BUG: IndexError when header rows have unequal column counts

[MrCreosote]

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

I couldn't find it with a search on indexerror read_csv anyway

• I have confirmed this bug exists on the latest version of pandas.

• (optional) I have confirmed this bug exists on the master branch of pandas.

---

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Code Sample, a copy-pastable example

In [1]: import pandas

In [2]: from io import StringIO

In [3]: data = """
   ...: head1, head2, head3
   ...: sub1, sub2
   ...: """[1:]

In [4]: data
Out[4]: 'head1, head2, head3\nsub1, sub2\n'

In [5]: pandas.read_csv(StringIO(data), sep=",", header=[0, 1], on_bad_lines="sk
   ...: ip")
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-5-1bf8982a1449> in <module>
----> 1 pandas.read_csv(StringIO(data), sep=",", header=[0, 1], on_bad_lines="skip")

*snip - I can provide the entire trace on request, but leave it out here for brevity*

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py in <genexpr>(.0)
    343 
    344         def extract(r):
--> 345             return tuple(r[i] for i in range(field_count) if i not in sic)
    346 
    347         columns = list(zip(*(extract(r) for r in header)))

IndexError: list index out of range

Problem description

A generic index error is thrown rather than a pandas specific error, or skipping the row as per on_bad_lines.

Expected Output

I would expect one of two things:

1. a pandas.errors.ParseError describing the problem
2. skipping the header. This seems a little odd to me so maybe 1 is the better option.

Maybe there are other reasonable responses as well.

Output of pd.show_versions()

INSTALLED VERSIONS

commit : 5f648bf
python : 3.9.6.final.0
python-bits : 64
OS : Linux
OS-release : 4.15.0-154-generic
Version : #161-Ubuntu SMP Fri Jul 30 13:04:17 UTC 2021
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8

pandas : 1.3.2
numpy : 1.21.2
pytz : 2021.1
dateutil : 2.8.2
pip : 20.3.3
setuptools : 51.3.3
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 : 7.26.0
pandas_datareader: None
bs4 : None
bottleneck : None
fsspec : None
fastparquet : None
gcsfs : None
matplotlib : None
numexpr : None
odfpy : None
openpyxl : 3.0.7
pandas_gbq : None
pyarrow : None
pyxlsb : None
s3fs : None
scipy : None
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : 2.0.1
xlwt : None
numba : None

[MrCreosote]

Here's the entire stacktrace:

<ipython-input-5-1bf8982a1449> in <module>
----> 1 pandas.read_csv(StringIO(data), sep=",", header=[0, 1], on_bad_lines="skip")

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/util/_decorators.py in wrapper(*args, **kwargs)
    309                     stacklevel=stacklevel,
    310                 )
--> 311             return func(*args, **kwargs)
    312 
    313         return wrapper

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/readers.py 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)
    584     kwds.update(kwds_defaults)
    585 
--> 586     return _read(filepath_or_buffer, kwds)
    587 
    588 

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/readers.py in _read(filepath_or_buffer, kwds)
    480 
    481     # Create the parser.
--> 482     parser = TextFileReader(filepath_or_buffer, **kwds)
    483 
    484     if chunksize or iterator:

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/readers.py in __init__(self, f, engine, **kwds)
    809             self.options["has_index_names"] = kwds["has_index_names"]
    810 
--> 811         self._engine = self._make_engine(self.engine)
    812 
    813     def close(self):

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/readers.py in _make_engine(self, engine)
   1038             )
   1039         # error: Too many arguments for "ParserBase"
-> 1040         return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
   1041 
   1042     def _failover_to_python(self):

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py in __init__(self, src, **kwds)
     90                     self.col_names,
     91                     passed_names,
---> 92                 ) = self._extract_multi_indexer_columns(
     93                     self._reader.header,
     94                     self.index_names,  # type: ignore[has-type]

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py in _extract_multi_indexer_columns(self, header, index_names, col_names, passed_names)
    345             return tuple(r[i] for i in range(field_count) if i not in sic)
    346 
--> 347         columns = list(zip(*(extract(r) for r in header)))
    348         names = ic + columns
    349 

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py in <genexpr>(.0)
    345             return tuple(r[i] for i in range(field_count) if i not in sic)
    346 
--> 347         columns = list(zip(*(extract(r) for r in header)))
    348         names = ic + columns
    349 

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py in extract(r)
    343 
    344         def extract(r):
--> 345             return tuple(r[i] for i in range(field_count) if i not in sic)
    346 
    347         columns = list(zip(*(extract(r) for r in header)))

~/.local/share/virtualenvs/py3.9playground--W4ZB8cD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py in <genexpr>(.0)
    343 
    344         def extract(r):
--> 345             return tuple(r[i] for i in range(field_count) if i not in sic)
    346 
    347         columns = list(zip(*(extract(r) for r in header)))

IndexError: list index out of range

[quantumalaviya]

So, just to confirm: an exception needs to be thrown if the length of the row (r) is not equal to the value of field_count inside the extract function, like so:

def extract(r):
            try:
                return tuple(r[i] for i in range(field_count) if i not in sic)
            except IndexError:
                raise Exception("Error") from None

This changes the stack trace to:

  File "<ipython-input-4-1bf8982a1449>", line 1, in <module>
    pandas.read_csv(StringIO(data), sep=",", header=[0, 1], on_bad_lines="skip")

  File "pandas\util\_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)

  File "pandas\io\parsers\readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)

  File "pandas\io\parsers\readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)

  File "pandas\io\parsers\readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)

  File "pandas\io\parsers\readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]

  File "pandas\io\parsers\c_parser_wrapper.py", line 92, in __init__
    ) = self._extract_multi_indexer_columns(

  File "pandas\io\parsers\base_parser.py", line 350, in _extract_multi_indexer_columns
    columns = list(zip(*(extract(r) for r in header)))

  File "pandas\io\parsers\base_parser.py", line 350, in <genexpr>
    columns = list(zip(*(extract(r) for r in header)))

  File "pandas\io\parsers\base_parser.py", line 348, in extract
    raise Exception("Error") from None

Exception: Error

If someone can guide me as to which exception I should raise and if there's anything else that needs to be added, I would love to work on this issue.

Also, I did confirm; the bug also exists on the master branch

[MrCreosote]

It'd be good if the exception could provide information regarding the header row on which the error occured

[phofl]

@quantumalaviya
You could do this before the extract, simply validating if all lists in header have the same length.

ParserError would be good here.

[quantumalaviya]

@phofl Something like this?

#check if header lengths are equal
for l in range(len(header)):
    if len(header[l])!=field_count:
        raise ParserError(f"Header rows must have equal number of columns")

[quantumalaviya]

@MrCreosote How would you suggest dealing with it in cases where there is more than one discrepancy? For example, if 3 rows are chosen to be headers and all have different values?

[MrCreosote]

Personally I'd probably just throw an error for the first discrepancy found, top to bottom, and ignore the others, but I'm a brand new Pandas user and not a dev, so the weight of my opinion is pretty low.

[MrCreosote]

Although I would definitely want the row index of the first offending row in the exception

[quantumalaviya]

Have a look at the PR and let me know if it's satisfactory.

The traceback now looks like this:

File "<ipython-input-4-1bf8982a1449>", line 1, in <module>
    pandas.read_csv(StringIO(data), sep=",", header=[0, 1], on_bad_lines="skip")

  File "pandas\util\_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)

  File "pandas\io\parsers\readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)

  File "pandas\io\parsers\readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)

  File "pandas\io\parsers\readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)

  File "pandas\io\parsers\readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]

  File "pandas\io\parsers\c_parser_wrapper.py", line 92, in __init__
    ) = self._extract_multi_indexer_columns(

  File "pandas\io\parsers\base_parser.py", line 347, in _extract_multi_indexer_columns
    raise ParserError("Header rows must have equal number of columns."

ParserError: Header rows must have equal number of columns. Mismatch found at row 1