Add logs and metadata directories for centralized file organization (Fixes #308)

[abuzarmahmood]

Summary

This PR addresses issue #308 by reorganizing log and metadata file storage in the blech_clust project:

Changes Made

1. Created centralized logs/ directory for all log files:

• output.log (via Tee class)
• results.log (blech_init.py)
• ram_usage.log (ram_monitor.py)
• blech_process.log (blech_process.py)
• umap_results.log (umap_plots.py)
• execution_log.json (pipeline_graph_check in blech_utils.py)

2. Created centralized metadata/ directory for all metadata files:

• electrode_layout_frame.csv (blech_exp_info.py)
• trial_info_frame.csv (blech_make_arrays.py, ephys_data.py, and others)
• dig_in_frame.csv (read_file.py)
• *.info file (blech_utils.py - imp_metadata class)
• *.params file (blech_utils.py - imp_metadata class)
• aggregated_characteristics.csv (blech_units_characteristics.py)
• unit_descriptor.csv (blech_post_process.py)
• unit_profile.csv (ephys_data.py)
• waveform_classifier_recommendations.csv (blech_process_utils.py)

3. Added helper functions in blech_utils.py:

• ensure_dir(data_dir, subdir) - Creates a subdirectory if it doesn't exist
• get_metadata_dir(data_dir) - Returns path to metadata directory
• get_logs_dir(data_dir) - Returns path to logs directory
• find_file_in_dir(data_dir, filename_pattern) - Helper for backward compatibility

4. Maintained backward compatibility:

• All reading functions check both the new location (metadata/ or logs/) and the old location (data directory root)
• If files exist in the old location, they are used; otherwise, files are created in the new location

Files Modified

• blech_exp_info.py
• blech_init.py
• blech_make_arrays.py
• blech_post_process.py
• blech_process.py
• blech_units_characteristics.py
• emg/emg_freq_setup.py
• utils/blech_data_summary.py
• utils/blech_process_utils.py
• utils/blech_utils.py
• utils/ephys_data/ephys_data.py
• utils/qa_utils/elbo_drift.py
• utils/ram_monitor.py
• utils/read_file.py
• utils/umap_plotting/umap_plots.py

Tests Added

• test_logs_metadata_dirs.py - Tests to verify the new directory structure

Fixes #308

@abuzarmahmood can click here to continue refining the PR