remove py2neo as primary database driver #235
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At this stage a full replacement of the subgraph class makes things too complicated. Instead, we'll make new functions take in subgraphs as arguments and operate on those at a lower level.
More spot fixes
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #235 +/- ##
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+ Coverage 81.65% 81.66% +0.01%
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Files 24 25 +1
Lines 2943 3049 +106
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+ Hits 2403 2490 +87
- Misses 540 559 +19 ☔ View full report in Codecov by Sentry. |
| graph = Graph( | ||
| settings.NEO4J_URL, | ||
| auth=(settings.NEO4J_USER, settings.NEO4J_PASS), | ||
| name=settings.NEO4J_DBNAME, |
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Let's also drop NEO4J_DBNAME from the settings, since we don't actually use it anywhere, such as in our execute_query calls.
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Nevermind, added it back in a commit I've pushed, but in transaction instead. Also added Neo4jStore.execute_query method that includes use of database_ kwarg to ensure this gets passed through, and adjusted all uses of self.graph.execute_query to use this instead.
alchemiscale/storage/statestore.py
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| def __init__(self, graph: "py2neo.Graph"): | ||
| self.graph: Graph = graph | ||
| def __init__(self, graph: Driver): | ||
| self.graph: Driver = graph | ||
| self.gufe_nodes = weakref.WeakValueDictionary() | ||
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| @contextmanager | ||
| def transaction(self, readonly=False, ignore_exceptions=False) -> Transaction: |
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Removed readonly kwarg, since this doesn't exist in new driver.
We currently use the EOL
py2neolibrary for handling communication betweenalchemiscaleand the Neo4j database. This PR removes this responsibility frompy2neoand instead shifts it to the official Neo4j Python driver. This PR does not remove py2neo entirely since we rely heavily on thepy2neoSubgraphdata structure and query generation.