3.1.3: pytest warnings

[kloczek]

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 </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

[dfm]

Thanks! That DeprecationWarning is expected (it's testing backwards compatibility) and has been happening since v3.0 🤦 We should catch it and silence it! Otherwise, things look fine to me.