Long overdue cleanup

[chick]

• Move to Stage/Phase
• Stop test output noise
• Stop opening diagrams in tests
• Format code
• Fix warnings

[jackkoenig]

@Mergifyio backport 1.3.x

[mergify[bot]]

Command backport 1.3.x: success

Backports have been created

• #79 Long overdue cleanup (bp #67) has been created for branch 1.3.x