HPI/my/core/pandas.py
2024-08-20 00:15:15 +01:00

285 lines
9 KiB
Python

'''
Various pandas helpers and convenience functions
'''
from __future__ import annotations
# todo not sure if belongs to 'core'. It's certainly 'more' core than actual modules, but still not essential
# NOTE: this file is meant to be importable without Pandas installed
import dataclasses
from datetime import datetime, timezone
from pprint import pformat
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterable,
Iterator,
Literal,
Type,
TypeVar,
)
from decorator import decorator
from . import warnings
from .error import Res, error_to_json, extract_error_datetime
from .logging import make_logger
from .types import Json, asdict
logger = make_logger(__name__)
if TYPE_CHECKING:
import pandas as pd
DataFrameT = pd.DataFrame
SeriesT = pd.Series
from pandas._typing import S1 # meh
FuncT = TypeVar('FuncT', bound=Callable[..., DataFrameT])
# huh interesting -- with from __future__ import annotations don't even need else clause here?
# but still if other modules import these we do need some fake runtime types here..
else:
from typing import Optional
DataFrameT = Any
SeriesT = Optional # just some type with one argument
S1 = Any
def _check_dateish(s: SeriesT[S1]) -> Iterable[str]:
import pandas as pd # noqa: F811 not actually a redefinition
ctype = s.dtype
if str(ctype).startswith('datetime64'):
return
s = s.dropna()
if len(s) == 0:
return
all_timestamps = s.apply(lambda x: isinstance(x, (pd.Timestamp, datetime))).all()
if not all_timestamps:
return # not sure why it would happen, but ok
tzs = s.map(lambda x: x.tzinfo).drop_duplicates() # type: ignore[union-attr, var-annotated, arg-type, return-value, unused-ignore]
examples = s[tzs.index]
# todo not so sure this warning is that useful... except for stuff without tz
yield f'''
All values are timestamp-like, but dtype is not datetime. Most likely, you have mixed timezones:
{pformat(list(zip(examples, tzs)))}
'''.strip()
def test_check_dateish() -> None:
import pandas as pd
from .compat import fromisoformat
# empty series shouldn't warn
assert list(_check_dateish(pd.Series([]))) == []
# if no dateimes, shouldn't return any warnings
assert list(_check_dateish(pd.Series([1, 2, 3]))) == []
# all values are datetimes, shouldn't warn
# fmt: off
assert list(_check_dateish(pd.Series([
fromisoformat('2024-08-19T01:02:03'),
fromisoformat('2024-08-19T03:04:05'),
]))) == []
# fmt: on
# mixture of timezones -- should warn
# fmt: off
assert len(list(_check_dateish(pd.Series([
fromisoformat('2024-08-19T01:02:03'),
fromisoformat('2024-08-19T03:04:05Z'),
])))) == 1
# fmt: on
# TODO hmm. maybe this should actually warn?
# fmt: off
assert len(list(_check_dateish(pd.Series([
'whatever',
fromisoformat('2024-08-19T01:02:03'),
])))) == 0
# fmt: on
# fmt: off
ErrorColPolicy = Literal[
'add_if_missing', # add error column if it's missing
'warn' , # warn, but do not modify
'ignore' , # no warnings
]
# fmt: on
def check_error_column(df: DataFrameT, *, policy: ErrorColPolicy) -> Iterable[str]:
if 'error' in df:
return
if policy == 'ignore':
return
wmsg = '''
No 'error' column detected. You probably forgot to handle errors defensively, which means a single bad entry might bring the whole dataframe down.
'''.strip()
if policy == 'add_if_missing':
# todo maybe just add the warnings text as well?
df['error'] = None
wmsg += "\nAdding empty 'error' column (see 'error_col_policy' if you want to change this behaviour)"
pass
yield wmsg
# TODO ugh. typing this is a mess... perhaps should use .compat.ParamSpec?
@decorator
def check_dataframe(f: FuncT, error_col_policy: ErrorColPolicy = 'add_if_missing', *args, **kwargs) -> DataFrameT:
df: DataFrameT = f(*args, **kwargs)
tag = '{f.__module__}:{f.__name__}'
# makes sense to keep super defensive
try:
for col, data in df.reset_index().items():
for w in _check_dateish(data):
warnings.low(f"{tag}, column '{col}': {w}")
except Exception as e:
logger.exception(e)
try:
for w in check_error_column(df, policy=error_col_policy):
warnings.low(f"{tag}, {w}")
except Exception as e:
logger.exception(e)
return df
# todo doctor: could have a suggesion to wrap dataframes with it?? discover by return type?
def error_to_row(e: Exception, *, dt_col: str = 'dt', tz: timezone | None = None) -> Json:
edt = extract_error_datetime(e)
if edt is not None and edt.tzinfo is None and tz is not None:
edt = edt.replace(tzinfo=tz)
err_dict: Json = error_to_json(e)
err_dict[dt_col] = edt
return err_dict
def _to_jsons(it: Iterable[Res[Any]]) -> Iterable[Json]:
for r in it:
if isinstance(r, Exception):
yield error_to_row(r)
else:
yield asdict(r)
# mm. https://github.com/python/mypy/issues/8564
# no type for dataclass?
Schema = Any
def _as_columns(s: Schema) -> Dict[str, Type]:
# todo would be nice to extract properties; add tests for this as well
if dataclasses.is_dataclass(s):
return {f.name: f.type for f in dataclasses.fields(s)}
# else must be NamedTuple??
# todo assert my.core.common.is_namedtuple?
return getattr(s, '_field_types')
# todo add proper types
@check_dataframe
def as_dataframe(it: Iterable[Res[Any]], schema: Schema | None = None) -> DataFrameT:
# todo warn if schema isn't specified?
# ok nice supports dataframe/NT natively
# https://github.com/pandas-dev/pandas/pull/27999
# but it dispatches dataclass based on the first entry...
# https://github.com/pandas-dev/pandas/blob/fc9fdba6592bdb5d0d1147ce4d65639acd897565/pandas/core/frame.py#L562
# same for NamedTuple -- seems that it takes whatever schema the first NT has
# so we need to convert each individually... sigh
import pandas as pd # noqa: F811 not actually a redefinition
columns = None if schema is None else list(_as_columns(schema).keys())
return pd.DataFrame(_to_jsons(it), columns=columns)
# ugh. in principle this could be inside the test
# might be due to use of from __future__ import annotations
# can quickly reproduce by running pytest tests/tz.py tests/core/test_pandas.py
# possibly will be resolved after fix in pytest?
# see https://github.com/pytest-dev/pytest/issues/7856
@dataclasses.dataclass
class _X:
# FIXME try moving inside?
x: int
def test_as_dataframe() -> None:
import numpy as np
import pandas as pd
import pytest
from pandas.testing import assert_frame_equal
from .compat import fromisoformat
it = (dict(i=i, s=f'str{i}') for i in range(5))
with pytest.warns(UserWarning, match=r"No 'error' column") as record_warnings: # noqa: F841
df: DataFrameT = as_dataframe(it)
# todo test other error col policies
# fmt: off
assert_frame_equal(
df,
pd.DataFrame({
'i' : [0 , 1 , 2 , 3 , 4 ],
's' : ['str0', 'str1', 'str2', 'str3', 'str4'],
# NOTE: error column is always added
'error': [None , None , None , None , None ],
}),
)
# fmt: on
assert_frame_equal(as_dataframe([]), pd.DataFrame(columns=['error']))
df2: DataFrameT = as_dataframe([], schema=_X)
assert_frame_equal(
df2,
# FIXME hmm. x column type should be an int?? and error should be string (or object??)
pd.DataFrame(columns=['x', 'error']),
)
@dataclasses.dataclass
class S:
value: str
def it2() -> Iterator[Res[S]]:
yield S(value='test')
yield RuntimeError('i failed')
df = as_dataframe(it2())
# fmt: off
assert_frame_equal(
df,
pd.DataFrame(data={
'value': ['test', np.nan ],
'error': [np.nan, 'RuntimeError: i failed\n'],
'dt' : [np.nan, np.nan ],
}).astype(dtype={'dt': 'float'}), # FIXME should be datetime64 as below
)
# fmt: on
def it3() -> Iterator[Res[S]]:
yield S(value='aba')
yield RuntimeError('whoops')
yield S(value='cde')
yield RuntimeError('exception with datetime', fromisoformat('2024-08-19T22:47:01Z'))
df = as_dataframe(it3())
# fmt: off
assert_frame_equal(df, pd.DataFrame(data={
'value': ['aba' , np.nan , 'cde' , np.nan ],
'error': [np.nan, 'RuntimeError: whoops\n', np.nan, "RuntimeError: ('exception with datetime', datetime.datetime(2024, 8, 19, 22, 47, 1, tzinfo=datetime.timezone.utc))\n"],
# note: dt column is added even if errors don't have an associated datetime
'dt' : [np.nan, np.nan , np.nan, '2024-08-19 22:47:01+00:00'],
}).astype(dtype={'dt': 'datetime64[ns, UTC]'}))
# fmt: on