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  • 2022.03.0: sphinx fails on generate documentation · 10 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1265849564 https://github.com/pydata/xarray/issues/6454#issuecomment-1265849564 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85Lc1Tc kloczek 31284574 2022-10-03T18:20:09Z 2022-10-03T18:20:09Z NONE

So someting is messing with sys.path. Most likepy some of the modules is using pkg_resources module which is known that it trashes sys.path https://github.com/pypa/setuptools/issues/3279. If that it the cause solution would be migration from use pkg_resources to importlib_metadata (I've checked and xarray already done such migration).

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1265416330 https://github.com/pydata/xarray/issues/6454#issuecomment-1265416330 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85LbLiK keewis 14808389 2022-10-03T13:10:30Z 2022-10-03T13:10:30Z MEMBER

if you look at your traceback, it says ModuleNotFoundError: No module named 'xarray' (i.e. most likely your sys.path patch does not work / points to the wrong directory).

We tried the sys.path patch before, but couldn't get it to build correctly because one of the optional dependencies depends on xarray (cfgrib, in this case).

I'm not sure for which OS you're building packages for, but you should have some sort of isolated build environment (chroot / docker / something else?). The most reliable way to fix this issue then is to install the built package (a wheel?) into that development environment.

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1261230922 https://github.com/pydata/xarray/issues/6454#issuecomment-1261230922 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85LLNtK kloczek 31284574 2022-09-28T17:27:37Z 2022-09-28T17:27:37Z NONE

I'll close this as the reason for the failure is that xarray was never actually installed (python -m build -w --no-isolation will only build a wheel, it will not install, and the .egg-info directory is a build artifact).

Please have look one more time on top patch. I'm building documentation after build which created directory with module metadata (because xarray uses as pep517 backednd setuptools) and patch adds to sys.path path to the directoey where metadata are available.

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1198033505 https://github.com/pydata/xarray/issues/6454#issuecomment-1198033505 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85HaIph keewis 14808389 2022-07-28T11:46:39Z 2022-07-28T11:46:39Z MEMBER

I'll close this as the reason for the failure is that xarray was never actually installed (python -m build -w --no-isolation will only build a wheel, it will not install, and the .egg-info directory is a build artifact).

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1102134733 https://github.com/pydata/xarray/issues/6454#issuecomment-1102134733 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BsT3N kloczek 31284574 2022-04-19T06:17:35Z 2022-04-19T06:17:35Z NONE

It seems like you're missing the pip install -e . step.

Please see https://docs.xarray.dev/en/stable/contributing.html#how-to-build-the-xarray-documentation for instructions

If you will follow procedure which I've provided by executing python3 -sBm build -w --no-isolation you will find that xarray.egg-info directory in project root with modules metadata is already created (as part of the pep517 build when setuptools as build backend is used). In other words pip install -e . is not needed and it is not the cause of the reported issue.

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1101542550 https://github.com/pydata/xarray/issues/6454#issuecomment-1101542550 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BqDSW dcherian 2448579 2022-04-18T16:25:23Z 2022-04-18T16:25:23Z MEMBER

It seems like you're missing the pip install -e . step.

Please see https://docs.xarray.dev/en/stable/contributing.html#how-to-build-the-xarray-documentation for instructions 

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   2022.03.0: sphinx fails on generate documentation 1196425693
1100283959 https://github.com/pydata/xarray/issues/6454#issuecomment-1100283959 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BlQA3 kloczek 31284574 2022-04-15T18:37:22Z 2022-04-15T18:37:22Z NONE

Everything should work if you create an environment using https://github.com/pydata/xarray/blob/main/ci/requirements/doc.yml . Can you try that please?

Issue seems is in other place after add patch ```patch --- a/doc/conf.py~ 2022-03-02 15:49:23.000000000 +0000 +++ b/doc/conf.py 2022-04-15 18:32:06.848726986 +0000 @@ -17,6 +17,9 @@ import os import subprocess import sys + +sys.path.append(os.path.abspath('..')) + from contextlib import suppress

import sphinx_autosummary_accessors build-shinx shows:console [tkloczko@devel-g2v xarray-2022.03.0]$ /usr/bin/sphinx-build -n -T -b man doc build/sphinx/man Running Sphinx v4.5.0 python exec: /usr/bin/python3 sys.path: ['/usr/bin', '/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '/home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0'] xarray: 2022.3.0, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/xarray/init.py making output directory... done [autosummary] generating autosummary for: README.rst, api-hidden.rst, api.rst, contributing.rst, developers-meeting.rst, ecosystem.rst, examples/ERA5-GRIB-example.ipynb, examples/ROMS_ocean_model.ipynb, examples/apply_ufunc_vectorize_1d.ipynb, examples/area_weighted_temperature.ipynb, ..., user-guide/indexing.rst, user-guide/interpolation.rst, user-guide/io.rst, user-guide/pandas.rst, user-guide/plotting.rst, user-guide/reshaping.rst, user-guide/terminology.rst, user-guide/time-series.rst, user-guide/weather-climate.rst, whats-new.rst [autosummary] generating autosummary for: /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.T.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.all.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.any.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.append.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argmax.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argmin.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argsort.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.array.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.asi8.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.asof.rst, ..., /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sin.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sinh.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sqrt.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.square.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.tan.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.tanh.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.trunc.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.unify_chunks.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.where.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.zeros_like.rst loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://scitools-iris.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory from https://numba.pydata.org/numba-doc/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory from https://docs.dask.org/en/latest/objects.inv... loading intersphinx inventory from https://unidata.github.io/cftime/objects.inv... loading intersphinx inventory from https://rasterio.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://sparse.pydata.org/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: [new config] 1282 added, 0 changed, 0 removed reading sources... [ 0%] examples/ERA5-GRIB-example Traceback (most recent call last): File "/usr/lib/python3.8/site-packages/nbsphinx.py", line 1032, in parse rststring, resources = exporter.from_notebook_node(nb, resources) File "/usr/lib/python3.8/site-packages/nbsphinx.py", line 842, in from_notebook_node nb, resources = pp.preprocess(nb, resources) File "/usr/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 83, in preprocess self.preprocess_cell(cell, resources, index) File "/usr/lib/python3.8/site-packages/nbconvert/preprocessors/execute.py", line 104, in preprocess_cell cell = self.execute_cell(cell, index, store_history=True) File "/usr/lib/python3.8/site-packages/nbclient/util.py", line 84, in wrapped return just_run(coro(args, *kwargs)) File "/usr/lib/python3.8/site-packages/nbclient/util.py", line 62, in just_run return loop.run_until_complete(coro) File "/usr/lib64/python3.8/asyncio/base_events.py", line 616, in run_until_complete return future.result() File "/usr/lib/python3.8/site-packages/nbclient/client.py", line 965, in async_execute_cell await self._check_raise_for_error(cell, cell_index, exec_reply) File "/usr/lib/python3.8/site-packages/nbclient/client.py", line 862, 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:

import xarray as xr import matplotlib.pyplot as plt

ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_1995816/830426931.py in <module> ----> 1 import xarray as xr 2 import matplotlib.pyplot as plt

ModuleNotFoundError: No module named 'xarray' ModuleNotFoundError: No module named 'xarray'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/lib/python3.8/site-packages/sphinx/cmd/build.py", line 276, in build_main app.build(args.force_all, filenames) File "/usr/lib/python3.8/site-packages/sphinx/application.py", line 330, in build self.builder.build_update() File "/usr/lib/python3.8/site-packages/sphinx/builders/init.py", line 283, in build_update self.build(['all'], to_build) File "/usr/lib/python3.8/site-packages/sphinx/builders/init.py", line 300, in build updated_docnames = set(self.read()) File "/usr/lib/python3.8/site-packages/sphinx/builders/init.py", line 407, in read self._read_serial(docnames) File "/usr/lib/python3.8/site-packages/sphinx/builders/init.py", line 428, in _read_serial self.read_doc(docname) File "/usr/lib/python3.8/site-packages/sphinx/builders/init.py", line 468, in read_doc doctree = read_doc(self.app, self.env, self.env.doc2path(docname)) File "/usr/lib/python3.8/site-packages/sphinx/io.py", line 181, in read_doc pub.publish() File "/usr/lib/python3.8/site-packages/docutils/core.py", line 217, in publish self.document = self.reader.read(self.source, self.parser, File "/usr/lib/python3.8/site-packages/sphinx/io.py", line 101, in read self.parse() File "/usr/lib/python3.8/site-packages/docutils/readers/init.py", line 78, in parse self.parser.parse(self.input, document) File "/usr/lib/python3.8/site-packages/nbsphinx.py", line 1039, in parse raise NotebookError('\n'.join(lines)) nbsphinx.NotebookError: CellExecutionError in examples/ERA5-GRIB-example.ipynb:

import xarray as xr import matplotlib.pyplot as plt

ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_1995816/830426931.py in <module> ----> 1 import xarray as xr 2 import matplotlib.pyplot as plt

ModuleNotFoundError: No module named 'xarray' ModuleNotFoundError: No module named 'xarray'

You can ignore this error by setting the following in conf.py:

nbsphinx_allow_errors = True

Notebook error: CellExecutionError in examples/ERA5-GRIB-example.ipynb:

import xarray as xr import matplotlib.pyplot as plt

ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_1995816/830426931.py in <module> ----> 1 import xarray as xr 2 import matplotlib.pyplot as plt

ModuleNotFoundError: No module named 'xarray' ModuleNotFoundError: No module named 'xarray'

You can ignore this error by setting the following in conf.py:

nbsphinx_allow_errors = True

So for some reason at some point it cannot locate `xarray` module even if your diagnostics shows:console Running Sphinx v4.5.0 python exec: /usr/bin/python3 sys.path: ['/usr/bin', '/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '/home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0'] `` Because i see usedsubprocessmodule I'm gueassing that that path is executed without injected..tosys.path` and that part fails.

Could ypu please try to reproduce this issue by uninstall xarray and using only source tree please try to execute build-sphinx command as same as I'm doing that?

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1092171997 https://github.com/pydata/xarray/issues/6454#issuecomment-1092171997 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BGTjd dcherian 2448579 2022-04-07T20:29:20Z 2022-04-07T20:29:20Z MEMBER

Everything should work if you create an environment using https://github.com/pydata/xarray/blob/main/ci/requirements/doc.yml . Can you try that please?

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1092170184 https://github.com/pydata/xarray/issues/6454#issuecomment-1092170184 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BGTHI kloczek 31284574 2022-04-07T20:26:56Z 2022-04-07T20:26:56Z NONE

I've added ipykernel to build dependencies and build moved few steps forward and failed again ```console + PYTHONPATH=/home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0 + /usr/bin/python3 setup.py build_sphinx -b man --build-dir build/sphinx /usr/lib/python3.8/site-packages/setuptools/dist.py:505: UserWarning: Normalizing '2022.03.0' to '2022.3.0' warnings.warn(tmpl.format(**locals())) running build_sphinx Running Sphinx v4.5.0 python exec: /usr/bin/python3 sys.path: ['/home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0', '/home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0', '/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages'] xarray: 2022.3.0, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/xarray/init.py making output directory... done [autosummary] generating autosummary for: README.rst, api-hidden.rst, api.rst, contributing.rst, developers-meeting.rst, ecosystem.rst, examples/ERA5-GRIB-example.ipynb, examples/ROMS_ocean_model.ipynb, examples/apply_ufunc_vectorize_1d.ipynb, examples/area_weighted_temperature.ipynb, ..., user-guide/indexing.rst, user-guide/interpolation.rst, user-guide/io.rst, user-guide/pandas.rst, user-guide/plotting.rst, user-guide/reshaping.rst, user-guide/terminology.rst, user-guide/time-series.rst, user-guide/weather-climate.rst, whats-new.rst [autosummary] generating autosummary for: /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.T.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.all.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.any.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.append.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argmax.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argmin.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.argsort.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.array.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.asi8.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.CFTimeIndex.asof.rst, ..., /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sin.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sinh.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.sqrt.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.square.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.tan.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.tanh.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.ufuncs.trunc.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.unify_chunks.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.where.rst, /home/tkloczko/rpmbuild/BUILD/xarray-2022.03.0/doc/generated/xarray.zeros_like.rst loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://scitools-iris.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory from https://numba.pydata.org/numba-doc/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory from https://docs.dask.org/en/latest/objects.inv... loading intersphinx inventory from https://unidata.github.io/cftime/objects.inv... loading intersphinx inventory from https://rasterio.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://sparse.pydata.org/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: [new config] 1282 added, 0 changed, 0 removed reading sources... [ 0%] examples/ERA5-GRIB-example Notebook error: CellExecutionError in examples/ERA5-GRIB-example.ipynb:

ds = xr.tutorial.load_dataset("era5-2mt-2019-03-uk.grib", engine="cfgrib")

ValueError Traceback (most recent call last) /tmp/ipykernel_599775/3699872736.py in <module> ----> 1 ds = xr.tutorial.load_dataset("era5-2mt-2019-03-uk.grib", engine="cfgrib")

~/rpmbuild/BUILD/xarray-2022.03.0/xarray/tutorial.py in load_dataset(args, kwargs) 223 open_dataset 224 """ --> 225 with open_dataset(args, **kwargs) as ds: 226 return ds.load() 227

~/rpmbuild/BUILD/xarray-2022.03.0/xarray/tutorial.py in open_dataset(name, cache, cache_dir, engine, kws) 141 # retrieve the file 142 filepath = pooch.retrieve(url=url, known_hash=None, path=cache_dir) --> 143 ds = _open_dataset(filepath, engine=engine, kws) 144 if not cache: 145 ds = ds.load()

~/rpmbuild/BUILD/xarray-2022.03.0/xarray/backends/api.py in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, backend_kwargs, args, *kwargs) 479 engine = plugins.guess_engine(filename_or_obj) 480 --> 481 backend = plugins.get_backend(engine) 482 483 decoders = _resolve_decoders_kwargs(

~/rpmbuild/BUILD/xarray-2022.03.0/xarray/backends/plugins.py in get_backend(engine) 154 engines = list_engines() 155 if engine not in engines: --> 156 raise ValueError( 157 f"unrecognized engine {engine} must be one of: {list(engines)}" 158 )

ValueError: unrecognized engine cfgrib must be one of: ['store'] ValueError: unrecognized engine cfgrib must be one of: ['store']

You can ignore this error by setting the following in conf.py:

nbsphinx_allow_errors = True

```

 
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   2022.03.0: sphinx fails on generate documentation 1196425693
1092089273 https://github.com/pydata/xarray/issues/6454#issuecomment-1092089273 https://api.github.com/repos/pydata/xarray/issues/6454 IC_kwDOAMm_X85BF_W5 keewis 14808389 2022-04-07T18:50:40Z 2022-04-07T18:50:40Z MEMBER

not sure, but that might be because your environment is missing the ipykernel package

 
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   2022.03.0: sphinx fails on generate documentation 1196425693

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