Fix entry points

Description

• fix executables recording for atmo-related tools
• update dependecies
  • introduce temporary solutions for unpublished dependencies
• update installation instructions

Related Issue

Closes #23 (closed), #22 (closed)

How Has This Been Tested?

Tested locally, executables are now discoverable. Current CI tests would probably fail due to dependencies resolution

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.