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kushal-thakkar / pytest

The pytest framework makes it easy to write small tests, yet scales to support complex functional testing
https://pytest.org
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4 errors running pytest for downloading tangos #3

Open kushal-thakkar opened 2 days ago

kushal-thakkar commented 2 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 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 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_simulationoutputs.py tests/test_simulation_outputs.py:187: in class DummyHaloClass(pynbody.halo.number_array.HaloNumberCatalogue): E AttributeError: module 'pynbody.halo' has no attribute 'numberarray' ____ 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 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```

github-actions[bot] commented 2 days ago

Thanks for reporting this issue. To help us investigate, we'll need more information:

  1. Please provide the complete error messages you're seeing
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# test_example.py
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    # Your minimal test case here
    pass

# The command you're running:
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