legend-pydataobj 1.14.1__tar.gz → 1.14.3__tar.gz

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: legend_pydataobj
-Version: 1.14.1
+Version: 1.14.3
 Summary: LEGEND Python Data Objects
 Author: The LEGEND Collaboration
 Maintainer: The LEGEND Collaboration

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/legend_pydataobj.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: legend_pydataobj
-Version: 1.14.1
+Version: 1.14.3
 Summary: LEGEND Python Data Objects
 Author: The LEGEND Collaboration
 Maintainer: The LEGEND Collaboration

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.14.1'
-__version_tuple__ = version_tuple = (1, 14, 1)
+__version__ = version = '1.14.3'
+__version_tuple__ = version_tuple = (1, 14, 3)

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/lh5/_serializers/write/composite.py

@@ -59,7 +59,7 @@ def _h5_write_lgdo(
         try:
             fh = h5py.File(lh5_file, mode=mode, **file_kwargs)
         except OSError as oe:
-            raise LH5EncodeError(str(oe), lh5_file, None) from oe
+            raise LH5EncodeError(oe, lh5_file) from oe
 
         opened_here = True
     else:

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/lh5/core.py

@@ -118,7 +118,7 @@ def read(
         try:
             lh5_file = h5py.File(str(Path(lh5_file)), mode="r", locking=locking)
         except (OSError, FileExistsError) as oe:
-            raise LH5DecodeError(str(oe), lh5_file, None) from oe
+            raise LH5DecodeError(oe, lh5_file) from oe
 
         close_after = True
         try:

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/lh5/store.py

@@ -19,6 +19,7 @@ from numpy.typing import ArrayLike
 from .. import types
 from . import _serializers, utils
 from .core import read
+from .exceptions import LH5DecodeError
 
 log = logging.getLogger(__name__)
 
@@ -125,7 +126,10 @@ class LH5Store:
                     "fs_page_size": page_buffer,
                 }
             )
-        h5f = h5py.File(full_path, mode, **file_kwargs)
+        try:
+            h5f = h5py.File(full_path, mode, **file_kwargs)
+        except (OSError, FileExistsError) as oe:
+            raise LH5DecodeError(oe, full_path) from oe
 
         if self.keep_open:
             if isinstance(self.keep_open, int) and len(self.files) >= self.keep_open:

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/lh5/tools.py

@@ -8,6 +8,7 @@ from pathlib import Path
 import h5py
 
 from . import utils
+from .exceptions import LH5DecodeError
 from .store import LH5Store
 
 log = logging.getLogger(__name__)
@@ -123,7 +124,10 @@ def show(
 
     # open file
     if isinstance(lh5_file, (str, Path)):
-        lh5_file = h5py.File(utils.expand_path(Path(lh5_file)), "r", locking=False)
+        try:
+            lh5_file = h5py.File(utils.expand_path(Path(lh5_file)), "r", locking=False)
+        except (OSError, FileExistsError) as oe:
+            raise LH5DecodeError(oe, lh5_file) from oe
 
     # go to group
     if lh5_group != "/":
@@ -145,17 +149,27 @@ def show(
 
     # loop over keys
     while True:
-        val = lh5_file[key]
-        # we want to print the LGDO datatype
-        dtype = val.attrs.get("datatype", default="no datatype")
-        if dtype == "no datatype" and isinstance(val, h5py.Group):
-            dtype = "HDF5 group"
-
-        _attrs = ""
-        if attrs:
-            attrs_d = dict(val.attrs)
-            attrs_d.pop("datatype", "")
-            _attrs = "── " + str(attrs_d) if attrs_d else ""
+        is_link = False
+        link_type = lh5_file.get(key, getlink=True)
+        if isinstance(link_type, (h5py.SoftLink, h5py.ExternalLink)):
+            desc = f"-> {link_type.path}"
+            is_link = True
+
+        else:
+            val = lh5_file[key]
+
+            # we want to print the LGDO datatype
+            dtype = val.attrs.get("datatype", default="no datatype")
+            if dtype == "no datatype" and isinstance(val, h5py.Group):
+                dtype = "HDF5 group"
+
+            _attrs = ""
+            if attrs:
+                attrs_d = dict(val.attrs)
+                attrs_d.pop("datatype", "")
+                _attrs = "── " + str(attrs_d) if attrs_d else ""
+
+            desc = f"· {dtype} {_attrs}"
 
         # is this the last key?
         killme = False
@@ -167,9 +181,10 @@ 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 {desc}")  # noqa: T201
 
-        if detail and isinstance(val, h5py.Dataset):
+        if not is_link and detail and isinstance(val, h5py.Dataset):
+            val = lh5_file[key]
             char = "|       "
             if killme:
                 char = "        "
@@ -203,9 +218,9 @@ def show(
             print(toprint)  # noqa: T201
 
         # if it's a group, call this function recursively
-        if isinstance(val, h5py.Group):
+        if not is_link and isinstance(val, h5py.Group):
             show(
-                val,
+                lh5_file[key],
                 indent=indent + ("    " if killme else "│   "),
                 header=False,
                 attrs=attrs,

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/src/lgdo/lh5/utils.py

@@ -45,7 +45,10 @@ def read_n_rows(name: str, h5f: str | Path | h5py.File) -> int | None:
     Return ``None`` if `name` is a :class:`.Scalar` or a :class:`.Struct`.
     """
     if not isinstance(h5f, h5py.File):
-        h5f = h5py.File(h5f, "r", locking=False)
+        try:
+            h5f = h5py.File(h5f, "r", locking=False)
+        except (OSError, FileExistsError) as oe:
+            raise LH5DecodeError(oe, h5f, None) from oe
 
     try:
         h5o = h5f[name].id
@@ -61,7 +64,10 @@ def read_size_in_bytes(name: str, h5f: str | Path | h5py.File) -> int | None:
     recursively through members of a Struct or Table
     """
     if not isinstance(h5f, h5py.File):
-        h5f = h5py.File(h5f, "r", locking=False)
+        try:
+            h5f = h5py.File(h5f, "r", locking=False)
+        except (OSError, FileExistsError) as oe:
+            raise LH5DecodeError(oe, h5f) from oe
 
     try:
         h5o = h5f[name].id

{legend_pydataobj-1.14.1 → legend_pydataobj-1.14.3}/tests/lh5/test_exceptions.py

@@ -12,6 +12,19 @@ from lgdo import lh5, types
 from lgdo.lh5.exceptions import LH5DecodeError, LH5EncodeError
 
 
+def test_tools(tmptestdir):
+    thefile = tmptestdir / "already-open-file-tools.lh5"
+    lh5.write(types.Struct({}), "/empty", thefile)
+
+    for mode in ("r", "r+", "w", "a"):
+        f = h5py.File(thefile, mode)
+        with pytest.raises(LH5DecodeError):
+            lh5.ls(thefile)
+        with pytest.raises(LH5DecodeError):
+            lh5.show(thefile)
+        f.close()
+
+
 def test_interact_with_already_open_files(tmptestdir):
     thefile = tmptestdir / "already-open-file.lh5"
     lh5.write(types.Struct({}), "/empty", thefile)