Resolve remaining doctests, enable doctest in CI #1124

clarkgwillison · 2020-06-23T20:47:45Z

Closes Possible regression in UnitRegistry.get_compatible_units() #1115
Executed black -t py36 . && isort -rc . && flake8 with no errors
The change is fully covered by automated unit tests
Documented in docs/ as appropriate
Added an entry to the CHANGES file

This PR pushes off fixing the get_compatible_units(..., group_or_system='...') feature mentioned in #1115, removing references to it from the docs for now.

It also enables doctests in CI now that all remaining doctests are passing

closes hgrecco#1115

some configurations in Travis skip optional dependencies, which causes the doctests that rely on them to fail. This fixes that by checking for those dependencies and skipping the affected doctests with :skipif:

clarkgwillison · 2020-07-12T05:14:48Z

@hgrecco this is ready for review

hgrecco · 2020-07-13T16:45:09Z

bors r+

bors · 2020-07-13T16:55:04Z

Build succeeded:

continuous-integration/travis-ci/push

hgrecco · 2020-07-13T19:01:48Z

awesome, thianks. I am getting an error on read the docs, lack of pint-pandas?

Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading intersphinx inventory from http://docs.python.org/objects.inv...
intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 20 source files that are out of date
updating environment: 20 added, 0 changed, 0 removed
reading sources... [  5%] contexts
reading sources... [ 10%] contributing
reading sources... [ 15%] currencies
reading sources... [ 20%] defining
reading sources... [ 25%] developers_reference
reading sources... [ 30%] faq
reading sources... [ 35%] getting
reading sources... [ 40%] index
reading sources... [ 45%] measurement
reading sources... [ 50%] nonmult
reading sources... [ 55%] numpy
reading sources... [ 60%] performance
reading sources... [ 65%] pint-convert
reading sources... [ 70%] pint-pandas
/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py:358: FutureWarning: Method cleanup(connection_file=True) is deprecated, use cleanup_resources(restart=False).
  FutureWarning)
/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/jupyter_client/manager.py:358: FutureWarning: Method cleanup(connection_file=True) is deprecated, use cleanup_resources(restart=False).
  FutureWarning)

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 994, in parse
    rststring, resources = exporter.from_notebook_node(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 805, in from_notebook_node
    nb, resources = pp.preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 405, in preprocess
    nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbconvert/preprocessors/base.py", line 69, in preprocess
    nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 448, in preprocess_cell
    raise CellExecutionError.from_cell_and_msg(cell, out)
nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
------------------
df = pd.DataFrame({
    "torque": pd.Series([1, 2, 2, 3], dtype="pint[lbf ft]"),
    "angular_velocity": pd.Series([1, 2, 2, 3], dtype="pint[rpm]"),
})
df
------------------

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�[0;31mTypeError�[0m                                 Traceback (most recent call last)
�[0;32m~/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pandas/core/dtypes/common.py�[0m in �[0;36mpandas_dtype�[0;34m(dtype)�[0m
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During handling of the above exception, another exception occurred:

�[0;31mTypeError�[0m                                 Traceback (most recent call last)
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�[1;32m      1�[0m df = pd.DataFrame({
�[0;32m----> 2�[0;31m     �[0;34m"torque"�[0m�[0;34m:�[0m �[0mpd�[0m�[0;34m.�[0m�[0mSeries�[0m�[0;34m(�[0m�[0;34m[�[0m�[0;36m1�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m3�[0m�[0;34m]�[0m�[0;34m,�[0m �[0mdtype�[0m�[0;34m=�[0m�[0;34m"pint[lbf ft]"�[0m�[0;34m)�[0m�[0;34m,�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0m�[1;32m      3�[0m     �[0;34m"angular_velocity"�[0m�[0;34m:�[0m �[0mpd�[0m�[0;34m.�[0m�[0mSeries�[0m�[0;34m(�[0m�[0;34m[�[0m�[0;36m1�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m3�[0m�[0;34m]�[0m�[0;34m,�[0m �[0mdtype�[0m�[0;34m=�[0m�[0;34m"pint[rpm]"�[0m�[0;34m)�[0m�[0;34m,�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[1;32m      4�[0m })
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�[1;32m    227�[0m                     �[0mdtype�[0m �[0;34m=�[0m �[0mdata�[0m�[0;34m.�[0m�[0mdtype�[0m�[0;34m�[0m�[0;34m�[0m�[0m
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�[0;32m--> 231�[0;31m             �[0mdtype�[0m �[0;34m=�[0m �[0mpandas_dtype�[0m�[0;34m(�[0m�[0mdtype�[0m�[0;34m)�[0m�[0;34m�[0m�[0;34m�[0m�[0m
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�[1;32m   2054�[0m             �[0;32mraise�[0m �[0mTypeError�[0m�[0;34m(�[0m�[0;34m"data type not understood"�[0m�[0;34m)�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0;32m-> 2055�[0;31m         �[0;32mraise�[0m �[0mTypeError�[0m�[0;34m(�[0m�[0;34m"data type '{}' not understood"�[0m�[0;34m.�[0m�[0mformat�[0m�[0;34m(�[0m�[0mdtype�[0m�[0;34m)�[0m�[0;34m)�[0m�[0;34m�[0m�[0;34m�[0m�[0m
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�[0;31mTypeError�[0m: data type 'pint[lbf ft]' not understood
TypeError: data type 'pint[lbf ft]' not understood


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 304, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 341, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 347, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 360, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 468, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 490, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 534, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/sphinx/io.py", line 318, in read_doc
    pub.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/docutils/core.py", line 217, in publish
    self.settings)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/docutils/readers/__init__.py", line 72, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/pint/envs/latest/lib/python3.7/site-packages/nbsphinx.py", line 1001, in parse
    raise NotebookError('\n'.join(lines))
nbsphinx.NotebookError: CellExecutionError in pint-pandas.ipynb:
------------------
df = pd.DataFrame({
    "torque": pd.Series([1, 2, 2, 3], dtype="pint[lbf ft]"),
    "angular_velocity": pd.Series([1, 2, 2, 3], dtype="pint[rpm]"),
})
df
------------------

�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mTypeError�[0m                                 Traceback (most recent call last)
�[0;32m~/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pandas/core/dtypes/common.py�[0m in �[0;36mpandas_dtype�[0;34m(dtype)�[0m
�[1;32m   2049�[0m     �[0;32mtry�[0m�[0;34m:�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0;32m-> 2050�[0;31m         �[0mnpdtype�[0m �[0;34m=�[0m �[0mnp�[0m�[0;34m.�[0m�[0mdtype�[0m�[0;34m(�[0m�[0mdtype�[0m�[0;34m)�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0m�[1;32m   2051�[0m     �[0;32mexcept�[0m �[0mException�[0m�[0;34m:�[0m�[0;34m�[0m�[0;34m�[0m�[0m

�[0;31mTypeError�[0m: data type "pint[lbf ft]" not understood

During handling of the above exception, another exception occurred:

�[0;31mTypeError�[0m                                 Traceback (most recent call last)
�[0;32m<ipython-input-2-381c91812326>�[0m in �[0;36m<module>�[0;34m�[0m
�[1;32m      1�[0m df = pd.DataFrame({
�[0;32m----> 2�[0;31m     �[0;34m"torque"�[0m�[0;34m:�[0m �[0mpd�[0m�[0;34m.�[0m�[0mSeries�[0m�[0;34m(�[0m�[0;34m[�[0m�[0;36m1�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m3�[0m�[0;34m]�[0m�[0;34m,�[0m �[0mdtype�[0m�[0;34m=�[0m�[0;34m"pint[lbf ft]"�[0m�[0;34m)�[0m�[0;34m,�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0m�[1;32m      3�[0m     �[0;34m"angular_velocity"�[0m�[0;34m:�[0m �[0mpd�[0m�[0;34m.�[0m�[0mSeries�[0m�[0;34m(�[0m�[0;34m[�[0m�[0;36m1�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m2�[0m�[0;34m,�[0m �[0;36m3�[0m�[0;34m]�[0m�[0;34m,�[0m �[0mdtype�[0m�[0;34m=�[0m�[0;34m"pint[rpm]"�[0m�[0;34m)�[0m�[0;34m,�[0m�[0;34m�[0m�[0;34m�[0m�[0m
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�[1;32m    227�[0m                     �[0mdtype�[0m �[0;34m=�[0m �[0mdata�[0m�[0;34m.�[0m�[0mdtype�[0m�[0;34m�[0m�[0;34m�[0m�[0m
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�[0;31mTypeError�[0m: data type 'pint[lbf ft]' not understood
TypeError: data type 'pint[lbf ft]' not understood

You can ignore this error by setting the following in conf.py:

    nbsphinx_allow_errors = True


Notebook error:
CellExecutionError in pint-pandas.ipynb:
------------------
df = pd.DataFrame({
    "torque": pd.Series([1, 2, 2, 3], dtype="pint[lbf ft]"),
    "angular_velocity": pd.Series([1, 2, 2, 3], dtype="pint[rpm]"),
})
df
------------------

�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mTypeError�[0m                                 Traceback (most recent call last)
�[0;32m~/.pyenv/versions/3.7.3/lib/python3.7/site-packages/pandas/core/dtypes/common.py�[0m in �[0;36mpandas_dtype�[0;34m(dtype)�[0m
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�[0;32m-> 2050�[0;31m         �[0mnpdtype�[0m �[0;34m=�[0m �[0mnp�[0m�[0;34m.�[0m�[0mdtype�[0m�[0;34m(�[0m�[0mdtype�[0m�[0;34m)�[0m�[0;34m�[0m�[0;34m�[0m�[0m
�[0m�[1;32m   2051�[0m     �[0;32mexcept�[0m �[0mException�[0m�[0;34m:�[0m�[0;34m�[0m�[0;34m�[0m�[0m

�[0;31mTypeError�[0m: data type "pint[lbf ft]" not understood

During handling of the above exception, another exception occurred:

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�[0;31mTypeError�[0m: data type 'pint[lbf ft]' not understood
TypeError: data type 'pint[lbf ft]' not understood

You can ignore this error by setting the following in conf.py:

    nbsphinx_allow_errors = True

resolve remaining doctests, enable doctest in CI

d2db231

closes hgrecco#1115

clarkgwillison force-pushed the fix-last-doctests branch from 4b73ae4 to d2db231 Compare July 12, 2020 01:53

clarkgwillison added 2 commits July 11, 2020 20:51

update install instructions for pint-pandas in docs

c7edd2e

skip doctests that rely on missing dependencies

1da80f4

some configurations in Travis skip optional dependencies, which causes the doctests that rely on them to fail. This fixes that by checking for those dependencies and skipping the affected doctests with :skipif:

clarkgwillison force-pushed the fix-last-doctests branch from 0f7595b to 1da80f4 Compare July 12, 2020 05:00

clarkgwillison changed the title ~~WIP: resolve remaining doctests, enable doctest in CI~~ Resolve remaining doctests, enable doctest in CI Jul 12, 2020

bors bot merged commit b6e1811 into hgrecco:master Jul 13, 2020

clarkgwillison deleted the fix-last-doctests branch July 13, 2020 19:52

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Resolve remaining doctests, enable doctest in CI #1124

Resolve remaining doctests, enable doctest in CI #1124

clarkgwillison commented Jun 23, 2020

clarkgwillison commented Jul 12, 2020

hgrecco commented Jul 13, 2020

bors bot commented Jul 13, 2020

hgrecco commented Jul 13, 2020

Resolve remaining doctests, enable doctest in CI #1124

Resolve remaining doctests, enable doctest in CI #1124

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clarkgwillison commented Jun 23, 2020

clarkgwillison commented Jul 12, 2020

hgrecco commented Jul 13, 2020

bors bot commented Jul 13, 2020

hgrecco commented Jul 13, 2020