Error in examples/diagnostics_and_criticism/model_averaging.ipynb

[williambdean]

The body_fat.csv from pm.get_data("body_fat.csv") is not found.

───────────────────────────────────── Error running examples/diagnostics_and_criticism/model_averaging.ipynb ─────────────────────────────────────

---------------------------------------------------------------------------
Exception encountered at "In [4]":
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[4], line 2
      1 try:
----> 2     d = pd.read_csv(os.path.join("..", "data", "body_fat.csv"))
      3 except FileNotFoundError:

File ~/micromamba/envs/pymc-examples/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)
   1024 kwds.update(kwds_defaults)
-> 1026 return _read(filepath_or_buffer, kwds)

File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pandas/io/parsers/readers.py:620, in _read(filepath_or_buffer, kwds)
    619 # Create the parser.
--> 620 parser = TextFileReader(filepath_or_buffer, **kwds)
    622 if chunksize or iterator:

File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1620, in TextFileReader.__init__(self, f, engine,
**kwds)
   1619 self.handles: IOHandles | None = None
-> 1620 self._engine = self._make_engine(f, self.engine)

File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pandas/io/parsers/readers.py:1880, in TextFileReader._make_engine(self, f,
engine)
   1879         mode += "b"
-> 1880 self.handles = get_handle(
   1881     f,
   1882     mode,
   1883     encoding=self.options.get("encoding", None),
   1884     compression=self.options.get("compression", None),
   1885     memory_map=self.options.get("memory_map", False),
   1886     is_text=is_text,
   1887     errors=self.options.get("encoding_errors", "strict"),
   1888     storage_options=self.options.get("storage_options", None),
   1889 )
   1890 assert self.handles is not None

File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pandas/io/common.py:873, in get_handle(path_or_buf, mode, encoding, compression,
memory_map, is_text, errors, storage_options)
    871 if ioargs.encoding and "b" not in ioargs.mode:
    872     # Encoding
--> 873     handle = open(
    874         handle,
    875         ioargs.mode,
    876         encoding=ioargs.encoding,
    877         errors=errors,
    878         newline="",
    879     )
    880 else:
    881     # Binary mode

FileNotFoundError: [Errno 2] No such file or directory: '../data/body_fat.csv'

During handling of the above exception, another exception occurred:

HTTPError                                 Traceback (most recent call last)
Cell In[4], line 4
      2     d = pd.read_csv(os.path.join("..", "data", "body_fat.csv"))
      3 except FileNotFoundError:
----> 4     d = pd.read_csv(pm.get_data("body_fat.csv"))
      6 d.head()

File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/data.py:67, in get_data(filename)
     55 def get_data(filename):
     56     """Return a BytesIO object for a package data file.
     57
     58     Parameters
   (...)
     65     BytesIO of the data
     66     """
---> 67     with urllib.request.urlopen(BASE_URL.format(filename=filename)) as handle:
     68         content = handle.read()
     69     return io.BytesIO(content)

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:216, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    214 else:
    215     opener = _opener
--> 216 return opener.open(url, data, timeout)

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:525, in OpenerDirector.open(self, fullurl, data, timeout)
    523 for processor in self.process_response.get(protocol, []):
    524     meth = getattr(processor, meth_name)
--> 525     response = meth(req, response)
    527 return response

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:634, in HTTPErrorProcessor.http_response(self, request, response)
    631 # According to RFC 2616, "2xx" code indicates that the client's
    632 # request was successfully received, understood, and accepted.
    633 if not (200 <= code < 300):
--> 634     response = self.parent.error(
    635         'http', request, response, code, msg, hdrs)
    637 return response

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:563, in OpenerDirector.error(self, proto, *args)
    561 if http_err:
    562     args = (dict, 'default', 'http_error_default') + orig_args
--> 563     return self._call_chain(*args)

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:496, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
    494 for handler in handlers:
    495     func = getattr(handler, meth_name)
--> 496     result = func(*args)
    497     if result is not None:
    498         return result

File ~/micromamba/envs/pymc-examples/lib/python3.11/urllib/request.py:643, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg,
hdrs)
    642 def http_error_default(self, req, fp, code, msg, hdrs):
--> 643     raise HTTPError(req.full_url, code, msg, hdrs, fp)

HTTPError: HTTP Error 404: Not Found

[OriolAbril]

cc @aloctavodia who will have the file used which looks like wasn't commited as part of the PR

[williambdean]

cc @aloctavodia who will have the file used which looks like wasn't commited as part of the PR

Could also look back in the pymc commit history to grab