BUG: pd.read_csv with use_nullable_dtypes incompatible with dtype coercion

[coroa]

Pandas version checks

• I have checked that this issue has not already been reported.

• [ ] I have confirmed this bug exists on the latest version of pandas. use_nullable_dtypes has been added by ENH: Add option to use nullable dtypes in read_csv #48776 .

• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

from io import StringIO
from textwrap import dedent
csv = dedent("""
    epoch_1,epoch_2
    1665045912937687151,1665045912937689151
    ,
""")[1:]
pd.read_csv(StringIO(csv), dtype="Int64", use_nullable_dtypes=True).assign(diff=lambda df: df.epoch_2 - df.epoch_1)

Issue Description

Fails with KeyError: Int64Dtype() in File [...]/pandas/_libs/parsers.pyx:1417, in pandas._libs.parsers._maybe_upcast(). (Also refer to full stacktrace below).

KeyError                                  Traceback (most recent call last)
Cell In [39], line 1
----> 1 pd.read_csv(StringIO(csv), dtype="Int64", use_nullable_dtypes=True).assign(diff=lambda df: df.epoch_2 - df.epoch_1)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.<locals>._deprecate_kwarg.<locals>.wrapper(*args, **kwargs)
    209     else:
    210         kwargs[new_arg_name] = new_arg_value
--> 211 return func(*args, **kwargs)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/util/_decorators.py:331, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
    325 if len(args) > num_allow_args:
    326     warnings.warn(
    327         msg.format(arguments=_format_argument_list(allow_args)),
    328         FutureWarning,
    329         stacklevel=find_stack_level(),
    330     )
--> 331 return func(*args, **kwargs)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/io/parsers/readers.py:963, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, use_nullable_dtypes)
    948 kwds_defaults = _refine_defaults_read(
    949     dialect,
    950     delimiter,
   (...)
    959     defaults={"delimiter": ","},
    960 )
    961 kwds.update(kwds_defaults)
--> 963 return _read(filepath_or_buffer, kwds)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/io/parsers/readers.py:619, in _read(filepath_or_buffer, kwds)
    616     return parser
    618 with parser:
--> 619     return parser.read(nrows)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1796, in TextFileReader.read(self, nrows)
   1789 nrows = validate_integer("nrows", nrows)
   1790 try:
   1791     # error: "ParserBase" has no attribute "read"
   1792     (
   1793         index,
   1794         columns,
   1795         col_dict,
-> 1796     ) = self._engine.read(  # type: ignore[attr-defined]
   1797         nrows
   1798     )
   1799 except Exception:
   1800     self.close()

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py:231, in CParserWrapper.read(self, nrows)
    229 try:
    230     if self.low_memory:
--> 231         chunks = self._reader.read_low_memory(nrows)
    232         # destructive to chunks
    233         data = _concatenate_chunks(chunks)

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/_libs/parsers.pyx:818, in pandas._libs.parsers.TextReader.read_low_memory()

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/_libs/parsers.pyx:900, in pandas._libs.parsers.TextReader._read_rows()

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/_libs/parsers.pyx:1065, in pandas._libs.parsers.TextReader._convert_column_data()

File ~/.local/conda/envs/test_pandas_nightly/lib/python3.10/site-packages/pandas/_libs/parsers.pyx:1417, in pandas._libs.parsers._maybe_upcast()

KeyError: Int64Dtype()

use_nullable_dtypes works well without dtype="Int64".

In [40]: pd.read_csv(StringIO(csv), use_nullable_dtypes=True).assign(diff=lambda df: df.epoch_2 - df.epoch_1)
Out[40]:
               epoch_1              epoch_2  diff
0  1665045912937687151  1665045912937689151  2000
1                 <NA>                 <NA>  <NA>

Without use_nullable_dtypes the coercion works, but there is a loss of precision (ie the diff is reported as 1792 instead of 2000 on my machine).

In [41]: pd.read_csv(StringIO(csv), dtype="Int64").assign(diff=lambda df: df.epoch_2 - df.epoch_1)
Out[41]:
               epoch_1              epoch_2  diff
0  1665045912937687296  1665045912937689088  1792
1                 <NA>                 <NA>  <NA>

Expected Behavior

Produces dataframe with:

               epoch_1              epoch_2  diff
0  1665045912937687151  1665045912937689151  2000
1                 <NA>                 <NA>  <NA>

Installed Versions

INSTALLED VERSIONS

commit : 2f7dce4
python : 3.10.6.final.0
python-bits : 64
OS : Darwin
OS-release : 21.6.0
Version : Darwin Kernel Version 21.6.0: Mon Aug 22 20:17:10 PDT 2022; root:xnu-8020.140.49~2/RELEASE_X86_64
machine : x86_64
processor : i386
byteorder : little
LC_ALL : None
LANG : en_GB.UTF-8
LOCALE : en_GB.UTF-8

pandas : 1.6.0.dev0+350.g2f7dce4e6e
numpy : 1.23.3
pytz : 2022.4
dateutil : 2.8.2
setuptools : 65.5.0
pip : 22.3
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : None
IPython : 8.5.0
pandas_datareader: None
bs4 : None
bottleneck : None
brotli : None
fastparquet : None
fsspec : None
gcsfs : None
matplotlib : None
numba : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pyreadstat : None
pyxlsb : None
s3fs : None
scipy : None
snappy : None
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlwt : None
zstandard : None
tzdata : None