3.1.3: pytest warnings
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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
buildwith--no-isolationI'm using during all processes only locally installed modules - install .whl file in </install/prefix>
- run pytest with PYTHONPATH pointing to sitearch and sitelib inside </install/prefix>
Here is pytest output:
+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-emcee-3.1.3-2.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-emcee-3.1.3-2.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra -p no:cacheprovider
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.14, pytest-7.1.3, pluggy-1.0.0
rootdir: /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3
collected 93 items
src/emcee/tests/integration/test_de.py ... [ 3%]
src/emcee/tests/integration/test_de_snooker.py .. [ 5%]
src/emcee/tests/integration/test_gaussian.py ............ [ 18%]
src/emcee/tests/integration/test_kde.py ... [ 21%]
src/emcee/tests/integration/test_longdouble.py .. [ 23%]
src/emcee/tests/integration/test_stretch.py ..... [ 29%]
src/emcee/tests/integration/test_walk.py .. [ 31%]
src/emcee/tests/unit/test_autocorr.py .... [ 35%]
src/emcee/tests/unit/test_backends.py s..ssss.s [ 45%]
src/emcee/tests/unit/test_blobs.py .......... [ 55%]
src/emcee/tests/unit/test_ensemble.py ....... [ 63%]
src/emcee/tests/unit/test_sampler.py .............................. [ 95%]
src/emcee/tests/unit/test_state.py ... [ 98%]
src/emcee/tests/unit/test_stretch.py . [100%]
============================================================================= warnings summary =============================================================================
src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_run_mcmc
/home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/utils.py:23: DeprecationWarning: 'chain' is deprecated. Use 'get_chain()' instead.
deprecation_warning(msg)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] src/emcee/tests/unit/test_backends.py:64: HDF5 not available
SKIPPED [1] src/emcee/tests/unit/test_backends.py:101: got empty parameter set ['backend', 'dtype', 'blobs'], function test_backend at /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/tests/unit/test_backends.py:100
SKIPPED [1] src/emcee/tests/unit/test_backends.py:142: got empty parameter set ['backend', 'dtype'], function test_reload at /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/tests/unit/test_backends.py:141
SKIPPED [1] src/emcee/tests/unit/test_backends.py:186: got empty parameter set ['backend', 'dtype'], function test_restart at /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/tests/unit/test_backends.py:185
SKIPPED [1] src/emcee/tests/unit/test_backends.py:218: HDF5 not available
SKIPPED [1] src/emcee/tests/unit/test_backends.py:268: HDF5 not available
=========================================================== 87 passed, 6 skipped, 1 warning in 136.15s (0:02:16) ===========================================================
Here is list of installed modules in build env
Package Version
----------------------------- -----------------
alabaster 0.7.12
appdirs 1.4.4
asttokens 2.0.5
attrs 22.1.0
Babel 2.10.2
backcall 0.2.0
Brlapi 0.8.3
build 0.8.0
charset-normalizer 2.1.0
click 8.1.3
codespell 2.2.1
cssselect 1.1.0
debugpy 1.6.3
decorator 5.1.1
distro 1.7.0
dnspython 2.2.1
docutils 0.18.1
entrypoints 0.4
executing 1.1.0
extras 1.0.0
fastjsonschema 2.16.1
fixtures 4.0.0
gpg 1.17.1-unknown
greenlet 1.1.2
idna 3.4
imagesize 1.4.1
importlib-metadata 4.12.0
importlib-resources 5.9.0
iniconfig 1.1.1
ipykernel 6.16.0
ipython 8.4.0
jedi 0.18.1
Jinja2 3.1.1
jsonschema 4.16.0
jupyter-cache 0.5.0
jupyter_client 7.3.5
jupyter_core 4.11.1
libcomps 0.1.19
louis 3.23.0
lxml 4.9.1
markdown-it-py 2.1.0
MarkupSafe 2.1.1
matplotlib-inline 0.1.5
mdit-py-plugins 0.3.0
mdurl 0.1.1
myst-nb 0.16.0
myst-parser 0.18.0
nbclient 0.6.8
nbformat 5.6.1
nest-asyncio 1.5.5
numpy 1.23.1
packaging 21.3
parso 0.8.3
pbr 5.9.0
pep517 0.12.0
pexpect 4.8.0
pickleshare 0.7.5
pip 22.2.2
pkgutil_resolve_name 1.3.10
pluggy 1.0.0
prompt-toolkit 3.0.29
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
Pygments 2.13.0
PyGObject 3.42.2
pyparsing 3.0.9
pyrsistent 0.18.1
pytest 7.1.3
python-dateutil 2.8.2
pytz 2022.1
PyYAML 6.0
pyzmq 24.0.0
requests 2.28.1
rpm 4.17.0
ruamel.yaml 0.17.21
ruamel.yaml.clib 0.2.6
scour 0.38.2
setuptools 65.4.0
setuptools-scm 7.0.5
six 1.16.0
snowballstemmer 2.2.0
Sphinx 5.2.2
sphinx-togglebutton 0.3.2
sphinxcontrib-applehelp 1.0.2.dev20220730
sphinxcontrib-devhelp 1.0.2.dev20220730
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1.dev20220730
sphinxcontrib-qthelp 1.0.3.dev20220730
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.41.dev0
stack-data 0.5.1
tabulate 0.8.10
testtools 2.5.0
tomli 2.0.1
tornado 6.2
traitlets 5.4.0
typing_extensions 4.3.0
urllib3 1.26.12
wcwidth 0.2.5
wheel 0.37.1
xmltodict 0.12.0
zipp 3.8.1
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing src/emcee/utils.py:23 and the warning-producing test, src/emcee/tests/unit/test_ensemble.py::TestNamedParameters::test_run_mcmc. Run the reported pytest command in the packaged installation environment and determine what change is needed for the deprecation warning to disappear while the existing tests continue to pass.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- testing-qa
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100