Move common code to a separate script

[VladimirShitov]

Currently, there is a code, which is repeated across different components. The examples that I faced are:

• Setting up a logger
• Subsetting HVG
• Extracting a particular layer from AnnData object (e.g. X or specified layer)
• Validation of the data in the layer. E.g. check that a matrix contains not-normalized counts

Code copy-pasting is not a good practice. If we decide to change a logging format or a bug is found (see recent PR #385), we must change the code in each component. To prevent this, we should move common code to a separate script or component.

I created such a script in src/ directory in this PR: #385. After merging it, I can move other reused code to this script. Other suggestions about common code location or examples of copy-pasting are welcome :)

[VladimirShitov]

Upd: the folder for the utils scripts is now src/utils