Add overwrite-dependencies flag for dependency graph checks (fixes #766)

[abuzarmahmood]

Summary

This PR addresses issue #766 by adding an override dependency flag (--overwrite_dependencies) for all scripts in the pipeline that use the dependency graph check.

Changes Made

1. Modified utils/blech_utils.py:

   • Added overwrite_dependencies parameter to pipeline_graph_check.__init__() (defaults to False)
   • Updated check_previous() method to:
     • Skip dependency check and return True when overwrite_dependencies=True
     • Ask user interactively whether to continue when check fails and overwrite_dependencies=False

2. Added --overwrite_dependencies argument to all pipeline scripts:

   • blech_init.py
   • blech_exp_info.py
   • blech_common_avg_reference.py
   • blech_make_arrays.py
   • blech_process.py
   • blech_post_process.py
   • blech_units_plot.py
   • blech_units_characteristics.py
   • utils/infer_rnn_rates.py
   • utils/qa_utils/drift_check.py
   • utils/qa_utils/elbo_drift.py
   • utils/qa_utils/unit_similarity.py

3. Added tests in tests/test_pipeline_graph_check.py

Usage

Users can now:

• Use --overwrite_dependencies flag to bypass dependency checks entirely
• If the flag is not provided and the dependency check fails, they will be prompted interactively to continue or exit

This follows the requirements from the issue comments:

1. ✅ Add over-ride dependency flag for all scripts in pipeline
2. ✅ If flag is not supplied and dependency graph check fails, ask user interactively whether they would like to continue