Release notes
=============

.. contents:: :local:
    :depth: 3

.. toctree::
   :maxdepth: 10

   *


v0.1.7
------

* Enable compatibility of in-place filtering with the latest anndata releases

* :func:`muon.pp.tfidf` when using data from a layer

* Fix custom chromosome names in :func:`muon.atac.tl.count_fragments_features`

* Prepare to count unique fragments in :func:`muon.atac.tl.count_fragments_features` from the next version

* Improve :func:`muon.pl.scatter`

v0.1.6
------

* Compatibility with scanpy 1.10

* Extend ``_l2norm`` to sparse inputs.

v0.1.5
------

This release comes with fixes:

* for handling and saving colour palettes in MuData for categorical and continuous variables in :func:`muon.pl.embedding`,

* for using sparse matrices in the MOFA interface to combine modalities with missing samples in :func:`muon.tl.mofa`,

* for error messages and mixing metadata and features when plotting across modalities with :func:`muon.pl.embedding`.

v0.1.4
------

This release comes with improvements and fixes:

* :func:`muon.pp.intersect_obs` now works for modalities that have no ``.X``

* :func:`muon.pl.embedding` now saves the colour palette in ``.uns``

* :func:`muon.atac.pl.fragment_histogram` and :func:`muon.pl.histogram` now have save/show arguments

* :func:`muon.atac.tl.count_fragments_features` now has a ``stranded`` argument

* :func:`muon.atac.tl.nucleosome_signal` now works on more ``pysam`` setups

* support for numpy 1.24 and newer scanpy versions

   
v0.1.3
------

This release comes with new features and improvements:

* MOFA can be now run in the stochastic mode (SVI) using the new arguments for :func:`muon.tl.mofa`.

* MOFA model weights can be visualised with :func:`muon.pl.mofa_loadings`.

* Plotting module has gained new plots such as :func:`muon.pl.scatter`.

* It is now possible to define layers as ``{modality: layer}`` in :func:`mu.pl.embedding`.

* Improvements to the TF-IDF normalisation interface including view handling.

* Dependencies are handled better now such as ``pysam`` and ``scikit-learn``.

v0.1.2
------

* In-place filtering functions (:func:`muon.pp.filter_obs` and :func:`muon.pp.filter_var`) can be now run one after another without requiring :func:`muon.MuData.update`).

v0.1.1
------

``MuData`` is now provided `as a separate package <https://mudata.readthedocs.io/>`_. Since this release, ``mudata`` is a hard dependency of ``muon``. Making the codebase more modular, this will also help developing tools around ``MuData`` that do not depend on ``scanpy`` or ``muon``.

We fixed a few things including reading ``.h5mu`` files in backed mode when modalities have ``.raw`` attributes (this is live in the ``mudata`` library), ``SNF`` functionality (:func:`muon.tl.snf`) and colouring plots by ``var_names`` that are present in ``.raw`` but not in the root ``AnnData`` object.

We also introduced some new features for the ATAC module including:
    
    * handling fragments files with barcodes different than ``obs_names`` and

    * supporting ``atac_peak_annotation.tsv`` files produced by Cell Ranger ARC 2.0.0.

v0.1.0
------

Initial ``muon`` release with ``MuData`` (:class:`muon.MuData`), ``atac`` and ``prot`` submodules (:mod:`muon.atac` and :mod:`muon.prot`), and multi-omics integration with ``MOFA`` (:func:`muon.tl.mofa`) and ``WNN`` (:func:`muon.pp.neighbors`).