doubletdetection v4.3.0.post1

What's Changed

• test.yml branch main by @adamgayoso in #169
• HOTFIX: fix rng by @adamgayoso in #170

Full Changelog: v4.3...v4.3.0.post1

doubletdetection v4.3

What's Changed

• Use hatch instead of poetry and bump minimum versions by @adamgayoso in #160
• Fix test.yml by @adamgayoso in #164
• Drop removed .A1 for asarray(...).ravel() by @adamgayoso in #161
• add louvain and leidenalg to dev dependencies by @adamgayoso in #165
• Add python typing by @adamgayoso in #162
• Use numpy default rng instead of setting global seed by @adamgayoso in #163
• readthedocs update by @adamgayoso in #166
• Update docs by @adamgayoso in #167
• Fix usage of pseudocount by @adamgayoso in #168

Full Changelog: v4.2...v4.3

doubletdetection v4.2

Fixes a bug in 4.0, where default louvain used directed=True, when it should use False.

doubletdetection v4.1

Merge pull request #151 from JonathanShor/dev_4.1

Dev 4.1

doubletdetection v4.0

Merge pull request #139 from JonathanShor/cluster_opts

Dev 4.0

doubletdetection v3.0

• Distributed via PyPI
• Remove unnecessary plotting code

HOTFIX: Correct setup.py installation

Fix an misconfiguration in setup.py.
Improved README while we're at it.

HOTFIX: Correct Defaults & Docstrings

Minor corrections to align parameter defaults with documentation around use_phenograph and standard_scaling parameters.

Sparse Scanpy Speedups

• Improves installation process through one pip install command and removes requirements.txt
• Adds documentation
• Uses sparse matrices for raw counts in the backend for speedups
• Uses scanpy for log normalization and PCA and optionally clustering
• New use_phenograph option to disable PhenoGraph and use Louvain as implemented in scanpy (much faster)
• Adds binary verbose option. Set to True to turn on informational messages (previous default behavior).
• Replaces tsne plot with umap and no longer clusters data, just visualizes doublets on the umap
• With new scanpy integration, doubletdetection requires at least Python 3.6.

DOI

Minor release updating the front README to reflect the work's DOI.