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CHANGELOG.md

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Changelog

  • 0.15.0 (August 21 2024)
    • Backwards-incompatible changes:
      • Removed the Docker container provisioning functionality from the Neo4jExecutor class. To continue using this functionality, please use the tamarind package directly, or install dotmotif==0.14.0
    • Housekeeping:
      • Removed codecov from CI
      • Added Python 3.11 to the test matrix
  • 0.14.0 (May 16 2023)
    • Housekeeping:
      • Upgraded the package manager to Poetry, with version-pinning now handled by the pyproject.toml file.
  • 0.13.0 (October 11 2022)
    • Features:
      • Introduced propagation of constraints when nodes are explicitly marked as automorphic to one another.
      • Nested lookup support for JSON attributes of neuPrint datasets (thanks @jakobtroidl!)
      • Allow users to specify EdgelistIngest column data types
  • 0.12.0 (June 7 2022)
    • Housekeeping:
      • Removed old, deprecated code like the v1 parser (deprecated in v0.5.0) and some unused ingest tools (#113)
    • Features:
      • Added edge aliases and inter-edge attribute constraints
  • 0.11.0 (April 12 2022)
    • Features:
      • Added support for attributes that include spaces and other non-word/variable characters, and updated Cypher syntax for these attributes when searching with Neo4j and neuPrint (#112)
  • 0.10.1 (January 26 2022)
    • Bugfixes: Fixed compatibility with grandiso 2.1 and up
  • 0.10.0 (September 30 2021)
    • Features:
      • GrandIsoExecutor and NetworkXExecutor: Support for networkx.MultiGraph and networkx.MultiDiGraph search through the use of the multigraph_edge_match executor argument (#107).
    • Deprecations:
      • Removed dotmotif.dotmotif method-style API (#107).
  • 0.9.2 (May 28 2021)
    • Features:
      • GrandIsoExecutor: Utilizes the node attribute matching flow available in grandiso≥2.0.0 to reduce complexity of attribute-heavy searches (#104)
  • 0.9.1 (May 6 2021)
    • Features:
      • GrandIsoExecutor: Adds support for the grandiso.find_motifs_iter generator API in grandiso v1.2.0; this reduces the runtime of queries with nonzero limit (#102)
  • 0.9.0 (March 23 2021)
    • Features:
      • Neo4jExecutor#create_index. This function call adds an index to the database on the node attribute specified, in order to improve query performance (#95)
      • dotmotif.ingest.EdgelistConverter now supports importing from a dask or pandas dataframe edgelist in addition to files on disk (#99)
    • Chores:
      • Put lingering top-level tests into their own directory (#100)
  • 0.8.1
    • Chores:
      • Upgraded to the latest version of Tamarind, with Neo4j v4.2 support (#93)
      • Upgraded to the latest version of GrandIso, v1.1.0
  • 0.8.0 (January 12 2021)
    • Features:
      • Add !contains and !in attribute constraints to the parser. (#88)
      • Neo4j and NeuPrintExecutors now support custom node/edge labels (#91)
    • Bugfixes:
      • Fix issue where lark grammar file is excluded from pip-based installs (#89)
      • Fix an issue introduced in 0.8.0 where !contains/!in operators failed to parse for Neo4j/NeuPrint executors. If you are installing DotMotif from pip/pypi, this issue is already fixed. (#92)
  • 0.7.0 (October 14 2020)
    • Executors:
      • Add new NeuPrintExecutor with motif-search support for neuPrint databases (#76)
      • Add new GrandIsoExecutor as a Python-only drop-in replacement for NetworkXExecutor (#80). If you're still using NetworkXExecutor, you should really switch!
    • Features:
      • Improve utils.draw_motif rendering style
      • Improve networkx import for Neo4j databases to use better datatype inference
      • New dotmotif.Motif class. This is just a naming thing; all your old dotmotif.dotmotif code will still work! (#84)
      • Short motifs can now be written on a single line, with semicolons to delimit commands (#84)
    • Bugfixes:
      • Improve pip-installation process by including EBNF grammar definitions
    • Documentation:
      • Moved documentation from docs/ to the wiki for a more permanent and organized home (#81)
  • 0.6.0 (July 23 2020)
    • Features:
      • Add dynamic node constraints for comparisons at runtime (#74)
    • DSL:
      • Add dynamic node constraints with Node.key [op] Node.key syntax (#74)
    • Executors:
      • NetworkXExecutor: Support dynamic node constraints
      • Neo4jExecutor: Support dynamic node constraints
    • Housekeeping:
      • Add GitHub actions for Python 3.6, 3.7, and 3.8 tests
  • 0.5.1
    • Features:
      • Better search-operator support in NetworkXExecutor
    • Housekeeping:
      • Upgrade to networkx v2.4
      • Include Neo4jExecutor in default package imports
  • 0.5.0 (April 07 2020)
    • Features:
      • Add Executor#count() function call to return only a motif count rather than a complete result set.
      • Improve speed response of automorphism detection (use internal Neo4j IDs)
      • Add optional wait when creating a Neo4jExecutor
    • Bugfixes:
      • Fix indexing of automorphisms to better jive with Neo4j's internal result ordering.
      • Fix issue where NetworkXExecutor would fail to identify all isomorphisms. This was due to a nomenclature mismatch between NetworkX and other executors. More details here.
      • Automatically add exists=True condition to edges added using dotmotif#from_nx().
    • Deprecations:
      • Warnings:
        • dotmotif.parsers.v1.ParserV1
        • dotmotif.from_nx
  • 0.4.2
    • Features:
      • Add dotmotif#save and dotmotif#load to save and load configuration files.
      • Add dotmotif constructor flag to automatically detect automorphisms (#47)
    • DSL:
    • Parsers:
      • Fix #35, wherein a WHERE clause was omitted from the cypher query constructed from the Neo4jExecutor under certain conditions
    • Bugfixes:
      • Fix #26 by raising an explanatory error message when graphs with integer IDs are imported.
      • Fix #25 to allow pip-installability outside of edit-mode
  • 0.4.1 (April 13, 2019)
    • Backend tamarind for provisioning Docker containers.
    • Resolved issue with improper tokenization of variables in DSL
    • Resolved failure to wait the appropriate amount of time before failing to connect to a Neo4jExecutor provisioned container
  • 0.4.0 (February 26, 2019)
    • DSL:
      • Support for node and edge attributes in non-template contexts
    • Executors:
      • NetworkxExecutor
        • Support for node and edge constraints
      • Neo4jExecutor
        • Support for node and edge constraints
  • 0.3.0
    • Overhaul of DotMotif Parsers
      • Implement EBNF spec of language, and complete parser (lark)
      • Support for macros (templating engine)
      • Inline validation
    • Faster motif construction
    • Executors (dotmotif.executors)
      • Neo4jExecutor automatically spins up/down docker containers for out-of-RAM search
      • NetworkXExecutor for small-scale subgraph isomorphism
    • Comprehensive test suite
    • Base implementations of Validators
    • Move query generators to the appropriate Executors for separation of responsibility
  • 0.2.1
    • Remove CSV support
    • Abstract parser syntax to dotmotif.parsers
    • Abstract validator to dotmotif.validators
  • 0.2.0 (May 7 2018)
    • Negative-edge support
  • 0.1.0