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Adopt code from py2neo to remove the use of the id function in cyph…
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…er queries (#302)

We are adopting the query generators from within py2neo and modifying them 
to satisfy our needs in alchemiscale. This is needed because the `id` function 
is deprecated, flooding outputs with deprecation warnings.

Code included from py2neo is under the Apache v2.0 license and therefore
we need to include a copy of Apache v2.0 along with a NOTICE with
information on our changes to the code.
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ianmkenney authored Nov 7, 2024
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211 changes: 210 additions & 1 deletion LICENSE
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MIT License
## MIT License

Copyright (c) 2022 Open Force Field Initiative

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## Apache 2.0 Licensed Code

This project includes code from py2neo, which is licensed under the Apache License 2.0. The Apache License 2.0 text is included below for reference.

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38 changes: 38 additions & 0 deletions NOTICE
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# NOTICE

This project includes software developed by py2neo (https://github.com/neo4j-contrib/py2neo/tree/master).

## Original NOTICE

py2neo
Copyright (c) "Neo4j"
Neo4j Sweden AB [https://neo4j.com]

This product includes software developed by
Neo4j, Inc. <drivers@neo4j.com>.

This product includes software developed by
Nigel Small <technige@nige.tech>.

This product includes software developed by
Simon Harrison <noisyboiler@googlemail.com>.

This product includes software developed by
Marcel Hellkamp <https://bottlepy.org>.

## Modifications

- alchemiscale/storage/cypher.py
- Functions modified from the py2neo.cypher.queries module:
- _match_clause
- Modifications made:
- switched all usage of the id function to elementId

- alchemiscale/storage/subgraph.py
- Functions modified from the py2neo.data module:
- Subgraph.__db_merge__ (moved to merge_subgraph)
- Subgraph.__db_create__ (moved to create_subgraph)
- Modifications made:
- switched all usage of the id function to elementId
- removed the usage of py2neo database connections
and replaced them with the official neo4j driver
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