API: idx.get_indexer(keys) fails if idx is non-unique, even if keys in idx are unique

[ivirshup]

Code Sample, a copy-pastable example

import pandas as pd

pd.Index(["a", "a", "b", "c"]).get_indexer(pd.Index(["b", "c"]))
# InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Came across this here: #38745 (comment)

Problem description

It makes sense to me why this would error:

pd.Index(["a", "a", "b", "c"]).get_indexer(pd.Index(["a", "c"]))

There isn't a unique solution. For the case presented at the top, there is a unique solution.

Expected Output

pd.Index(["a", "a", "b", "c"]).get_indexer(pd.Index(["b", "c"]))
# array([2, 3])

Note, this is the behaviour of pd.Index._get_indexer on master

Output of pd.show_versions()

master

INSTALLED VERSIONS
------------------
commit           : 7f912a4009da963b5eacdcebb638c38eec06e7a7
python           : 3.8.5.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 19.6.0
Version          : Darwin Kernel Version 19.6.0: Tue Nov 10 00:10:30 PST 2020; root:xnu-6153.141.10~1/RELEASE_X86_64
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.3.0.dev0+228.g7f912a4009
numpy            : 1.18.5
pytz             : 2020.1
dateutil         : 2.8.1
pip              : 20.1.1
setuptools       : 49.2.0.post20200712
Cython           : 0.29.21
pytest           : 5.4.3
hypothesis       : 5.20.3
sphinx           : 3.1.1
blosc            : None
feather          : None
xlsxwriter       : 1.2.9
lxml.etree       : 4.5.2
html5lib         : 1.1
pymysql          : None
psycopg2         : None
jinja2           : 2.11.2
IPython          : 7.16.1
pandas_datareader: None
bs4              : 4.9.1
bottleneck       : 1.3.2
fsspec           : 0.7.4
fastparquet      : 0.4.1
gcsfs            : 0.6.2
matplotlib       : 3.2.2
numexpr          : 2.7.1
odfpy            : None
openpyxl         : 3.0.4
pandas_gbq       : None
pyarrow          : 0.17.1
pyxlsb           : None
s3fs             : 0.4.2
scipy            : 1.5.1
sqlalchemy       : 1.3.18
tables           : 3.6.1
tabulate         : 0.8.7
xarray           : 0.16.0
xlrd             : 1.2.0
xlwt             : 1.3.0
numba            : 0.50.1

1.2.0

pd.show_versions() is failing with: ImportError: Can't determine version for numba, so here's conda list:

$ conda list
# packages in environment at /Users/isaac/miniconda3/envs/pandas-1.2:
#
# Name                    Version                   Build  Channel
appnope                   0.1.2           py38hecd8cb5_1001  
backcall                  0.2.0                      py_0  
blas                      1.0                         mkl  
ca-certificates           2020.12.8            hecd8cb5_0  
certifi                   2020.12.5        py38hecd8cb5_0  
decorator                 4.4.2                      py_0  
intel-openmp              2019.4                      233  
ipython                   7.19.0           py38h01d92e1_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
jedi                      0.17.0                   py38_0  
libcxx                    11.0.0               h4c3b8ed_1    conda-forge
libedit                   3.1.20191231         h1de35cc_1  
libffi                    3.3                  hb1e8313_2  
mkl                       2019.4                      233  
mkl-service               2.3.0            py38h9ed2024_0  
mkl_fft                   1.2.0            py38hc64f4ea_0  
mkl_random                1.1.1            py38h959d312_0  
ncurses                   6.2                  h0a44026_1  
numpy                     1.19.2           py38h456fd55_0  
numpy-base                1.19.2           py38hcfb5961_0  
openssl                   1.1.1i               h9ed2024_0  
pandas                    1.2.0            py38he9f00de_0    conda-forge
parso                     0.8.1              pyhd3eb1b0_0  
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pip                       20.3.3           py38hecd8cb5_0  
prompt-toolkit            3.0.8                      py_0  
ptyprocess                0.6.0              pyhd3eb1b0_2  
pygments                  2.7.3              pyhd3eb1b0_0  
python                    3.8.5                h26836e1_1  
python-dateutil           2.8.1                      py_0  
python_abi                3.8                      1_cp38    conda-forge
pytz                      2020.4             pyhd3eb1b0_0  
readline                  8.0                  h1de35cc_0  
setuptools                51.0.0           py38hecd8cb5_2  
six                       1.15.0           py38hecd8cb5_0  
sqlite                    3.33.0               hffcf06c_0  
tk                        8.6.10               hb0a8c7a_0  
traitlets                 5.0.5                      py_0  
wcwidth                   0.2.5                      py_0  
wheel                     0.36.2             pyhd3eb1b0_0  
xz                        5.2.5                h1de35cc_0  
zlib                      1.2.11               h1de35cc_3