v0.2.0

What's Changed

This release improves the overall ergonomics of the package, enhances and clarifies the documentation, and adds compatibility with the latest Python versions.

New Features

• Add basic QC metrics functions by @shanibmo in #180
• Fix scatterplot ordering for categorical values by @vbrennsteiner in #186
• Support covariates in combat batch correction by @lucas-diedrich in #220
• IO: Add column mappings in read_pg_table by @lucas-diedrich in #216
• Proteome Discoverer reader functionality with alphabase v1.9.0

Breaking Changes

• Adjust plot labels interface by @vbrennsteiner in #182
• [API] Add copy argument to PCA and BPCA functions by @lucas-diedrich in #206
• [API] Set copy=False for median imputation by @lucas-diedrich in #207
• Remove Plots wrapper class from plots.py by @vbrennsteiner in #209
• FEATURE_LEVEL_CONFIG in reader_columns.py has a mistaken singular key by @vbrennsteiner in #219

Bug fixes

• [Dep] Fix docutils dependency due to bug in sphinx-tabs by @lucas-diedrich in #185
• [Fix] Include scDVP notebook in the documentation by @lucas-diedrich in #205
• fix failing unit test on pre-release: by @vbrennsteiner in #222

Other Changes / unlabeled

• Sc dvp nb review vb by @vbrennsteiner in #171
• [VERSION] Bump version to 0.1.1-dev0 (merge after release) by @github-actions[bot] in #184
• [Dep] Remove numpy+pandas dependency by @lucas-diedrich in #162
• [Dep] Drop python 3.10 support by @lucas-diedrich in #172
• Python3.14 by @lucas-diedrich in #159
• Sc dvp nb by @shanibmo in #169
• CI/CD: Separate notebook tests by @lucas-diedrich in #204
• Refactor tl.embeddings.py docstrings by @vbrennsteiner in #198
• reformat tl.tools.py docstrings and examples by @vbrennsteiner in #203
• refactor tl.utils.py docstrings and add examples by @vbrennsteiner in #202
• refactor tl.stats.py docstrings by @vbrennsteiner in #201
• refactor tl.plot_data_handling.py and add user-facing functions to init by @vbrennsteiner in #200
• refactor tl.defaults.py docstring by @vbrennsteiner in #199
• refactor tl.diff_exp docstrings and rerun notebooks by @vbrennsteiner in #197
• refactor pp.norm.py docstrings by @vbrennsteiner in #196
• refactor pp.transform.pydocstrings and add examples by @vbrennsteiner in #195
• refactor pp.impute.py docstrings by @vbrennsteiner in #194
• refactor pp.batch_correction.pydocstrings by @vbrennsteiner in #193
• refactor pp.data.py docstrings by @vbrennsteiner in #192
• refactor metrics docstrings by @vbrennsteiner in #191
• refactor data.datasets.py docstrings by @vbrennsteiner in #190
• refactor io.anndata_factory.py docstrings by @vbrennsteiner in #189
• refactor pl.figure.py docstrings by @vbrennsteiner in #188
• refactor pl.defaults.py docstrings by @vbrennsteiner in #187
• Refactor pl.colors.py docstrings by @vbrennsteiner in #174
• Refactor pl.plots.py docstrings by @vbrennsteiner in #173
• Updated draft for the volcanoplot function by @vbrennsteiner in #167
• fix volcano docstring which had a merge typo and unclear description of layer tuples by @vbrennsteiner in #210
• Reduction plot - accommodate bpca embeddings by @shanibmo in #208
• Scalability: 2000 Plasma samples by @lucas-diedrich in #168
• add grouped CVs and simplify metrics module by @vbrennsteiner in #211
• Reformat study 02 by @vbrennsteiner in #221
• [VERSION] Bump version to 0.2.0 by @github-actions[bot] in #214

Full Changelog: v0.1.0...v0.2.0