Scarf

CHANGELOG

**Improvements**
Fixes in `get_markers` in `DataStore` to allow backward compatibility with marker search results.

CHANGELOG

CHANGELOG


**New features**
Multimodal data integration by graph merging. Integrated graphs are supported by `run_umap`, `run_clustering` and `run_leiden_clustering`
Added `smart_label` method to `DataStore`


**Added tutorials**
Expanded the multi-modal data handling tutorial to demonstrate graph integration functionality
Added MNIST dataset notebook

**Improvements**
MtxDirReader now supports custom index offset
Warning suppression for `division by zero` in `run_umap`
`plot_cluster_tree` supports non-integer labels

**Dev notes**
`.codecov.yml` moved to `github` dir and edited to not show checks along with github tests
removed `push_pypi.sh` from root as pypi released are now handled by github actions

CHANGELOG


*Breaking changes introduced in `run_umap` and `run_unified_umap` method of `DataStore`*
`fit_n_epochs` parameter renamed to `n_epochs`. `tx_n_epochs` parameter is no longer valid.

**Improvements**
~100% coverage in docstrings in `assays` module
Fixed a bug in file counter in `fetch_dataset`
Improved iteration counter in `smoothen_dists`. Potentially more memory optimized now.
Removed unnecessary `transform` method in `umap` module. Disabled removal of low weight edges. Removed call to `fuzzy_simplical_set` because steps are already performed upstream.

**New feature**
Added DensMap algorithm to umap module.

CHANGELOG

**Improvements**
Removed `holoviews` and `EoN` as dependencies.
Added `hierarchy_pos` from EoN directly into `plots.py`
Added docstrings in `assays` module
Added few FAQs and minor improvements to documentation

CHANGELOG

**Improvements**
Improved logging. Moved a lot of unnecessary log messages to DEBUG level so that they will not be shown by default.
Progress bars for dask operations are now rendered through tqdm.
tqdm progress bar now can be modified by users. Optimized tqdm usage for jupyter notebooks.
`handle_download` now uses the requests library rather than OS specific download utilities. Shows progress of the download.
More API tests were added for scATAC-Seq data, utilities, mapping functions and downloading.

**New feature**
Added `set_verbosity` global function that can change the verbosity of log messages. This exposes the loguru log levels.
Exposed verbosity in `DataStore.run_umap`

**For developers**
Switched to 'black' code style.
Docs theme was switched to jupyter-book-theme. Most of the docs file converted from rst to md format and are now parsed using My-ST parser.