sdf-xarray 0.2.5__cp313-cp313-win_amd64.whl → 0.3.0__cp313-cp313-win_amd64.whl

sdf_xarray/__init__.py

@@ -2,12 +2,15 @@ import os
 import re
 from collections import Counter, defaultdict
 from collections.abc import Callable, Iterable
+from importlib.metadata import version
 from itertools import product
+from os import PathLike as os_PathLike
 from pathlib import Path
 from typing import ClassVar
 
 import numpy as np
 import xarray as xr
+from packaging.version import Version
 from xarray.backends import AbstractDataStore, BackendArray, BackendEntrypoint
 from xarray.backends.file_manager import CachingFileManager
 from xarray.backends.locks import ensure_lock
@@ -21,6 +24,12 @@ import sdf_xarray.plotting  # noqa: F401
 
 from .sdf_interface import Constant, SDFFile  # type: ignore  # noqa: PGH003
 
+# TODO Remove this once the new kwarg options are fully implemented
+if Version(version("xarray")) >= Version("2025.8.0"):
+    xr.set_options(use_new_combine_kwarg_defaults=True)
+
+PathLike = str | os_PathLike
+
 
 def _rename_with_underscore(name: str) -> str:
     """A lot of the variable names have spaces, forward slashes and dashes in them, which
@@ -51,14 +60,32 @@ def _process_latex_name(variable_name: str) -> str:
     return variable_name
 
 
+def _resolve_glob(path_glob: PathLike | Iterable[PathLike]):
+    """
+    Normalise input path_glob into a sorted list of absolute, resolved Path objects.
+    """
+
+    try:
+        p = Path(path_glob)
+        paths = list(p.parent.glob(p.name)) if p.name == "*.sdf" else list(p)
+    except TypeError:
+        paths = list({Path(p) for p in path_glob})
+
+    paths = sorted(p.resolve() for p in paths)
+    if not paths:
+        raise FileNotFoundError(f"No files matched pattern or input: {path_glob!r}")
+    return paths
+
+
 def combine_datasets(path_glob: Iterable | str, **kwargs) -> xr.Dataset:
     """Combine all datasets using a single time dimension"""
 
     return xr.open_mfdataset(
         path_glob,
-        data_vars="minimal",
-        coords="minimal",
-        compat="override",
+        data_vars="all",
+        coords="different",
+        compat="no_conflicts",
+        join="outer",
         preprocess=SDFPreprocess(),
         **kwargs,
     )
@@ -69,6 +96,7 @@ def open_mfdataset(
     *,
     separate_times: bool = False,
     keep_particles: bool = False,
+    probe_names: list[str] | None = None,
 ) -> xr.Dataset:
     """Open a set of EPOCH SDF files as one `xarray.Dataset`
 
@@ -98,20 +126,21 @@ def open_mfdataset(
         different output frequencies
     keep_particles :
         If ``True``, also load particle data (this may use a lot of memory!)
+    probe_names :
+        List of EPOCH probe names
     """
 
-    # TODO: This is not very robust, look at how xarray.open_mfdataset does it
-    if isinstance(path_glob, str):
-        path_glob = Path().glob(path_glob)
-
-    # Coerce to list because we might need to use the sequence multiple times
-    path_glob = sorted(list(path_glob))  # noqa: C414
-
+    path_glob = _resolve_glob(path_glob)
     if not separate_times:
-        return combine_datasets(path_glob, keep_particles=keep_particles)
+        return combine_datasets(
+            path_glob, keep_particles=keep_particles, probe_names=probe_names
+        )
 
-    time_dims, var_times_map = make_time_dims(path_glob)
-    all_dfs = [xr.open_dataset(f, keep_particles=keep_particles) for f in path_glob]
+    _, var_times_map = make_time_dims(path_glob)
+    all_dfs = [
+        xr.open_dataset(f, keep_particles=keep_particles, probe_names=probe_names)
+        for f in path_glob
+    ]
 
     for df in all_dfs:
         for da in df:
@@ -128,7 +157,12 @@ def open_mfdataset(
                 )
 
     return xr.combine_by_coords(
-        all_dfs, data_vars="minimal", combine_attrs="drop_conflicts"
+        all_dfs,
+        data_vars="all",
+        coords="different",
+        combine_attrs="drop_conflicts",
+        join="outer",
+        compat="no_conflicts",
     )
 
 
@@ -211,14 +245,23 @@ class SDFDataStore(AbstractDataStore):
         "drop_variables",
         "keep_particles",
         "lock",
+        "probe_names",
     )
 
-    def __init__(self, manager, drop_variables=None, keep_particles=False, lock=None):
+    def __init__(
+        self,
+        manager,
+        drop_variables=None,
+        keep_particles=False,
+        lock=None,
+        probe_names=None,
+    ):
         self._manager = manager
         self._filename = self.ds.filename
         self.drop_variables = drop_variables
         self.keep_particles = keep_particles
         self.lock = ensure_lock(lock)
+        self.probe_names = probe_names
 
     @classmethod
     def open(
@@ -227,6 +270,7 @@ class SDFDataStore(AbstractDataStore):
         lock=None,
         drop_variables=None,
         keep_particles=False,
+        probe_names=None,
     ):
         if isinstance(filename, os.PathLike):
             filename = os.fspath(filename)
@@ -237,6 +281,7 @@ class SDFDataStore(AbstractDataStore):
             lock=lock,
             drop_variables=drop_variables,
             keep_particles=keep_particles,
+            probe_names=probe_names,
         )
 
     def _acquire(self, needs_lock=True):
@@ -347,7 +392,28 @@ class SDFDataStore(AbstractDataStore):
 
             if value.is_point_data:
                 # Point (particle) variables are 1D
-                var_coords = (f"ID_{_process_grid_name(key, _grid_species_name)}",)
+
+                # Particle data does not maintain a fixed dimension size
+                # throughout the simulation. An example of a particle name comes
+                # in the form of `Particles/Px/Ion_H` which is then modified
+                # using `_process_grid_name()` into `Ion_H`. This is fine as the
+                # other components of the momentum (`Py`, `Pz`) will have the same
+                # size as they represent the same bunch of particles.
+
+                # Probes however have names in the form of `Electron_Front_Probe/Px`
+                # which are changed to just `Px`; this is fine when there is only one
+                # probe in the system but when there are multiple they will have
+                # conflicting sizes so we can't keep the names as simply `Px` so we
+                # instead set their dimension as the full name `Electron_Front_Probe_Px`.
+                is_probe_name_match = self.probe_names is not None and any(
+                    name in key for name in self.probe_names
+                )
+                name_processor = (
+                    _rename_with_underscore
+                    if is_probe_name_match
+                    else _grid_species_name
+                )
+                var_coords = (f"ID_{_process_grid_name(key, name_processor)}",)
             else:
                 # These are DataArrays
 
@@ -414,6 +480,7 @@ class SDFEntrypoint(BackendEntrypoint):
         *,
         drop_variables=None,
         keep_particles=False,
+        probe_names=None,
     ):
         if isinstance(filename_or_obj, Path):
             # sdf library takes a filename only
@@ -424,6 +491,7 @@ class SDFEntrypoint(BackendEntrypoint):
             filename_or_obj,
             drop_variables=drop_variables,
             keep_particles=keep_particles,
+            probe_names=probe_names,
         )
         with close_on_error(store):
             return store.load()
@@ -432,6 +500,7 @@ class SDFEntrypoint(BackendEntrypoint):
         "filename_or_obj",
         "drop_variables",
         "keep_particles",
+        "probe_names",
     ]
 
     def guess_can_open(self, filename_or_obj):

sdf_xarray/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '0.2.5'
-__version_tuple__ = version_tuple = (0, 2, 5)
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)
+
+__commit_id__ = commit_id = 'gcca942b3f'

sdf_xarray/plotting.py

@@ -114,8 +114,8 @@ def animate(
     --------
     >>> dataset["Derived_Number_Density_Electron"].epoch.animate()
     """
-    import matplotlib.pyplot as plt
-    from matplotlib.animation import FuncAnimation
+    import matplotlib.pyplot as plt  # noqa: PLC0415
+    from matplotlib.animation import FuncAnimation  # noqa: PLC0415
 
     kwargs_original = kwargs.copy()
 

{sdf_xarray-0.2.5.dist-info → sdf_xarray-0.3.0.dist-info}/METADATA

@@ -1,47 +1,20 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: sdf-xarray
-Version: 0.2.5
+Version: 0.3.0
 Summary: Provides a backend for xarray to read SDF files as created by the EPOCH plasma PIC code.
 Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>
-License: Copyright 2024, Peter Hill, Joel Adams, epochpic team
-         
-         Redistribution and use in source and binary forms, with or without
-         modification, are permitted provided that the following conditions are
-         met:
-         
-         1. Redistributions of source code must retain the above copyright
-         notice, this list of conditions and the following disclaimer.
-         
-         2. Redistributions in binary form must reproduce the above copyright
-         notice, this list of conditions and the following disclaimer in the
-         documentation and/or other materials provided with the distribution.
-         
-         3. Neither the name of the copyright holder nor the names of its
-         contributors may be used to endorse or promote products derived from
-         this software without specific prior written permission.
-         
-         THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-         “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-         LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-         A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-         HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-         SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-         LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-         DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-         THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-         (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-         
+License-Expression: BSD-3-Clause
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.10
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: xarray>=2024.1.0
 Requires-Dist: dask>=2024.7.1
@@ -88,6 +61,9 @@ sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files
 [EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.
 Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
 
+> [!IMPORTANT]
+> To install this package make sure you are using one of the Python versions listed above.
+
 ## Installation
 
 Install from PyPI with:

{sdf_xarray-0.2.5.dist-info → sdf_xarray-0.3.0.dist-info}/RECORD

@@ -6,19 +6,19 @@ include/SDFC_14.4.7/sdf_list_type.h,sha256=Quu8v0-SEsQuJpGtEZnm09tAyXqWNitx0sXl5
 include/SDFC_14.4.7/sdf_vector_type.h,sha256=dbKjhzRRsvhzrnTwVjtVlvnuisEnRMKY-vvdm94ok_Q,1595
 include/SDFC_14.4.7/stack_allocator.h,sha256=L7U9vmGiVSw3VQLIv9EzTaVq7JbFxs9aNonKStTkUSg,1335
 include/SDFC_14.4.7/uthash.h,sha256=rIyy_-ylY6S_7WaZCCC3VtvXaC9q37rFyA0f1U9xc4w,63030
-lib/SDFC_14.4.7/sdfc.lib,sha256=D-ZfTK-UI85tD9nBu2i4Bb8mfo48Lc8TDDF6hDBJK4k,350410
+lib/SDFC_14.4.7/sdfc.lib,sha256=a6io2pN2IuTiSejxXjJkOEqPsluzQiksXQkZLnRdeCU,350158
 lib/SDFC_14.4.7/SDFCConfig.cmake,sha256=IOA1eusC-KvUK4LNTEiOAmEdaPH1ZvNvbYPgiG1oZio,802
 lib/SDFC_14.4.7/SDFCConfigVersion.cmake,sha256=pN7Qqyf04s3izw7PYQ0XK6imvmhaVegSdR_nEl3Ok_o,2830
 lib/SDFC_14.4.7/SDFCTargets-release.cmake,sha256=G4zdx5PyjePigeD_a6rmZAxbk7L8Nf0klUnV78Lm2fI,828
 lib/SDFC_14.4.7/SDFCTargets.cmake,sha256=OVt1Gm8n7Ew4fiTmA9yHoef3vIIGwsXUZfqeG9p9Bys,4152
-sdf_xarray/__init__.py,sha256=MgATg9E6Jyo1fW3_li3lIEm-yxTHgJbNfZf5qeAvuyY,18073
-sdf_xarray/_version.py,sha256=XjF4m8_cMkXrbRU7Rim3aBSkgXL9DCvwDPeFFTVyWd8,532
+sdf_xarray/__init__.py,sha256=RGtaYtX9Iqc7TMB305py2qW2HhILYkIidsDpjO6N8dI,20548
+sdf_xarray/_version.py,sha256=iQCqXuCEb7bAhie1qOwoyJuqOm0k4QDq4mp-_ILwsSk,746
 sdf_xarray/csdf.pxd,sha256=ADPjAuHsodAvdOz96Z_XlFF7VL3KmVaXcTifWDP3rK0,4205
-sdf_xarray/plotting.py,sha256=ze1paC1Uw42WOWspdqkyNsUviDt-Z7AwQlPyO7JB90o,7007
-sdf_xarray/sdf_interface.cp313-win_amd64.pyd,sha256=UNph8MYHwpjg33jAijyaWZibVVOK4TakPln62O7Fnn0,357888
+sdf_xarray/plotting.py,sha256=PnbEspR4XkA5SHkpoFKA2G7BYj5J3mVgR1TEeGol6Vw,7041
+sdf_xarray/sdf_interface.cp313-win_amd64.pyd,sha256=aRouLMNZbxA8Byqg3Fp9Q-ENzODSbzRv0FyaXsbenrk,359936
 sdf_xarray/sdf_interface.pyx,sha256=PFC6upg14OZBqiGInLgBoxztIIKBk-HOh3WC9Ro4YUw,11975
-sdf_xarray-0.2.5.dist-info/METADATA,sha256=ybk80dZjGpoDSonOcmjyIO5HdCP4zUJRbqWjuxBn68c,9129
-sdf_xarray-0.2.5.dist-info/WHEEL,sha256=sy0UFHejwb8HKZF4TZKxRLz0uqFoYZA7Xu3tB1pL5yA,106
-sdf_xarray-0.2.5.dist-info/entry_points.txt,sha256=gP7BIQpXNg6vIf7S7p-Rw_EJZTC1X50BsVTkK7dA7g0,57
-sdf_xarray-0.2.5.dist-info/licenses/LICENCE,sha256=aHWuyELjtzIL1jTXFHTbI3tr9vyVyhnw3I9_QYPdEX8,1515
-sdf_xarray-0.2.5.dist-info/RECORD,,
+sdf_xarray-0.3.0.dist-info/METADATA,sha256=q9WJBhz2Su52p14Q6b1ZBJRjCeepN7yfao9PdVnVbtU,7582
+sdf_xarray-0.3.0.dist-info/WHEEL,sha256=vkL3wTIkhjZa3RmEXX20hldNp6Q8qtwRjrXW6K5sw_Q,106
+sdf_xarray-0.3.0.dist-info/entry_points.txt,sha256=gP7BIQpXNg6vIf7S7p-Rw_EJZTC1X50BsVTkK7dA7g0,57
+sdf_xarray-0.3.0.dist-info/licenses/LICENCE,sha256=aHWuyELjtzIL1jTXFHTbI3tr9vyVyhnw3I9_QYPdEX8,1515
+sdf_xarray-0.3.0.dist-info/RECORD,,

{sdf_xarray-0.2.5.dist-info → sdf_xarray-0.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.2
+Generator: scikit-build-core 0.11.6
 Root-Is-Purelib: false
 Tag: cp313-cp313-win_amd64