Changelog

Version 0.5.4 - 0.5.5

  • Coercions from SE to RSE and vice-versa.

  • Adapting changes from genomic ranges’s search and overlap methods.

  • Update set_assay to accept either an assay name or an index position of the assay to replace.

Version 0.5.1 - 0.5.3

  • Add wrapper methods to combine Summarized and RangedSummarized by rows or columns.

  • Implement getters and setters to access and modify an assay.

  • Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils’s subset functions to perform these operations.

Version 0.5.0

  • chore: Remove Python 3.8 (EOL)

  • precommit: Replace docformatter with ruff’s formatter

Version 0.4.2 - 0.4.5

  • Fix issue coercing SummarizedExperiments to AnnData objects and vice-versa.

  • Handling coercions when matrices are delayed arrays (for SE/RSE) or backed (for AnnData).

  • Update sphinx configuration to run snippets in the documentation.

Version 0.4.0 to 0.4.1

This is a complete rewrite of the package, following the functional paradigm from our developer notes.

  • Implements functional paradigm to access and set attributes on SE/RSE

  • Can initialize SE/RSE without assays, also initialize an empty SE/RSE

  • row_data and column_data are expected to be BiocFrame objects and will be converted if a pandas DataFrame is provided. This allows us to reduce complexity and implement consistent downstream operations. If these are not provided, an empty BiocFrame is set as default.

  • On RSE, if row_ranges is not provided, an empty GenomicRangesList is set as default.

  • SE/RSE now contain row_names and column_names that are separate from row_data’s and column_data’s row names, also helps in simplifying subset operations.

  • Printing SE/RSE objects now looks almost similar to R/Bioc’s printing of these objects.

  • Support combine operations, both strict and a flexible combine option when rows or columns do not exactly match between multiple objects.

  • Streamlines subset operation for SE/RSE and probably downstream derivates; they only need to update the slice method.

In addition the following rules are set to access or update row_names and column_names either from the SE or the row_data or column_data slots.

  • On construction, if row_names or column_names are not provided, these are automatically inferred from row_data and column_data objects.

  • On extraction of these objects, the row_names in row_data and column_data are replaced by the equivalents from the SE level.

  • On setting these objects, especially with the functional style (set_row_data and set_column_data methods), additional options are available to replace the names in the SE object.

Other changes

  • Reduce dependency on a number of external packages.

  • Update docstrings, tests and docs.

Version 0.3.0

This release migrates the package to a more palatable Google’s Python style guide. A major modification to the package is with casing, all camelCase methods, functions and parameters are now snake_case.

With respect to the classes, BaseSE is an intenal-only class. RangedSummarizedExperiment now extends SummarizedExperiment and so do all derivates. Typehints have been updated to reflect these changes.

In addition, docstrings and documentation has been updated to use sphinx’s features of linking objects to their types. Sphinx now also documents private and special dunder methods (e.g. __getitem__, __copy__ etc). Intersphinx has been updated to link to references from dependent packages.

Configuration for flake8, ruff and black has been added to pyproject.toml and setup.cfg to be less annoying.

Finally, pyscaffold has been updated to use “myst-parser” as the markdown compiler instead of recommonmark. As part of the pyscaffold setup, one may use pre-commits to run some of the routine tasks of linting and formatting before every commit. While this is sometimes annoying and can be ignored with --no-verify, it brings some consistency to the code base.

Version 0.1.4

  • rewriting Base classes, SE and RSE

  • implement range methods specific to RSE

  • tests

  • docs

Version 0.1.3

  • more accessors to assays

  • fix bug with defining shape of an experiment

  • tests

  • docs

Version 0.1.2

  • row/col data can be empty/None

  • update tests and documentation

Version 0.1.1

  • Add subset, shape and custom print for the class

  • Tests for subset

  • Documentation update

Version 0.1

  • Initial creation of SE and RSE classes

  • Tests

  • Documentation