Scarf

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.

CHANGELOG

**Improvements**
Added several more tests
Small bug fixes plots, reader and writers modules

CHANGELOG:

**Improvements**
- Improved testing for DataStore class (thanks to JohanRodhe for contribution)
- Improved default color palettes (inspired by Scanpy)
- Improve legends display for `plot_layout`. Cleaned up code in `plots.plot_scatter` and all affected `DataStore` wrappers.

**Known issues**
- Tests fail on MacOS
- Unable to reproduce results of Leiden and UMAP on Github actions. Can reproduce locally

**Other changes**
- Minimized README for Github repo
- Improved logo layout for Github README
- Improved logo formats for Github and RTD
- Using Github actions for testing now. Not using CircleCI anymore. This was motivated by difficulty of changing testing OS.

CHANGELOG

Package name on PyPi changed to `scarf`
To install Scarf:
`pip install scarf`

CHANGELOG:

Fixes in github publish workflow

CHANGELOG:

Several fixes in Manifest.in including renaming from Manifest.ini
This release is to test if github actions based pypi upload works