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

@@ -84,16 +84,16 @@ def make_initial_parser(**kwargs):
                              ' report')
 
     parser.add_argument('--not-reproducible', action='store_true',
-                        help='Disable checks or confirmations that may cause '
-                             'the processed result to not be reproducible at '
-                             'a later point in time.')
+                        help='Disable checks to allow the processing result '
+                             'to not be reproducible based on its metadata.')
 
     parser.add_argument('--skip-report', action='store_true',
                         help='Skip report generation in finalize step.')
 
     parser.add_argument('--skip-env-freeze', action='store_true',
                         help='Skip recording the Python environment for '
-                             'reproducibility purposes.')
+                             'reproducibility purposes, requires '
+                             '--not-reproducible to run.')
 
     parser.add_argument('--concurrency-par', type=str,
                         help='Name of concurrency parameter.'
@@ -995,7 +995,7 @@ def run():
     # canonical representation.
     not_reproducible_args = sorted(
         ('--' + x.replace('_', '-')
-         for x in ['not_reproducible', 'skip_report', 'skip_env_freeze']
+         for x in ['skip_env_freeze']
          if args[x]))
 
     # If any of these arguments are set, present a warning.
@@ -1009,13 +1009,11 @@ def run():
               'needs.'.format(', '.join(not_reproducible_args)))
 
         if not args['not_reproducible']:
-            # If reproducibility has not been permitted to be broken
-            # explicitly, force the user to confirm this explicitly.
-            try:
-                input('Press ENTER to continue or CTRL+C to abort...')
-            except KeyboardInterrupt:
-                # Catch the interrupt and silently exit.
-                sys.exit(0)
+            # If not explicitly specified that reproducibility may be
+            # broken, remind the user and exit.
+            print('To proceed, you can explicitly allow reproducibility to '
+                  'be broken by adding --not-reproducible')
+            sys.exit(1)
 
         reproducible = False
     else: