Merge pull request #1688 from braingram/cleanup_util

Cleanup `asdf.util`

CHANGES.rst

@@ -1,3 +1,12 @@
+3.1.0 (unreleased)
+------------------
+
+The ASDF Standard is at v1.6.0
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Cleanup ``asdf.util`` including deprecating: ``human_list``
+  ``resolve_name`` ``minversion`` and ``iter_subclasses`` [#1688]
+
 3.0.1 (2023-10-30)
 ------------------
 

asdf/_block/external.py

@@ -40,7 +40,7 @@ def load(self, base_uri, uri, memmap=False, validate_checksums=False):
             ) as af:
                 blk = af._blocks.blocks[0]
                 if memmap and blk.header["compression"] == b"\0\0\0\0":
-                    parsed_url = util.patched_urllib_parse.urlparse(resolved_uri)
+                    parsed_url = util._patched_urllib_parse.urlparse(resolved_uri)
                     if parsed_url.scheme == "file":
                         # deal with leading slash for windows file://
                         filename = urllib.request.url2pathname(parsed_url.path)
@@ -58,7 +58,7 @@ def clear(self):
 
 def relative_uri_for_index(uri, index):
     # get the os-native separated path for this uri
-    path = util.patched_urllib_parse.urlparse(uri).path
+    path = util._patched_urllib_parse.urlparse(uri).path
     dirname, filename = os.path.split(path)
     filename = os.path.splitext(filename)[0] + f"{index:04d}.asdf"
     return filename

asdf/_block/io.py

@@ -15,7 +15,7 @@
 
 from .exceptions import BlockIndexError
 
-BLOCK_HEADER = util.BinaryStruct(
+BLOCK_HEADER = util._BinaryStruct(
     [
         ("flags", "I"),
         ("compression", "4s"),
@@ -83,7 +83,7 @@ def read_block_header(fd, offset=None):
     -------
     header : dict
         Dictionary containing the read ASDF header as parsed by the
-        `BLOCK_HEADER` `asdf.util.BinaryStruct`.
+        `BLOCK_HEADER` `asdf.util._BinaryStruct`.
 
     Raises
     ------

asdf/_tests/test_deprecated.py

@@ -2,6 +2,7 @@
 
 import pytest
 
+import asdf
 from asdf.exceptions import AsdfDeprecationWarning
 
 
@@ -15,3 +16,23 @@ def test_asdf_stream_deprecation():
 def test_asdf_asdf_SerializationContext_import_deprecation():
     with pytest.warns(AsdfDeprecationWarning, match="importing SerializationContext from asdf.asdf"):
         from asdf.asdf import SerializationContext  # noqa: F401
+
+
+def test_asdf_util_human_list_deprecation():
+    with pytest.warns(AsdfDeprecationWarning, match="asdf.util.human_list is deprecated"):
+        asdf.util.human_list("a")
+
+
+def test_asdf_util_resolve_name_deprecation():
+    with pytest.warns(AsdfDeprecationWarning, match="asdf.util.resolve_name is deprecated"):
+        asdf.util.resolve_name("asdf.AsdfFile")
+
+
+def test_asdf_util_minversion_deprecation():
+    with pytest.warns(AsdfDeprecationWarning, match="asdf.util.minversion is deprecated"):
+        asdf.util.minversion("yaml", "3.1")
+
+
+def test_asdf_util_iter_subclasses_deprecation():
+    with pytest.warns(AsdfDeprecationWarning, match="asdf.util.iter_subclasses is deprecated"):
+        list(asdf.util.iter_subclasses(asdf.AsdfFile))

asdf/_tests/test_util.py

@@ -1,8 +1,10 @@
 import io
+import warnings
 
 import pytest
 
 from asdf import generic_io, util
+from asdf.exceptions import AsdfDeprecationWarning
 
 
 def test_is_primitive():
@@ -35,12 +37,12 @@ def test_get_class_name():
 
 
 def test_patched_urllib_parse():
-    assert "asdf" in util.patched_urllib_parse.uses_relative
-    assert "asdf" in util.patched_urllib_parse.uses_netloc
+    assert "asdf" in util._patched_urllib_parse.uses_relative
+    assert "asdf" in util._patched_urllib_parse.uses_netloc
 
     import urllib.parse
 
-    assert urllib.parse is not util.patched_urllib_parse
+    assert urllib.parse is not util._patched_urllib_parse
     assert "asdf" not in urllib.parse.uses_relative
     assert "asdf" not in urllib.parse.uses_netloc
 
@@ -103,12 +105,14 @@ def test_minversion():
 
     good_versions = ["1.16", "1.16.1", "1.16.0.dev", "1.16dev"]
     bad_versions = ["100000", "100000.2rc1"]
-    for version in good_versions:
-        assert util.minversion(np, version)
-        assert util.minversion("numpy", version)
-    for version in bad_versions:
-        assert not util.minversion(np, version)
-        assert not util.minversion("numpy", version)
-
-    assert util.minversion(yaml, "3.1")
-    assert util.minversion("yaml", "3.1")
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", "asdf.util.minversion", AsdfDeprecationWarning)
+        for version in good_versions:
+            assert util.minversion(np, version)
+            assert util.minversion("numpy", version)
+        for version in bad_versions:
+            assert not util.minversion(np, version)
+            assert not util.minversion("numpy", version)
+
+        assert util.minversion(yaml, "3.1")
+        assert util.minversion("yaml", "3.1")

asdf/commands/diff.py

@@ -33,7 +33,6 @@
 import asdf
 from asdf.extension._serialization_context import BlockAccess
 from asdf.tagged import Tagged
-from asdf.util import human_list
 
 from .main import Command
 
@@ -256,6 +255,34 @@ def _load_array(asdf_file, array_dict):
     return conv.from_yaml_tree(array_dict, array_dict._tag, sctx)
 
 
+def _human_list(line, separator="and"):
+    """
+    Formats a list for human readability.
+
+    Parameters
+    ----------
+    line : sequence
+        A sequence of strings
+
+    separator : string, optional
+        The word to use between the last two entries.  Default:
+        ``"and"``.
+
+    Returns
+    -------
+    formatted_list : string
+
+    Examples
+    --------
+    >>> _human_list(["vanilla", "strawberry", "chocolate"], "or")
+    'vanilla, strawberry or chocolate'
+    """
+    if len(line) == 1:
+        return line[0]
+
+    return ", ".join(line[:-1]) + " " + separator + " " + line[-1]
+
+
 def compare_ndarrays(diff_ctx, array0, array1, keys):
     """Compares two ndarray objects"""
     if isinstance(array0, list):
@@ -278,7 +305,7 @@ def compare_ndarrays(diff_ctx, array0, array1, keys):
         differences.append("contents")
 
     if differences:
-        msg = f"ndarrays differ by {human_list(differences)}"
+        msg = f"ndarrays differ by {_human_list(differences)}"
         print_in_tree(diff_ctx, keys, msg, False, ignore_lwl=True)
         print_in_tree(diff_ctx, keys, msg, True, ignore_lwl=True)
 

asdf/commands/main.py

@@ -37,7 +37,7 @@ def help_(args):
     help_parser = subparsers.add_parser("help", help="Display usage information")
     help_parser.set_defaults(func=help_)
 
-    commands = {x.__name__: x for x in util.iter_subclasses(Command)}
+    commands = {x.__name__: x for x in util._iter_subclasses(Command)}
 
     for command in command_order:
         commands[str(command)].setup_arguments(subparsers)

asdf/core/_converters/complex.py

@@ -14,7 +14,7 @@
 class ComplexConverter(Converter):
     tags = ["tag:stsci.edu:asdf/core/complex-1.0.0"]
 
-    types = [*list(util.iter_subclasses(np.complexfloating)), complex]
+    types = [*list(util._iter_subclasses(np.complexfloating)), complex]
 
     def to_yaml_tree(self, obj, tag, ctx):
         return str(obj)

asdf/generic_io.py

@@ -22,7 +22,7 @@
 from . import util
 from .exceptions import DelimiterNotFoundError
 from .extern import atomicfile
-from .util import patched_urllib_parse
+from .util import _patched_urllib_parse
 
 __all__ = ["get_file", "get_uri", "resolve_uri", "relative_uri"]
 
@@ -69,8 +69,8 @@ def resolve_uri(base, uri):
     """
     if base is None:
         base = ""
-    resolved = patched_urllib_parse.urljoin(base, uri)
-    parsed = patched_urllib_parse.urlparse(resolved)
+    resolved = _patched_urllib_parse.urljoin(base, uri)
+    parsed = _patched_urllib_parse.urlparse(resolved)
     if parsed.path != "" and not parsed.path.startswith("/"):
         msg = "Resolved to relative URL"
         raise ValueError(msg)
@@ -81,8 +81,8 @@ def relative_uri(source, target):
     """
     Make a relative URI from source to target.
     """
-    su = patched_urllib_parse.urlparse(source)
-    tu = patched_urllib_parse.urlparse(target)
+    su = _patched_urllib_parse.urlparse(source)
+    tu = _patched_urllib_parse.urlparse(target)
     extra = list(tu[3:])
     relative = None
     if tu[0] == "" and tu[1] == "":
@@ -98,7 +98,7 @@ def relative_uri(source, target):
     if relative == ".":
         relative = ""
 
-    return patched_urllib_parse.urlunparse(["", "", relative, *extra])
+    return _patched_urllib_parse.urlunparse(["", "", relative, *extra])
 
 
 class _TruncatedReader:
@@ -187,7 +187,7 @@ def read(self, nbytes=None):
         return content
 
 
-class GenericFile(metaclass=util.InheritDocstrings):
+class GenericFile(metaclass=util._InheritDocstrings):
     """
     Base class for an abstraction layer around a number of different
     file-like types.  Each of its subclasses handles a particular kind
@@ -1094,7 +1094,7 @@ def get_file(init, mode="r", uri=None, close=False):
         return GenericWrapper(init)
 
     if isinstance(init, (str, pathlib.Path)):
-        parsed = patched_urllib_parse.urlparse(str(init))
+        parsed = _patched_urllib_parse.urlparse(str(init))
         if parsed.scheme in ["http", "https"]:
             if "w" in mode:
                 msg = "HTTP connections can not be opened for writing"

asdf/reference.py

@@ -12,7 +12,7 @@
 import numpy as np
 
 from . import generic_io, treeutil, util
-from .util import patched_urllib_parse
+from .util import _patched_urllib_parse
 
 __all__ = ["resolve_fragment", "Reference", "find_references", "resolve_references", "make_reference"]
 
@@ -22,7 +22,7 @@ def resolve_fragment(tree, pointer):
     Resolve a JSON Pointer within the tree.
     """
     pointer = pointer.lstrip("/")
-    parts = patched_urllib_parse.unquote(pointer).split("/") if pointer else []
+    parts = _patched_urllib_parse.unquote(pointer).split("/") if pointer else []
 
     for part in parts:
         part_ = part.replace("~1", "/").replace("~0", "~")
@@ -57,7 +57,7 @@ def _get_target(self, **kwargs):
                 base_uri = self._asdffile().uri
             uri = generic_io.resolve_uri(base_uri, self._uri)
             asdffile = self._asdffile().open_external(uri, **kwargs)
-            parts = patched_urllib_parse.urlparse(self._uri)
+            parts = _patched_urllib_parse.urlparse(self._uri)
             fragment = parts.fragment
             self._target = resolve_fragment(asdffile.tree, fragment)
         return self._target

asdf/schema.py

@@ -17,7 +17,7 @@
 from . import constants, generic_io, reference, tagged, treeutil, util, versioning, yamlutil
 from .config import get_config
 from .exceptions import AsdfDeprecationWarning, AsdfWarning
-from .util import patched_urllib_parse
+from .util import _patched_urllib_parse
 
 YAML_SCHEMA_METASCHEMA_ID = "http://stsci.edu/schemas/yaml-schema/draft-01"
 
@@ -381,7 +381,7 @@ def get_schema(url):
 
     # Supplying our own implementation of urljoin_cache
     # allows asdf:// URIs to be resolved correctly.
-    urljoin_cache = lru_cache(1024)(patched_urllib_parse.urljoin)
+    urljoin_cache = lru_cache(1024)(_patched_urllib_parse.urljoin)
 
     # We set cache_remote=False here because we do the caching of
     # remote schemas here in `load_schema`, so we don't need