⬆️ Bump cryptography from 41.0.3 to 41.0.4 #123
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Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.3 to 41.0.4. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@41.0.3...41.0.4) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
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Make non-required dependencies optional again! Workaround by running `poetry lock --no-update` until dependabot/dependabot-core#3104 is resolved.
weiji14
approved these changes
Sep 21, 2023
The latest stackstac 0.5.0 version installed via readthedocs does sets the dtype on read-in using rasterio, instead of after reading with `np.astype`, see gjoseph92/stackstac#208. Ideally, this should be fixed upstream in rasterio and GDAL by supporting reading of GeoTIFFs into float16 dtype. Alternative is to cast to float32 instead, though it would be a waste of memory if doing 16-bit precision training.
weiji14
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| post_install: | ||
| # Install stackstac=0.4.4 instead of 0.5.0 to prevent | ||
| # TypeError: Unsupported data type float16 | ||
| # because stackstac casts to float16 at read-in instead of post-read | ||
| # see https://github.com/gjoseph92/stackstac/pull/208 | ||
| # Need to wait for rasterio/GDAL to support float16 | ||
| # see https://gdal.org/api/raster_c_api.html#_CPPv412GDALDataType | ||
| - "pip install stackstac==0.4.4" |
There was a problem hiding this comment.
Was getting this error with stackstac==0.5.0 at https://readthedocs.org/projects/zen3geo/builds/21996237/:
/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/checkouts/123/docs/stacking.md: WARNING: Executing notebook failed: CellExecutionError
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
executenb(
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/nbclient/client.py", line 1305, in execute
return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
return loop.run_until_complete(inner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/docs/.asdf/installs/python/3.11.4/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/nbclient/client.py", line 705, in async_execute
await self.async_execute_cell(
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/nbclient/client.py", line 1058, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/home/docs/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
dataslice = datacube.sel(time="2022-02-23T11:41:54.329096000").compute()
fig, ax = plt.subplots(nrows=2, ncols=2, figsize=(11, 12), sharex=True, sharey=True)
dataslice.vh.plot.imshow(ax=ax[0][0], cmap="bone", robust=True)
ax[0][0].set_title("Sentinel-1 RTC 20220223 VH")
dataslice.vv.plot.imshow(ax=ax[0][1], cmap="bone", robust=True)
ax[0][1].set_title("Sentinel-1 RTC 20220223 VV")
dataslice.dem.plot.imshow(ax=ax[1][0], cmap="gist_earth")
ax[1][0].set_title("Copernicus DEM")
dataslice.mask.plot.imshow(ax=ax[1][1], cmap="binary_r")
ax[1][1].set_title("Landslide mask")
plt.show()
------------------
�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mKeyError�[0m Traceback (most recent call last)
File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/rasterio/dtypes.py:66�[0m, in �[0;36m_get_gdal_dtype�[0;34m(type_name)�[0m
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�[0;31mKeyError�[0m: 'float16'
During handling of the above exception, another exception occurred:
�[0;31mTypeError�[0m Traceback (most recent call last)
File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/stackstac/rio_reader.py:387�[0m, in �[0;36mAutoParallelRioReader.read�[0;34m(self, window, **kwargs)�[0m
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�[1;32m 391�[0m �[43m �[49m�[38;5;66;43;03m# ^ NOTE: we always do a masked array, so we can safely apply scales and offsets�[39;49;00m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/stackstac/rio_reader.py:228�[0m, in �[0;36mThreadLocalRioDataset.read�[0;34m(self, window, **kwargs)�[0m
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File �[0;32mrasterio/_warp.pyx:1240�[0m, in �[0;36mrasterio._warp.WarpedVRTReaderBase.read�[0;34m()�[0m
File �[0;32mrasterio/_io.pyx:651�[0m, in �[0;36mrasterio._io.DatasetReaderBase.read�[0;34m()�[0m
File �[0;32mrasterio/_io.pyx:975�[0m, in �[0;36mrasterio._io.DatasetReaderBase._read�[0;34m()�[0m
File �[0;32mrasterio/_io.pyx:140�[0m, in �[0;36mrasterio._io.io_multi_band�[0;34m()�[0m
File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/rasterio/dtypes.py:68�[0m, in �[0;36m_get_gdal_dtype�[0;34m(type_name)�[0m
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�[1;32m 69�[0m �[38;5;124mf�[39m�[38;5;124m"�[39m�[38;5;124mUnsupported data type �[39m�[38;5;132;01m{�[39;00mtype_name�[38;5;132;01m}�[39;00m�[38;5;124m. �[39m�[38;5;124m"�[39m
�[1;32m 70�[0m �[38;5;124mf�[39m�[38;5;124m"�[39m�[38;5;124mAllowed data types: �[39m�[38;5;132;01m{�[39;00m�[38;5;28mlist�[39m(dtype_rev)�[38;5;132;01m}�[39;00m�[38;5;124m.�[39m�[38;5;124m"�[39m
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The above exception was the direct cause of the following exception:
�[0;31mRuntimeError�[0m Traceback (most recent call last)
Cell �[0;32mIn[26], line 1�[0m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/xarray/core/dataset.py:991�[0m, in �[0;36mDataset.compute�[0;34m(self, **kwargs)�[0m
�[1;32m 972�[0m �[38;5;250m�[39m�[38;5;124;03m"""Manually trigger loading and/or computation of this dataset's data�[39;00m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/xarray/core/dataset.py:825�[0m, in �[0;36mDataset.load�[0;34m(self, **kwargs)�[0m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/xarray/core/daskmanager.py:70�[0m, in �[0;36mDaskManager.compute�[0;34m(self, *data, **kwargs)�[0m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/dask/base.py:628�[0m, in �[0;36mcompute�[0;34m(traverse, optimize_graph, scheduler, get, *args, **kwargs)�[0m
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File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/stackstac/to_dask.py:189�[0m, in �[0;36mfetch_raster_window�[0;34m(reader_table, slices, dtype, fill_value)�[0m
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�[1;32m 198�[0m �[38;5;66;03m# Unless the data we just read is all empty anyway�[39;00m
File �[0;32m~/checkouts/readthedocs.org/user_builds/zen3geo/envs/123/lib/python3.11/site-packages/stackstac/rio_reader.py:401�[0m, in �[0;36mAutoParallelRioReader.read�[0;34m(self, window, **kwargs)�[0m
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�[0;32m--> 401�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mRuntimeError�[39;00m(msg) �[38;5;28;01mfrom�[39;00m �[38;5;21;01me�[39;00m
�[1;32m 403�[0m �[38;5;66;03m# When the GeoTIFF doesn't have a nodata value, and we're using a VRT, pixels�[39;00m
�[1;32m 404�[0m �[38;5;66;03m# outside the dataset don't get properly masked (they're just 0). Using `add_alpha`�[39;00m
�[1;32m 405�[0m �[38;5;66;03m# in the `WarpedVRT`, we get an explicit alpha channel, which we use as a mask instead.�[39;00m
�[1;32m 406�[0m �[38;5;66;03m# See https://github.com/gjoseph92/stackstac/issues/217.�[39;00m
�[1;32m 407�[0m �[38;5;28;01mif�[39;00m result�[38;5;241m.�[39mshape[�[38;5;241m0�[39m] �[38;5;241m==�[39m �[38;5;241m2�[39m:
�[0;31mRuntimeError�[0m: Error reading Window(col_off=0, row_off=0, width=491, height=579) from 'https://elevationeuwest.blob.core.windows.net/copernicus-dem/COP30_hh/Copernicus_DSM_COG_10_S01_00_E100_00_DEM.tif?st=2023-09-20T21%3A28%3A02Z&se=2023-09-22T21%3A28%3A02Z&sp=rl&sv=2021-06-08&sr=c&skoid=c85c15d6-d1ae-42d4-af60-e2ca0f81359b&sktid=72f988bf-86f1-41af-91ab-2d7cd011db47&skt=2023-09-21T05%3A22%3A55Z&ske=2023-09-28T05%3A22%3A55Z&sks=b&skv=2021-06-08&sig=WelnMcHXxjdEuDHJJ1i9%2BV83uQXToDYmOkbL3WVGWpc%3D': TypeError("Unsupported data type float16. Allowed data types: [None, 'uint8', 'uint16', 'int16', 'uint32', 'int32', 'float32', 'float64', 'complex_int16', 'complex64', 'complex128', 'int64', 'uint64', 'complex', 'int8'].")Not exactly stackstac's fault as rasterio/GDAL doesn't support reading GeoTIFFs into float16 dtype directly (and probably won't soon given the effort).
Will have a follow-up PR to make things compatible with stackstac=0.5.0. Key is on how to deal with NaNs, since only float types support having NaNs. Either cast things to float32 instead of float16, or use native uint16 and cast back to float16? If only there were nullable uint16 dtype 🤔
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Bumps cryptography from 41.0.3 to 41.0.4.
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Sourced from cryptography's changelog.
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fc11bcebump for 41.0.4 (#9629)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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