COMPAT: recent numpy deprecation warnings

[jreback]

getting lots of deprecation warnings from numpy.

(pandas) bash-3.2$ pytest pandas/tests/test_resample.py pandas/tests/io/json/test_json_table_schema.py 
============================================================================================================ test session starts ============================================================================================================
platform darwin -- Python 3.6.3, pytest-3.3.0, py-1.5.2, pluggy-0.6.0
rootdir: /Users/jreback/pandas, inifile: setup.cfg
plugins: xdist-1.20.1, forked-0.2, cov-2.5.1, hypothesis-3.38.5
collected 350 items                                                                                                                                                                                                                         

pandas/tests/test_resample.py ...................................................................................................................ssss................................................................................ [ 56%]
...............................ssss..................................                                                                                                                                                                 [ 76%]
pandas/tests/io/json/test_json_table_schema.py ...................................................x..x..x..x..xxxx..x..x..X..X...                                                                                                     [100%]

============================================================================================================= warnings summary ==============================================================================================================
pandas/tests/io/json/test_json_table_schema.py::TestTableOrientReader::()::test_read_json_table_orient[vals2-None]
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)

pandas/tests/io/json/test_json_table_schema.py::TestTableOrientReader::()::test_read_json_table_orient[vals2-idx]
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)

pandas/tests/io/json/test_json_table_schema.py::TestTableOrientReader::()::test_read_json_table_orient[vals2-index]
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)

pandas/tests/io/json/test_json_table_schema.py::TestTableOrientReader::()::test_comprehensive
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)
  /Users/jreback/pandas/pandas/core/dtypes/cast.py:706: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
    return arr.astype(dtype)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
================================================================================ 330 passed, 8 skipped, 10 xfailed, 2 xpassed, 16 warnings in 12.85 seconds =================================================================================

In [1]: arr = np.array(['2016-01-01T00:00:00.000Z', '2016-01-02T00:00:00.000Z',
   ...:        '2016-01-03T00:00:00.000Z', '2016-01-04T00:00:00.000Z'], dtype=object)
   ...: 

In [2]: arr.astype('<M8[ns]')
/Users/jreback/miniconda3/envs/pandas/bin/ipython:1: DeprecationWarning: parsing timezone aware datetimes is deprecated; this will raise an error in the future
  #!/Users/jreback/miniconda3/envs/pandas/bin/python
Out[2]: 
array(['2016-01-01T00:00:00.000000000', '2016-01-02T00:00:00.000000000',
       '2016-01-03T00:00:00.000000000', '2016-01-04T00:00:00.000000000'], dtype='datetime64[ns]')

I haven't seen these before, so a recent change must have triggered

[jreback]

cc @jbrockmendel cc @jschendel cc @WillAyd

[WillAyd]

Just ran on upstream/master and did not get any warnings - are we running the same version?

pd.show_versions()

INSTALLED VERSIONS

commit: 16d0262
python: 3.6.3.final.0
python-bits: 64
OS: Darwin
OS-release: 17.3.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

pandas: 0.23.0.dev0+79.g16d026212
pytest: 3.2.1
pip: 9.0.1
setuptools: 36.5.0.post20170921
Cython: 0.26.1
numpy: 1.13.3
scipy: 1.0.0
pyarrow: 0.8.0
xarray: 0.10.0
IPython: 6.2.1
sphinx: 1.6.3
patsy: 0.4.1
dateutil: 2.6.1
pytz: 2017.2
blosc: None
bottleneck: 1.2.1
tables: 3.4.2
numexpr: 2.6.4
feather: 0.4.0
matplotlib: 2.1.1
openpyxl: 2.5.0b1
xlrd: 1.1.0
xlwt: 1.3.0
xlsxwriter: 1.0.2
lxml: 4.1.1
bs4: 4.6.0
html5lib: 1.0.1
sqlalchemy: 1.1.13
pymysql: 0.7.11.None
psycopg2: None
jinja2: 2.10
s3fs: 0.1.2
fastparquet: 0.1.3
pandas_gbq: None
pandas_datareader: None

[jreback]

export PANDAS_TESTING_MODE=deprecate
first ; DeprecationWarnings are normally suppressed
we enable them in CI

[WillAyd]

Hmm OK. It appears the line

pd.date_range('2016-01-01', freq='d', periods=4)

Is triggering this within the tests. Not immediately apparent to me why that would be the case but will take a look

[WillAyd]

So it looks like write_json is outputting the date range in the format that you provided above. Are we on the same page that we would have to change that behavior to support this?

[chris-b1]

This is without digging into the json code, but I suspect rather than changing the output format, we should instead replace uses of numpy conversion .astype(<datetime>) with our internal parser pd.to_datetime(...)

[gfyoung]

Odd how this is case, since I think that warning was created partially in response to pandas:

https://github.com/numpy/numpy/blob/2bacec9ecb0fc665117a22027b73812509a99f56/doc/release/1.11.0-notes.rst#compatibility-notes