Changelog

v0.3.7

Released on 2023-11-22 - GitHub

Major Changes:

  • Added MontyDB to the dependencies and semi-officially started supporting it for all implemented methods so far. However, it is important to point out that not all future methods ported from the ULTERA project will work.
  • Added tutorial CustomDatasetFromBSON.ipynb showing how to utilize a custom BSON snapshot of a database in-memory; for instance, based on a snapshot we provide in devTools.
  • Added tests for the custom collection override methods.

Minor Changes:

  • README improved all around and in the Install section in particular.

Full Changelog: v0.3.6...v0.3.7

v0.3.6

Released on 2023-11-19 - GitHub

Major Changes:

  • Added a subset of ULTERA Database (300 entries) in bf8bf50 for PyQAlloy users to play with. You can insert them quickly into your initialized MongoDB collection with a simple:

    with open('../ULTERA_sample.bson', 'rb+') as f:
    collection.insert_many(bson.decode_all(f.read()))

    and it should also work well with in-memory databases like MontyDB, as shown in dev/jDummyDatabaseInMemory.ipynb

  • Added ability to manually specify an already initialized MongoDB-like collection in collectionManualOverride for any Analyzer. As of now, all methods should work, but in the future, some functionalities may be limited because, for instance, MongoDB aggregation may be irreplaceable.

  • Reimplemented Analyzer's get_allDOIs function to use (slower) find instead of aggregate if collectionManualOverride is declared, as most users override with Mongo-like tools with limited capabilities.

  • Dropped testing on Windows (temporarily) as there seems to be an issue that causes tests to time out when outputting excel spreadsheets, and it appears to be related to GitHub runners rather than code.

  • Added Apple M1 Macs to the testing matrix, and everything seems to run smoothly.

Minor Changes:

  • Typo fixes and style improvements in the documentation.
  • Codebase style improvements.

Full Changelog: v0.3.5...v0.3.6

v0.3.5.post2

Released on 2023-04-04 - GitHub

Major Changes:

  • PyPI release
  • Official support for Python 3.11
  • Automated testing in GitHub CLI on every code change; run across all 9 Windows/Mac/Linux and Python 3.9/3.10/3.11 combinations
  • Automated test coverage analysis; reported to Codecov service

Minor Changes:

  • Documentation imporvements
  • Minor bug fixes

Full Changelog: v0.3.4...v0.3.5

v0.3.4

Released on 2023-03-27 - GitHub

Minor Updates:

  • Added configuration for ReadTheDocs and published it.
  • Added autogenerating changelog to the ReadTheDocs.

Full Changelog: v0.3.3...v0.3.4

v0.3.3

Released on 2023-03-27 - GitHub

Changes Breaking Backward-Compatibility:

  • Changed the submodules naming scheme to be cleaner and more intuitive, e.g. curation.analysis and core.pyqalloy. In the future, the core will primarily serve user-facing features and GUI, while others will be specialized. The curation will also include things like property and structure name unifiers from the ULTERA project (but user-definable). The future database will include functions handling and setting up a MongoDB (or a substitute) database.

Minor Changes:

  • Optimized requirements.

Full Changelog: v0.3.1...v0.3.3

v0.3.1

Released on 2023-03-27 - GitHub

Major Changes:

  • Added automatically generated documentation of software (using Sphinx) and API
  • Completed the doc strings coverage to include all files

Full Changelog: v0.3.0...v0.3.1

v0.3.0

Released on 2023-03-19 - GitHub

Internal Release

Major Changes:

  • Completed implementing all abnormality detection in the context of the entire database (to the degree we are confident with).
  • The AllDataAnalyzer now allows performing DBSCAN/TSNE-based analysis. The automated combining of them is not yet included.
  • Completed implementing a lot of tests, allowing 95% coverage.

Minor Changes:

  • Added README and installation instructions to the repository.
  • UserCuration Jupyter notebook was updated and turned into a mini-tutorial.
  • Many small improvements to the tool.

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Released on 2023-03-14 - GitHub

(Internal Release)

Major Points

  • Contains completed docstrings for all functions (directly ingestable into API documentation later using Sphinx).
  • Full test coverage of the functions.
  • Included in the release are (1) single composition abnormal data detection tools and (2) single study / DOI abnormal data detection tools, along with (3) Analyzer() class (which they extend) and helper functions.
  • Tentative name: PyQAlloy