Add warning if xfel-calibrate may not be reproducible

Description

This adds a warning to xfel-calibrate if the chosen configuration may cause the result not be reproducible by xfel_calibrate.repeat, currently based on the presence of argument line flags. The user is forced to confirm this by pressing ENTER except when the additional --not-reproducible flag is passed. In the future, we may also use the latter flag to disable other checks or work only relevant for reproducibility.

Also, there's a new flag --skip-env-freeze to skip the pip freeze stage, which obviously breaks reproducibility.

Most important question and the reason I tag @calibration: Do you think the wording is good enough?

How Has This Been Tested?

Extensive testing of the HED fast path.

Types of changes

• New feature (non-breaking change which adds functionality)

Checklist:

Reviewers

@calibration

src/xfel_calibrate/calibrate.py

@@ -93,7 +93,7 @@ def make_initial_parser(**kwargs):
     parser.add_argument('--skip-env-freeze', action='store_true',
                         help='Skip recording the Python environment for '
                              'reproducibility purposes, requires '
-                             '--non-reproducible to run.')
+                             '--not-reproducible to run.')
 
     parser.add_argument('--concurrency-par', type=str,
                         help='Name of concurrency parameter.'