Update stage.py to close inprogress files

[drewoldag]

Problem & Solution Description (including issue #)

Code Quality

• [x] My code follows the code style of this project
• [ ] I have written unit tests or justified all instances of #pragma: no cover; in the case of a bugfix, a new test that breaks as a result of the bug has been added
• [ ] My code contains relevant comments and necessary documentation for future maintainers; the change is reflected in applicable demos/tutorials (with output cleared!) and added/updated docstrings use the NumPy docstring format
• [ ] Any breaking changes, described above, are accompanied by backwards compatibility and deprecation warnings

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 96.78%. Comparing base (c51868d) to head (a98cb54).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #91 +/- ## ========================================== - Coverage 96.78% 96.78% -0.01% ========================================== Files 31 31 Lines 1585 1584 -1 ========================================== - Hits 1534 1533 -1 Misses 51 51 ```

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