id,node_id,number,title,user,state,locked,assignee,milestone,comments,created_at,updated_at,closed_at,author_association,active_lock_reason,draft,pull_request,body,reactions,performed_via_github_app,state_reason,repo,type
357156174,MDU6SXNzdWUzNTcxNTYxNzQ=,2399,DataArray.loc fails for duplicates where DataFrame works,514522,closed,0,,,11,2018-09-05T10:03:12Z,2020-09-11T04:32:16Z,2020-09-11T04:32:16Z,CONTRIBUTOR,,,,"
```python
import pandas as pd
import xarray as xr
df = pd.DataFrame(data=[0, 1], index=list(""aa""))
da = xr.DataArray(df)
print(df.loc[list(""a"")]) # works
print(da.loc[{""dim_0"": list(""a"")}]) # fails
```
Xarray fails with the exception
```
Traceback (most recent call last):
File ""session4.py"", line 7, in <module>
print(da.loc[{""dim_0"": list(""a"")}]) # fails
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/dataarray.py"", line 104, in __getitem__
return self.data_array.sel(**key)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/dataarray.py"", line 784, in sel
indexers=indexers, drop=drop, method=method, tolerance=tolerance)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/dataset.py"", line 1509, in sel
self, indexers=indexers, method=method, tolerance=tolerance)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/coordinates.py"", line 355, in remap_label_indexers
obj, v_indexers, method=method, tolerance=tolerance
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/indexing.py"", line 250, in remap_label_indexers
dim, method, tolerance)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/indexing.py"", line 186, in convert_label_indexer
indexer = get_indexer_nd(index, label, method, tolerance)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/xarray/core/indexing.py"", line 117, in get_indexer_nd
flat_indexer = index.get_indexer(flat_labels, **kwargs)
File ""/usr/local/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/base.py"", line 3244, in get_indexer
raise InvalidIndexError('Reindexing only valid with uniquely'
pandas.core.indexes.base.InvalidIndexError: Reindexing only valid with uniquely valued Index objects
```
#### Output of ``xr.show_versions()``
```
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.6.final.0
python-bits: 64
OS: Darwin
OS-release: 17.7.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_GB.UTF-8
LOCALE: en_GB.UTF-8
xarray: 0.10.8
pandas: 0.23.4
numpy: 1.15.1
scipy: 1.1.0
netCDF4: 1.4.1
h5netcdf: None
h5py: 2.8.0
Nio: None
zarr: None
bottleneck: 1.2.1
cyordereddict: None
dask: 0.19.0
distributed: 1.23.0
matplotlib: 2.2.3
cartopy: None
seaborn: 0.9.0
setuptools: 40.2.0
pip: 18.0
conda: 4.5.11
pytest: 3.7.3
IPython: 6.5.0
sphinx: 1.7.7
```","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/2399/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue
384051686,MDExOlB1bGxSZXF1ZXN0MjMzMzU4NjU4,2574,Remove py37 collections.abc deprecation warnings,514522,closed,0,,,3,2018-11-25T06:19:18Z,2019-01-25T01:16:05Z,2019-01-25T01:16:05Z,CONTRIBUTOR,,0,pydata/xarray/pulls/2574,,"{""url"": ""https://api.github.com/repos/pydata/xarray/issues/2574/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,,13221727,pull
383057458,MDU6SXNzdWUzODMwNTc0NTg=,2560,Lock related problem in on travis-ci but not on local machine,514522,closed,0,,,10,2018-11-21T10:42:19Z,2018-12-23T20:11:32Z,2018-12-23T20:11:32Z,CONTRIBUTOR,,,,"There is a `KeyError` at `xarray.backends.file_manager.CachingFileManager` for the `acquire` method on these lines:
```
with self._lock:
try:
file = self._cache[self._key]
```
which does not happen when I test on my macos.
Let me know if you require further testing on my part.
Full log:
```
=================================== FAILURES ===================================
________________________________ test_qtl_xarr _________________________________
self = <xarray.backends.file_manager.CachingFileManager object at 0x7f59e2cab978>
def acquire(self):
""""""Acquiring a file object from the manager.
A new file is only opened if it has expired from the
least-recently-used cache.
This method uses a reentrant lock, which ensures that it is
thread-safe. You can safely acquire a file in multiple threads at the
same time, as long as the underlying file object is thread-safe.
Returns
-------
An open file object, as returned by ``opener(*args, **kwargs)``.
""""""
with self._lock:
try:
> file = self._cache[self._key]
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/file_manager.py:137:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <xarray.backends.lru_cache.LRUCache object at 0x7f5a04a9c630>
key = [<function _open_netcdf4_group at 0x7f5a04abc1e0>, ('/tmp/tmprj8lwlat/xarr.hdf5', CombinedLock([<SerializableLock: 447...>])), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('group', '/foo/chr1'), ('persist', False))]
def __getitem__(self, key):
# record recent use of the key by moving it to the front of the list
with self._lock:
> value = self._cache[key]
E KeyError: [<function _open_netcdf4_group at 0x7f5a04abc1e0>, ('/tmp/tmprj8lwlat/xarr.hdf5', CombinedLock([<SerializableLock: 4471090f-419e-49bd-9d27-4156e09febdd>, <SerializableLock: b9eb5ba1-2830-402e-b48f-3ef45768b7c2>])), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('group', '/foo/chr1'), ('persist', False))]
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/lru_cache.py:43: KeyError
During handling of the above exception, another exception occurred:
def test_qtl_xarr():
with limix.example.file_example(""xarr.hdf5.bz2"") as filepath:
filepath = limix.sh.extract(filepath, verbose=False)
sample_ids = limix.io.hdf5.fetch(filepath, ""/foo/chr1/col_header/sample_ids"")
rsid = dict()
for i in range(1, 3):
rsid[i] = limix.io.hdf5.fetch(
filepath, ""/foo/chr{}/row_header/rsid"".format(i)
)
G = []
for i in range(1, 3):
> g = xr.open_dataset(filepath, ""/foo/chr{}"".format(i))[""matrix""]
miniconda/envs/test-environment/lib/python3.6/site-packages/limix/qtl/test/test_qtl_xarr.py:20:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/api.py:320: in open_dataset
filename_or_obj, group=group, lock=lock, **backend_kwargs)
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/netCDF4_.py:355: in open
return cls(manager, lock=lock, autoclose=autoclose)
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/netCDF4_.py:314: in __init__
self.format = self.ds.data_model
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/netCDF4_.py:359: in ds
return self._manager.acquire().value
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/file_manager.py:143: in acquire
file = self._opener(*self._args, **kwargs)
miniconda/envs/test-environment/lib/python3.6/site-packages/xarray/backends/netCDF4_.py:247: in _open_netcdf4_group
ds = nc4.Dataset(filename, mode=mode, **kwargs)
netCDF4/_netCDF4.pyx:2135: in netCDF4._netCDF4.Dataset.__init__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E OSError: [Errno -101] NetCDF: HDF error: b'/tmp/tmprj8lwlat/xarr.hdf5'
netCDF4/_netCDF4.pyx:1752: OSError
===================== 1 failed, 50 passed in 65.82 seconds =====================
The command ""bash <(curl -fsSL https://raw.githubusercontent.com/horta/ci/master/travis.sh)"" exited with 1.
Done. Your build exited with 1.
```","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/2560/reactions"", ""total_count"": 1, ""+1"": 1, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue
384050983,MDExOlB1bGxSZXF1ZXN0MjMzMzU4MjY4,2573,python setup.py test now works by default,514522,closed,0,,,2,2018-11-25T06:06:58Z,2018-11-25T20:00:03Z,2018-11-25T19:59:57Z,CONTRIBUTOR,,0,pydata/xarray/pulls/2573,You don't need to have pytest-runner before-hand.,"{""url"": ""https://api.github.com/repos/pydata/xarray/issues/2573/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,,13221727,pull