Data fixes

[percevalw]

Description

Added

• Support for a filesystem parameter in every edsnlp.data.read_* and edsnlp.data.write_* functions
• Pipes of a pipeline are now easily accessible with nlp.pipes.xxx instead of nlp.get_pipe("xxx")

• Support builtin Span attributes in converters span_attributes parameter, e.g.

  import edsnlp
  
  nlp = ...
  nlp.add_pipe("eds.sentences")
  
  data = edsnlp.data.from_xxx(...)
  data = data.map_pipeline(nlp)
  data.to_pandas(converters={"ents": {"span_attributes": ["sent.text", "start", "end"]}})

• Support assigning Brat AnnotatorNotes as span attributes: edsnlp.data.read_standoff(..., notes_as_span_attribute="cui")

• Support for mapping full batches in edsnlp.processing pipelines with map_batches lazy collection method:

  import edsnlp
  
  data = edsnlp.data.from_xxx(...)
  data = data.map_batches(lambda batch: do_something(batch))
  data.to_pandas()

Changed

• nlp.preprocess_many now uses lazy collections to enable parallel processing

Fixed

• Flatten list outputs (such as "ents" converter) when iterating: nlp.map(data).to_iterable("ents") is now a list of entities, and not a list of lists of entities

Checklist

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

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 97.13%. Comparing base (a06cd11) to head (27fcb66).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #275 +/- ## ========================================== + Coverage 97.12% 97.13% +0.01% ========================================== Files 257 257 Lines 8703 8734 +31 ========================================== + Hits 8453 8484 +31 Misses 250 250 ```

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