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andreagemelli / doc2graph

Doc2Graph transforms documents into graphs and exploit a GNN to solve several tasks.
https://link.springer.com/chapter/10.1007/978-3-031-25069-9_22
MIT License
114 stars 20 forks source link

Pydantic problems with dependency mismatches #17

Open 0000F8 opened 10 months ago

0000F8 commented 10 months ago

I get some conflicts where I can't run the main.py script. 


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 3.3.0 requires pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4, but you have pydantic 2.5.3 which is incompatible.
thinc 8.0.17 requires pydantic!=1.8,!=1.8.1,<1.9.0,>=1.7.4, but you have pydantic 2.5.3 which is incompatible.
doc2graph 0.2.0b0.post7+git.99ac9e69 requires pydantic==1.8.2, but you have pydantic 2.5.3 which is incompatible.

then if I install pydantic 1.8.2

I get


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.
dglgo 0.0.2 requires pydantic>=1.9.0, but you have pydantic 1.8.2 which is incompatible.

and back and forth.

[edit] Here is what I get when I run main.py for set-up.

Traceback (most recent call last):
  File "/Users/z1ggy/projects/forma/doc2graph/src/main.py", line 4, in <module>
    from src.inference import inference
  File "/Users/z1ggy/projects/forma/doc2graph/src/inference.py", line 7, in <module>
    from src.data.feature_builder import FeatureBuilder
  File "/Users/z1ggy/projects/forma/doc2graph/src/data/feature_builder.py", line 3, in <module>
    import spacy
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/__init__.py", line 14, in <module>
    from . import pipeline  # noqa: F401
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/pipeline/__init__.py", line 1, in <module>
    from .attributeruler import AttributeRuler
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/pipeline/attributeruler.py", line 6, in <module>
    from .pipe import Pipe
  File "spacy/pipeline/pipe.pyx", line 8, in init spacy.pipeline.pipe
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/training/__init__.py", line 11, in <module>
    from .callbacks import create_copy_from_base_model  # noqa: F401
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/training/callbacks.py", line 3, in <module>
    from ..language import Language
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/language.py", line 25, in <module>
    from .training.initialize import init_vocab, init_tok2vec
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/training/initialize.py", line 14, in <module>
    from .pretrain import get_tok2vec_ref
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/training/pretrain.py", line 16, in <module>
    from ..schemas import ConfigSchemaPretrain
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/schemas.py", line 216, in <module>
    class TokenPattern(BaseModel):
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/main.py", line 299, in __new__
    fields[ann_name] = ModelField.infer(
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 411, in infer
    return cls(
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 342, in __init__
    self.prepare()
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 451, in prepare
    self._type_analysis()
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 545, in _type_analysis
    self._type_analysis()
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 550, in _type_analysis
    if issubclass(origin, Tuple):  # type: ignore
  File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/typing.py", line 852, in __subclasscheck__
    return issubclass(cls, self.__origin__)
TypeError: issubclass() arg 1 must be a class

any protips here?

VimukthiRandika1997 commented 9 months ago

I got the same issue!

comment out spacy in requirements.txt file, then run the command pip install -e . After that conda install spacy

You might get an error with opencv, in that case

pip uninstall opencv-contrib-python
pip uninstall opencv-python
pip uninstall opencv-python-headless

pip install opencv-python====4.6.0.66

After all, run python src/main.py --init

andreagemelli commented 9 months ago

Sorry for the late answer @0000F8 and thank you @VimukthiRandika1997 for the solution! I will try again in local, solve the conflicts and push the changes! Leaving the issue open for now, closing with next commit!

VimukthiRandika1997 commented 9 months ago

@andreagemelli Thank you very much!

0000F8 commented 9 months ago

Still get

Traceback (most recent call last): File "/Users/z1ggy/projects/forma/doc2graph/src/main.py", line 4, in from src.inference import inference File "/Users/z1ggy/projects/forma/doc2graph/src/inference.py", line 7, in from src.data.feature_builder import FeatureBuilder File "/Users/z1ggy/projects/forma/doc2graph/src/data/feature_builder.py", line 3, in import spacy File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/init.py", line 13, in from . import pipeline # noqa: F401 File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/pipeline/init.py", line 1, in from .attributeruler import AttributeRuler File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/pipeline/attributeruler.py", line 8, in from ..language import Language File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/language.py", line 43, in from .pipe_analysis import analyze_pipes, print_pipe_analysis, validate_attrs File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/pipe_analysis.py", line 6, in from .tokens import Doc, Span, Token File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/tokens/init.py", line 1, in from ._serialize import DocBin File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/tokens/_serialize.py", line 14, in from ..vocab import Vocab File "spacy/vocab.pyx", line 1, in init spacy.vocab File "spacy/tokens/doc.pyx", line 49, in init spacy.tokens.doc File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/spacy/schemas.py", line 287, in class TokenPattern(BaseModel): File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/main.py", line 299, in new fields[ann_name] = ModelField.infer( File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 411, in infer return cls( File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 342, in init self.prepare() File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 451, in prepare self._type_analysis() File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 545, in _type_analysis self._type_analysis() File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/pydantic/fields.py", line 550, in _type_analysis if issubclass(origin, Tuple): # type: ignore File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/typing.py", line 852, in subclasscheck return issubclass(cls, self.origin) TypeError: issubclass() arg 1 must be a class

0000F8 commented 9 months ago

Sorry for the late answer @0000F8 and thank you @VimukthiRandika1997 for the solution! I will try again in local, solve the conflicts and push the changes! Leaving the issue open for now, closing with next commit!

Any chance of a timeline?

0000F8 commented 9 months ago

Tried this:

conda install -c conda-forge spacy conda install -c conda-forge pydantic

ended up here: /Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: dlopen(/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/image.so, 0x0006): Symbol not found: (ZN3c106detail19maybe_wrap_dim_slowExxb) Referenced from: '/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/image.so' Expected in: '/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torch/lib/libc10.dylib' warn(f"Failed to load image Python extension: {e}") DGL backend not selected or invalid. Assuming PyTorch for now. Setting the default backend to "pytorch". You can change it in the ~/.dgl/config.json file or export the DGLBACKEND environment variable. Valid options are: pytorch, mxnet, tensorflow (all lowercase) Traceback (most recent call last): File "/Users/z1ggy/projects/forma/doc2graph/src/main.py", line 4, in from src.inference import inference File "/Users/z1ggy/projects/forma/doc2graph/src/inference.py", line 8, in from src.data.graph_builder import GraphBuilder File "/Users/z1ggy/projects/forma/doc2graph/src/data/graph_builder.py", line 6, in import dgl File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/dgl/init.py", line 14, in from .backend import backend_name, load_backend # usort: skip File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/dgl/backend/init.py", line 122, in load_backend(get_preferred_backend()) File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/dgl/backend/init__.py", line 57, in load_backend mod = importlib.import_module(".%s" % mod_name, name) File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/dgl/backend/pytorch/init.py", line 2, in from .tensor import * File "/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/dgl/backend/pytorch/tensor.py", line 16, in raise RuntimeError("DGL requires PyTorch >= 1.13.0") RuntimeError: DGL requires PyTorch >= 1.13.0

Performed conda install pytorch

finally got to here:

(doc2graph) ➜ doc2graph git:(master) ✗ python src/main.py --init /Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: dlopen(/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/image.so, 0x0006): Symbol not found: (__ZN2at4_ops19empty_memory_format4callEN3c108ArrayRefIxEENS2_8optionalINS2_10ScalarTypeEEENS5_INS2_6LayoutEEENS5_INS2_6DeviceEEENS5_IbEENS5_INS2_12MemoryFormatEEE) Referenced from: '/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torchvision/image.so' Expected in: '/Users/z1ggy/anaconda3/envs/doc2graph/lib/python3.9/site-packages/torch/lib/libtorch_cpu.dylib' warn(f"Failed to load image Python extension: {e}") Namespace(init=True, add_geom=False, add_embs=False, add_hist=False, add_visual=False, add_eweights=False, src_data='FUNSD', data_type='img', edge_type='fully', node_granularity='gt', num_polar_bins=8, model='e2e', gpu=-1, test=False, weights=None, inference=False, docs=None) Downloading FUNSD 100% [..............................................................................] 36590 / 36590Downloading PAU 100% [................................................................................] 7264 / 7264Initialization completed!