Inaccessible examples

[nicodomschke]

Hi,

I wanted to run some of the examples, but it seems like the dropbox links inside

gptchem/data.py

only lead to dropbox page saying "That didn't work for some reason"

trying any get_xxx_data() function leads to something like this:

---------------------------------------------------------------------------
ParserError                               Traceback (most recent call last)
Cell In[4], line 1
----> 1 data = get_lipophilicity_data()

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/gptchem/data.py:225, in get_lipophilicity_data()
    221 def get_lipophilicity_data() -> pd.DataFrame:
    222     """Return the Lipophilicity data parsed from ChEMBL [chembl]_"""
    223     return (
    224         pystow.module("gptchem")
--> 225         .ensure_csv(
    226             "lipophilicity",
    227             url="https://www.dropbox.com/s/secesuqvqrdexz4/lipophilicity.csv?dl=1",
    228             read_csv_kwargs=dict(sep=","),
    229         )
    230         .reset_index(drop=True)
    231     )

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/pystow/impl.py:632, in Module.ensure_csv(self, url, name, force, download_kwargs, read_csv_kwargs, *subkeys)
    627 import pandas as pd
    629 path = self.ensure(
    630     *subkeys, url=url, name=name, force=force, download_kwargs=download_kwargs
    631 )
--> 632 return pd.read_csv(path, **_clean_csv_kwargs(read_csv_kwargs))

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1026, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, 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, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)
   1013 kwds_defaults = _refine_defaults_read(
   1014     dialect,
   1015     delimiter,
   (...)
   1022     dtype_backend=dtype_backend,
   1023 )
   1024 kwds.update(kwds_defaults)
-> 1026 return _read(filepath_or_buffer, kwds)

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/pandas/io/parsers/readers.py:626, in _read(filepath_or_buffer, kwds)
    623     return parser
    625 with parser:
--> 626     return parser.read(nrows)

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1923, in TextFileReader.read(self, nrows)
   1916 nrows = validate_integer("nrows", nrows)
   1917 try:
   1918     # error: "ParserBase" has no attribute "read"
   1919     (
   1920         index,
   1921         columns,
   1922         col_dict,
-> 1923     ) = self._engine.read(  # type: ignore[attr-defined]
   1924         nrows
   1925     )
   1926 except Exception:
   1927     self.close()

File ~/.conda/envs/zstruct-llm/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py:234, in CParserWrapper.read(self, nrows)
    232 try:
    233     if self.low_memory:
--> 234         chunks = self._reader.read_low_memory(nrows)
    235         # destructive to chunks
    236         data = _concatenate_chunks(chunks)

File parsers.pyx:838, in pandas._libs.parsers.TextReader.read_low_memory()

File parsers.pyx:905, in pandas._libs.parsers.TextReader._read_rows()

File parsers.pyx:874, in pandas._libs.parsers.TextReader._tokenize_rows()

File parsers.pyx:891, in pandas._libs.parsers.TextReader._check_tokenize_status()

File parsers.pyx:2061, in pandas._libs.parsers.raise_parser_error()

ParserError: Error tokenizing data. C error: Expected 1 fields in line 4, saw 3

[kjappelbaum]

Indeed, that is a bug. Let me move the data somewhere else. I am busy with something else this week but planned to spend one day of maintaining this next week

[kjappelbaum]

Thanks for raising this issue!

[kjappelbaum]

I'll upload them onto Zenodo to keep them in a stable place

[kjappelbaum]

datasets are on Hugginface https://huggingface.co/datasets/kjappelbaum/gptchem/tree/main but I still need to adjust the code in the library. Sorry for the delay on this!