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allenai / scispacy

A full spaCy pipeline and models for scientific/biomedical documents.
https://allenai.github.io/scispacy/
Apache License 2.0
1.68k stars 225 forks source link

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed #438

Closed EmanuelFaria closed 2 years ago

EmanuelFaria commented 2 years ago

Any fix or workaround for this issue:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
scispacy 0.4.0 requires spacy<3.1.0,>=3.0.0, but you have spacy 3.2.4 which is incompatible.
en-core-web-sm 3.0.0 requires spacy<3.1.0,>=3.0.0, but you have spacy 3.2.4 which is incompatible.
docanalysis 0.1.1 requires spacy==3.0.7, but you have spacy 3.2.4 which is incompatible.

Here's my terminal log:

Last login: Mon Jun 20 11:58:15 on ttys000
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % pip2 install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.0/en_core_sci_scibert-0.5.0.tar.gz
zsh: command not found: pip2
emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % pip3 install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.0/en_core_sci_scibert-0.5.0.tar.gz
Collecting https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.0/en_core_sci_scibert-0.5.0.tar.gz
  Using cached https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.0/en_core_sci_scibert-0.5.0.tar.gz (417.6 MB)
  Preparing metadata (setup.py) ... done
Collecting spacy<3.3.0,>=3.2.3
  Using cached spacy-3.2.4-cp310-cp310-macosx_10_9_x86_64.whl (6.3 MB)
Requirement already satisfied: spacy-transformers in /usr/local/lib/python3.10/site-packages (from en-core-sci-scibert==0.5.0) (1.1.6)
Requirement already satisfied: click<8.1.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (7.1.2)
Requirement already satisfied: tqdm<5.0.0,>=4.38.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (4.62.3)
Requirement already satisfied: typer<0.5.0,>=0.3.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (0.3.2)
Requirement already satisfied: pathy>=0.3.5 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (0.6.1)
Requirement already satisfied: wasabi<1.1.0,>=0.8.1 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (0.9.1)
Requirement already satisfied: murmurhash<1.1.0,>=0.28.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (1.0.7)
Requirement already satisfied: numpy>=1.15.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (1.22.4)
Requirement already satisfied: srsly<3.0.0,>=2.4.1 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.4.3)
Requirement already satisfied: cymem<2.1.0,>=2.0.2 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.0.6)
Requirement already satisfied: jinja2 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.1.2)
Requirement already satisfied: preshed<3.1.0,>=3.0.2 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.0.6)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (21.3)
Requirement already satisfied: setuptools in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (60.3.1)
Requirement already satisfied: blis<0.8.0,>=0.4.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (0.7.7)
Requirement already satisfied: requests<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.28.0)
Requirement already satisfied: spacy-loggers<2.0.0,>=1.0.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (1.0.2)
Requirement already satisfied: thinc<8.1.0,>=8.0.12 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (8.0.17)
Requirement already satisfied: spacy-legacy<3.1.0,>=3.0.8 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.0.9)
Requirement already satisfied: catalogue<2.1.0,>=2.0.6 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.0.7)
Requirement already satisfied: langcodes<4.0.0,>=3.2.0 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.3.0)
Requirement already satisfied: pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4 in /usr/local/lib/python3.10/site-packages (from spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (1.8.2)
Requirement already satisfied: spacy-alignments<1.0.0,>=0.7.2 in /usr/local/lib/python3.10/site-packages (from spacy-transformers->en-core-sci-scibert==0.5.0) (0.8.5)
Requirement already satisfied: torch>=1.6.0 in /usr/local/lib/python3.10/site-packages (from spacy-transformers->en-core-sci-scibert==0.5.0) (1.11.0)
Requirement already satisfied: transformers<4.20.0,>=3.4.0 in /usr/local/lib/python3.10/site-packages (from spacy-transformers->en-core-sci-scibert==0.5.0) (4.19.4)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/local/lib/python3.10/site-packages (from packaging>=20.0->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.0.9)
Requirement already satisfied: smart-open<6.0.0,>=5.0.0 in /usr/local/lib/python3.10/site-packages (from pathy>=0.3.5->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (5.2.1)
Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (4.2.0)
Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/site-packages (from requests<3.0.0,>=2.13.0->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (3.3)
Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/site-packages (from requests<3.0.0,>=2.13.0->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/site-packages (from requests<3.0.0,>=2.13.0->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (1.26.9)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/site-packages (from requests<3.0.0,>=2.13.0->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2022.5.18.1)
Requirement already satisfied: filelock in /usr/local/lib/python3.10/site-packages (from transformers<4.20.0,>=3.4.0->spacy-transformers->en-core-sci-scibert==0.5.0) (3.7.1)
Requirement already satisfied: huggingface-hub<1.0,>=0.1.0 in /usr/local/lib/python3.10/site-packages (from transformers<4.20.0,>=3.4.0->spacy-transformers->en-core-sci-scibert==0.5.0) (0.7.0)
Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.10/site-packages (from transformers<4.20.0,>=3.4.0->spacy-transformers->en-core-sci-scibert==0.5.0) (6.0)
Requirement already satisfied: regex!=2019.12.17 in /usr/local/lib/python3.10/site-packages (from transformers<4.20.0,>=3.4.0->spacy-transformers->en-core-sci-scibert==0.5.0) (2022.6.2)
Requirement already satisfied: tokenizers!=0.11.3,<0.13,>=0.11.1 in /usr/local/lib/python3.10/site-packages (from transformers<4.20.0,>=3.4.0->spacy-transformers->en-core-sci-scibert==0.5.0) (0.12.1)
Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/site-packages (from jinja2->spacy<3.3.0,>=3.2.3->en-core-sci-scibert==0.5.0) (2.1.1)
Installing collected packages: spacy
  Attempting uninstall: spacy
    Found existing installation: spacy 3.0.7
    Uninstalling spacy-3.0.7:
      Successfully uninstalled spacy-3.0.7
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
scispacy 0.4.0 requires spacy<3.1.0,>=3.0.0, but you have spacy 3.2.4 which is incompatible.
en-core-web-sm 3.0.0 requires spacy<3.1.0,>=3.0.0, but you have spacy 3.2.4 which is incompatible.
docanalysis 0.1.1 requires spacy==3.0.7, but you have spacy 3.2.4 which is incompatible.
Successfully installed spacy-3.2.4
dakinggg commented 2 years ago

You will need to stick with compatible versions of spacy and scispacy. It looks like you can just upgrade scispacy to resolve your particular issue.

EmanuelFaria commented 2 years ago

When installing scispacy, I get similar resolver issues. Am I doing something wrong?

emanuelfarruda@Mannys-MacBook-Pro-2021 ~ % pip3 install scispacy
Requirement already satisfied: scispacy in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (0.4.0)
Requirement already satisfied: scikit-learn>=0.20.3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (1.1.1)
Requirement already satisfied: joblib in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (1.1.0)
Requirement already satisfied: nmslib>=1.7.3.6 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (2.1.1)
Requirement already satisfied: pysbd in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (0.3.4)
Collecting spacy<3.1.0,>=3.0.0
  Using cached spacy-3.0.8-cp310-cp310-macosx_10_9_x86_64.whl (6.1 MB)
Requirement already satisfied: conllu in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (4.4.2)
Requirement already satisfied: requests<3.0.0,>=2.0.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (2.15.1)
Requirement already satisfied: numpy in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scispacy) (1.22.4)
Requirement already satisfied: psutil in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from nmslib>=1.7.3.6->scispacy) (5.9.1)
Requirement already satisfied: pybind11<2.6.2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from nmslib>=1.7.3.6->scispacy) (2.6.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scikit-learn>=0.20.3->scispacy) (3.1.0)
Requirement already satisfied: scipy>=1.3.2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from scikit-learn>=0.20.3->scispacy) (1.8.1)
Requirement already satisfied: thinc<8.1.0,>=8.0.3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (8.0.17)
Requirement already satisfied: typer<0.4.0,>=0.3.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (0.3.2)
Requirement already satisfied: pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (1.8.2)
Requirement already satisfied: tqdm<5.0.0,>=4.38.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (4.62.3)
Requirement already satisfied: blis<0.8.0,>=0.4.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (0.7.7)
Requirement already satisfied: preshed<3.1.0,>=3.0.2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (3.0.6)
Requirement already satisfied: packaging>=20.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (21.3)
Requirement already satisfied: spacy-legacy<3.1.0,>=3.0.5 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (3.0.9)
Requirement already satisfied: cymem<2.1.0,>=2.0.2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (2.0.6)
Requirement already satisfied: catalogue<2.1.0,>=2.0.4 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (2.0.7)
Requirement already satisfied: wasabi<1.1.0,>=0.8.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (0.9.1)
Requirement already satisfied: srsly<3.0.0,>=2.4.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (2.4.3)
Requirement already satisfied: pathy>=0.3.5 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (0.6.1)
Requirement already satisfied: murmurhash<1.1.0,>=0.28.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (1.0.7)
Requirement already satisfied: jinja2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (3.1.2)
Requirement already satisfied: setuptools in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from spacy<3.1.0,>=3.0.0->scispacy) (60.3.1)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from packaging>=20.0->spacy<3.1.0,>=3.0.0->scispacy) (3.0.9)
Requirement already satisfied: smart-open<6.0.0,>=5.0.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from pathy>=0.3.5->spacy<3.1.0,>=3.0.0->scispacy) (5.2.1)
Requirement already satisfied: typing-extensions>=3.7.4.3 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4->spacy<3.1.0,>=3.0.0->scispacy) (4.2.0)
Requirement already satisfied: click<7.2.0,>=7.1.1 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from typer<0.4.0,>=0.3.0->spacy<3.1.0,>=3.0.0->scispacy) (7.1.2)
Requirement already satisfied: MarkupSafe>=2.0 in /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages (from jinja2->spacy<3.1.0,>=3.0.0->scispacy) (2.1.1)
Installing collected packages: spacy
  Attempting uninstall: spacy
    Found existing installation: spacy 3.2.4
    Uninstalling spacy-3.2.4:
      Successfully uninstalled spacy-3.2.4
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
spacy-transformers 1.1.6 requires spacy<4.0.0,>=3.1.3, but you have spacy 3.0.8 which is incompatible.
medspacy 0.2.0.0 requires spacy<3.2.0,>=3.1.3, but you have spacy 3.0.8 which is incompatible.
en-core-sci-scibert 0.5.0 requires spacy<3.3.0,>=3.2.3, but you have spacy 3.0.8 which is incompatible.
docanalysis 0.1.1 requires spacy==3.0.7, but you have spacy 3.0.8 which is incompatible.
Successfully installed spacy-3.0.8