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  • xarray · 8 ✖
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
783985506 MDExOlB1bGxSZXF1ZXN0NTUzMjUxMzEz 4795 Expand user dir paths (~) in open_mfdataset. juseg 1186928 closed 0     3 2021-01-12T07:22:56Z 2021-01-15T17:22:37Z 2021-01-15T17:22:28Z CONTRIBUTOR   0 pydata/xarray/pulls/4795
  • [x] Closes #4783
  • [ ] Tests added
  • [x] Passes pre-commit run --all-files
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

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    xarray 13221727 pull
782335748 MDU6SXNzdWU3ODIzMzU3NDg= 4783 User directories (~) not expanded by open_mfdataset(). juseg 1186928 closed 0     0 2021-01-08T19:08:25Z 2021-01-15T17:22:28Z 2021-01-15T17:22:27Z CONTRIBUTOR      

What happened:

Hi. Perhaps a trivially minor issue, but I have noticed that open_dataset and to_netcdf expand user directories (~), while open_mfdataset does so on file lists, but not on patterns or single files.

What you expected to happen:

I would expect consistent behaviour across all file reading and writing methods.

Minimal Complete Verifiable Example:

```python

import xarray as xr xr.Dataset().to_netcdf('~/dataset.nc') # works xr.open_dataset('~/dataset.nc') # works xr.open_mfdataset(['~/dataset.nc']) # works xr.open_mfdataset('~/dataset.nc') # error Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.9/site-packages/xarray/backends/api.py", line 891, in open_mfdataset raise OSError("no files to open") OSError: no files to open ```

Anything else we need to know?:

This is done by private method _normalize_paths, which is called in open_dataset and to_netcdf but not open_mfdataset.

https://github.com/pydata/xarray/blob/1525fb0b23b8e92420ab428dc3d918a658e92dd4/xarray/backends/api.py#L170-L177

Environment:

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.9.1 (default, Dec 13 2020, 11:55:53) [GCC 10.2.0] python-bits: 64 OS: Linux OS-release: 5.4.80-2-MANJARO machine: x86_64 processor: byteorder: little LC_ALL: None LANG: en_GB.utf8 LOCALE: en_GB.UTF-8 libhdf5: 1.12.0 libnetcdf: 4.7.4 xarray: 0.16.1 pandas: 1.1.5 numpy: 1.19.4 scipy: 1.5.4 netCDF4: 1.5.4 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.2.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.30.0 distributed: None matplotlib: 3.3.3 cartopy: None seaborn: None numbagg: None pint: None setuptools: 51.0.0 pip: 20.2.2 conda: None pytest: 6.1.2 IPython: 7.19.0 sphinx: 3.4.0
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  completed xarray 13221727 issue
558140877 MDU6SXNzdWU1NTgxNDA4Nzc= 3735 Contour plot with norm and int or no levels fails. juseg 1186928 closed 0     1 2020-01-31T13:45:07Z 2020-05-12T22:47:51Z 2020-05-12T22:47:51Z CONTRIBUTOR      

MCVE Code Sample

python import numpy as np import xarray as xr import matplotlib as mpl data = xr.DataArray(np.arange(24).reshape(4, 6)) data.plot.contour(norm=mpl.colors.Normalize(vmin=5, vmax=10))

Yields:

python Traceback (most recent call last): File "<stdin>", line 1, in <module> File ".../xarray/xarray/plot/plot.py", line 816, in plotmethod return newplotfunc(**allargs) File ".../xarray/xarray/plot/plot.py", line 694, in newplotfunc cmap_params, cbar_kwargs = _process_cmap_cbar_kwargs( File ".../xarray/xarray/plot/utils.py", line 772, in _process_cmap_cbar_kwargs cmap_params = _determine_cmap_params(**cmap_kwargs) File ".../xarray/xarray/plot/utils.py", line 278, in _determine_cmap_params cmap, newnorm = _build_discrete_cmap(cmap, levels, extend, filled) File ".../xarray/xarray/plot/utils.py", line 94, in _build_discrete_cmap n_colors = len(levels) + ext_n - 1

Expected Output

A plot.

Problem Description

I think this has to do with:

https://github.com/pydata/xarray/blob/95e4f6c7a636878c94b892ee8d49866823d0748f/xarray/plot/utils.py#L744

And the line where the code fails:

https://github.com/pydata/xarray/blob/95e4f6c7a636878c94b892ee8d49866823d0748f/xarray/plot/utils.py#L94

There should be an easy fix, I think.

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.8.1 (default, Jan 22 2020, 06:38:00) [GCC 9.2.0] python-bits: 64 OS: Linux OS-release: 4.19.98-1-MANJARO machine: x86_64 processor: byteorder: little LC_ALL: None LANG: fr_CH.utf8 LOCALE: fr_CH.UTF-8 libhdf5: 1.10.5 libnetcdf: 4.7.3 xarray: 0.14.1 pandas: 0.25.3 numpy: 1.18.1 scipy: 1.4.1 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.4.2 nc_time_axis: None PseudoNetCDF: None rasterio: 1.1.1 cfgrib: None iris: None bottleneck: None dask: 2.8.0 distributed: None matplotlib: 3.1.2 cartopy: 0.17.0 seaborn: None numbagg: None setuptools: 44.0.0 pip: 19.3 conda: None pytest: 5.3.4 IPython: 7.11.1 sphinx: 2.2.1
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  completed xarray 13221727 issue
520110180 MDExOlB1bGxSZXF1ZXN0MzM4NzU1NzM5 3498 Add option to choose mfdataset attributes source. juseg 1186928 closed 0     9 2019-11-08T16:30:33Z 2020-04-05T20:44:43Z 2020-01-11T15:22:56Z CONTRIBUTOR   0 pydata/xarray/pulls/3498

Add a master_file keyword arguments to open_mfdataset to choose the source of global attributes in a multi-file dataset.

  • [x] Closes #2382
  • [x] Tests added
  • [x] Passes black . && mypy . && flake8
  • [x] Fully documented, including whats-new.rst for all changes and api.rst for new API
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    xarray 13221727 pull
548413554 MDExOlB1bGxSZXF1ZXN0MzYxNzE4MTAy 3685 Allow binned coordinates on 1D plots y-axis. juseg 1186928 closed 0     5 2020-01-11T10:39:13Z 2020-01-23T08:57:07Z 2020-01-22T21:09:39Z CONTRIBUTOR   0 pydata/xarray/pulls/3685

Currently 1D plot functions only allow binned coordinates (of pd.Interval type, produced with groupby_bins) on the y-axis (issue #3571). This pull request enables plotting intervals on either or both axes of 1D plots.

  • [x] Closes #3571
  • [x] Tests added
  • [x] Passes black . && mypy . && flake8
  • [x] Fully documented, including whats-new.rst for all changes and api.rst for new API
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    xarray 13221727 pull
528062816 MDU6SXNzdWU1MjgwNjI4MTY= 3571 Binned coordinates (pd.Interval) not plottable on the y-axis. juseg 1186928 closed 0     1 2019-11-25T12:44:40Z 2020-01-22T21:09:39Z 2020-01-22T21:09:39Z CONTRIBUTOR      

Minimal Code Sample

```python import numpy as np import xarray as xr import matplotlib.pyplot as plt

create fake data

data = xr.DataArray(np.random.rand(101)).rename('data')

group by bins and compute sum

bins = np.linspace(0, 1, 11) data = data.groupby_bins(data, bins).sum()

plot group means

data.plot() # works data.plot(x='data_bins') # works plt.plot((bins[:-1]+bins[1:])/2, data) # works

plot with axes transposed

data.plot(y='data_bins') # TypeError data.plot.line(y='data_bins') # TypeError plt.plot(data, (bins[:-1]+bins[1:])/2) # workaround ```

Expected Output

I would like to plot binned data (produced with groupby_bins) with transposed axes, i.e. data on the x-axis, and bins on the y-axis.

Problem Description

Attempting to plot using an array of pd.Interval on the y-axis yields the following TypeError. The error message reports data should be numeric, dates or pd.Interval, which they are.

Traceback (most recent call last): File "./groupbybug.py", line 19, in <module> data.plot(y='data_bins') # TypeError File "~/.local/lib/python3.7/site-packages/xarray/plot/plot.py", line 465, in __call__ return plot(self._da, **kwargs) File "~/.local/lib/python3.7/site-packages/xarray/plot/plot.py", line 202, in plot return plotfunc(darray, **kwargs) File "~/.local/lib/python3.7/site-packages/xarray/plot/plot.py", line 323, in line _ensure_plottable(xplt_val, yplt_val) File "~/.local/lib/python3.7/site-packages/xarray/plot/utils.py", line 512, in _ensure_plottable "Plotting requires coordinates to be numeric " TypeError: Plotting requires coordinates to be numeric or dates of type np.datetime64, datetime.datetime, cftime.datetime or pd.Interval.

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.7.4 (default, Oct 4 2019, 06:57:26) [GCC 9.2.0] python-bits: 64 OS: Linux OS-release: 4.19.84-1-MANJARO machine: x86_64 processor: byteorder: little LC_ALL: None LANG: fr_CH.utf8 LOCALE: fr_CH.UTF-8 libhdf5: 1.10.5 libnetcdf: 4.7.2 xarray: 0.14.1 pandas: 0.25.2 numpy: 1.17.3 scipy: 1.3.1 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.4.2 nc_time_axis: None PseudoNetCDF: None rasterio: 1.1.0 cfgrib: None iris: None bottleneck: None dask: 2.5.2 distributed: 0+untagged.1.gd096901.dirty matplotlib: 3.1.1 cartopy: 0.17.0 seaborn: None numbagg: None setuptools: 41.2.0 pip: 19.2.3 conda: None pytest: 5.2.1 IPython: 7.9.0 sphinx: 2.2.1
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  completed xarray 13221727 issue
354151953 MDU6SXNzdWUzNTQxNTE5NTM= 2382 Add option to choose the source of global attributes in mfdataset. juseg 1186928 closed 0     0 2018-08-27T01:45:23Z 2020-01-11T15:22:56Z 2020-01-11T15:22:56Z CONTRIBUTOR      

Code Sample

```python import numpy as np import xarray as xr

prepare fake data

time = np.arange(1000) data = time**2

write to multiple netcdf files

for i in range(10): filename = 'ds{:d}.nc'.format(i) ds = xr.Dataset({'data': (['time'], data[100i:100i+100])}, coords={'time': time[100i:100i+100]}, attrs={'history': 'Created ' + filename + '.'}) ds.to_netcdf(filename)

open as mfdataset

with xr.open_mfdataset('ds?.nc') as ds: print ds.history ```

Problem description

Currently, global attributes of multi-file datasets are taken from the first file in the list.

https://github.com/pydata/xarray/blob/b87b684b36cf5adbe4dca208aed0c69c44fc44c4/xarray/backends/api.py#L649

I think this is a problem in the context of consecutive model runs where history is appended in each subsequent run. When opening the results as mfdataset, history is taken from the first run file all subsequent history is lost.

NetCDF4 has a new keyword argument to set the master_file in a MFDataset (Unidata/netcdf4-python#835). Would it be possible to add a similar option in xarray?

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 2.7.15.final.0 python-bits: 64 OS: Linux OS-release: 4.14.65-1-MANJARO machine: x86_64 processor: byteorder: little LC_ALL: None LANG: fr_CH.utf8 LOCALE: None.None xarray: 0.10.8 pandas: 0.23.4 numpy: 1.15.0 scipy: 1.1.0 netCDF4: 1.4.2 h5netcdf: None h5py: None Nio: None zarr: None bottleneck: None cyordereddict: None dask: 0.18.2 distributed: None matplotlib: 2.2.3 cartopy: 0.15.1 seaborn: None setuptools: 40.0.0 pip: 18.0 conda: None pytest: None IPython: 5.8.0 sphinx: 1.7.6
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  completed xarray 13221727 issue
353623661 MDU6SXNzdWUzNTM2MjM2NjE= 2381 Plotting norm is superseded by xarray vmin and vmax juseg 1186928 closed 0     6 2018-08-24T02:47:17Z 2018-10-08T05:23:35Z 2018-10-08T05:23:35Z CONTRIBUTOR      

Code Sample

```python import numpy as np import xarray as xr import matplotlib.pyplot as plt import matplotlib.colors as mcolors

prepare array with values between 1e0 and 1e3

da = xr.DataArray(np.logspace(0, 3, 24).reshape(4, 6), dims=('x', 'y'))

but we want to log-normalize between 1e0 and 1e2

norm = mcolors.LogNorm(1e1, 1e2)

plot with log norm

da.plot.imshow(norm=norm) # log norm is applied but bounds are replaced

da.plot.imshow(norm=norm, vmin=norm.vmin, vmax=norm.vmax) # works, but redundant

show results

plt.show()

```

Problem description

When passing a norm argument to imshow etc, the norm is forwarded to matplotlib but its data bounds are replaced with those calculated by xarray.

Expected Output

I think that the norm's vmin and vmax should take precedence over xarray-generated vmin and vmax.

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 2.7.15.final.0 python-bits: 64 OS: Linux OS-release: 4.14.65-1-MANJARO machine: x86_64 processor: byteorder: little LC_ALL: None LANG: fr_CH.utf8 LOCALE: None.None xarray: 0.10.8 pandas: 0.23.4 numpy: 1.15.0 scipy: 1.1.0 netCDF4: 1.4.1 h5netcdf: None h5py: None Nio: None zarr: None bottleneck: None cyordereddict: None dask: 0.18.2 distributed: None matplotlib: 2.2.3 cartopy: 0.15.1 seaborn: None setuptools: 40.0.0 pip: 18.0 conda: None pytest: None IPython: 5.8.0 sphinx: 1.7.6
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  completed xarray 13221727 issue

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