jupyter / jupyter/nbformat

5.7.0: pytest is failing

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Python
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Description

I'm packaging your module as an rpm package so I'm using the typical PEP517 based build, install and test cycle used on building packages from non-root account.
- `python3 -sBm build -w --no-isolation`
- because I'm calling `build` with `--no-isolation` I'm using during all processes only locally installed modules
- install .whl file in
- run pytest with PYTHONPATH pointing to sitearch and sitelib inside

Here is pytest output:

```console
+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-nbformat-5.7.0-2.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-nbformat-5.7.0-2.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.15, pytest-7.2.0, pluggy-1.0.0
rootdir: /home/tkloczko/rpmbuild/BUILD/nbformat-5.7.0, configfile: pyproject.toml, testpaths: tests/
plugins: anyio-3.6.2
collected 169 items / 2 errors

================================================================================== ERRORS ==================================================================================
___________________________________________________________________ ERROR collecting tests/test_sign.py ____________________________________________________________________
tests/test_sign.py:19: in
from nbformat import read, sign, write
nbformat/sign.py:25: in
from jupyter_core.application import JupyterApp, base_flags
/usr/lib/python3.8/site-packages/jupyter_core/application.py:21: in
from .paths import (
/usr/lib/python3.8/site-packages/jupyter_core/paths.py:176: in
deprecation(
/usr/lib/python3.8/site-packages/jupyter_core/utils/__init__.py:87: in deprecation
warnings.warn(message, DeprecationWarning, stacklevel=stacklevel + 1)
E DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
E given by the platformdirs library. To remove this warning and
E see the appropriate new directories, set the environment variable
E `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`.
E The use of platformdirs will be the default in `jupyter_core` v6
___________________________________________________________________ ERROR collecting tests/test_sign.py ____________________________________________________________________
tests/test_sign.py:19: in
from nbformat import read, sign, write
nbformat/sign.py:25: in
from jupyter_core.application import JupyterApp, base_flags
/usr/lib/python3.8/site-packages/jupyter_core/application.py:21: in
from .paths import (
/usr/lib/python3.8/site-packages/jupyter_core/paths.py:176: in
deprecation(
/usr/lib/python3.8/site-packages/jupyter_core/utils/__init__.py:87: in deprecation
warnings.warn(message, DeprecationWarning, stacklevel=stacklevel + 1)
E DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
E given by the platformdirs library. To remove this warning and
E see the appropriate new directories, set the environment variable
E `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`.
E The use of platformdirs will be the default in `jupyter_core` v6
========================================================================= short test summary info ==========================================================================
ERROR tests/test_sign.py - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
ERROR tests/test_sign.py - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================ 2 errors in 0.80s =============================================================================
```

Here is list of installed modules in build env

```console
Package Version
----------------------------- -----------------
alabaster 0.7.12
anyio 3.6.2
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.2.0
attrs 22.1.0
Babel 2.11.0
backcall 0.2.0
beautifulsoup4 4.11.1
bleach 5.0.0
Brlapi 0.8.3
build 0.9.0
cffi 1.15.1
charset-normalizer 3.0.1
comm 0.1.0
contourpy 1.0.6
cssselect 1.1.0
cycler 0.11.0
debugpy 1.6.4
decorator 5.1.1
defusedxml 0.7.1
distro 1.8.0
dnspython 2.2.1
docutils 0.19
editables 0.3
entrypoints 0.4
exceptiongroup 1.0.0
executing 1.2.0
extras 1.0.0
fastjsonschema 2.16.1
fixtures 4.0.0
fonttools 4.38.0
gpg 1.17.1-unknown
hatch-nodejs-version 0.3.1
hatchling 1.11.1
html5lib 1.1
idna 3.4
imagesize 1.4.1
importlib-metadata 5.1.0
importlib-resources 5.9.0
iniconfig 1.1.1
ipython 8.6.0
ipython-genutils 0.2.0
jedi 0.18.2
Jinja2 3.1.2
jsonschema 4.17.3
jupyter_client 7.4.8
jupyter_core 5.1.0
jupyter-server 1.23.3
jupyterlab-pygments 0.1.2
kiwisolver 1.4.4
libcomps 0.1.19
louis 3.23.0
lxml 4.9.1
MarkupSafe 2.1.1
matplotlib 3.6.2
matplotlib-inline 0.1.6
mistune 2.0.4
nbclient 0.7.2
nbconvert 7.2.6
nbformat 5.7.0
nest-asyncio 1.5.6
numpy 1.23.1
olefile 0.46
packaging 21.3
pandocfilters 1.5.0
parso 0.8.3
pathspec 0.10.2
pbr 5.9.0
pep440 0.1.2
pep517 0.13.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.3.0
pip 22.3.1
pkgutil_resolve_name 1.3.10
platformdirs 2.5.2
pluggy 1.0.0
ply 3.11
prometheus-client 0.15.0
prompt-toolkit 3.0.29
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.4.8
pycparser 2.21
Pygments 2.13.0
PyGObject 3.42.2
pyparsing 3.0.9
pyrsistent 0.19.2
pytest 7.2.0
python-dateutil 2.8.2
pytz 2022.4
pyzmq 24.0.0
requests 2.28.1
rpm 4.17.0
scour 0.38.2
Send2Trash 1.8.0
six 1.16.0
sniffio 1.2.0
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 5.3.0
sphinxcontrib-applehelp 1.0.2.dev20221204
sphinxcontrib-devhelp 1.0.2.dev20221204
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1.dev20221204
sphinxcontrib-qthelp 1.0.3.dev20221204
sphinxcontrib-serializinghtml 1.1.5
stack-data 0.6.2
terminado 0.15.0
testpath 0.6.0
testtools 2.5.0
tinycss2 1.2.1
tomli 2.0.1
tornado 6.2
traitlets 5.4.0
urllib3 1.26.12
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.4.2
wheel 0.38.4
zipp 3.11.0
```

Contributor guide

Open the contributing guide

Research direction

Reproduce the reported PEP 517 installation and `pytest -ra` run, starting with `pyproject.toml` and `tests/test_sign.py`. Trace the `jupyter_core` deprecation warning during test collection and define the fix so the installed package's tests collect and pass without these errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
build-system, testing-qa
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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