    value = getattr(importlib.import_module(module_name), name)
+    globals()[name] = value  # cache: later lookups bypass __getattr__
+    return value
+
+
+def __dir__():
+    return sorted(set(globals()) | set(_LAZY_API))

struphy-3.4.0/src/struphy/api/compiler/__init__.py

@@ -0,0 +1,3 @@
+from struphy.utils.compiler import Compiler
+
+__all__ = ["Compiler"]

{struphy-3.2.0 → struphy-3.4.0}/src/struphy/api/options/__init__.py

@@ -1,3 +1,5 @@
+from scope_profiler import ProfilingOptions
+
 from struphy.io.options import (
     BaseUnits,
     DerhamOptions,
@@ -10,6 +12,7 @@ __all__ = [
     "EnvironmentOptions",
     "BaseUnits",
     "Time",
+    "ProfilingOptions",
     #
     "DerhamOptions",
     "FieldsBackground",

struphy-3.4.0/src/struphy/api/post_processing/__init__.py

@@ -0,0 +1,3 @@
+from struphy.post_processing.output import Output, open_output
+
+__all__ = ["Output", "open_output"]

{struphy-3.2.0 → struphy-3.4.0}/src/struphy/bsplines/bsplines.py

@@ -611,8 +611,8 @@ def make_knots(breaks, degree, periodic):
 
     if periodic:
         period = breaks[-1] - breaks[0]
-        T[0:p] = [xi - period for xi in breaks[-p - 1 : -1]]
-        T[-p:] = [xi + period for xi in breaks[1 : p + 1]]
+        T[0:p] = xp.asarray([xi - period for xi in breaks[-p - 1 : -1]])
+        T[-p:] = xp.asarray([xi + period for xi in breaks[1 : p + 1]])
     else:
         T[0:p] = breaks[0]
         T[-p:] = breaks[-1]

{struphy-3.2.0 → struphy-3.4.0}/src/struphy/compile_struphy.mk

@@ -10,8 +10,7 @@ struphy_path := $(shell $(PYTHON) -c "import struphy; print(struphy.__path__[0])
 # Arguments to this script are: 
 STRUPHY_SOURCES := $(sources)
 FLAGS := --libdir $(LIBDIR) $(flags) #--debug
-FLAGS_openmp_pic := $(flags_openmp_pic)
-FLAGS_openmp_mhd := $(flags_openmp_mhd)
+FLAGS_openmp := $(flags_openmp)
 
 #--------------------------------------
 # SOURCE FILES 
@@ -35,7 +34,7 @@ all: $(OUTPUTS)
 	@for dep in $^ ; do \
 		echo $$dep ; \
     done
-	pyccel compile -v $(FLAGS) $(FLAGS_openmp_pic) $(FLAGS_openmp_mhd) $<
+	pyccel compile $(FLAGS) $(FLAGS_openmp) $<
 	@echo ""
 
 #--------------------------------------