deprecating old function

GooseHDF5/__init__.py

@@ -619,7 +619,9 @@ def copy(
     :param source_root: Path prefix for all ``source_datasets``.
     :param recursive: If the source is a group, copy all objects within that group recursively.
     :param skip: Skip datasets that are not present in source.
-    :param expand_soft: Copy the underlying data of a link, or copy as link with the same path.
+    :param expand_soft:
+        If True: create a copy of the source dataset.
+        If False: create a link (with identical path as in the source).
     """
 
     if len(source_datasets) == 0:
@@ -679,34 +681,6 @@ def copy(
         )
 
 
-def copydatasets(
-    source: h5py.File,
-    dest: h5py.File,
-    source_datasets: list[str],
-    dest_datasets: list[str] = None,
-    root: str = None,
-):
-    """
-    Copy datasets from one HDF5-archive ``source`` to another HDF5-archive ``dest``.
-    The datasets can be renamed by specifying a list of ``dest_datasets``
-    (whose entries should correspond to the ``source_datasets``).
-    If the source is a Group object,
-    by default all objects within that group will be copied recursively.
-
-    In addition, a ``root`` (path prefix) for the destination datasets name can be specified.
-
-    :param source: The source HDF5-archive.
-    :param dest: The destination HDF5-archive.
-    :param source_datasets: List of dataset-paths in ``source``.
-    :param dest_datasets: List of dataset-paths in ``dest``, defaults to ``source_datasets``.
-    :param root: Path prefix for all ``dest_datasets``.
-    """
-
-    warnings.warn("copydatasets() is deprecated, use copy().", category=DeprecationWarning)
-
-    return copy(source, dest, source_datasets, dest_datasets, root)
-
-
 def isnumeric(a):
     """
     Returns ``True`` is an array contains numeric values.

docs/examples.rst

@@ -3,7 +3,7 @@ Examples
 ********
 
 Copy part of a file
-====================
+===================
 
 Suppose that you want to copy all but some dataset from a file.
 In that case you can use
@@ -16,7 +16,4 @@ Consider the following example.
 .. literalinclude:: examples/copy_modify-selection.py
    :language: python
 
-.. note::
-
-   The copy functions from *h5py* copy attributes as well.
-   By extension also :py:meth:`GooseHDF5.copy` copies all attributes.
+The last line includes an example on how to verify if a set of datasets is indeed the same.

docs/examples/copy_modify-selection.py

@@ -3,17 +3,19 @@
 
 import GooseHDF5 as g5
 
-with h5py.File("foo.h5", "w") as data:
+with h5py.File("foo.h5", "w") as file:
 
-    data["/a"] = np.arange(5)
-    data["/b/c"] = np.arange(5)
-    data["/d/e/f"] = np.arange(5)
+    file["/a"] = np.arange(5)
+    file["/b/c"] = np.arange(5)
+    file["/d/e/f"] = np.arange(5)
 
-with h5py.File("foo.h5", "r") as data:
+with h5py.File("foo.h5", "r") as file:
 
-    paths = list(g5.getdatasets(data))
+    paths = list(g5.getdatasets(file))
     paths.remove("/d/e/f")
 
     with h5py.File("bar.h5", "w") as ret:
-        g5.copy(data, ret, paths)
-        ret["/d/e/f"] = data["/d/e/f"][...] * 2
+        g5.copy(file, ret, paths)
+        ret["/d/e/f"] = file["/d/e/f"][...] * 2
+
+    print(g5.compare(file, ret, paths))