docs: add usage details for blech_autosort.sh script in README.md

[abuzarmahmood]

Co-authored-by: aider (gpt-4o) aider@aider.chat

[abuzarmahmood]

Generated edit command:

Summary of User's Issues and Requests

The user has requested to add details about the blech_autosort.sh script to the README file of the blech_clust repository. The script's functionality and usage need to be documented to provide users with clear instructions on how to use it.

Overview of Plan to Address the Issues

1. Review the blech_autosort.sh script to understand its functionality and usage.
2. Update the README.md file to include a section that describes the purpose and usage of the blech_autosort.sh script.

Specific Details of Changes to be Made

1. Add Details to README

   • File: /home/exouser/Desktop/blech_github_bot/repos/katzlabbrandeis/blech_clust/README.md

   • Line: After line 166 (before "Operations Workflow Visual")

   • Description of Change: Add a new section titled "blech_autosort.sh Script" that explains the purpose and usage of the script.

   • Code Snippet of Edits:

     ### blech_autosort.sh Script
     
     The `blech_autosort.sh` script is designed to automate the process of clustering and post-processing electrophysiology data. It ensures that the necessary parameters are set correctly and executes the pre-processing, clustering, and post-processing steps in sequence.
     
     **Usage:**
     ```bash
     bash blech_autosort.sh <data_directory> [--force]

     • <data_directory>: Path to the directory containing the raw data files.
     • --force: Optional flag to force re-processing even if previous results exist.

     Functionality:

     • Checks for the existence of required parameter files and verifies that specific settings are enabled.
     • Executes the blech_clust_pre.sh script to perform initial processing.
     • Runs blech_post_process.py to add sorted units to the HDF5 file.
     • Completes the workflow with blech_clust_post.sh for further processing.

     Ensure that the parameter files sorting_params_template.json and waveform_classifier_params.json are correctly configured before running this script.

By implementing these changes, users will have a clear understanding of how to use the blech_autosort.sh script within the blech_clust project.

---

This response was automatically generated by blech_bot using model gpt-4o

Aider output:

View Aider Output

Aider v0.85.2
Main model: gpt-4o with diff edit format
Weak model: gpt-4o-mini
Git repo: .git with 115 files
Repo-map: using 4096 tokens, auto refresh


README.md

blech_autosort.sh

blech_clust_post.sh

blech_clust_pre.sh

blech_post_process.py

params/_templates/sorting_params_template.json

params/_templates/waveform_classifier_params.json
To add details about the blech_autosort.sh script to the README file, we will insert a new section describing its purpose and usage. Here is the     
SEARCH/REPLACE block to update the README.md file:                                                                                                   

                                                                                                                                                     
README.md                                                                                                                                            
<<<<<<< SEARCH                                                                                                                                       
### Operations Workflow Visual                                                                                                                       
=======                                                                                                                                              
### blech_autosort.sh Script                                                                                                                         
                                                                                                                                                     
The `blech_autosort.sh` script is designed to automate the process of clustering and post-processing electrophysiology data. It ensures that the     
necessary parameters are set correctly and executes the pre-processing, clustering, and post-processing steps in sequence.                           
                                                                                                                                                     
**Usage:**                                                                                                                                           
```bash                                                                                                                                              
bash blech_autosort.sh <data_directory> [--force]                                                                                                    

• <data_directory>: Path to the directory containing the raw data files.
• --force: Optional flag to force re-processing even if previous results exist.

Functionality:

• Checks for the existence of required parameter files and verifies that specific settings are enabled.
• Executes the blech_clust_pre.sh script to perform initial processing.
• Runs blech_post_process.py to add sorted units to the HDF5 file.
• Completes the workflow with blech_clust_post.sh for further processing.

Ensure that the parameter files sorting_params_template.json and waveform_classifier_params.json are correctly configured before running this
script.

Operations Workflow Visual

REPLACE

Please apply this change to the README.md file.

Tokens: 17k sent, 308 received. Cost: $0.05 message, $0.05 session.
Applied edit to README.md
Commit 68f30c0 docs: add usage details for blech_autosort.sh script in README.md

</details>