legend-pydataobj 1.7.0__py3-none-any.whl → 1.7.1__py3-none-any.whl

{legend_pydataobj-1.7.0.dist-info → legend_pydataobj-1.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: legend_pydataobj
-Version: 1.7.0
+Version: 1.7.1
 Summary: LEGEND Python Data Objects
 Author: The LEGEND Collaboration
 Maintainer: The LEGEND Collaboration
@@ -707,7 +707,7 @@ Requires-Dist: numexpr
 Requires-Dist: numpy >=1.21
 Requires-Dist: pandas >=1.4.4
 Requires-Dist: parse
-Requires-Dist: pint
+Requires-Dist: pint !=0.24
 Requires-Dist: pint-pandas
 Provides-Extra: all
 Requires-Dist: legend-pydataobj[docs,test] ; extra == 'all'

{legend_pydataobj-1.7.0.dist-info → legend_pydataobj-1.7.1.dist-info}/RECORD

@@ -1,10 +1,10 @@
 lgdo/__init__.py,sha256=nv9kORuX2FCA6rQLbH959E0fuGMfZvHb0H5uyrLr2WI,3046
-lgdo/_version.py,sha256=2fEqxujmrV2dsREie2BmOYFLu66FowyHtZT2AoLuIzU,411
+lgdo/_version.py,sha256=kn-QYzzAhfbnfKK6EpE9gJz8TDZkEk52evaid1DHkG4,411
 lgdo/cli.py,sha256=vB1Oj6kZ5gWaY9HBPBRRRyiepp72hm3bFvQeUUWeMYg,8214
 lgdo/lgdo_utils.py,sha256=6a2YWEwpyEMXlAyTHZMO01aqxy6SxJzPZkGNWKNWuS0,2567
 lgdo/lh5_store.py,sha256=xHwzbKNueEtFwScxrgfvCo2_bWKS6j7ojrpeF9kQflc,8483
 lgdo/logging.py,sha256=82wIOj7l7xr3WYyeHdpSXbbjzHJsy-uRyKYUYx2vMfQ,1003
-lgdo/units.py,sha256=nbJ0JTNqlhHUXiBXT3k6qhRpSfMk5_9yW7EeC0dhMuQ,151
+lgdo/units.py,sha256=VQYME86_ev9S7Fq8RyCOQNqYr29MphTTYemmEouZafk,161
 lgdo/utils.py,sha256=9t_GYdB8aQhZ4Vz6ujmASzwCgTuP7ZdINtPTVPyIR6E,3661
 lgdo/compression/__init__.py,sha256=gqbdx4NnpCcW-C7kUXV-hVUZFiNlbCwIbs3uzFe4AFE,1127
 lgdo/compression/base.py,sha256=82cQJujfvoAOKBFx761dEcx_xM02TBCBBuBo6i78tuI,838
@@ -18,12 +18,12 @@ lgdo/lh5/datatype.py,sha256=VhPWeWv3FW8XM6ZOFOdTZOYK3_hRZ3i0fYsBOEOIF5U,1623
 lgdo/lh5/exceptions.py,sha256=QWStQD27Qrm4oYs5Z3UAIoq4y7X-f_Z6QWCBCH0DXwE,1006
 lgdo/lh5/iterator.py,sha256=eqH9a_ZjEhgqJUZbMj36jXK_1Xbx86450DVw7LHNB3Y,12369
 lgdo/lh5/store.py,sha256=sYX1harVGRyP0oq1LGq2qrFhorutkev9MOovwhzEWZ4,6670
-lgdo/lh5/tools.py,sha256=MqYvyag2Uo3RxO0jLphml6UfScLPI2a2MCz3kjkIwmU,9430
+lgdo/lh5/tools.py,sha256=nb4zaBbVbQZTEzawi_faMhRvaPQf9Iea2xbuN6MPSQg,9922
 lgdo/lh5/utils.py,sha256=7QYhKd8MqpeFevLyWuasv63WfzEPx7Fd9wA-l3JjnIQ,6984
 lgdo/lh5/_serializers/__init__.py,sha256=7zvTmBdp-pqS0ium6cKKjEvcqIND-kBC7319G5wMq5Y,1213
 lgdo/lh5/_serializers/read/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 lgdo/lh5/_serializers/read/array.py,sha256=DLguBkiVNXZuUk7LdalixA8uISx_SETVPXWk-26HYmk,933
-lgdo/lh5/_serializers/read/composite.py,sha256=M3RR4SEyFGtb4qsscJOtB-P4HhdMQw0_JDIWKkUOsKA,12066
+lgdo/lh5/_serializers/read/composite.py,sha256=xyi1raVlflgBwc855Bfj8m0zTLIme-LPXxQcMrKUhGA,12069
 lgdo/lh5/_serializers/read/encoded.py,sha256=LTdSqEH5tJOdqcSCrMLWutYiQ4FwBFIPF7FDZ-iallw,3744
 lgdo/lh5/_serializers/read/ndarray.py,sha256=4vdgHwj_yIon1KvSiOkDSHq7CJhYtFcjjSHijsvp1aU,3481
 lgdo/lh5/_serializers/read/scalar.py,sha256=YwvA6kyNUh6H0kh2L7bzfgLkA8Et2dQFjp2nFnRmeGI,755
@@ -33,22 +33,22 @@ lgdo/lh5/_serializers/write/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 lgdo/lh5/_serializers/write/array.py,sha256=Gosg8rOCH_2dRMj_oNSWyXuoYXDjy0OK--GCYWswR4U,2803
 lgdo/lh5/_serializers/write/composite.py,sha256=f3b4YeOoUr8y1wA7zsKEFT5mIwX8SD0MYQ40unMRyQc,8460
 lgdo/lh5/_serializers/write/scalar.py,sha256=gkcF2WVBR3aQYl0EynbVUocx4y3r8tvPfQYQJjkPvP4,643
-lgdo/lh5/_serializers/write/vector_of_vectors.py,sha256=mZuC7NIb-IkmJ9wgn37TTvFTLLAFR71iivrY4yiSJZM,2912
+lgdo/lh5/_serializers/write/vector_of_vectors.py,sha256=puGQX9XF5P_5DVbm_Cc6TvPrsDywgBLSYtkqFNltbB4,3493
 lgdo/types/__init__.py,sha256=_cHZEpsh7OGsA243WBK2a2UmCp3NSA0MjXYf95y728k,771
 lgdo/types/array.py,sha256=sUxh1CNCaefrnybt5qdjmmMpVQa_RqFxUv1tJ_pyBbc,6537
 lgdo/types/arrayofequalsizedarrays.py,sha256=DOGJiTmc1QCdm7vLbE6uIRXoMPtt8uuCfmwQawgWf5s,4949
 lgdo/types/encoded.py,sha256=JW4U5ow7KLMzhKnmhdnxbC3SZJAs4bOEDZWKG4KY1uU,15293
-lgdo/types/fixedsizearray.py,sha256=7Fj4QS9ubaeEf2tM3HwjSs6AuG8hKSYaT6Hy7Y_VHdQ,1525
+lgdo/types/fixedsizearray.py,sha256=7RjUwTz1bW0pcrdy27JlfrXPAuOU89Kj7pOuSUCojK8,1527
 lgdo/types/lgdo.py,sha256=UnJDi1emQYVgH_H29Vipfs4LelPopxG5pgZUu1eKOlw,2761
 lgdo/types/scalar.py,sha256=c5Es2vyDqyWTPV6mujzfIzMpC1jNWkEIcvYyWQUxH3Q,1933
 lgdo/types/struct.py,sha256=Q0OWLVd4B0ciLb8t6VsxU3MPbmGLZ7WfQNno1lSQS0Q,4918
 lgdo/types/table.py,sha256=PYxHXRmuNZkz1UK6MzUVWGhEsRFf6t-xXGFFrXUP0EY,17936
-lgdo/types/vectorofvectors.py,sha256=d_n0lK6rut3_DdPcmMro0ObJAIRhMQnYj0cqAEpckPc,24368
+lgdo/types/vectorofvectors.py,sha256=Q53K8wiHwRHpGw3ARqrLnOXu3kLHptTYMp0ay9KK1vs,24386
 lgdo/types/vovutils.py,sha256=7BWPP0BSj-92ifbCIUBcfqxG5-TS8uxujTyJJuDFI04,10302
 lgdo/types/waveformtable.py,sha256=f2tS4f1OEoYaTM5ldCX9zmw8iSISCT3t3wS1SrPdu_o,9901
-legend_pydataobj-1.7.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-legend_pydataobj-1.7.0.dist-info/METADATA,sha256=rcfERzQLFd45YcFRMTusx2x7i1LuU7faypmwka_83Ws,44353
-legend_pydataobj-1.7.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-legend_pydataobj-1.7.0.dist-info/entry_points.txt,sha256=Uu5MTlppBZxB4QGlLv-oX8FqACWjAZDNii__TBDJwLQ,72
-legend_pydataobj-1.7.0.dist-info/top_level.txt,sha256=KyR-EUloqiXcQ62IWnzBmtInDtvsHl4q2ZJAZgTcLXE,5
-legend_pydataobj-1.7.0.dist-info/RECORD,,
+legend_pydataobj-1.7.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+legend_pydataobj-1.7.1.dist-info/METADATA,sha256=ZHdaQ1DJm7BXQEsppDekmab5BZFFuBtjjCF3fQagPh0,44360
+legend_pydataobj-1.7.1.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+legend_pydataobj-1.7.1.dist-info/entry_points.txt,sha256=Uu5MTlppBZxB4QGlLv-oX8FqACWjAZDNii__TBDJwLQ,72
+legend_pydataobj-1.7.1.dist-info/top_level.txt,sha256=KyR-EUloqiXcQ62IWnzBmtInDtvsHl4q2ZJAZgTcLXE,5
+legend_pydataobj-1.7.1.dist-info/RECORD,,

{legend_pydataobj-1.7.0.dist-info → legend_pydataobj-1.7.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

lgdo/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.7.0'
-__version_tuple__ = version_tuple = (1, 7, 0)
+__version__ = version = '1.7.1'
+__version_tuple__ = version_tuple = (1, 7, 1)

lgdo/lh5/_serializers/read/composite.py

@@ -56,7 +56,7 @@ def _h5_read_lgdo(
         lh5_file = list(h5f)
         n_rows_read = 0
 
-        for i, h5f in enumerate(lh5_file):
+        for i, _h5f in enumerate(lh5_file):
             if isinstance(idx, list) and len(idx) > 0 and not np.isscalar(idx[0]):
                 # a list of lists: must be one per file
                 idx_i = idx[i]
@@ -65,7 +65,7 @@ def _h5_read_lgdo(
                 if not (isinstance(idx, tuple) and len(idx) == 1):
                     idx = (idx,)
                 # idx is a long continuous array
-                n_rows_i = read_n_rows(name, h5f)
+                n_rows_i = read_n_rows(name, _h5f)
                 # find the length of the subset of idx that contains indices
                 # that are less than n_rows_i
                 n_rows_to_read_i = bisect.bisect_left(idx[0], n_rows_i)
@@ -78,7 +78,7 @@ def _h5_read_lgdo(
 
             obj_buf, n_rows_read_i = _h5_read_lgdo(
                 name,
-                h5f,
+                _h5f,
                 start_row=start_row,
                 n_rows=n_rows_i,
                 idx=idx_i,

lgdo/lh5/_serializers/write/vector_of_vectors.py

@@ -2,6 +2,8 @@ from __future__ import annotations
 
 import logging
 
+import numpy as np
+
 from .... import types
 from ... import utils
 from ...exceptions import LH5EncodeError
@@ -31,12 +33,15 @@ def _h5_write_vector_of_vectors(
 
     # if appending we need to add an appropriate offset to the
     # cumulative lengths as appropriate for the in-file object
-    offset = 0  # declare here because we have to subtract it off at the end
+    # declare here because we have to subtract it off at the end
+    offset = np.int64(0)
     if (wo_mode in ("a", "o")) and "cumulative_length" in group:
         len_cl = len(group["cumulative_length"])
+        # if append, ignore write_start and set it to total number of vectors
         if wo_mode == "a":
             write_start = len_cl
         if len_cl > 0:
+            # set offset to correct number of elements in flattened_data until write_start
             offset = group["cumulative_length"][write_start - 1]
 
     # First write flattened_data array. Only write rows with data.
@@ -71,15 +76,23 @@ def _h5_write_vector_of_vectors(
     )
 
     # now offset is used to give appropriate in-file values for
-    # cumulative_length. Need to adjust it for start_row
+    # cumulative_length. Need to adjust it for start_row, if different from zero
     if start_row > 0:
         offset -= obj.cumulative_length.nda[start_row - 1]
 
     # Add offset to obj.cumulative_length itself to avoid memory allocation.
     # Then subtract it off after writing! (otherwise it will be changed
     # upon return)
-    cl_dtype = obj.cumulative_length.nda.dtype.type
-    obj.cumulative_length.nda += cl_dtype(offset)
+
+    # NOTE: this operation is not numerically safe (uint overflow in the lower
+    # part of the array), but this is not a problem because those values are
+    # not written to disk and we are going to restore the offset at the end
+    np.add(
+        obj.cumulative_length.nda,
+        offset,
+        out=obj.cumulative_length.nda,
+        casting="unsafe",
+    )
 
     _h5_write_array(
         obj.cumulative_length,
@@ -92,4 +105,10 @@ def _h5_write_vector_of_vectors(
         write_start=write_start,
         **h5py_kwargs,
     )
-    obj.cumulative_length.nda -= cl_dtype(offset)
+
+    np.subtract(
+        obj.cumulative_length.nda,
+        offset,
+        out=obj.cumulative_length.nda,
+        casting="unsafe",
+    )

lgdo/lh5/tools.py

@@ -188,7 +188,20 @@ def show(
                 else:
                     toprint += f", \033[3mnumchunks\033[0m={val.id.get_num_chunks()}"
                     toprint += f", \033[3mchunkshape\033[0m={chunkshape}"
-                toprint += f", \033[3mcompression\033[0m={val.compression}"
+                toprint += ", \033[3mfilters\033[0m="
+
+                numfilters = val.id.get_create_plist().get_nfilters()
+                if numfilters == 0:
+                    toprint += "None"
+                else:
+                    toprint += "("
+                    for i in range(numfilters):
+                        thisfilter = val.id.get_create_plist().get_filter(i)[3].decode()
+                        if "lz4" in thisfilter:
+                            thisfilter = "lz4"
+                        toprint += f"{thisfilter},"
+                    toprint += ")"
+
             except TypeError:
                 toprint += "(scalar)"
 
@@ -268,7 +281,7 @@ def load_nda(
         f = sto.gimme_file(ff, "r")
         for par in par_list:
             if f"{lh5_group}/{par}" not in f:
-                msg = f"'{lh5_group}/{par}' not in file {f_list[ii]}"
+                msg = f"'{lh5_group}/{par}' not in file {ff}"
                 raise RuntimeError(msg)
 
             if idx_list is None:

lgdo/types/fixedsizearray.py

@@ -50,4 +50,4 @@ class FixedSizeArray(Array):
         --------
         .LGDO.view_as
         """
-        return super.view_as(library, with_units=with_units)
+        return super().view_as(library, with_units=with_units)

lgdo/types/vectorofvectors.py

@@ -480,7 +480,7 @@ class VectorOfVectors(LGDO):
                 lens = np.array([lens], dtype="u4")
 
             # calculate stop index in flattened_data
-            cum_lens = start + lens.cumsum()
+            cum_lens = np.add(start, lens.cumsum(), dtype=int)
 
             # fill with fast vectorized routine
             vovutils._nb_fill(vec, lens, self.flattened_data.nda[start : cum_lens[-1]])

lgdo/units.py

@@ -3,4 +3,4 @@ from __future__ import annotations
 import pint
 
 default_units_registry = pint.get_application_registry()
-default_units_registry.default_format = "~P"
+default_units_registry.formatter.default_format = "~P"