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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| cff-version: 1.2.0 | ||
| message: "If you use this software, please cite it as below." | ||
| authors: | ||
| - family-names: "Hoyer" | ||
| given-names: "Stephan" | ||
| orcid: "https://orcid.org/0000-0002-5207-0380" | ||
| - family-names: "Roos" | ||
| given-names: "Maximilian" | ||
| - family-names: "Joseph" | ||
| given-names: "Hamman" | ||
| orcid: "https://orcid.org/0000-0001-7479-8439" | ||
| - family-names: "Magin" | ||
| given-names: "Justus" | ||
| - family-names: "Cherian" | ||
| given-names: "Deepak" | ||
| orcid: "https://orcid.org/0000-0002-6861-8734" | ||
| - family-names: "Fitzgerald" | ||
| given-names: "Clark" | ||
| orcid: "https://orcid.org/0000-0003-3446-6389" | ||
| - family-names: "Hauser" | ||
| given-names: "Mathias" | ||
| orcid: "https://orcid.org/0000-0002-0057-4878" | ||
| - family-names: "Fujii" | ||
| given-names: "Keisuke" | ||
| orcid: "https://orcid.org/0000-0003-0390-9984" | ||
| - family-names: "Maussion" | ||
| given-names: "Fabien" | ||
| orcid: "https://orcid.org/0000-0002-3211-506X" | ||
| - family-names: "Imperiale" | ||
| given-names: "Guido" | ||
| - family-names: "Clark" | ||
| given-names: "Spencer" | ||
| orcid: "https://orcid.org/0000-0001-5595-7895" | ||
| - family-names: "Kleeman" | ||
| given-names: "Alex" | ||
| - family-names: "Nicholas" | ||
| given-names: "Thomas" | ||
| orcid: "https://orcid.org/0000-0002-2176-0530" | ||
| - family-names: "Kluyver" | ||
| given-names: "Thomas" | ||
| orcid: "https://orcid.org/0000-0003-4020-6364" | ||
| - family-names: "Westling" | ||
| given-names: "Jimmy" | ||
| - family-names: "Munroe" | ||
| given-names: "James" | ||
| orcid: "https://orcid.org/0000-0001-9098-6309" | ||
| - family-names: "Amici" | ||
| given-names: "Alessandro" | ||
| orcid: "https://orcid.org/0000-0002-1778-4505" | ||
| - family-names: "Barghini" | ||
| given-names: "Aureliana" | ||
| - family-names: "Banihirwe" | ||
| given-names: "Anderson" | ||
| orcid: "https://orcid.org/0000-0001-6583-571X" | ||
| - family-names: "Bell" | ||
| given-names: "Ray" | ||
| orcid: "https://orcid.org/0000-0003-2623-0587" | ||
| - family-names: "Hatfield-Dodds" | ||
| given-names: "Zac" | ||
| orcid: "https://orcid.org/0000-0002-8646-8362" | ||
| - family-names: "Abernathey" | ||
| given-names: "Ryan" | ||
| orcid: "https://orcid.org/0000-0001-5999-4917" | ||
| - family-names: "Bovy" | ||
| given-names: "Benoît" | ||
| - family-names: "Omotani" | ||
| given-names: "John" | ||
| orcid: "https://orcid.org/0000-0002-3156-8227" | ||
| - family-names: "Mühlbauer" | ||
| given-names: "Kai" | ||
| orcid: "https://orcid.org/0000-0001-6599-1034" | ||
| - family-names: "Roszko" | ||
| given-names: "Maximilian K." | ||
| orcid: "https://orcid.org/0000-0001-9424-2526" | ||
| - family-names: "Wolfram" | ||
| given-names: "Phillip J." | ||
| orcid: "https://orcid.org/0000-0001-5971-4241" | ||
| title: "xarray" | ||
| doi: 10.5281/zenodo.598201 | ||
| url: "https://github.com/pydata/xarray" | ||
| preferred-citation: | ||
| type: article | ||
| authors: | ||
| - family-names: "Hoyer" | ||
| given-names: "Stephan" | ||
| orcid: "https://orcid.org/0000-0002-5207-0380" | ||
| - family-names: "Joseph" | ||
| given-names: "Hamman" | ||
| orcid: "https://orcid.org/0000-0001-7479-8439" | ||
| doi: "10.5334/jors.148" | ||
| journal: "Journal of Open Research Software" | ||
| month: 4 | ||
| title: "xarray: N-D labeled Arrays and Datasets in Python" | ||
| volume: 5 | ||
| issue: 1 | ||
| year: 2017 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,98 @@ | ||
| import numpy as np | ||
| import pandas as pd | ||
|
|
||
| import xarray as xr | ||
|
|
||
| from . import parameterized, requires_dask | ||
| from . import _skip_slow, parameterized, requires_dask | ||
|
|
||
|
|
||
| class GroupBy: | ||
| def setup(self, *args, **kwargs): | ||
| self.ds = xr.Dataset( | ||
| self.n = 100 | ||
| self.ds1d = xr.Dataset( | ||
| { | ||
| "a": xr.DataArray(np.r_[np.arange(500.0), np.arange(500.0)]), | ||
| "b": xr.DataArray(np.arange(1000.0)), | ||
| "a": xr.DataArray(np.r_[np.repeat(1, self.n), np.repeat(2, self.n)]), | ||
| "b": xr.DataArray(np.arange(2 * self.n)), | ||
| } | ||
| ) | ||
| self.ds2d = self.ds1d.expand_dims(z=10) | ||
|
|
||
| @parameterized(["method"], [("sum", "mean")]) | ||
| def time_agg(self, method): | ||
| return getattr(self.ds.groupby("a"), method)() | ||
| @parameterized(["ndim"], [(1, 2)]) | ||
| def time_init(self, ndim): | ||
| getattr(self, f"ds{ndim}d").groupby("b") | ||
|
|
||
| @parameterized(["method", "ndim"], [("sum", "mean"), (1, 2)]) | ||
| def time_agg_small_num_groups(self, method, ndim): | ||
| ds = getattr(self, f"ds{ndim}d") | ||
| getattr(ds.groupby("a"), method)() | ||
|
|
||
| @parameterized(["method", "ndim"], [("sum", "mean"), (1, 2)]) | ||
| def time_agg_large_num_groups(self, method, ndim): | ||
| ds = getattr(self, f"ds{ndim}d") | ||
| getattr(ds.groupby("b"), method)() | ||
|
|
||
|
|
||
| class GroupByDask(GroupBy): | ||
| def setup(self, *args, **kwargs): | ||
| requires_dask() | ||
| super().setup(**kwargs) | ||
| self.ds = self.ds.chunk({"dim_0": 50}) | ||
| self.ds1d = self.ds1d.sel(dim_0=slice(None, None, 2)).chunk({"dim_0": 50}) | ||
| self.ds2d = self.ds2d.sel(dim_0=slice(None, None, 2)).chunk( | ||
| {"dim_0": 50, "z": 5} | ||
| ) | ||
|
|
||
|
|
||
| class GroupByDataFrame(GroupBy): | ||
| class GroupByPandasDataFrame(GroupBy): | ||
| """Run groupby tests using pandas DataFrame.""" | ||
|
|
||
| def setup(self, *args, **kwargs): | ||
| # Skip testing in CI as it won't ever change in a commit: | ||
| _skip_slow() | ||
|
|
||
| super().setup(**kwargs) | ||
| self.ds = self.ds.to_dataframe() | ||
| self.ds1d = self.ds1d.to_dataframe() | ||
|
|
||
|
|
||
| class GroupByDaskDataFrame(GroupBy): | ||
| """Run groupby tests using dask DataFrame.""" | ||
|
|
||
| def setup(self, *args, **kwargs): | ||
| # Skip testing in CI as it won't ever change in a commit: | ||
| _skip_slow() | ||
|
|
||
| requires_dask() | ||
| super().setup(**kwargs) | ||
| self.ds1d = self.ds1d.chunk({"dim_0": 50}).to_dataframe() | ||
|
|
||
|
|
||
| class Resample: | ||
| def setup(self, *args, **kwargs): | ||
| self.ds1d = xr.Dataset( | ||
| { | ||
| "b": ("time", np.arange(365.0 * 24)), | ||
| }, | ||
| coords={"time": pd.date_range("2001-01-01", freq="H", periods=365 * 24)}, | ||
| ) | ||
| self.ds2d = self.ds1d.expand_dims(z=10) | ||
|
|
||
| @parameterized(["ndim"], [(1, 2)]) | ||
| def time_init(self, ndim): | ||
| getattr(self, f"ds{ndim}d").resample(time="D") | ||
|
|
||
| @parameterized(["method", "ndim"], [("sum", "mean"), (1, 2)]) | ||
| def time_agg_small_num_groups(self, method, ndim): | ||
| ds = getattr(self, f"ds{ndim}d") | ||
| getattr(ds.resample(time="3M"), method)() | ||
|
|
||
| @parameterized(["method", "ndim"], [("sum", "mean"), (1, 2)]) | ||
| def time_agg_large_num_groups(self, method, ndim): | ||
| ds = getattr(self, f"ds{ndim}d") | ||
| getattr(ds.resample(time="48H"), method)() | ||
|
|
||
|
|
||
| class ResampleDask(Resample): | ||
| def setup(self, *args, **kwargs): | ||
| requires_dask() | ||
| super().setup(**kwargs) | ||
| self.ds = self.ds.chunk({"dim_0": 50}).to_dataframe() | ||
| self.ds1d = self.ds1d.chunk({"time": 50}) | ||
| self.ds2d = self.ds2d.chunk({"time": 50, "z": 4}) |
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