Integrate DataStore with MultiPack

[mylibrar]

This PR fixes #833.

Description of changes

• base_pack.py
  • Refactor _pending_entries
  • Add pack version checking in deserialization
  • Implement delete_entry
  • Update on_entry_creation to support new approach for entry creation
• base_store.py
  • Update some interfaces to make it consistent with data_store.py
• multi_pack.py
  • Remove all the SortedList containers and store the entries to DataStore
  • Update _add_entry_with_check, get, delete_entry accordingly
• data_pack.py
  • Move some of the implementation to BasePack
  • Create a separate file for EntryConverter: entry_converter.py
• data_store.py
  • Add add_multipack_entries_raw()
  • Remove allow_duplicate option when adding some some non-annotation entries
• top.py
  • Refactor the MultiEntrys and store their attributes to DataStore. Any calls that may update these entries' attributes will be directed to DataStore.

Possible influences of this PR.

The integration is not fully tested and it might be unstable.

Test Conducted

The integration should successfully pass all the current CI tests. Will need more dedicated test cases in future #808.

[codecov]

Codecov Report

Merging #834 (06dfacc) into master (3ed661e) will increase coverage by 0.08%.
The diff coverage is 85.89%.

@@            Coverage Diff             @@
##           master     #834      +/-   ##
==========================================
+ Coverage   80.54%   80.63%   +0.08%     
==========================================
  Files         252      253       +1     
  Lines       19363    19295      -68     
==========================================
- Hits        15596    15558      -38     
+ Misses       3767     3737      -30     

Impacted Files	Coverage Δ
forte/data/container.py	76.47% <ø> (-1.03%)	⬇️
forte/processors/nlp/ner_predictor.py	18.00% <0.00%> (ø)
forte/data/base_store.py	73.19% <67.74%> (-2.93%)	⬇️
forte/data/entry_converter.py	82.66% <82.66%> (ø)
forte/data/ontology/top.py	74.39% <86.66%> (+2.11%)	⬆️
forte/data/multi_pack.py	82.12% <86.79%> (+3.34%)	⬆️
forte/data/base_pack.py	77.15% <87.67%> (+1.53%)	⬆️
forte/data/data_pack.py	84.29% <100.00%> (-0.31%)	⬇️
forte/data/data_store.py	92.53% <100.00%> (+1.35%)	⬆️
forte/data/ontology/core.py	76.47% <100.00%> (+0.85%)	⬆️
... and 10 more

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[hunterhector]

Looks like there is quite a bit changes in the code, but we probably need to add test cases specifically designed for them.

[hunterhector]

• Remember to add the parameter documentation to the functions
• Some of the complex cases are not tested, like here: https://app.codecov.io/gh/asyml/forte/compare/834/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=checks&utm_campaign=pr%20comments&utm_term=asyml#D7L151

[hunterhector]

1. there is a big decrease in coverage on core.py for 43 lines: https://app.codecov.io/gh/asyml/forte/compare/834/changes. What happens?
2. Ci failed after merging to master

[mylibrar]

1. there is a big decrease in coverage on core.py for 43 lines: https://app.codecov.io/gh/asyml/forte/compare/834/changes. What happens?
2. Ci failed after merging to master

1. I guess this is because we discard the entry serialization/deserialization approach which uses Pointer and MpPointer to resolve tid. Maybe we can just remove them.
2. This is caused by the changes in BasePack.__del__. I'll fix it in the next update.

[hunterhector]

1. there is a big decrease in coverage on core.py for 43 lines: https://app.codecov.io/gh/asyml/forte/compare/834/changes. What happens?
2. Ci failed after merging to master

1. I guess this is because we discard the entry serialization/deserialization approach which uses Pointer and MpPointer to resolve tid. Maybe we can just remove them.
2. This is caused by the changes in BasePack.__del__. I'll fix it in the next update.

If the test cases are no longer needed (using pointers), we can delete those branches.