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spyder-ide / spyder

Official repository for Spyder - The Scientific Python Development Environment
https://www.spyder-ide.org
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"missing dependencies" not actually missing #20455

Closed mct-lrh closed 1 year ago

mct-lrh commented 1 year ago

Description

What steps will reproduce the problem?

In Navigator, make new env, python=3.7 In Navigator, install pytorch In Navigator, open terminal in env Install AllenNLP: pip install allennlp To resolve a dependency conflict: pip uninstall pyyaml Try again: pip install allennlp Install AllenNLP-models: pip install allennlp-models In Navigator, install Spyder From Navigator, launch Spyder On launch, an error message appears: "You have missing dependencies!

Mandatory:

nbconvert >=4.0 : None (NOK) Please install them to avoid this message." Navigator shows nbconvert 6.5.4 installed.

Versions

Dependencies

# Mandatory:
atomicwrites >=1.2.0          :  1.4.0 (OK)
chardet >=2.0.0               :  4.0.0 (OK)
cloudpickle >=0.5.0           :  2.0.0 (OK)
cookiecutter >=1.6.0          :  1.7.3 (OK)
diff_match_patch >=20181111   :  20200713 (OK)
intervaltree >=3.0.2          :  3.1.0 (OK)
IPython >=7.31.1;<8.0.0       :  7.31.1 (OK)
jedi >=0.17.2;<0.19.0         :  0.18.1 (OK)
jellyfish >=0.7               :  0.9.0 (OK)
jsonschema >=3.2.0            :  4.16.0 (OK)
keyring >=17.0.0              :  23.9.3 (OK)
nbconvert >=4.0               :  None (NOK)
numpydoc >=0.6.0              :  1.5.0 (OK)
paramiko >=2.4.0              :  2.8.1 (OK)
parso >=0.7.0;<0.9.0          :  0.8.3 (OK)
pexpect >=4.4.0               :  4.8.0 (OK)
pickleshare >=0.4             :  0.7.5 (OK)
psutil >=5.3                  :  5.9.0 (OK)
pygments >=2.0                :  2.11.2 (OK)
pylint >=2.5.0;<3.0           :  2.14.5 (OK)
pyls_spyder >=0.4.0           :  0.4.0 (OK)
pylsp >=1.5.0;<1.6.0          :  1.5.0 (OK)
pylsp_black >=1.2.0           :  1.2.1 (OK)
qdarkstyle >=3.0.2;<3.1.0     :  3.0.2 (OK)
qstylizer >=0.1.10            :  0.2.2 (OK)
qtawesome >=1.0.2             :  1.2.2 (OK)
qtconsole >=5.3.2;<5.4.0      :  5.3.2 (OK)
qtpy >=2.1.0                  :  2.2.0 (OK)
rtree >=0.9.7                 :  0.9.7 (OK)
setuptools >=49.6.0           :  67.0.0 (OK)
sphinx >=0.6.6                :  4.2.0 (OK)
spyder_kernels >=2.3.3;<2.4.0 :  2.3.3 (OK)
textdistance >=4.2.0          :  4.2.1 (OK)
three_merge >=0.1.1           :  0.1.1 (OK)
watchdog >=0.10.3             :  2.2.1 (OK)
zmq >=22.1.0                  :  23.2.0 (OK)

# Optional:
cython >=0.21                 :  None (NOK)
matplotlib >=3.0.0            :  3.5.3 (OK)
numpy >=1.7                   :  1.21.5 (OK)
pandas >=1.1.1                :  1.3.5 (OK)
scipy >=0.17.0                :  1.7.3 (OK)
sympy >=0.7.3                 :  None (NOK)

Environment

Environment ``` # packages in environment at C:\Users\laura\anaconda3\envs\allen: # # Name Version Build Channel aiohttp 3.8.3 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi alabaster 0.7.12 py37_0 allennlp 2.10.1 pypi_0 pypi allennlp-models 2.10.1 pypi_0 pypi anyio 3.6.2 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi argon2-cffi 21.3.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arrow 1.2.3 py37haa95532_0 astroid 2.11.7 py37haa95532_0 async-timeout 4.0.2 pypi_0 pypi asynctest 0.13.0 pypi_0 pypi atomicwrites 1.4.0 py_0 attrs 22.2.0 pypi_0 pypi autocommand 2.2.2 pypi_0 pypi autopep8 1.6.0 pyhd3eb1b0_1 babel 2.11.0 py37haa95532_0 backcall 0.2.0 pyhd3eb1b0_0 backports-csv 1.0.7 pypi_0 pypi base58 2.1.1 pypi_0 pypi bcrypt 3.2.0 py37h2bbff1b_1 beautifulsoup4 4.11.1 py37haa95532_0 binaryornot 0.4.4 pyhd3eb1b0_1 black 22.6.0 py37haa95532_0 blas 1.0 mkl bleach 6.0.0 pypi_0 pypi blis 0.7.9 pypi_0 pypi boto3 1.26.60 pypi_0 pypi botocore 1.29.60 pypi_0 pypi brotlipy 0.7.0 py37h2bbff1b_1003 ca-certificates 2023.01.10 haa95532_0 cached-path 1.3.1 pypi_0 pypi cachetools 5.3.0 pypi_0 pypi catalogue 2.0.8 pypi_0 pypi certifi 2022.12.7 py37haa95532_0 cffi 1.15.1 py37h2bbff1b_3 chardet 4.0.0 py37haa95532_1003 charset-normalizer 2.1.1 pypi_0 pypi checklist 0.0.11 pypi_0 pypi cheroot 9.0.0 pypi_0 pypi cherrypy 18.8.0 pypi_0 pypi click 8.1.3 pypi_0 pypi cloudpickle 2.0.0 pyhd3eb1b0_0 codecov 2.1.12 pypi_0 pypi colorama 0.4.6 py37haa95532_0 confection 0.0.4 pypi_0 pypi conllu 4.4.2 pypi_0 pypi cookiecutter 1.7.3 pyhd3eb1b0_0 coverage 7.1.0 pypi_0 pypi cryptography 39.0.0 pypi_0 pypi cycler 0.11.0 pypi_0 pypi cymem 2.0.7 pypi_0 pypi databind-core 1.5.3 pypi_0 pypi databind-json 1.5.3 pypi_0 pypi datasets 2.9.0 pypi_0 pypi debugpy 1.6.6 pypi_0 pypi decorator 5.1.1 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 deprecated 1.2.13 pypi_0 pypi diff-match-patch 20200713 pyhd3eb1b0_0 dill 0.3.6 py37haa95532_0 docker-pycreds 0.4.0 pypi_0 pypi docspec 1.1.0 pypi_0 pypi docspec-python 1.1.0 pypi_0 pypi docutils 0.19 pypi_0 pypi entrypoints 0.4 py37haa95532_0 exceptiongroup 1.1.0 pypi_0 pypi fairscale 0.4.6 pypi_0 pypi feedparser 6.0.10 pypi_0 pypi filelock 3.9.0 pypi_0 pypi flake8 5.0.4 pypi_0 pypi flaky 3.7.0 pypi_0 pypi flit-core 3.6.0 pyhd3eb1b0_0 fonttools 4.38.0 pypi_0 pypi frozenlist 1.3.3 pypi_0 pypi fsspec 2023.1.0 pypi_0 pypi ftfy 6.1.1 pypi_0 pypi future 0.18.3 pypi_0 pypi ghp-import 2.1.0 pypi_0 pypi gitdb 4.0.10 pypi_0 pypi gitpython 3.1.30 pypi_0 pypi glib 2.69.1 h5dc1a3c_2 google-api-core 2.11.0 pypi_0 pypi google-auth 2.16.0 pypi_0 pypi google-cloud-core 2.3.2 pypi_0 pypi google-cloud-storage 2.7.0 pypi_0 pypi google-crc32c 1.5.0 pypi_0 pypi google-resumable-media 2.4.1 pypi_0 pypi googleapis-common-protos 1.58.0 pypi_0 pypi gst-plugins-base 1.18.5 h9e645db_0 gstreamer 1.18.5 hd78058f_0 h5py 3.8.0 pypi_0 pypi huggingface-hub 0.11.1 pypi_0 pypi icu 58.2 ha925a31_3 idna 3.4 py37haa95532_0 imagesize 1.4.1 py37haa95532_0 importlib-metadata 4.2.0 pypi_0 pypi importlib-resources 5.10.2 pypi_0 pypi importlib_metadata 3.10.0 hd3eb1b0_0 importlib_resources 5.2.0 pyhd3eb1b0_1 inflect 6.0.2 pypi_0 pypi inflection 0.5.1 py37haa95532_0 iniconfig 2.0.0 pypi_0 pypi intel-openmp 2021.4.0 haa95532_3556 intervaltree 3.1.0 pyhd3eb1b0_0 ipykernel 6.16.2 pypi_0 pypi ipython 7.34.0 pypi_0 pypi ipython_genutils 0.2.0 pyhd3eb1b0_1 ipywidgets 8.0.4 pypi_0 pypi iso-639 0.4.5 pypi_0 pypi isort 5.9.3 pyhd3eb1b0_0 jaraco-classes 3.2.3 pypi_0 pypi jaraco-collections 3.8.0 pypi_0 pypi jaraco-context 4.3.0 pypi_0 pypi jaraco-functools 3.5.2 pypi_0 pypi jaraco-text 3.11.1 pypi_0 pypi jedi 0.18.2 pypi_0 pypi jellyfish 0.9.0 py37h2bbff1b_0 jinja2 3.0.3 pypi_0 pypi jinja2-time 0.2.0 pyhd3eb1b0_3 jmespath 1.0.1 pypi_0 pypi joblib 1.2.0 pypi_0 pypi jpeg 9e h2bbff1b_0 jsonschema 4.17.3 pypi_0 pypi jupyter 1.0.0 pypi_0 pypi jupyter-client 7.4.9 pypi_0 pypi jupyter-console 6.4.4 pypi_0 pypi jupyter-core 4.12.0 pypi_0 pypi jupyter-server 1.23.5 pypi_0 pypi jupyter_client 7.4.8 py37haa95532_0 jupyter_core 4.11.2 py37haa95532_0 jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-widgets 3.0.5 pypi_0 pypi jupyterlab_pygments 0.1.2 py_0 keyring 23.9.3 pypi_0 pypi kiwisolver 1.4.4 pypi_0 pypi langcodes 3.3.0 pypi_0 pypi lazy-object-proxy 1.6.0 py37h2bbff1b_0 libclang 12.0.0 default_h627e005_2 libffi 3.4.2 hd77b12b_6 libiconv 1.16 h2bbff1b_2 libogg 1.3.5 h2bbff1b_1 libpng 1.6.37 h2a8f88b_0 libsodium 1.0.18 h62dcd97_0 libspatialindex 1.9.3 h6c2663c_0 libuv 1.40.0 he774522_0 libvorbis 1.3.7 he774522_0 libwebp 1.2.4 h2bbff1b_0 libwebp-base 1.2.4 h2bbff1b_0 libxml2 2.9.14 h0ad7f3c_0 libxslt 1.1.35 h2bbff1b_0 lmdb 1.4.0 pypi_0 pypi lxml 4.9.2 pypi_0 pypi lz4-c 1.9.4 h2bbff1b_0 markdown 3.3.4 pypi_0 pypi markdown-include 0.6.0 pypi_0 pypi markdown-it-py 2.1.0 pypi_0 pypi markupsafe 2.1.2 pypi_0 pypi matplotlib 3.5.3 pypi_0 pypi matplotlib-inline 0.1.6 py37haa95532_0 mccabe 0.7.0 pyhd3eb1b0_0 mdurl 0.1.2 pypi_0 pypi mergedeep 1.3.4 pypi_0 pypi mistune 2.0.4 pypi_0 pypi mkdocs 1.2.4 pypi_0 pypi mkdocs-material 8.2.7 pypi_0 pypi mkdocs-material-extensions 1.1.1 pypi_0 pypi mkl 2021.4.0 haa95532_640 mkl-service 2.4.0 py37h2bbff1b_0 mkl_fft 1.3.1 py37h277e83a_0 mkl_random 1.2.2 py37hf11a4ad_0 more-itertools 9.0.0 pypi_0 pypi multidict 6.0.4 pypi_0 pypi multiprocess 0.70.14 pypi_0 pypi munch 2.5.0 pypi_0 pypi murmurhash 1.0.9 pypi_0 pypi mypy 0.961 pypi_0 pypi mypy-extensions 0.4.3 pypi_0 pypi mypy_extensions 0.4.3 py37haa95532_1 nbclassic 0.5.1 pypi_0 pypi nbclient 0.7.2 pypi_0 pypi nbconvert 7.2.9 pypi_0 pypi nbformat 5.7.3 pypi_0 pypi nest-asyncio 1.5.6 py37haa95532_0 ninja 1.10.2 haa95532_5 ninja-base 1.10.2 h6d14046_5 nltk 3.8.1 pypi_0 pypi notebook 6.5.2 pypi_0 pypi notebook-shim 0.2.2 pypi_0 pypi nr-fs 1.6.3 pypi_0 pypi nr-pylang-utils 0.1.3 pypi_0 pypi nr-stream 0.2.3 pypi_0 pypi nr-util 0.8.12 pypi_0 pypi numpy 1.21.6 pypi_0 pypi numpy-base 1.21.5 py37hca35cd5_3 numpydoc 1.5.0 py37haa95532_0 openssl 1.1.1s h2bbff1b_0 packaging 23.0 pypi_0 pypi pandas 1.3.5 pypi_0 pypi pandocfilters 1.5.0 pyhd3eb1b0_0 paramiko 2.8.1 pyhd3eb1b0_0 parso 0.8.3 pyhd3eb1b0_0 pathspec 0.11.0 pypi_0 pypi pathtools 0.1.2 pypi_0 pypi pathy 0.10.1 pypi_0 pypi patternfork-nosql 3.6 pypi_0 pypi pcre 8.45 hd77b12b_0 pdfminer-six 20221105 pypi_0 pypi pexpect 4.8.0 pyhd3eb1b0_3 pickleshare 0.7.5 pyhd3eb1b0_1003 pillow 9.4.0 pypi_0 pypi pip 23.0 pypi_0 pypi pkginfo 1.9.6 pypi_0 pypi pkgutil-resolve-name 1.3.10 py37haa95532_0 platformdirs 2.6.2 pypi_0 pypi pluggy 1.0.0 py37haa95532_1 ply 3.11 py37_0 portend 3.1.0 pypi_0 pypi poyo 0.5.0 pyhd3eb1b0_0 preshed 3.0.8 pypi_0 pypi prometheus-client 0.16.0 pypi_0 pypi prompt-toolkit 3.0.36 py37haa95532_0 protobuf 3.19.6 pypi_0 pypi psutil 5.9.4 pypi_0 pypi ptyprocess 0.7.0 pyhd3eb1b0_2 py-cpuinfo 9.0.0 pypi_0 pypi py-rouge 1.1 pypi_0 pypi pyarrow 11.0.0 pypi_0 pypi pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pycodestyle 2.9.1 pypi_0 pypi pycparser 2.21 pyhd3eb1b0_0 pydantic 1.10.4 pypi_0 pypi pydoc-markdown 4.3.2 pypi_0 pypi pydocstyle 6.1.1 pyhd3eb1b0_0 pyflakes 2.5.0 pypi_0 pypi pygments 2.14.0 pypi_0 pypi pylint 2.14.5 py37haa95532_0 pyls-spyder 0.4.0 pyhd3eb1b0_0 pymdown-extensions 9.9.2 pypi_0 pypi pynacl 1.5.0 py37h8cc25b3_0 pyopenssl 22.0.0 pyhd3eb1b0_0 pyparsing 3.0.9 pypi_0 pypi pyqt 5.15.7 py37hd77b12b_0 pyqt5-sip 12.11.0 py37hd77b12b_0 pyqtwebengine 5.15.7 py37hd77b12b_0 pyrsistent 0.19.3 pypi_0 pypi pysocks 1.7.1 py37_1 pytest 7.2.1 pypi_0 pypi pytest-benchmark 4.0.0 pypi_0 pypi pytest-cov 4.0.0 pypi_0 pypi python 3.7.16 h6244533_0 python-dateutil 2.8.2 pyhd3eb1b0_0 python-docx 0.8.11 pypi_0 pypi python-fastjsonschema 2.16.2 py37haa95532_0 python-lsp-black 1.2.1 py37haa95532_0 python-lsp-jsonrpc 1.0.0 pyhd3eb1b0_0 python-lsp-server 1.5.0 py37haa95532_0 python-slugify 5.0.2 pyhd3eb1b0_0 pytorch 1.12.1 cpu_py37h5e1f01c_0 pytz 2022.7.1 pypi_0 pypi pywin32 305 pypi_0 pypi pywin32-ctypes 0.2.0 py37_1001 pywinpty 2.0.10 pypi_0 pypi pyyaml 5.4.1 pypi_0 pypi pyyaml-env-tag 0.1 pypi_0 pypi pyzmq 25.0.0 pypi_0 pypi qdarkstyle 3.0.2 pyhd3eb1b0_0 qstylizer 0.2.2 py37haa95532_0 qt-main 5.15.2 he8e5bd7_7 qt-webengine 5.15.9 hb9a9bb5_5 qtawesome 1.2.2 py37haa95532_0 qtconsole 5.4.0 pypi_0 pypi qtpy 2.3.0 pypi_0 pypi qtwebkit 5.212 h3ad3cdb_4 readme-renderer 37.3 pypi_0 pypi regex 2022.10.31 pypi_0 pypi requests 2.28.2 pypi_0 pypi requests-toolbelt 0.10.1 pypi_0 pypi responses 0.18.0 pypi_0 pypi rfc3986 2.0.0 pypi_0 pypi rich 13.3.1 pypi_0 pypi rope 0.22.0 pyhd3eb1b0_0 rsa 4.9 pypi_0 pypi rtree 0.9.7 py37h2eaa2aa_1 ruamel-yaml 0.17.21 pypi_0 pypi ruamel-yaml-clib 0.2.7 pypi_0 pypi s3transfer 0.6.0 pypi_0 pypi sacremoses 0.0.53 pypi_0 pypi scikit-learn 1.0.2 pypi_0 pypi scipy 1.7.3 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi sentencepiece 0.1.97 pypi_0 pypi sentry-sdk 1.14.0 pypi_0 pypi setproctitle 1.3.2 pypi_0 pypi setuptools 67.0.0 pypi_0 pypi sgmllib3k 1.0.0 pypi_0 pypi sip 6.6.2 py37hd77b12b_0 six 1.16.0 pyhd3eb1b0_1 smart-open 6.3.0 pypi_0 pypi smmap 5.0.0 pypi_0 pypi sniffio 1.3.0 pypi_0 pypi snowballstemmer 2.2.0 pyhd3eb1b0_0 sortedcontainers 2.4.0 pyhd3eb1b0_0 soupsieve 2.3.2.post1 py37haa95532_0 spacy 3.5.0 pypi_0 pypi spacy-legacy 3.0.12 pypi_0 pypi spacy-loggers 1.0.4 pypi_0 pypi sphinx 4.2.0 pyhd3eb1b0_1 sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0 sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0 sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0 sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0 spyder 5.3.3 py37haa95532_0 spyder-kernels 2.3.3 py37haa95532_0 sqlite 3.40.1 h2bbff1b_0 srsly 2.4.5 pypi_0 pypi tempora 5.2.1 pypi_0 pypi tensorboardx 2.5.1 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.17.1 pypi_0 pypi text-unidecode 1.3 pyhd3eb1b0_0 textdistance 4.2.1 pyhd3eb1b0_0 thinc 8.1.7 pypi_0 pypi threadpoolctl 3.1.0 pypi_0 pypi three-merge 0.1.1 pyhd3eb1b0_0 tinycss2 1.2.1 py37haa95532_0 tokenizers 0.13.2 pypi_0 pypi toml 0.10.2 pyhd3eb1b0_0 tomli 2.0.1 py37haa95532_0 tomlkit 0.11.1 py37haa95532_0 torch 1.12.1 pypi_0 pypi torchvision 0.13.1 pypi_0 pypi tornado 6.2 py37h2bbff1b_0 tqdm 4.64.1 pypi_0 pypi traitlets 5.9.0 pypi_0 pypi transformers 4.26.0 pypi_0 pypi twine 4.0.2 pypi_0 pypi typed-ast 1.5.4 pypi_0 pypi typer 0.7.0 pypi_0 pypi types-toml 0.10.8.1 pypi_0 pypi typing-extensions 4.4.0 py37haa95532_0 typing_extensions 4.4.0 py37haa95532_0 ujson 5.4.0 py37hd77b12b_0 unidecode 1.2.0 pyhd3eb1b0_0 urllib3 1.26.14 py37haa95532_0 vc 14.2 h21ff451_1 vs2015_runtime 14.27.29016 h5e58377_2 wandb 0.13.9 pypi_0 pypi wasabi 1.1.1 pypi_0 pypi watchdog 2.2.1 pypi_0 pypi wcwidth 0.2.6 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.5.0 pypi_0 pypi whatthepatch 1.0.2 py37haa95532_0 wheel 0.38.4 pypi_0 pypi widgetsnbextension 4.0.5 pypi_0 pypi win_inet_pton 1.1.0 py37haa95532_0 wincertstore 0.2 py37haa95532_2 word2number 1.1 pypi_0 pypi wrapt 1.14.1 py37h2bbff1b_0 xxhash 3.2.0 pypi_0 pypi yaml 0.2.5 he774522_0 yapf 0.31.0 pyhd3eb1b0_0 yarl 1.8.2 pypi_0 pypi zc-lockfile 2.0 pypi_0 pypi zeromq 4.3.4 hd77b12b_0 zipp 3.12.0 pypi_0 pypi zlib 1.2.13 h8cc25b3_0 zstd 1.5.2 h19a0ad4_0 ```
mct-lrh commented 1 year ago

Installing Spyder first resolved this issue. This still does not explain why a package in the environment was not accessible to Spyder.

dalthviz commented 1 year ago

Hi @mct-lrh my guess is that mixing conda and pip packages caused the nbconvert installation in the env to become faulty. You mentioned that when installing a package with pip you had to resolve a conflict uninstalling something else and then reinstalling things, right? To prevent issue like this we suggest not mixing pip and conda packages. Maybe this entry in the Spyder docs FAQ page could be useful: https://docs.spyder-ide.org/current/faq.html#using-install-packages

However, I think you are able to use Spyder now, right?

mct-lrh commented 1 year ago

I see, I recall being warned about mixing pip and conda packages. Unfortunately, some packages, like allennlp, are not available from conda.

I am able to use Spyder now and I think I can consider this issue resolved.