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The pytest framework makes it easy to write small tests, yet scales to support complex functional testing
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4 errors running pytest for downloading tangos #12825

Open alliemolle opened 4 days ago

alliemolle commented 4 days ago

Hi, I am trying to test my download of tangos in the ubuntu shell using pytest. I encountered 4 errors. I am on a windows computer but running linux through ubuntu. The pip list:

Package                           Version            Editable project location
--------------------------------- ------------------ ---------------------------------------------------
aiobotocore                       2.12.3
aiohttp                           3.9.5
aioitertools                      0.7.1
aiosignal                         1.2.0
alabaster                         0.7.16
altair                            5.0.1
anaconda-anon-usage               0.4.4
anaconda-catalogs                 0.2.0
anaconda-client                   1.12.3
anaconda-cloud-auth               0.5.1
anaconda-navigator                2.6.0
anaconda-project                  0.11.1
annotated-types                   0.6.0
anyio                             4.2.0
appdirs                           1.4.4
archspec                          0.2.3
argon2-cffi                       21.3.0
argon2-cffi-bindings              21.2.0
arrow                             1.2.3
astroid                           2.14.2
astropy                           6.1.0
astropy-iers-data                 0.2024.6.3.0.31.14
asttokens                         2.0.5
async-lru                         2.0.4
atomicwrites                      1.4.0
attrs                             23.1.0
Automat                           20.2.0
autopep8                          2.0.4
Babel                             2.11.0
bcrypt                            3.2.0
beautifulsoup4                    4.12.3
binaryornot                       0.4.4
black                             24.4.2
bleach                            4.1.0
blinker                           1.6.2
bokeh                             3.4.1
boltons                           23.0.0
botocore                          1.34.69
Bottleneck                        1.3.7
Brotli                            1.0.9
cachetools                        5.3.3
certifi                           2024.8.30
cffi                              1.16.0
chardet                           4.0.0
charset-normalizer                2.0.4
click                             8.1.7
cloudpickle                       2.2.1
cmyt                              2.0.0
colorama                          0.4.6
colorcet                          3.1.0
comm                              0.2.1
conda                             24.7.1
conda-build                       24.5.1
conda-content-trust               0.2.0
conda_index                       0.5.0
conda-libmamba-solver             24.1.0
conda-pack                        0.7.1
conda-package-handling            2.3.0
conda_package_streaming           0.10.0
conda-repo-cli                    1.0.88
conda-token                       0.5.0+1.g2209e04
constantly                        23.10.4
contourpy                         1.2.0
cookiecutter                      2.6.0
cryptography                      42.0.5
cssselect                         1.2.0
cycler                            0.11.0
Cython                            3.0.11
cytoolz                           0.12.2
dask                              2024.5.0
dask-expr                         1.1.0
datashader                        0.16.2
debugpy                           1.6.7
decorator                         5.1.1
defusedxml                        0.7.1
diff-match-patch                  20200713
dill                              0.3.8
distributed                       2024.5.0
distro                            1.9.0
docstring-to-markdown             0.11
docutils                          0.18.1
entrypoints                       0.4
et-xmlfile                        1.1.0
ewah_bool_utils                   1.2.2
executing                         0.8.3
fastjsonschema                    2.16.2
filelock                          3.13.1
flake8                            7.0.0
Flask                             3.0.3
fonttools                         4.51.0
frozendict                        2.4.2
frozenlist                        1.4.0
fsspec                            2024.3.1
gensim                            4.3.2
gitdb                             4.0.7
GitPython                         3.1.37
greenlet                          3.0.1
h5py                              3.11.0
HeapDict                          1.0.1
holoviews                         1.19.0
hupper                            1.12.1
hvplot                            0.10.0
hyperlink                         21.0.0
idna                              3.7
imagecodecs                       2023.1.23
imageio                           2.33.1
imagesize                         1.4.1
imbalanced-learn                  0.12.3
importlib-metadata                7.0.1
incremental                       22.10.0
inflection                        0.5.1
iniconfig                         1.1.1
intake                            0.7.0
intervaltree                      3.1.0
ipykernel                         6.28.0
ipython                           8.25.0
ipython-genutils                  0.2.0
ipywidgets                        8.1.5
isort                             5.13.2
itemadapter                       0.3.0
itemloaders                       1.1.0
itsdangerous                      2.2.0
jaraco.classes                    3.2.1
jedi                              0.18.1
jeepney                           0.7.1
jellyfish                         1.0.1
Jinja2                            3.1.4
jmespath                          1.0.1
joblib                            1.4.2
json5                             0.9.6
jsonpatch                         1.33
jsonpointer                       2.1
jsonschema                        4.19.2
jsonschema-specifications         2023.7.1
jupyter                           1.0.0
jupyter_client                    8.6.0
jupyter-console                   6.6.3
jupyter_core                      5.7.2
jupyter-events                    0.10.0
jupyter-lsp                       2.2.0
jupyter_server                    2.14.1
jupyter_server_terminals          0.4.4
jupyterlab                        4.0.11
jupyterlab-pygments               0.1.2
jupyterlab_server                 2.25.1
jupyterlab_widgets                3.0.13
keyring                           24.3.1
kiwisolver                        1.4.4
lazy_loader                       0.4
lazy-object-proxy                 1.10.0
lckr_jupyterlab_variableinspector 3.1.0
libarchive-c                      2.9
libmambapy                        1.5.8
linkify-it-py                     2.0.0
llvmlite                          0.42.0
lmdb                              1.4.1
locket                            1.0.0
lxml                              5.2.1
lz4                               4.3.2
Mako                              1.3.5
Markdown                          3.4.1
markdown-it-py                    2.2.0
MarkupSafe                        2.1.3
matplotlib                        3.8.4
matplotlib-inline                 0.1.6
mccabe                            0.7.0
mdit-py-plugins                   0.3.0
mdurl                             0.1.0
menuinst                          2.1.1
mistune                           2.0.4
mkl-fft                           1.3.8
mkl-random                        1.2.4
mkl-service                       2.4.0
more-itertools                    10.1.0
mpmath                            1.3.0
msgpack                           1.0.3
multidict                         6.0.4
multipledispatch                  0.6.0
mypy                              1.10.0
mypy-extensions                   1.0.0
navigator-updater                 0.5.1
nbclient                          0.8.0
nbconvert                         7.10.0
nbformat                          5.9.2
nest-asyncio                      1.6.0
networkx                          3.2.1
nltk                              3.8.1
notebook                          7.0.8
notebook_shim                     0.2.3
numba                             0.59.1
numexpr                           2.8.7
numpy                             1.26.4
numpydoc                          1.7.0
openpyxl                          3.1.2
overrides                         7.4.0
packaging                         23.2
pandas                            2.2.2
pandocfilters                     1.5.0
panel                             1.4.4
param                             2.1.0
parsel                            1.8.1
parso                             0.8.3
partd                             1.4.1
PasteDeploy                       3.1.0
pathspec                          0.10.3
patsy                             0.5.6
pexpect                           4.8.0
pickleshare                       0.7.5
pillow                            10.3.0
pip                               24.2
pkce                              1.0.3
pkginfo                           1.10.0
plaster                           1.1.2
plaster-pastedeploy               1.0.1
platformdirs                      3.10.0
plotly                            5.22.0
pluggy                            1.0.0
ply                               3.11
prometheus-client                 0.14.1
prompt-toolkit                    3.0.43
Protego                           0.1.16
protobuf                          3.20.3
psutil                            5.9.0
ptyprocess                        0.7.0
pure-eval                         0.2.2
py-cpuinfo                        9.0.0
pyarrow                           14.0.2
pyasn1                            0.4.8
pyasn1-modules                    0.2.8
pycodestyle                       2.11.1
pycosat                           0.6.6
pycparser                         2.21
pyct                              0.5.0
pycurl                            7.45.2
pydantic                          2.5.3
pydantic_core                     2.14.6
pydeck                            0.8.0
PyDispatcher                      2.0.5
pydocstyle                        6.3.0
pyerfa                            2.0.1.4
pyflakes                          3.2.0
Pygments                          2.15.1
PyJWT                             2.8.0
pylint                            2.16.2
pylint-venv                       3.0.3
pyls-spyder                       0.4.0
pynbody                           1.6.0.post0
pyodbc                            5.0.1
pyOpenSSL                         24.0.0
pyparsing                         3.0.9
PyQt5                             5.15.10
PyQt5-sip                         12.13.0
PyQtWebEngine                     5.15.6
pyquery                           2.0.1
pyramid                           2.0.2
pyramid_debugtoolbar              4.12.1
pyramid_jinja2                    2.10.1
pyramid-mako                      1.1.0
pyramid-retry                     2.1.1
pyramid-tm                        2.5
PySocks                           1.7.1
pytest                            7.4.4
python-dateutil                   2.9.0.post0
python-dotenv                     0.21.0
python-json-logger                2.0.7
python-lsp-black                  2.0.0
python-lsp-jsonrpc                1.1.2
python-lsp-server                 1.10.0
python-slugify                    5.0.2
python-snappy                     0.6.1
pytoolconfig                      1.2.6
pytz                              2024.1
pyviz_comms                       3.0.2
pywavelets                        1.5.0
pyxdg                             0.27
PyYAML                            6.0.1
pyzmq                             25.1.2
QDarkStyle                        3.2.3
qstylizer                         0.2.2
QtAwesome                         1.2.2
qtconsole                         5.5.1
QtPy                              2.4.1
queuelib                          1.6.2
referencing                       0.30.2
regex                             2023.10.3
repoze.lru                        0.7
requests                          2.32.2
requests-file                     1.5.1
requests-toolbelt                 1.0.0
rfc3339-validator                 0.1.4
rfc3986-validator                 0.1.1
rich                              13.3.5
rope                              1.12.0
rpds-py                           0.10.6
Rtree                             1.0.1
ruamel.yaml                       0.17.21
ruamel-yaml-conda                 0.17.21
s3fs                              2024.3.1
scikit-image                      0.23.2
scikit-learn                      1.4.2
scipy                             1.13.1
Scrapy                            2.11.1
seaborn                           0.13.2
SecretStorage                     3.3.1
semver                            3.0.2
Send2Trash                        1.8.2
service-identity                  18.1.0
setuptools                        69.5.1
sip                               6.7.12
six                               1.16.0
smart-open                        5.2.1
smmap                             4.0.0
sniffio                           1.3.0
snowballstemmer                   2.2.0
sortedcontainers                  2.4.0
soupsieve                         2.5
Sphinx                            7.3.7
sphinxcontrib-applehelp           1.0.2
sphinxcontrib-devhelp             1.0.2
sphinxcontrib-htmlhelp            2.0.0
sphinxcontrib-jsmath              1.0.1
sphinxcontrib-qthelp              1.0.3
sphinxcontrib-serializinghtml     1.1.10
spyder                            5.5.1
spyder-kernels                    2.5.0
SQLAlchemy                        2.0.30
stack-data                        0.2.0
statsmodels                       0.14.2
streamlit                         1.32.0
sympy                             1.12
tables                            3.9.2
tabulate                          0.9.0
tangos                            1.9.1              /home/amolle/anaconda3/lib/python3.12/site-packages
tblib                             3.0.0
tenacity                          8.2.2
terminado                         0.17.1
text-unidecode                    1.3
textdistance                      4.2.1
threadpoolctl                     2.2.0
three-merge                       0.1.1
tifffile                          2023.4.12
tinycss2                          1.2.1
tldextract                        3.2.0
toml                              0.10.2
tomli                             2.0.1
tomli_w                           1.0.0
tomlkit                           0.11.1
toolz                             0.12.0
tornado                           6.4.1
tqdm                              4.66.4
traitlets                         5.14.3
transaction                       4.0
translationstring                 1.4
truststore                        0.8.0
Twisted                           23.10.0
typing_extensions                 4.11.0
tzdata                            2023.3
uc-micro-py                       1.0.1
ujson                             5.10.0
unicodedata2                      15.1.0
Unidecode                         1.2.0
unyt                              3.0.3
urllib3                           2.2.2
venusian                          3.1.0
w3lib                             1.21.0
waitress                          3.0.0
watchdog                          4.0.1
wcwidth                           0.2.5
webencodings                      0.5.1
WebOb                             1.8.8
websocket-client                  1.8.0
WebTest                           3.0.1
Werkzeug                          3.0.3
whatthepatch                      1.0.2
wheel                             0.43.0
widgetsnbextension                4.0.13
wrapt                             1.14.1
wurlitzer                         3.0.2
xarray                            2023.6.0
xyzservices                       2022.9.0
yapf                              0.40.2
yarl                              1.9.3
yt                                4.3.1
zict                              3.0.0
zipp                              3.17.0
zope.deprecation                  5.0
zope.interface                    5.4.0
zope.sqlalchemy                   3.1
zstandard                         0.22.0

When I run pytest, this is the warning / error list:



================================== ERRORS ==================================
___________ ERROR collecting tests/test_parallel_tasks_async.py ____________
ImportError while importing test module '/home/amolle/tangos/tests/test_parallel_tasks_async.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../anaconda3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_parallel_tasks_async.py:6: in <module>
    from tangos.parallel_tasks import async_message, message, testing
E   ImportError: cannot import name 'async_message' from 'tangos.parallel_tasks' (/home/amolle/anaconda3/lib/python3.12/site-packages/tangos/parallel_tasks/__init__.py)
______________ ERROR collecting tests/test_pynbody_server.py _______________
ImportError while importing test module '/home/amolle/tangos/tests/test_pynbody_server.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../anaconda3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_pynbody_server.py:14: in <module>
    from tangos.parallel_tasks.pynbody_server import shared_object_catalogue
E   ImportError: cannot import name 'shared_object_catalogue' from 'tangos.parallel_tasks.pynbody_server' (/home/amolle/anaconda3/lib/python3.12/site-packages/tangos/parallel_tasks/pynbody_server/__init__.py)
____________ ERROR collecting tests/test_simulation_outputs.py _____________
tests/test_simulation_outputs.py:187: in <module>
    class DummyHaloClass(pynbody.halo.number_array.HaloNumberCatalogue):
E   AttributeError: module 'pynbody.halo' has no attribute 'number_array'
_____________ ERROR collecting tests/test_timestep_thinner.py ______________
ImportError while importing test module '/home/amolle/tangos/tests/test_timestep_thinner.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../anaconda3/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_timestep_thinner.py:6: in <module>
    from tangos.tools import timestep_thinner
E   ImportError: cannot import name 'timestep_thinner' from 'tangos.tools' (/home/amolle/anaconda3/lib/python3.12/site-packages/tangos/tools/__init__.py)
============================= warnings summary
=============================
../anaconda3/lib/python3.12/site-packages/webob/compat.py:5
  /home/amolle/anaconda3/lib/python3.12/site-packages/webob/compat.py:5: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13
    from cgi import parse_header

../anaconda3/lib/python3.12/site-packages/pyramid/asset.py:2
  /home/amolle/anaconda3/lib/python3.12/site-packages/pyramid/asset.py:2: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('paste')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('repoze')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('ruamel')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
../anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832
  /home/amolle/anaconda3/lib/python3.12/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('zope')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================= short test summary info ==========================
ERROR tests/test_parallel_tasks_async.py
ERROR tests/test_pynbody_server.py
ERROR tests/test_simulation_outputs.py - AttributeError: module 'pynbody.halo' has no attribute 'number_array'
ERROR tests/test_timestep_thinner.py```
RonnyPfannschmidt commented 4 days ago

Install a older setuptools,the package you uses used a API that's deprecated since ages

alliemolle commented 4 days ago

I tried 19.2 and 19.1 and no luck. Should I go older?

alliemolle commented 4 days ago

Im also getting an extra error message:

ERROR test_web.py