Bug fixes for issues found while conda packaging

[mjuric]

Fixes # .

Describe your changes.

Review Checklist for Source Code Changes

• [x] Does pip install still work?
• [x] Have you written a unit test for any new functions?
• [x] Do all the units tests run successfully?
• [x] Does Sorcha run successfully on a test set of input files/databases?
• [x] Have you used black on the files you have updated to confirm python programming style guide enforcement?

[codecov[bot]]

Codecov Report

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

Project coverage is 80.61%. Comparing base (39cf35f) to head (59102a5). Report is 77 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #976 +/- ## ========================================== - Coverage 80.69% 80.61% -0.09% ========================================== Files 69 69 Lines 3139 3079 -60 ========================================== - Hits 2533 2482 -51 + Misses 606 597 -9 ```

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