Large refacto

[percevalw]

Description

Complete refacto and many new features in this PR 🎉 , already put to the test internally at APHP

Core features

• new pipeline system whose API is inspired by spaCy
• first-class support for pytorch
• hybrid model inference and training (rules + deep learning)
• moved from pandas DataFrame to dataclasses (attrs) for representing PDF documents
• new configuration system, whose API is inspired by thinc/confection, with support for instantiation of complex deep learning models, off-the-shelf CLI, ...

Functional features

• new extractors: pymupdf and poppler (separate packages for licensing reasons)
• many deep learning layers (box-transformer, 2d attention with relative position information, ...)
• deep learning classifier
• training recipes for deep learning models

Checklist

• If this PR is a bug fix, the bug is documented in the test suite.
• Changes were documented in the changelog (pending section).
• If necessary, changes were made to the documentation.

[codecov-commenter]

Codecov Report

Patch coverage: 94.98% and project coverage change: -4.95 ⚠️

Comparison is base (2efafd3) 100.00% compared to head (bc9e10e) 95.05%.

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Additional details and impacted files

@@             Coverage Diff             @@
##            master      #12      +/-   ##
===========================================
- Coverage   100.00%   95.05%   -4.95%     
===========================================
  Files           33       32       -1     
  Lines          594     1900    +1306     
===========================================
+ Hits           594     1806    +1212     
- Misses           0       94      +94     

Impacted Files	Coverage Δ
edspdf/utils/torch.py	53.84% <53.84%> (ø)
...f/components/embeddings/box_layout_preprocessor.py	86.66% <86.66%> (ø)
edspdf/layers/relative_attention.py	90.62% <90.62%> (ø)
edspdf/visualization/annotations.py	96.87% <90.90%> (-3.13%)	⬇️
edspdf/pipeline.py	94.30% <94.30%> (ø)
edspdf/layers/sinusoidal_embedding.py	95.00% <95.00%> (ø)
edspdf/utils/collections.py	95.29% <95.29%> (ø)
edspdf/utils/optimization.py	95.83% <95.83%> (ø)
edspdf/layers/vocabulary.py	96.00% <96.00%> (ø)
...pdf/components/embeddings/simple_text_embedding.py	96.18% <96.18%> (ø)
... and 22 more

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