[1888][eval] Refactor Reader class

[mtar]

Description

This PR introduces some refactoring on the Reader class in io_reader.

The changes include:

• Reader is an abstract class that cannot be instantiated
• docstrings are more descriptive
• helper functions to avoid code repetition
• change assertions into exceptions
• fix of spelling errors

Issue Number

Closes #1888

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Checklist before asking for review

• I have performed a self-review of my code
• My changes comply with basic sanity checks:
  • I have fixed formatting issues with ./scripts/actions.sh lint
  • I have run unit tests with ./scripts/actions.sh unit-test
  • I have documented my code and I have updated the docstrings.
  • I have added unit tests, if relevant
• I have tried my changes with data and code:
  • I have run the integration tests with ./scripts/actions.sh integration-test
  • (bigger changes) I have run a full training and I have written in the comment the run_id(s): launch-slurm.py --time 60
  • (bigger changes and experiments) I have shared a hegdedoc in the github issue with all the configurations and runs for this experiments
• I have informed and aligned with people impacted by my change:
  • for config changes: the MatterMost channels and/or a design doc
  • for changes of dependencies: the MatterMost software development channel