pygama 2.3.8.dev2__tar.gz → 2.3.9__tar.gz

{pygama-2.3.8.dev2/src/pygama.egg-info → pygama-2.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pygama
-Version: 2.3.8.dev2
+Version: 2.3.9
 Summary: Python package for data processing and analysis
 Author: The LEGEND collaboration
 Maintainer: The LEGEND collaboration
@@ -28,7 +28,8 @@ Requires-Dist: dbetto
 Requires-Dist: dspeed>=2.0
 Requires-Dist: h5py>=3.2
 Requires-Dist: iminuit
-Requires-Dist: legend-pydataobj>=1.16
+Requires-Dist: legend-pydataobj>=2
+Requires-Dist: legend-lh5io>=0.2.3
 Requires-Dist: pylegendmeta>=0.9
 Requires-Dist: matplotlib
 Requires-Dist: numba!=0.53.*,!=0.54.*,!=0.57

{pygama-2.3.8.dev2 → pygama-2.3.9}/pyproject.toml

@@ -36,7 +36,8 @@ dependencies = [
     "dspeed >=2.0",
     "h5py >=3.2",
     "iminuit",
-    "legend-pydataobj >=1.16",
+    "legend-pydataobj >=2",
+    "legend-lh5io >=0.2.3",
     "pylegendmeta >=0.9",
     "matplotlib",
     "numba !=0.53.*,!=0.54.*,!=0.57",
@@ -121,6 +122,7 @@ ignore-words-list = "hist, gaus, nd, ans, crate, nin, puls, spms, fom, FOM"
 minversion = "6.0"
 addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
 xfail_strict = true
+filterwarnings = "error"
 log_cli_level = "INFO"
 testpaths = "tests"
 

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.3.8.dev2'
-__version_tuple__ = version_tuple = (2, 3, 8, 'dev2')
+__version__ = version = '2.3.9'
+__version_tuple__ = version_tuple = (2, 3, 9)
 
-__commit_id__ = commit_id = 'g13d41716a'
+__commit_id__ = commit_id = 'g3a8a13814'

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/aggregators.py

@@ -5,9 +5,10 @@ This module provides aggregators to build the `evt` tier.
 from __future__ import annotations
 
 import awkward as ak
+import lh5
 import numpy as np
 import pandas as pd
-from lgdo import lh5, types
+from lgdo import types
 
 from . import utils
 

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/build_evt.py

@@ -13,8 +13,9 @@ from pathlib import Path
 from typing import Any
 
 import awkward as ak
+import lh5
 import numpy as np
-from lgdo import Array, ArrayOfEqualSizedArrays, Table, VectorOfVectors, lh5
+from lgdo import Array, ArrayOfEqualSizedArrays, Table, VectorOfVectors
 
 from ..utils import load_dict
 from . import aggregators, utils
@@ -130,7 +131,7 @@ def build_evt(
             }
 
     wo_mode
-        writing mode, see :func:`lgdo.lh5.core.write`.
+        writing mode, see :func:`lh5.io.core.write`.
     """
     if not isinstance(config, dict):
         config = load_dict(config)
@@ -252,7 +253,7 @@ def build_evt_cols(
     channels
         list of channels to be used in the event table.
     wo_mode
-        writing mode, see :func:`lgdo.lh5.core.write`.
+        writing mode, see :func:`lh5.io.core.write`.
     buffer_len
         number of rows to be processed at once.
     channel_mapping
@@ -308,6 +309,9 @@ def build_evt_cols(
                 if "lgdo_attrs" in v:
                     obj.attrs |= v["lgdo_attrs"]
 
+                if "description" in v:
+                    obj.attrs["description"] = v["description"]
+
             # else we build the event entry
             else:
                 if "channels" not in v:
@@ -357,6 +361,9 @@ def build_evt_cols(
                 if "lgdo_attrs" in v:
                     obj.attrs |= v["lgdo_attrs"]
 
+                if "description" in v:
+                    obj.attrs["description"] = v["description"]
+
             # cast to type, if required
             # hijack the poor LGDO
             if "dtype" in v:

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/build_tcm.py

@@ -6,7 +6,7 @@ from pathlib import Path
 
 import awkward as ak
 import lgdo
-from lgdo import lh5
+import lh5
 from lgdo.types import Struct, Table, VectorOfVectors
 
 from . import tcm as ptcm
@@ -85,7 +85,7 @@ def build_tcm(
     out_name
         name for the TCM table in the output file.
     wo_mode
-        mode to send to :meth:`~.lgdo.lh5.LH5Store.write`.
+        mode to send to :meth:`~lh5.io.store.LH5Store.write`.
 
     out_fields
         Optional additional fields to propagate from the input tables into the

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/modules/geds.py

@@ -5,8 +5,9 @@ from __future__ import annotations
 from collections.abc import Sequence
 
 import awkward as ak
+import lh5
 import numpy as np
-from lgdo import lh5, types
+from lgdo import types
 
 from .. import utils
 from . import xtalk

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/modules/spms.py

@@ -6,8 +6,9 @@ import logging
 from collections.abc import Sequence
 
 import awkward as ak
+import lh5
 import numpy as np
-from lgdo import lh5, types
+from lgdo import types
 
 from .. import utils
 from . import larveto

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/modules/xtalk.py

@@ -5,9 +5,10 @@ Module for cross talk correction of energies.
 from __future__ import annotations
 
 import awkward as ak
+import lh5
 import numpy as np
 from dbetto import Props
-from lgdo import lh5, types
+from lgdo import types
 from numpy.typing import ArrayLike
 
 from pygama.hit.build_hit import _remove_uneeded_operations, _reorder_table_operations
@@ -102,7 +103,7 @@ def gather_energy(
                 # read the energy data
                 data = lh5.read(f"ch{channel}/{group}/{column}", file, idx=tbl_idxs_ch)
                 tbl.add_column(name, data)
-            except (lh5.exceptions.LH5DecodeError, KeyError):
+            except (lh5.io.exceptions.LH5DecodeError, KeyError):
                 tbl.add_column(name, types.Array(np.full_like(evt_ids_ch, np.nan)))
 
         res = tbl.eval(observable)
@@ -169,7 +170,7 @@ def filter_hits(
                 data = lh5.read(f"ch{channel}/{group}/{column}", file, idx=tbl_idxs_ch)
 
                 tbl.add_column(name, data)
-            except (lh5.exceptions.LH5DecodeError, KeyError):
+            except (lh5.io.exceptions.LH5DecodeError, KeyError):
                 tbl.add_column(name, types.Array(np.full_like(evt_ids_ch, np.nan)))
 
         # add the corrected energy to the table

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/evt/utils.py

@@ -9,8 +9,8 @@ import re
 from collections import namedtuple
 
 import awkward as ak
+import lh5
 import numpy as np
-from lgdo import lh5
 from numpy.typing import NDArray
 
 H5DataLoc = namedtuple(

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/flow/data_loader.py

@@ -11,13 +11,13 @@ from itertools import product
 from keyword import iskeyword
 from typing import Iterator
 
-import lgdo.lh5 as lh5
+import lh5
 import numpy as np
 import pandas as pd
 from awkward_pandas import AwkwardDtype
 from dspeed.vis import WaveformBrowser
-from lgdo.lh5 import LH5Iterator
-from lgdo.lh5.utils import expand_vars
+from lh5 import LH5Iterator
+from lh5.io.utils import expand_vars
 from lgdo.types import Array, Struct, Table
 from lgdo.types.vovutils import build_cl, explode_arrays
 from tqdm.auto import tqdm
@@ -1420,6 +1420,7 @@ class DataLoader:
                             field_mask=field_mask,
                             buffer_len=buffer_len,
                             friend=lh5_it,
+                            safe_mode=False,
                         )
 
             return lh5_it
@@ -1516,6 +1517,7 @@ class DataLoader:
                 buffer_len=buffer_len,
                 field_mask={"tracelist": False},
                 friend=lh5_it,
+                safe_mode=False,
             )
 
         return WaveformBrowser(lh5_it, buffer_len=buffer_len, **kwargs)

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/flow/file_db.py

@@ -10,11 +10,11 @@ import string
 import warnings
 
 import h5py
-import lgdo.lh5 as lh5
+import lh5
 import numpy as np
 import pandas as pd
-from lgdo.lh5 import ls
-from lgdo.lh5.utils import expand_path, expand_vars
+from lh5 import ls
+from lh5.io.utils import expand_path, expand_vars
 from lgdo.types import Array, Scalar, VectorOfVectors
 from parse import parse
 
@@ -600,7 +600,7 @@ class FileDB:
         filename
             output LH5 file name.
         wo_mode
-            passed to :meth:`~.lgdo.lh5.write`.
+            passed to :func:`~lh5.io.core.write`.
         """
         log.debug(f"writing database to {filename}")
 

{pygama-2.3.8.dev2 → pygama-2.3.9}/src/pygama/hit/build_hit.py

@@ -10,9 +10,9 @@ from collections.abc import Iterable, Mapping
 from pathlib import Path
 
 import lgdo
+import lh5
 import numpy as np
-from lgdo import lh5
-from lgdo.lh5 import LH5Iterator, ls
+from lh5 import LH5Iterator, ls
 
 from .. import utils
 
@@ -76,7 +76,7 @@ def build_hit(
     n_max
         maximum number of rows to process
     wo_mode
-        forwarded to :meth:`lgdo.lh5.write`.
+        forwarded to :func:`lh5.io.core.write`.
 
     See Also
     --------
@@ -156,6 +156,9 @@ def build_hit(
                 if "lgdo_attrs" in info:
                     outcol.attrs |= info["lgdo_attrs"]
 
+                if "description" in info:
+                    outcol.attrs["description"] = info["description"]
+
                 log.debug("made new column %r=%r", outname, outcol)
                 outtbl_obj.add_column(outname, outcol)