Cannot build documentation: No such kernel named python3

Code Sample, a copy-pastable example if possible

# Run in local pandas repo
conda create -y -n pandas_dev python=3 -c conda-forge --file ci/requirements_all.txt
conda install -y -n pandas_dev -c conda-forge fastparquet feather-format pandas-datareader pandas-gbq python-blosc pyarrow psycopg2 pymysql s3fs xarray
source activate pandas_dev
python setup.py develop
cd doc
python make.py html

Output

Running Sphinx v1.5.6
WARNING: while setting up extension conf.py: directive 'autosummary' is already registered, it will be overridden
loading pickled environment... not yet created
[autosummary] generating autosummary for: 10min.rst, advanced.rst, api.rst, basics.rst, categorical.rst, comparison_with_r.rst, comparison_with_sas.rst, comparison_with_sql.rst, computation.rst, contributing.rst, ..., release.rst, remote_data.rst, reshaping.rst, sparse.rst, text.rst, timedeltas.rst, timeseries.rst, tutorials.rst, visualization.rst, whatsnew.rst
[autosummary] generating autosummary for: /Users/hayes/personal/pandas/doc/source/generated/pandas.Categorical.__array__.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.Categorical.from_codes.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.Categorical.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.add_categories.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.as_ordered.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.as_unordered.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.categories.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.codes.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.ordered.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.CategoricalIndex.remove_categories.rst, ..., /Users/hayes/personal/pandas/doc/source/generated/pandas.test.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.testing.assert_frame_equal.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.testing.assert_index_equal.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.testing.assert_series_equal.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.timedelta_range.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.to_datetime.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.to_numeric.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.to_timedelta.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.unique.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.wide_to_long.rst
WARNING: [autosummary] failed to import 'pandas.DataFrame.columns': no module named pandas.DataFrame.columns
WARNING: [autosummary] failed to import 'pandas.DataFrame.index': no module named pandas.DataFrame.index
WARNING: [autosummary] failed to import 'pandas.Panel.items': no module named pandas.Panel.items
WARNING: [autosummary] failed to import 'pandas.Panel.major_axis': no module named pandas.Panel.major_axis
WARNING: [autosummary] failed to import 'pandas.Panel.minor_axis': no module named pandas.Panel.minor_axis
WARNING: [autosummary] failed to import 'pandas.Series.index': no module named pandas.Series.index
[autosummary] generating autosummary for: /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.agg.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.as_blocks.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.at_time.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.between_time.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.bfill.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.blocks.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.bool.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.compound.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.consolidate.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.DataFrame.divide.rst, ..., /Users/hayes/personal/pandas/doc/source/generated/pandas.Timestamp.minute.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.Timestamp.offset.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.Timestamp.to_datetime.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.Timestamp.week.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.env.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.from_custom_template.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.loader.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.set_table_attributes.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.template.rst, /Users/hayes/personal/pandas/doc/source/generated/pandas.io.formats.style.Styler.to_excel.rst
loading intersphinx inventory from http://www.statsmodels.org/devel/objects.inv...
loading intersphinx inventory from http://matplotlib.org/objects.inv...
loading intersphinx inventory from http://docs.python.org/3/objects.inv...
intersphinx inventory has moved: http://docs.python.org/3/objects.inv -> https://docs.python.org/3/objects.inv
loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv...
intersphinx inventory has moved: http://docs.scipy.org/doc/numpy/objects.inv -> https://docs.scipy.org/doc/numpy/objects.inv
loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv...
intersphinx inventory has moved: http://docs.scipy.org/doc/scipy/reference/objects.inv -> https://docs.scipy.org/doc/scipy/reference/objects.inv
loading intersphinx inventory from https://pylib.readthedocs.io/en/latest/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 38 source files that are out of date
updating environment: 1794 added, 0 changed, 0 removed
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section Note
  warn("Unknown section %s" % key)
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section Note
  warn("Unknown section %s" % key)
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section :func:`datetime.datetime` Parameters
  warn("Unknown section %s" % key)
reading sources... [  0%] computation

>>>-------------------------------------------------------------------------
Warning in /Users/hayes/personal/pandas/doc/source/computation.rst at block ending on line None
Specify :okwarning: as an option in the ipython:: block to suppress this message
----------------------------------------------------------------------------
/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/numpy/core/_methods.py:135: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
<<<-------------------------------------------------------------------------
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section Note
  warn("Unknown section %s" % key)
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section Note
  warn("Unknown section %s" % key)
/Users/hayes/personal/pandas/doc/sphinxext/numpydoc/docscrape.py:119: UserWarning: Unknown section :func:`datetime.datetime` Parameters
  warn("Unknown section %s" % key)
reading sources... [ 99%] io

>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/io.rst at block ending on line 4531
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-510-8ba55b61d48c> in <module>()
----> 1 df.to_parquet('example_fp.parquet', engine='fastparquet')

~/personal/pandas/pandas/core/frame.py in to_parquet(self, fname, engine, compression, **kwargs)
   1643         from pandas.io.parquet import to_parquet
   1644         to_parquet(self, fname, engine,
-> 1645                    compression=compression, **kwargs)
   1646
   1647     @Substitution(header='Write out the column names. If a list of strings '

~/personal/pandas/pandas/io/parquet.py in to_parquet(df, path, engine, compression, **kwargs)
    176         raise ValueError("parquet must have string column names")
    177
--> 178     return impl.write(df, path, compression=compression)
    179
    180

~/personal/pandas/pandas/io/parquet.py in write(self, df, path, compression, **kwargs)
    114         with catch_warnings(record=True):
    115             self.api.write(path, df,
--> 116                            compression=compression, **kwargs)
    117
    118     def read(self, path):

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/writer.py in write(filename, data, row_group_offsets, compression, file_scheme, open_with, mkdirs, has_nulls, write_index, partition_on, fixed_text, append, object_encoding, times)
    800     if file_scheme == 'simple':
    801         write_simple(filename, data, fmd, row_group_offsets,
--> 802                      compression, open_with, has_nulls, append)
    803     elif file_scheme in ['hive', 'drill']:
    804         if append:

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/writer.py in write_simple(fn, data, fmd, row_group_offsets, compression, open_with, has_nulls, append)
    696                    else None)
    697             rg = make_row_group(f, data[start:end], fmd.schema,
--> 698                                 compression=compression)
    699             if rg is not None:
    700                 fmd.row_groups.append(rg)

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/writer.py in make_row_group(f, data, schema, compression)
    592                 comp = compression
    593             chunk = write_column(f, data[column.name], column,
--> 594                                  compression=comp)
    595             rg.columns.append(chunk)
    596     rg.total_byte_size = sum([c.meta_data.total_uncompressed_size for c in

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/writer.py in write_column(f, data, selement, compression)
    521
    522     if compression:
--> 523         bdata = compress_data(bdata, compression)
    524         l1 = len(bdata)
    525     else:

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/compression.py in compress_data(data, algorithm)
     71     if algorithm.upper() not in compressions:
     72         raise RuntimeError("Compression '%s' not available.  Options: %s" %
---> 73                 (algorithm, sorted(compressions)))
     74     return compressions[algorithm.upper()](data)
     75

RuntimeError: Compression 'snappy' not available.  Options: ['GZIP', 'UNCOMPRESSED']
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/io.rst at block ending on line 4540
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NotADirectoryError                        Traceback (most recent call last)
~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/api.py in __init__(self, fn, verify, open_with, sep, root)
     95                 self.fn = fn2
---> 96                 with open_with(fn2, 'rb') as f:
     97                     self._parse_header(f, verify)

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/util.py in default_open(f, mode)
     43 def default_open(f, mode='rb'):
---> 44     return open(f, mode)
     45

NotADirectoryError: [Errno 20] Not a directory: 'example_fp.parquet/_metadata'

During handling of the above exception, another exception occurred:

OSError                                   Traceback (most recent call last)
<ipython-input-512-d4bce7d5df53> in <module>()
----> 1 result = pd.read_parquet('example_fp.parquet', engine='fastparquet')

~/personal/pandas/pandas/io/parquet.py in read_parquet(path, engine, **kwargs)
    202
    203     impl = get_engine(engine)
--> 204     return impl.read(path)

~/personal/pandas/pandas/io/parquet.py in read(self, path)
    118     def read(self, path):
    119         path, _, _ = get_filepath_or_buffer(path)
--> 120         return self.api.ParquetFile(path).to_pandas()
    121
    122

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/api.py in __init__(self, fn, verify, open_with, sep, root)
    100                 self.fn = fn
    101                 with open_with(fn, 'rb') as f:
--> 102                     self._parse_header(f, verify)
    103         self.open = open_with
    104

~/miniconda/envs/pandas_dev/lib/python3.6/site-packages/fastparquet/api.py in _parse_header(self, f, verify)
    108             if verify:
    109                 assert f.read(4) == b'PAR1'
--> 110             f.seek(-8, 2)
    111             head_size = struct.unpack('<i', f.read(4))[0]
    112             if verify:

OSError: [Errno 22] Invalid argument
<<<-------------------------------------------------------------------------

reading sources... [ 99%] r_interface

>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 40
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-79b90b86f23f> in <module>()
----> 1 from rpy2.robjects import r, pandas2ri

ModuleNotFoundError: No module named 'rpy2'
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 40
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-2-0531561cbbe9> in <module>()
----> 1 pandas2ri.activate()

NameError: name 'pandas2ri' is not defined
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 51
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-3-8bdc5639fb0c> in <module>()
----> 1 r.data('iris')

~/personal/pandas/pandas/core/window.py in __getattr__(self, attr)
    177
    178         raise AttributeError("%r object has no attribute %r" %
--> 179                              (type(self).__name__, attr))
    180
    181     def _dir_additions(self):

AttributeError: 'Rolling' object has no attribute 'data'
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 51
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-4-b9fbcc010df6> in <module>()
----> 1 r['iris'].head()

~/personal/pandas/pandas/core/base.py in __getitem__(self, key)
    252         elif not getattr(self, 'as_index', False):
    253             if key not in self.obj.columns:
--> 254                 raise KeyError("Column not found: {key}".format(key=key))
    255             return self._gotitem(key, ndim=2)
    256

KeyError: 'Column not found: iris'
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 69
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-6-7620636bf651> in <module>()
----> 1 r_dataframe = pandas2ri.py2ri(df)

NameError: name 'pandas2ri' is not defined
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 69
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-7-4ab82496598b> in <module>()
----> 1 print(type(r_dataframe))

NameError: name 'r_dataframe' is not defined
<<<-------------------------------------------------------------------------



>>>-------------------------------------------------------------------------
Exception in /Users/hayes/personal/pandas/doc/source/r_interface.rst at block ending on line 69
Specify :okexcept: as an option in the ipython:: block to suppress this message
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-8-714489a67f8e> in <module>()
----> 1 print(r_dataframe)

NameError: name 'r_dataframe' is not defined
<<<-------------------------------------------------------------------------

Exception occurred while building, starting debugger:
Traceback (most recent call last):
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 201, in get_kernel_spec
    resource_dir = d[kernel_name.lower()]
KeyError: 'python3'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbsphinx.py", line 634, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbsphinx.py", line 578, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py", line 257, in preprocess
    cwd=path)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py", line 237, in start_new_kernel
    km.start_kernel(**kwargs)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/jupyter_client/manager.py", line 244, in start_kernel
    kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/jupyter_client/manager.py", line 175, in format_kernel_cmd
    cmd = self.kernel_spec.argv + extra_arguments
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/jupyter_client/manager.py", line 87, in kernel_spec
    self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/jupyter_client/kernelspec.py", line 203, in get_kernel_spec
    raise NoSuchKernel(kernel_name)
jupyter_client.kernelspec.NoSuchKernel: No such kernel named python3

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/cmdline.py", line 296, in main
    app.build(opts.force_all, filenames)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/application.py", line 333, in build
    self.builder.build_update()
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 251, in build_update
    'out of date' % len(to_build))
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 265, in build
    self.doctreedir, self.app))
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/environment/__init__.py", line 556, in update
    self._read_serial(docnames, app)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/environment/__init__.py", line 576, in _read_serial
    self.read_doc(docname, app)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/environment/__init__.py", line 684, in read_doc
    pub.publish()
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/sphinx/io.py", line 55, in read
    self.parse()
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbsphinx.py", line 645, in parse
    str(e))
nbsphinx.NotebookError: NoSuchKernel in style.ipynb:
No such kernel named python3
> /Users/hayes/miniconda/envs/pandas_dev/lib/python3.6/site-packages/nbsphinx.py(645)parse()
-> str(e))
(Pdb)

Problem description

I’m trying to build the documentation, following the instructions in the Contributing to pandas docs. Unfortunately, I hit a Python debugger along the way, causing the build to fail.

Do you have any advice on how to get past this issue?

Expected Output

No errors when building the documentation when following the documentation. Ideally no warnings either.

Output of pd.show_versions()

INSTALLED VERSIONS

commit: None python: 3.6.3.final.0 python-bits: 64 OS: Darwin OS-release: 16.7.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8

pandas: 0.22.0.dev0+20.g8449ffd90 pytest: 3.2.3 pip: 9.0.1 setuptools: 36.6.0 Cython: 0.27.2 numpy: 1.13.3 scipy: 0.19.1 pyarrow: None xarray: None IPython: 6.2.1 sphinx: 1.5.6 patsy: 0.4.1 dateutil: 2.6.1 pytz: 2017.3 blosc: None bottleneck: 1.2.1 tables: 3.4.2 numexpr: 2.6.4 feather: None matplotlib: 2.1.0 openpyxl: 2.5.0b1 xlrd: 1.1.0 xlwt: 1.3.0 xlsxwriter: 1.0.2 lxml: 4.1.0 bs4: 4.6.0 html5lib: 0.999999999 sqlalchemy: 1.1.13 pymysql: 0.7.11.None psycopg2: None jinja2: 2.9.6 s3fs: None fastparquet: None pandas_gbq: None pandas_datareader: None

[mattayes]

Awesome, installing ipykernel did the trick, thank you! And thanks for improving the docs, I appreciate it!

[jorisvandenbossche]

@mattayes We just had the same question on gitter, and there is was ipykernel that was missing. Can you install that one and see if it then works?