Repository: jsonpickle/jsonpickle (python)

Issue:
np.compat is deprecated
```
==================================== ERRORS ====================================
_______________ ERROR collecting examples/save_class_to_file.py ________________
examples/save_class_to_file.py:27: in <module>
    encoded_instance
E   AssertionError
=============================== warnings summary ===============================
tests/numpy_test.py:9
  /build/python-jsonpickle/src/jsonpickle/tests/numpy_test.py:9: DeprecationWarning: `np.compat`, which was used during the Python 2 to 3 transition, is deprecated since 1.26.0, and will be removed
    from numpy.compat import asbytes
```

https://github.com/jsonpickle/jsonpickle/blob/bc1d149ddc2facb4e8c575f51e8b3f16142bc161/tests/numpy_test.py#L39

Pull request description:
Fix numpy compat issues
Fixes #533. Rewrite a line of a test to use an equivalent for np.compat.asbytes found [here](https://github.com/harishsdev/scipy/commit/4dcb9d50705709e3083e3bd6aacc6f39538404b4#diff-d28fbb0be287769c763ce61b0695feb0a6ca0e67b28bafee20526b46be7aaa84R17), and remove np.compat.unicode from being tested as apparently it's just the Python 2 version of str which isn't supported anymore. This is on top of #534, so once that is merged, this can be merged too.

Patch:
diff --git a/CHANGES.rst b/CHANGES.rst
index b510619..105bf4a 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -18,6 +18,12 @@ Upcoming
     * ``yaml`` is now supported as a jsonpickle backend. (+528)
     * `OSSFuzz <https://github.com/google/oss-fuzz>`_ scripts are now available in
       the ``fuzzing/`` directory. (+525)
+    * Pure-python dtypes are now preserved across ``encode()``/``decode()`` roundtrips
+      for the pandas extension. (#407) (+534)
+    * Pandas dataframe columns with an ``object`` dtype that contain multiple different
+      types within (e.g. a column of type ``list[Union[str, int]]``) now preserve the types
+      upon being roundtripped. (#457) (#358) (+534)
+    * Fix warnings in the test suite regarding numpy.compat usage. (#533) (+535)
 
 v3.3.0
 ======
diff --git a/jsonpickle/ext/pandas.py b/jsonpickle/ext/pandas.py
index 475b77e..fd18634 100644
--- a/jsonpickle/ext/pandas.py
+++ b/jsonpickle/ext/pandas.py
@@ -1,10 +1,12 @@
+import warnings
 import zlib
-from io import StringIO
 
 import pandas as pd
+import numpy as np
 
 from .. import decode, encode
 from ..handlers import BaseHandler, register, unregister
+from ..tags_pd import TYPE_MAP, REVERSE_TYPE_MAP
 from ..util import b64decode, b64encode
 from .numpy import register_handlers as register_numpy_handlers
 from .numpy import unregister_handlers as unregister_numpy_handlers
@@ -12,6 +14,50 @@ from .numpy import unregister_handlers as unregister_numpy_handlers
 __all__ = ['register_handlers', 'unregister_handlers']
 
 
+def pd_encode(obj, **kwargs):
+    if isinstance(obj, np.generic):
+        # convert pandas/numpy scalar to native Python type
+        return obj.item()
+    return encode(obj, **kwargs)
+
+
+def pd_decode(s, **kwargs):
+    return decode(s, **kwargs)
+
+
+def rle_encode(types_list):
+    """
+    Encodes a list of type codes using Run-Length Encoding (RLE). This allows for object columns in dataframes to contain items of different types without massively bloating the encoded representation.
+    """
+    if not types_list:
+        return []
+
+    encoded = []
+    current_type = types_list[0]
+    count = 1
+
+    for typ in types_list[1:]:
+        if typ == current_type:
+            count += 1
+        else:
+            encoded.append([current_type, count])
+            current_type = typ
+            count = 1
+    encoded.append([current_type, count])
+
+    return encoded
+
+
+def rle_decode(encoded_list):
+    """
+    Decodes a Run-Length Encoded (RLE) list back into the original list of type codes.
+    """
+    decoded = []
+    for typ, count in encoded_list:
+        decoded.extend([typ] * count)
+    return decoded
+
+
 class PandasProcessor(object):
     def __init__(self, size_threshold=500, compression=zlib):
         """
@@ -85,44 +131,143 @@ def make_read_csv_params(meta, context):
 
 
 class PandasDfHandler(BaseHandler):
-    pp = PandasProcessor()
-
     def flatten(self, obj, data):
-        dtype = obj.dtypes.to_dict()
-
+        pp = PandasProcessor()
+        # handle multiindex columns
+        if isinstance(obj.columns, pd.MultiIndex):
+            columns = [tuple(col) for col in obj.columns]
+            column_names = obj.columns.names
+            is_multicolumns = True
+        else:
+            columns = obj.columns.tolist()
+            column_names = obj.columns.name
+            is_multicolumns = False
+
+        # handle multiindex index
+        if isinstance(obj.index, pd.MultiIndex):
+            index_values = [tuple(idx) for idx in obj.index.values]
+            index_names = obj.index.names
+            is_multiindex = True
+        else:
+            index_values = obj.index.tolist()
+            index_names = obj.index.name
+            is_multiindex = False
+
+        data_columns = {}
+        type_codes = []
+        for col in obj.columns:
+            col_data = obj[col]
+            dtype_name = col_data.dtype.name
+
+            if dtype_name == "object":
+                # check if items are complex types
+                if col_data.apply(
+                    lambda x: isinstance(x, (list, dict, set, tuple, np.ndarray))
+                ).any():
+                    # if items are complex, erialize each item individually
+                    serialized_values = col_data.apply(lambda x: encode(x)).tolist()
+                    data_columns[col] = serialized_values
+                    type_codes.append("py/jp")
+                else:
+                    # treat it as regular object dtype
+                    data_columns[col] = col_data.tolist()
+                    type_codes.append(TYPE_MAP.get(dtype_name, "object"))
+            else:
+                # for other dtypes, store their values directly
+                data_columns[col] = col_data.tolist()
+                type_codes.append(TYPE_MAP.get(dtype_name, "object"))
+
+        # store index data
+        index_encoded = encode(index_values, keys=True)
+
+        rle_types = rle_encode(type_codes)
+        # prepare metadata
         meta = {
-            'dtypes': self.context.flatten(
-                {k: str(dtype[k]) for k in dtype}, reset=False
-            ),
-            'index': encode(obj.index),
-            'column_level_names': obj.columns.names,
-            'header': list(range(len(obj.columns.names))),
+            "dtypes_rle": rle_types,
+            "index": index_encoded,
+            "index_names": index_names,
+            "columns": encode(columns, keys=True),
+            "column_names": column_names,
+            "is_multiindex": is_multiindex,
+            "is_multicolumns": is_multicolumns,
         }
 
-        data = self.pp.flatten_pandas(
-            obj.reset_index(drop=True).to_csv(index=False), data, meta
-        )
+        # serialize data_columns with keys=True to allow for non-object keys
+        data_encoded = encode(data_columns, keys=True)
+
+        # use PandasProcessor to flatten
+        data = pp.flatten_pandas(data_encoded, data, meta)
         return data
 
-    def restore(self, data):
-        csv, meta = self.pp.restore_pandas(data)
-        params, timedeltas, parse_datetime_v2 = make_read_csv_params(meta, self.context)
-        # None makes it compatible with objects serialized before
-        # column_levels_names has been introduced.
-        column_level_names = meta.get('column_level_names', None)
-        df = (
-            pd.read_csv(StringIO(csv), **params)
-            if data['values'].strip()
-            else pd.DataFrame()
-        )
-        for col in timedeltas:
-            df[col] = pd.to_timedelta(df[col])
-        df = df.astype(parse_datetime_v2)
-
-        df.set_index(decode(meta['index']), inplace=True)
-        # restore the column level(s) name(s)
-        if column_level_names:
-            df.columns.names = column_level_names
+    def restore(self, obj):
+        pp = PandasProcessor()
+        data_encoded, meta = pp.restore_pandas(obj)
+
+        data_columns = decode(data_encoded, keys=True)
+
+        # get type codes, un-RLE-ed
+        rle_types = meta["dtypes_rle"]
+        type_codes = rle_decode(rle_types)
+
+        # handle multicolumns
+        columns_decoded = decode(meta["columns"], keys=True)
+        if meta.get("is_multicolumns", False):
+            columns = pd.MultiIndex.from_tuples(
+                columns_decoded, names=meta.get("column_names")
+            )
+        else:
+            columns = columns_decoded
+
+        # progressively reconstruct dataframe as a dict
+        df_data = {}
+        dtypes = {}
+        for col, type_code in zip(columns, type_codes):
+            col_data = data_columns[col]
+            if type_code == "py/jp":
+                # deserialize each item in the column
+                col_values = [decode(item) for item in col_data]
+                df_data[col] = col_values
+            else:
+                df_data[col] = col_data
+                # used later to get correct dtypes
+                dtype_str = REVERSE_TYPE_MAP.get(type_code, "object")
+                dtypes[col] = dtype_str
+
+        # turn dict into df
+        df = pd.DataFrame(df_data)
+        df.columns = columns
+
+        # apply dtypes
+        for col in df.columns:
+            dtype_str = dtypes.get(col, "object")
+            try:
+                dtype = np.dtype(dtype_str)
+                df[col] = df[col].astype(dtype)
+            except Exception:
+                msg = (
+                    f"jsonpickle was unable to properly deserialize "
+                    f"the column {col} into its inferred dtype. "
+                    f"Please file a bugreport on the jsonpickle GitHub! "
+                )
+                warnings.warn(msg)
+
+        # decode and set the index
+        index_values = decode(meta["index"], keys=True)
+        if meta.get("is_multiindex", False):
+            index = pd.MultiIndex.from_tuples(
+                index_values, names=meta.get("index_names")
+            )
+        else:
+            index = pd.Index(index_values, name=meta.get("index_names"))
+        df.index = index
+
+        # restore column names for easy readability
+        if "column_names" in meta:
+            if meta.get("is_multicolumns", False):
+                df.columns.names = meta.get("column_names")
+            else:
+                df.columns.name = meta.get("column_names")
+
         return df
 
 
diff --git a/jsonpickle/tags_pd.py b/jsonpickle/tags_pd.py
new file mode 100644
index 0000000..314b986
--- /dev/null
+++ b/jsonpickle/tags_pd.py
@@ -0,0 +1,207 @@
+"""
+This file exists to automatically generate tags for numpy/pandas extensions. Because numpy/pandas follow a (relatively) rapid release schedule, updating types for new versions as bug reports come in could be infeasible, so we auto-generate them. Unfortunately, this file can't go into the ext folder because then the imports would break.
+"""
+
+import re
+
+import numpy as np
+import pandas as pd
+from pandas.api.extensions import ExtensionDtype
+
+
+def split_letters_numbers_brackets(s):
+    """
+    Split the string into letters, numbers, and brackets (with their content).
+    This is a helper function for getting the smallest unique substring, for determining tags.
+    """
+    # extract brackets and their content
+    brackets_match = re.search(r"\[.*?\]", s)
+    if brackets_match:
+        brackets_part = brackets_match.group()
+        s_clean = s.replace(brackets_part, "")
+    else:
+        brackets_part = ""
+        s_clean = s
+
+    # find where the trailing digits start
+    index = len(s_clean)
+    while index > 0 and s_clean[index - 1].isdigit():
+        index -= 1
+    letters_part = s_clean[:index]
+    numbers_part = s_clean[index:]
+    return letters_part, numbers_part, brackets_part
+
+
+def get_smallest_unique_substrings(strings, prefix="np"):
+    used_substrings = set()
+    used_letters_parts = set()
+    result = {}
+
+    for s in strings:
+        if not isinstance(s, str):
+            s2 = s.__name__
+        else:
+            s2 = s
+        letters_part, numbers_part, brackets_part = split_letters_numbers_brackets(s2)
+        letters_part = letters_part.lower()
+        unique_substring_found = False
+
+        # handle the weird datetime64[...] and timedelta64[...] cases
+        if letters_part == "datetime" and numbers_part == "64" and brackets_part:
+            substr = "d64" + brackets_part
+            if substr not in used_substrings:
+                result[s] = substr
+                used_substrings.add(substr)
+                unique_substring_found = True
+        elif letters_part == "timedelta" and numbers_part == "64" and brackets_part:
+            substr = "t64" + brackets_part
+            if substr not in used_substrings:
+                result[s] = substr
+                used_substrings.add(substr)
+                unique_substring_found = True
+        else:
+            if letters_part in used_letters_parts:
+                # letters have been seen before, so use letters + numbers_part + brackets_part
+                if numbers_part or brackets_part:
+                    # try first letter + numbers_part + brackets_part
+                    substr = letters_part[0]
+                    if numbers_part:
+                        substr += numbers_part
+                    if brackets_part:
+                        substr += brackets_part
+                    if substr not in used_substrings:
+                        result[s] = substr
+                        used_substrings.add(substr)
+                        unique_substring_found = True
+                    else:
+                        # try letters_part + numbers_part + brackets_part
+                        substr = letters_part
+                        if numbers_part:
+                            substr += numbers_part
+                        if brackets_part:
+                            substr += brackets_part
+                        if substr not in used_substrings:
+                            result[s] = substr
+                            used_substrings.add(substr)
+                            unique_substring_found = True
+                else:
+                    # find a unique substring of just letters_part
+                    for length in range(1, len(letters_part) + 1):
+                        substr = letters_part[:length]
+                        if substr not in used_substrings:
+                            result[s] = substr
+                            used_substrings.add(substr)
+                            unique_substring_found = True
+                            break
+            else:
+                # assign the smallest substring of letters_part
+                for length in range(1, len(letters_part) + 1):
+                    substr = letters_part[:length]
+                    if substr not in used_substrings:
+                        result[s] = substr
+                        used_substrings.add(substr)
+                        unique_substring_found = True
+                        break
+                used_letters_parts.add(letters_part)
+
+        # last resort: assign the entire string
+        if not unique_substring_found:
+            result[s] = s
+            used_substrings.add(s)
+
+    for key in result:
+        result[key] = f"{prefix}/" + result[key]
+
+    return result
+
+
+def all_subclasses(cls):
+    # use a set to avoid adding duplicates
+    subclasses = set()
+    for subclass in cls.__subclasses__():
+        subclasses.add(subclass)
+        subclasses.update(all_subclasses(subclass))
+    return list(subclasses)
+
+
+def get_all_numpy_dtype_strings():
+    dtypes = []
+
+    # sctypeDict is the dict of all possible numpy dtypes + some invalid dtypes too
+    for dtype in np.sctypeDict.values():
+        try:
+            dtype_obj = np.dtype(dtype)
+            dtypes.append(dtype_obj.name.lower())
+        except TypeError:
+            continue
+
+    try:
+        char_codes = np._typing._char_codes
+        # datetime64 and timedelta64 are special, they have multiple variants
+        # python internally compiles and caches regex like this to speed it up
+        dt_variants = list(
+            dict.fromkeys(
+                [
+                    "datetime64[" + re.search(r"\[(.*?)\]", var).group(1) + "]"
+                    for var in char_codes._DT64Codes.__args__
+                    if re.search(r"\[(.*?)\]", var)
+                ]
+            )
+        )
+        td_variants = list(
+            dict.fromkeys(
+                [
+                    "timedelta64[" + re.search(r"\[(.*?)\]", var).group(1) + "]"
+                    for var in char_codes._TD64Codes.__args__
+                    if re.search(r"\[(.*?)\]", var)
+                ]
+            )
+        )
+    except AttributeError:
+        # AttributeError happens on numpy <1.25 because _typing isn't exposed to users
+        dt_variants = ['datetime64[Y]', 'datetime64[M]', 'datetime64[W]', 'datetime64[D]', 'datetime64[h]', 'datetime64[m]', 'datetime64[s]', 'datetime64[ms]', 'datetime64[us]', 'datetime64[ns]', 'datetime64[ps]', 'datetime64[fs]', 'datetime64[as]']
+        td_variants = ['timedelta64[Y]', 'timedelta64[M]', 'timedelta64[W]', 'timedelta64[D]', 'timedelta64[h]', 'timedelta64[m]', 'timedelta64[s]', 'timedelta64[ms]', 'timedelta64[us]', 'timedelta64[ns]', 'timedelta64[ps]', 'timedelta64[fs]', 'timedelta64[as]']
+
+    dtypes += dt_variants + td_variants
+
+    return list(dict.fromkeys(dtypes))
+
+
+def get_all_pandas_dtype_strings():
+    dtypes = []
+
+    # get all pandas dtypes since it doesnt have a built-in api
+    extension_dtypes = all_subclasses(ExtensionDtype)
+
+    for dtype_cls in extension_dtypes:
+        # some ExtensionDtype subclasses might not have a name attribute
+        if hasattr(dtype_cls, "name"):
+            try:
+                dtype_name = dtype_cls.name
+                dtypes.append(dtype_name.lower())
+            except Exception:
+                continue
+
+    # use the class object for things that np.dtype can't reconstruct
+    dtypes.extend([pd.Timestamp, pd.Timedelta, pd.Period, pd.Interval])
+
+    return list(dict.fromkeys(dtypes))
+
+
+np_dtypes = list(
+    dict.fromkeys(
+        [dtype for dtype in get_all_numpy_dtype_strings() if isinstance(dtype, str)]
+    )
+)
+
+pd_dtypes = list(
+    dict.fromkeys(
+        [dtype for dtype in get_all_pandas_dtype_strings() if isinstance(dtype, str)]
+    )
+)
+
+
+TYPE_MAP = get_smallest_unique_substrings(np_dtypes, prefix="np")
+TYPE_MAP.update(get_smallest_unique_substrings(pd_dtypes, prefix="pd"))
+
+REVERSE_TYPE_MAP = {v: k for k, v in TYPE_MAP.items()}


Test patch:
diff --git a/tests/numpy_test.py b/tests/numpy_test.py
index 2e6725b..550ab2c 100644
--- a/tests/numpy_test.py
+++ b/tests/numpy_test.py
@@ -6,7 +6,6 @@ import pytest
 try:
     import numpy as np
     import numpy.testing as npt
-    from numpy.compat import asbytes
     from numpy.testing import assert_equal
 except ImportError:
     pytest.skip('numpy is not available', allow_module_level=True)
@@ -36,7 +35,6 @@ def test_dtype_roundtrip():
         np.complex128,
         np.str_,
         np.object_,
-        np.compat.unicode,
         np.dtype(np.void),
         np.dtype(np.int32),
         np.dtype(np.float32),
@@ -106,7 +104,7 @@ def test_ndarray_roundtrip():
         np.array(['foo', 'bar']),
         np.array(['baz'.encode('utf-8')]),
         np.array(['2010', 'NaT', '2030']).astype('M'),
-        np.rec.array(asbytes('abcdefg') * 100, formats='i2,a3,i4', shape=3),
+        np.rec.array('abcdefg'.encode('utf-8') * 100, formats='i2,a3,i4', shape=3),
         np.rec.array(
             [
                 (1, 11, 'a'),
diff --git a/tests/pandas_test.py b/tests/pandas_test.py
index 414bd65..b46a166 100644
--- a/tests/pandas_test.py
+++ b/tests/pandas_test.py
@@ -26,8 +26,8 @@ def pandas_extension():
     jsonpickle.ext.pandas.unregister_handlers()
 
 
-def roundtrip(obj):
-    return jsonpickle.decode(jsonpickle.encode(obj))
+def roundtrip(obj, **kwargs):
+    return jsonpickle.decode(jsonpickle.encode(obj, **kwargs))
 
 
 def test_series_roundtrip():
@@ -59,6 +59,8 @@ def test_dataframe_roundtrip():
             'an_inf': np.array([np.inf] * 3),
             'a_str': np.str_('foo'),
             'date': np.array([np.datetime64('2014-01-01')] * 3, dtype="datetime64[s]"),
+            'date_ns': np.array([np.datetime64('2014-01-01')] * 3, dtype="datetime64[ns]"),
+            'timedelta': np.array([np.timedelta64(1, "Y")] * 3, dtype="timedelta64[Y]"),
             'complex': np.complex128([1 - 2j, 2 - 1.2j, 3 - 1.3j]),
             # TODO: the following dtypes are not currently supported.
             # 'object': np.object_([{'a': 'b'}]*3),
@@ -67,6 +69,24 @@ def test_dataframe_roundtrip():
     decoded_df = roundtrip(df)
     assert_frame_equal(decoded_df, df)
 
+def test_dataframe_nested_containers():
+    # adapted from #407
+    a = pd.DataFrame({"date": ["20220921abc", 20220921.5], "date2": [20220921, "20220921"]})
+    b = roundtrip(a, keys=True)
+    assert a['date'][0] == b['date'][0]
+
+def test_dataframe_mixed_dtypes():
+    # adapted from #358
+    df = pd.DataFrame({'col1': [[1, 2, 3], ['a', 'b', 'c']]})
+    assert isinstance((df['col1'].iloc[0]), list)
+    result = roundtrip(df)
+    assert isinstance((result['col1'].iloc[0]), list)
+
+    # adapted from #457
+    # Create simple data frame of mixed data types
+    df1 = pd.DataFrame(([1, 2], [4, 'foo']))
+    df2 = roundtrip(df1)
+    assert (df1[0] == df2[0]).all()
 
 def test_multindex_dataframe_roundtrip():
     df = pd.DataFrame(
@@ -301,6 +321,7 @@ def test_multilevel_columns():
     assert isinstance(cloned_data_frame, pd.DataFrame)
     assert data_frame.columns.names == cloned_data_frame.columns.names
     assert_frame_equal(data_frame, cloned_data_frame)
+    assert names == cloned_data_frame.columns.names
 
 
 if __name__ == '__main__':