Peppy

Fixed
- Fixed disabling rich progress on small datasets bug
- Disabled progressbar if object variable `progressbar` is set False

Fixed
- Returning `NaN` value in initialization project from pandas df

Fixed
- Returning `NaN` value within `to_dict` method was fixed and method now returns `None` instead

Changed
- Organization of test files. Separated unittests from smoketests.

Fixed
- The root cause of `np.nan` values showing up in Pandas dataframes. Replaced the values with None right after reading the database, which made it possible to remove all custom `np.nan` to `None` converters used later in the code.
- Typing in some methods.
- Code redundancy in fixtures in conftest.

Added
- New test cases with test data

Changed

- Optimized converting Projects to and from dict. Now, `to_dict(extended=True)` returns only essential properties to save space and time.
- Small refactors.

Fixed

- Initialization of `peppy.Project` from `pandas.DataFrame`. Now `from_pandas()` can receive sample table, subsample table and config file
- Multiple bugs introduced during initialization of the project with custom index column names

Added
- New test cases and test data

Changed

- Way of initialization project from dictionary. Now it's possible as follows: `Project().from_dict()`

Fixed

- Fix error that was raised when duplicated sample in `sample_table` had different read types (single-end mixed with paired-end).

Added

- Feature of initializing `peppy.Project` from `pandas.DataFrame`