legend-pydataobj 1.0.0__tar.gz → 1.1.1__tar.gz

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: legend_pydataobj
-Version: 1.0.0
+Version: 1.1.1
 Summary: LEGEND Python Data Objects
 Home-page: https://github.com/legend-exp/legend-pydataobj
 Author: The LEGEND Collaboration

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/setup.cfg

@@ -31,7 +31,8 @@ classifiers =
 [options]
 packages = find:
 install_requires = 
-	h5py>=3.2.0
+	colorlog
+	h5py>=3.2
 	hdf5plugin
 	numba!=0.53.*,!=0.54.*
 	numexpr
@@ -48,6 +49,10 @@ zip_safe = False
 [options.packages.find]
 where = src
 
+[options.entry_points]
+console_scripts = 
+	lh5ls = lgdo.cli:lh5ls
+
 [options.extras_require]
 all = 
 	legend-pydataobj[docs,test]

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/legend_pydataobj.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: legend-pydataobj
-Version: 1.0.0
+Version: 1.1.1
 Summary: LEGEND Python Data Objects
 Home-page: https://github.com/legend-exp/legend-pydataobj
 Author: The LEGEND Collaboration

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/legend_pydataobj.egg-info/SOURCES.txt

@@ -6,13 +6,16 @@ setup.py
 src/legend_pydataobj.egg-info/PKG-INFO
 src/legend_pydataobj.egg-info/SOURCES.txt
 src/legend_pydataobj.egg-info/dependency_links.txt
+src/legend_pydataobj.egg-info/entry_points.txt
 src/legend_pydataobj.egg-info/not-zip-safe
 src/legend_pydataobj.egg-info/requires.txt
 src/legend_pydataobj.egg-info/top_level.txt
 src/lgdo/__init__.py
 src/lgdo/_version.py
+src/lgdo/cli.py
 src/lgdo/lgdo_utils.py
 src/lgdo/lh5_store.py
+src/lgdo/logging.py
 src/lgdo/compression/__init__.py
 src/lgdo/compression/base.py
 src/lgdo/compression/generic.py

legend_pydataobj-1.1.1/src/legend_pydataobj.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+lh5ls = lgdo.cli:lh5ls

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/legend_pydataobj.egg-info/requires.txt

@@ -1,4 +1,5 @@
-h5py>=3.2.0
+colorlog
+h5py>=3.2
 hdf5plugin
 numba!=0.53.*,!=0.54.*
 numexpr

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/lgdo/__init__.py

@@ -38,6 +38,7 @@ browsed easily in python like any `HDF5 <https://www.hdfgroup.org>`_ file using
 `h5py <https://www.h5py.org>`_.
 """
 
+from ._version import version as __version__
 from .lh5_store import LH5Iterator, LH5Store, load_dfs, load_nda, ls, show
 from .types import (
     LGDO,
@@ -71,5 +72,5 @@ __all__ = [
     "load_nda",
     "ls",
     "show",
-    "copy",
+    "__version__",
 ]

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/lgdo/_version.py

@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '1.0.0'
-__version_tuple__ = version_tuple = (1, 0, 0)
+__version__ = version = '1.1.1'
+__version_tuple__ = version_tuple = (1, 1, 1)

legend_pydataobj-1.1.1/src/lgdo/cli.py

@@ -0,0 +1,68 @@
+"""Command line interface utilities."""
+from __future__ import annotations
+
+import argparse
+import sys
+
+from . import __version__, logging, show
+
+
+def lh5ls():
+    """``lh5ls`` console command.
+
+    To learn more, have a look at the help section:
+
+    .. code-block:: console
+
+      $ lh5ls --help
+    """
+
+    parser = argparse.ArgumentParser(
+        prog="lh5ls", description="Inspect LEGEND HDF5 (LH5) file contents"
+    )
+
+    # global options
+    parser.add_argument(
+        "--version", action="store_true", help="""Print the program version and exit"""
+    )
+    parser.add_argument(
+        "--verbose",
+        "-v",
+        action="store_true",
+        help="""Increase the program verbosity""",
+    )
+    parser.add_argument(
+        "--debug",
+        "-d",
+        action="store_true",
+        help="""Increase the program verbosity to maximum""",
+    )
+
+    # show options
+    parser.add_argument(
+        "lh5_file",
+        help="""Input LH5 file.""",
+    )
+    parser.add_argument("lh5_group", nargs="?", help="""LH5 group.""", default="/")
+    parser.add_argument(
+        "--attributes",
+        "-a",
+        action="store_true",
+        default=False,
+        help="""Print HDF5 attributes too""",
+    )
+
+    args = parser.parse_args()
+
+    if args.verbose:
+        logging.setup(logging.DEBUG)
+    elif args.debug:
+        logging.setup(logging.DEBUG, logging.root)
+    else:
+        logging.setup()
+
+    if args.version:
+        print(__version__)  # noqa: T201
+        sys.exit()
+
+    show(args.lh5_file, args.lh5_group, attrs=args.attributes)

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/src/lgdo/lh5_store.py

@@ -1287,9 +1287,11 @@ def show(
         if dtype == "no datatype" and isinstance(val, h5py.Group):
             dtype = "HDF5 group"
 
-        attrs_d = dict(val.attrs)
-        attrs_d.pop("datatype", "")
-        attrs = "── " + str(attrs_d) if attrs_d else ""
+        _attrs = ""
+        if attrs:
+            attrs_d = dict(val.attrs)
+            attrs_d.pop("datatype", "")
+            _attrs = "── " + str(attrs_d) if attrs_d else ""
 
         # is this the last key?
         killme = False
@@ -1301,11 +1303,16 @@ def show(
         else:
             char = "├──"
 
-        print(f"{indent}{char} \033[1m{key}\033[0m · {dtype} {attrs}")  # noqa: T201
+        print(f"{indent}{char} \033[1m{key}\033[0m · {dtype} {_attrs}")  # noqa: T201
 
         # if it's a group, call this function recursively
         if isinstance(val, h5py.Group):
-            show(val, indent=indent + ("    " if killme else "│   "), header=False)
+            show(
+                val,
+                indent=indent + ("    " if killme else "│   "),
+                header=False,
+                attrs=attrs,
+            )
 
         # break or move to next key
         if killme:

legend_pydataobj-1.1.1/src/lgdo/logging.py

@@ -0,0 +1,40 @@
+"""This module implements some helpers for setting up logging."""
+import logging
+
+import colorlog
+
+DEBUG = logging.DEBUG
+INFO = logging.INFO
+WARNING = logging.WARNING
+ERROR = logging.ERROR
+FATAL = logging.FATAL
+CRITICAL = logging.CRITICAL
+
+
+def setup(level: int = logging.INFO, logger: logging.Logger = None) -> None:
+    """Setup a colorful logging output.
+
+    If `logger` is None, sets up only the ``pygama`` logger.
+
+    Parameters
+    ----------
+    level
+        logging level (see :mod:`logging` module).
+    logger
+        if not `None`, setup this logger.
+
+    Examples
+    --------
+    >>> from pygama import logging
+    >>> logging.setup(level=logging.DEBUG)
+    """
+    handler = colorlog.StreamHandler()
+    handler.setFormatter(
+        colorlog.ColoredFormatter("%(log_color)s%(name)s [%(levelname)s] %(message)s")
+    )
+
+    if logger is None:
+        logger = colorlog.getLogger("pygama")
+
+    logger.setLevel(level)
+    logger.addHandler(handler)

legend_pydataobj-1.1.1/tests/conftest.py

@@ -0,0 +1,28 @@
+import os
+import shutil
+import uuid
+from getpass import getuser
+from tempfile import gettempdir
+
+import pytest
+from legendtestdata import LegendTestData
+
+_tmptestdir = os.path.join(gettempdir(), f"lgdo-tests-{getuser()}-{str(uuid.uuid4())}")
+
+
+@pytest.fixture(scope="session")
+def tmptestdir():
+    os.mkdir(_tmptestdir)
+    return _tmptestdir
+
+
+def pytest_sessionfinish(session, exitstatus):
+    if exitstatus == 0:
+        shutil.rmtree(_tmptestdir)
+
+
+@pytest.fixture(scope="session")
+def lgnd_test_data():
+    ldata = LegendTestData()
+    ldata.checkout("c089a59")
+    return ldata

{legend_pydataobj-1.0.0 → legend_pydataobj-1.1.1}/tests/test_lh5_store.py

@@ -33,13 +33,13 @@ def test_gimme_file(lgnd_file):
         store.gimme_file("non-existent-file")
 
 
-def test_gimme_group(lgnd_file):
+def test_gimme_group(lgnd_file, tmptestdir):
     f = h5py.File(lgnd_file)
     store = LH5Store()
     g = store.gimme_group("/geds", f)
     assert isinstance(g, h5py.Group)
 
-    f = h5py.File("/tmp/testfile.lh5", mode="w")
+    f = h5py.File(f"{tmptestdir}/testfile.lh5", mode="w")
     g = store.gimme_group("/geds", f, grp_attrs={"attr1": 1}, overwrite=True)
     assert isinstance(g, h5py.Group)
 
@@ -95,7 +95,7 @@ def test_load_dfs(lgnd_file):
 
 
 @pytest.fixture(scope="module")
-def lh5_file():
+def lh5_file(tmptestdir):
     store = LH5Store()
 
     struct = lgdo.Struct()
@@ -161,7 +161,7 @@ def lh5_file():
     store.write_object(
         struct,
         "struct",
-        "/tmp/tmp-pygama-lgdo-types.lh5",
+        f"{tmptestdir}/tmp-pygama-lgdo-types.lh5",
         group="/data",
         start_row=1,
         n_rows=3,
@@ -171,12 +171,12 @@ def lh5_file():
     store.write_object(
         struct,
         "struct_full",
-        "/tmp/tmp-pygama-lgdo-types.lh5",
+        f"{tmptestdir}/tmp-pygama-lgdo-types.lh5",
         group="/data",
         wo_mode="append",
     )
 
-    return "/tmp/tmp-pygama-lgdo-types.lh5"
+    return f"{tmptestdir}/tmp-pygama-lgdo-types.lh5"
 
 
 def test_write_objects(lh5_file):
@@ -477,17 +477,17 @@ def test_read_lgnd_waveform_table_fancy_idx(lgnd_file):
 
 
 @pytest.fixture(scope="module")
-def enc_lgnd_file(lgnd_file):
+def enc_lgnd_file(lgnd_file, tmptestdir):
     store = LH5Store()
     wft, n_rows = store.read_object("/geds/raw/waveform", lgnd_file)
     wft.values.attrs["compression"] = RadwareSigcompress(codec_shift=-32768)
     store.write_object(
         wft,
         "/geds/raw/waveform",
-        "/tmp/tmp-pygama-compressed-wfs.lh5",
+        f"{tmptestdir}/tmp-pygama-compressed-wfs.lh5",
         wo_mode="overwrite_file",
     )
-    return "/tmp/tmp-pygama-compressed-wfs.lh5"
+    return f"{tmptestdir}/tmp-pygama-compressed-wfs.lh5"
 
 
 def test_write_compressed_lgnd_waveform_table(enc_lgnd_file):
@@ -502,21 +502,24 @@ def test_read_compressed_lgnd_waveform_table(lgnd_file, enc_lgnd_file):
 
 
 # First test that we can overwrite a table with the same name without deleting the original field
-def test_write_object_overwrite_table_no_deletion(caplog):
+def test_write_object_overwrite_table_no_deletion(caplog, tmptestdir):
     caplog.set_level(logging.DEBUG)
     caplog.clear()
 
-    if os.path.exists("/tmp/write_object_overwrite_test.lh5"):
-        os.remove("/tmp/write_object_overwrite_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_overwrite_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_overwrite_test.lh5")
 
     tb1 = lh5.Table(col_dict={"dset1": lh5.Array(np.zeros(10))})
     tb2 = lh5.Table(
         col_dict={"dset1": lh5.Array(np.ones(10))}
     )  # Same field name, different values
     store = LH5Store()
-    store.write_object(tb1, "my_group", "/tmp/write_object_overwrite_test.lh5")
+    store.write_object(tb1, "my_group", f"{tmptestdir}/write_object_overwrite_test.lh5")
     store.write_object(
-        tb2, "my_group", "/tmp/write_object_overwrite_test.lh5", wo_mode="overwrite"
+        tb2,
+        "my_group",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
+        wo_mode="overwrite",
     )  # Now, try to overwrite the same field
 
     # If the old field is deleted from the file before writing the new field, then we would get an extra debug statement
@@ -525,39 +528,46 @@ def test_write_object_overwrite_table_no_deletion(caplog):
     ]
 
     # Now, check that the data were overwritten
-    tb_dat, _ = store.read_object("my_group", "/tmp/write_object_overwrite_test.lh5")
+    tb_dat, _ = store.read_object(
+        "my_group", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     assert np.array_equal(tb_dat["dset1"].nda, np.ones(10))
 
 
 # Second: test that when we overwrite a table with fields with a different name, we delete the original field
-def test_write_object_overwrite_table_with_deletion(caplog):
+def test_write_object_overwrite_table_with_deletion(caplog, tmptestdir):
     caplog.set_level(logging.DEBUG)
     caplog.clear()
 
-    if os.path.exists("/tmp/write_object_overwrite_test.lh5"):
-        os.remove("/tmp/write_object_overwrite_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_overwrite_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_overwrite_test.lh5")
 
     tb1 = lh5.Table(col_dict={"dset1": lh5.Array(np.zeros(10))})
     tb2 = lh5.Table(
         col_dict={"dset2": lh5.Array(np.ones(10))}
     )  # Same field name, different values
     store = LH5Store()
-    store.write_object(tb1, "my_group", "/tmp/write_object_overwrite_test.lh5")
+    store.write_object(tb1, "my_group", f"{tmptestdir}/write_object_overwrite_test.lh5")
     store.write_object(
-        tb2, "my_group", "/tmp/write_object_overwrite_test.lh5", wo_mode="overwrite"
+        tb2,
+        "my_group",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
+        wo_mode="overwrite",
     )  # Now, try to overwrite with a different field
 
     # Now, check that the data were overwritten
-    tb_dat, _ = store.read_object("my_group", "/tmp/write_object_overwrite_test.lh5")
+    tb_dat, _ = store.read_object(
+        "my_group", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     assert np.array_equal(tb_dat["dset2"].nda, np.ones(10))
 
     # Also make sure that the first table's fields aren't lurking around the lh5 file!
-    with h5py.File("/tmp/write_object_overwrite_test.lh5", "r") as lh5file:
+    with h5py.File(f"{tmptestdir}/write_object_overwrite_test.lh5", "r") as lh5file:
         assert "dset1" not in list(lh5file["my_group"].keys())
 
     # Make sure the same behavior happens when we nest the table in a group
-    if os.path.exists("/tmp/write_object_overwrite_test.lh5"):
-        os.remove("/tmp/write_object_overwrite_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_overwrite_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_overwrite_test.lh5")
 
     tb1 = lh5.Table(col_dict={"dset1": lh5.Array(np.zeros(10))})
     tb2 = lh5.Table(
@@ -565,35 +575,38 @@ def test_write_object_overwrite_table_with_deletion(caplog):
     )  # Same field name, different values
     store = LH5Store()
     store.write_object(
-        tb1, "my_table", "/tmp/write_object_overwrite_test.lh5", group="my_group"
+        tb1,
+        "my_table",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
+        group="my_group",
     )
     store.write_object(
         tb2,
         "my_table",
-        "/tmp/write_object_overwrite_test.lh5",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
         group="my_group",
         wo_mode="overwrite",
     )  # Now, try to overwrite with a different field
 
     # Now, check that the data were overwritten
     tb_dat, _ = store.read_object(
-        "my_group/my_table", "/tmp/write_object_overwrite_test.lh5"
+        "my_group/my_table", f"{tmptestdir}/write_object_overwrite_test.lh5"
     )
     assert np.array_equal(tb_dat["dset2"].nda, np.ones(10))
 
     # Also make sure that the first table's fields aren't lurking around the lh5 file!
-    with h5py.File("/tmp/write_object_overwrite_test.lh5", "r") as lh5file:
+    with h5py.File(f"{tmptestdir}/write_object_overwrite_test.lh5", "r") as lh5file:
         assert "dset1" not in list(lh5file["my_group/my_table"].keys())
 
 
 # Third: test that when we overwrite other LGDO classes
-def test_write_object_overwrite_lgdo(caplog):
+def test_write_object_overwrite_lgdo(caplog, tmptestdir):
     caplog.set_level(logging.DEBUG)
     caplog.clear()
 
     # Start with an lgdo.WaveformTable
-    if os.path.exists("/tmp/write_object_overwrite_test.lh5"):
-        os.remove("/tmp/write_object_overwrite_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_overwrite_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_overwrite_test.lh5")
 
     tb1 = lh5.WaveformTable(
         t0=np.zeros(10),
@@ -613,12 +626,15 @@ def test_write_object_overwrite_lgdo(caplog):
     )  # Same field name, different values
     store = LH5Store()
     store.write_object(
-        tb1, "my_table", "/tmp/write_object_overwrite_test.lh5", group="my_group"
+        tb1,
+        "my_table",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
+        group="my_group",
     )
     store.write_object(
         tb2,
         "my_table",
-        "/tmp/write_object_overwrite_test.lh5",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
         wo_mode="overwrite",
         group="my_group",
     )
@@ -630,7 +646,7 @@ def test_write_object_overwrite_lgdo(caplog):
 
     # Now, check that the data were overwritten
     tb_dat, _ = store.read_object(
-        "my_group/my_table", "/tmp/write_object_overwrite_test.lh5"
+        "my_group/my_table", f"{tmptestdir}/write_object_overwrite_test.lh5"
     )
     assert np.array_equal(tb_dat["values"].nda, np.ones((10, 10)))
 
@@ -638,17 +654,21 @@ def test_write_object_overwrite_lgdo(caplog):
     array1 = lh5.Array(nda=np.zeros(10))
     array2 = lh5.Array(nda=np.ones(20))
     store = LH5Store()
-    store.write_object(array1, "my_array", "/tmp/write_object_overwrite_test.lh5")
+    store.write_object(
+        array1, "my_array", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     store.write_object(
         array2,
         "my_array",
-        "/tmp/write_object_overwrite_test.lh5",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
         wo_mode="overwrite",
         write_start=5,
     )
 
     # Now, check that the data were overwritten
-    array_dat, _ = store.read_object("my_array", "/tmp/write_object_overwrite_test.lh5")
+    array_dat, _ = store.read_object(
+        "my_array", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     expected_out_array = np.append(np.zeros(5), np.ones(20))
 
     assert np.array_equal(array_dat.nda, expected_out_array)
@@ -657,17 +677,19 @@ def test_write_object_overwrite_lgdo(caplog):
     scalar1 = lh5.Scalar(0)
     scalar2 = lh5.Scalar(1)
     store = LH5Store()
-    store.write_object(scalar1, "my_scalar", "/tmp/write_object_overwrite_test.lh5")
+    store.write_object(
+        scalar1, "my_scalar", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     store.write_object(
         scalar2,
         "my_scalar",
-        "/tmp/write_object_overwrite_test.lh5",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
         wo_mode="overwrite",
     )
 
     # Now, check that the data were overwritten
     scalar_dat, _ = store.read_object(
-        "my_scalar", "/tmp/write_object_overwrite_test.lh5"
+        "my_scalar", f"{tmptestdir}/write_object_overwrite_test.lh5"
     )
 
     assert scalar_dat.value == 1
@@ -676,17 +698,19 @@ def test_write_object_overwrite_lgdo(caplog):
     vov1 = lh5.VectorOfVectors(listoflists=[np.zeros(1), np.ones(2), np.zeros(3)])
     vov2 = lh5.VectorOfVectors(listoflists=[np.ones(1), np.zeros(2), np.ones(3)])
     store = LH5Store()
-    store.write_object(vov1, "my_vector", "/tmp/write_object_overwrite_test.lh5")
+    store.write_object(
+        vov1, "my_vector", f"{tmptestdir}/write_object_overwrite_test.lh5"
+    )
     store.write_object(
         vov2,
         "my_vector",
-        "/tmp/write_object_overwrite_test.lh5",
+        f"{tmptestdir}/write_object_overwrite_test.lh5",
         wo_mode="overwrite",
         write_start=1,
     )  # start overwriting the second list of lists
 
     vector_dat, _ = store.read_object(
-        "my_vector", "/tmp/write_object_overwrite_test.lh5"
+        "my_vector", f"{tmptestdir}/write_object_overwrite_test.lh5"
     )
 
     assert np.array_equal(vector_dat.cumulative_length.nda, [1, 2, 4, 7])
@@ -694,20 +718,22 @@ def test_write_object_overwrite_lgdo(caplog):
 
 
 # Test that when we try to overwrite an existing column in a table we fail
-def test_write_object_append_column():
+def test_write_object_append_column(tmptestdir):
     # Try to append an array to a table
-    if os.path.exists("/tmp/write_object_append_column_test.lh5"):
-        os.remove("/tmp/write_object_append_column_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_append_column_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_append_column_test.lh5")
 
     array1 = lh5.Array(np.zeros(10))
     tb1 = lh5.Table(col_dict={"dset1`": lh5.Array(np.ones(10))})
     store = LH5Store()
-    store.write_object(array1, "my_table", "/tmp/write_object_append_column_test.lh5")
+    store.write_object(
+        array1, "my_table", f"{tmptestdir}/write_object_append_column_test.lh5"
+    )
     with pytest.raises(RuntimeError) as exc_info:
         store.write_object(
             tb1,
             "my_table",
-            "/tmp/write_object_append_column_test.lh5",
+            f"{tmptestdir}/write_object_append_column_test.lh5",
             wo_mode="append_column",
         )  # Now, try to append a column to an array
 
@@ -717,8 +743,8 @@ def test_write_object_append_column():
     )
 
     # Try to append a table that has a same key as the old table
-    if os.path.exists("/tmp/write_object_append_column_test.lh5"):
-        os.remove("/tmp/write_object_append_column_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_append_column_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_append_column_test.lh5")
 
     tb1 = lh5.Table(
         col_dict={"dset1": lh5.Array(np.zeros(10)), "dset2": lh5.Array(np.zeros(10))}
@@ -727,12 +753,14 @@ def test_write_object_append_column():
         col_dict={"dset2": lh5.Array(np.ones(10))}
     )  # Same field name, different values
     store = LH5Store()
-    store.write_object(tb1, "my_table", "/tmp/write_object_append_column_test.lh5")
+    store.write_object(
+        tb1, "my_table", f"{tmptestdir}/write_object_append_column_test.lh5"
+    )
     with pytest.raises(ValueError) as exc_info:
         store.write_object(
             tb2,
             "my_table",
-            "/tmp/write_object_append_column_test.lh5",
+            f"{tmptestdir}/write_object_append_column_test.lh5",
             wo_mode="append_column",
         )  # Now, try to append a column with a same field
 
@@ -743,20 +771,22 @@ def test_write_object_append_column():
     )
 
     # try appending a column that is larger than one that exists
-    if os.path.exists("/tmp/write_object_append_column_test.lh5"):
-        os.remove("/tmp/write_object_append_column_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_append_column_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_append_column_test.lh5")
 
     tb1 = lh5.Table(col_dict={"dset1": lh5.Array(np.zeros(10))})
     tb2 = lh5.Table(
         col_dict={"dset2": lh5.Array(np.ones(20))}
     )  # different field name, different size
     store = LH5Store()
-    store.write_object(tb1, "my_table", "/tmp/write_object_append_column_test.lh5")
+    store.write_object(
+        tb1, "my_table", f"{tmptestdir}/write_object_append_column_test.lh5"
+    )
     with pytest.raises(ValueError) as exc_info:
         store.write_object(
             tb2,
             "my_table",
-            "/tmp/write_object_append_column_test.lh5",
+            f"{tmptestdir}/write_object_append_column_test.lh5",
             wo_mode="append_column",
         )  # Now, try to append a column with a different field size
 
@@ -767,8 +797,8 @@ def test_write_object_append_column():
     )
 
     # Finally successfully append a column
-    if os.path.exists("/tmp/write_object_append_column_test.lh5"):
-        os.remove("/tmp/write_object_append_column_test.lh5")
+    if os.path.exists(f"{tmptestdir}/write_object_append_column_test.lh5"):
+        os.remove(f"{tmptestdir}/write_object_append_column_test.lh5")
 
     tb1 = lh5.Table(col_dict={"dset1": lh5.Array(np.zeros(10))})
     tb2 = lh5.Table(
@@ -776,19 +806,22 @@ def test_write_object_append_column():
     )  # different field name, different size
     store = LH5Store()
     store.write_object(
-        tb1, "my_table", "/tmp/write_object_append_column_test.lh5", group="my_group"
+        tb1,
+        "my_table",
+        f"{tmptestdir}/write_object_append_column_test.lh5",
+        group="my_group",
     )
     store.write_object(
         tb2,
         "my_table",
-        "/tmp/write_object_append_column_test.lh5",
+        f"{tmptestdir}/write_object_append_column_test.lh5",
         group="my_group",
         wo_mode="append_column",
     )
 
     # Now, check that the data were appended
     tb_dat, _ = store.read_object(
-        "my_group/my_table", "/tmp/write_object_append_column_test.lh5"
+        "my_group/my_table", f"{tmptestdir}/write_object_append_column_test.lh5"
     )
     assert isinstance(tb_dat, lgdo.Table)
     assert np.array_equal(tb_dat["dset1"].nda, np.zeros(10))

legend_pydataobj-1.0.0/tests/conftest.py

@@ -1,54 +0,0 @@
-import os
-import shutil
-import uuid
-from getpass import getuser
-from tempfile import gettempdir
-
-import pytest
-from legendtestdata import LegendTestData
-
-_tmptestdir = os.path.join(
-    gettempdir(), "pygama-tests-" + getuser() + str(uuid.uuid4())
-)
-
-
-@pytest.fixture(scope="session")
-def tmptestdir():
-    os.mkdir(_tmptestdir)
-    yield _tmptestdir
-    shutil.rmtree(_tmptestdir)
-
-
-def pytest_sessionfinish(session, exitstatus):
-    if exitstatus is True:
-        os.rmdir(_tmptestdir)
-
-
-@pytest.fixture(scope="session")
-def lgnd_test_data():
-    ldata = LegendTestData()
-    ldata.checkout("c089a59")
-    return ldata
-
-
-# @pytest.fixture(scope="session")
-# def multich_raw_file(lgnd_test_data):
-#     out_file = "/tmp/L200-comm-20211130-phy-spms.lh5"
-#     out_spec = {
-#         "FCEventDecoder": {
-#             "ch{key}": {
-#                 "key_list": [[0, 6]],
-#                 "out_stream": out_file + ":{name}",
-#                 "out_name": "raw",
-#             }
-#         }
-#     }
-
-#     build_raw(
-#         in_stream=lgnd_test_data.get_path("fcio/L200-comm-20211130-phy-spms.fcio"),
-#         out_spec=out_spec,
-#         overwrite=True,
-#     )
-#     assert os.path.exists(out_file)
-
-#     return out_file