v0.1.0

What's Changed

Breaking Changes

• Fix diff exp ebayes bug & fix temp dirs in notebooks by @vbrennsteiner in #133
• [API,Fix] Make Nanlog consistent by @lucas-diedrich in #155

Bug fixes

• [Fix] Fix badge for documentation deployment by @lucas-diedrich in #124
• Fix clone command URL in README by @lucas-diedrich in #134
• [Docs,Fix] Add all tutorials to docs by @lucas-diedrich in #137
• [Hotfix] Include tutorials into documentation by @lucas-diedrich in #151
• Mock alphaquant file output in DE unittest by @lucas-diedrich in #157
• [Bug] Fix installation instructions and only use pip by @lucas-diedrich in #175
• Fix bug in dev installation instructions by @lucas-diedrich in #176
• replace fragile int/float check with more generalized type check by @vbrennsteiner in #181

New Features

• List all available readers by @lucas-diedrich in #125
• Make search filter configurable by @lucas-diedrich in #136
• Coefficient of variation 2 - Groupwise metric by @lucas-diedrich in #130
• Coefficient of variation 1 - Feature level metric by @lucas-diedrich in #129
• Custom naming for BPCA by @lucas-diedrich in #153
• Bayesian Principal Component Analysis 1 | Embedding by @lucas-diedrich in #141
• Bayesian Principal Component Analysis 2 | Imputation by @lucas-diedrich in #142

Other Changes / unlabeled

• Remove vscode by @mschwoer in #122
• Pelsa peptidomics notebook by @vbrennsteiner in #110
• [Doc] Add installation instructions for pypi by @lucas-diedrich in #126
• Data module integration by @lucas-diedrich in #127
• [Dep] Fix pandas dependency by @lucas-diedrich in #135
• Remove inits from tests (not a package) by @lucas-diedrich in #128
• [Dep] Update alphabase dependency to 1.8.0 by @lucas-diedrich in #146
• Update tool docs by @lucas-diedrich in #149
• Expose alphapepttools.tl.tools functions by @lucas-diedrich in #148
• Improve impute gaussian by @vbrennsteiner in #139
• Return pca anndata by @shanibmo in #138
• rename into study and demo notebooks by @vbrennsteiner in #143
• Remove redundancy between BPCA and PCA methods by @lucas-diedrich in #152
• [Doc] Examples for nanlog on copy/layer handling by @lucas-diedrich in #154
• Test loose and stable alphapepttools versions in CI/CD by @lucas-diedrich in #150
• [Dependencies] Remove most dependency restrictions by @lucas-diedrich in #147
• [CI/CD] Test with latest supported python version (3.13) by @lucas-diedrich in #158
• Fix README by @lucas-diedrich in #163
• Make alphaquant optional by @mschwoer in #165
• Make inmoose optional by @mschwoer in #166
• Remove sans serif font by @vbrennsteiner in #144
• remove leading underscore from metrics modules by @vbrennsteiner in #177

Full Changelog: v0.0.1...v0.1.0