From 9d02c2361e7805eac8bb88d526c12a5ac93305e5 Mon Sep 17 00:00:00 2001
From: Christian Tabedzki <35670232+tabedzki@users.noreply.github.com>
Date: Thu, 21 Mar 2024 10:22:23 -0400
Subject: [PATCH] updated indentation

---
 src/software/automation_pipeline_developer.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/software/automation_pipeline_developer.md b/src/software/automation_pipeline_developer.md
index 34f181a..75b39b4 100644
--- a/src/software/automation_pipeline_developer.md
+++ b/src/software/automation_pipeline_developer.md
@@ -44,10 +44,10 @@ The class that manages workflow at the recording level is (<a href="https://gith
 
 + **recording_status_dict** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/params_config.py">Params Config file</a>): This dictionary defines status definitions and corresponding functions to execute.
 + **pipeline_handler_main** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main function in recording workflow
-1. Executes corresponding functions based in status.
-2. Executed every 30 minutes to check for new recordings to be handled.
-3. Send notifications for processed and failed functions.
-+  **exception_handler** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Python decorator for error handling.
+  1. Executes corresponding functions based in status.
+  2. Executed every 30 minutes to check for new recordings to be handled.
+  3. Send notifications for processed and failed functions.
+  +  **exception_handler** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Python decorator for error handling.
 +  **modality_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Main ingestion function from recording to recording_process tables. There are subcalls depending on modality of recording (ephys or imaging).
 
 #### Imaging preingestion main steps:
@@ -55,9 +55,9 @@ The class that manages workflow at the recording level is (<a href="https://gith
 +  **imaging_preingestion** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/automatic_job/u19_pipeline/automatic_job/recording_handler.py">RecordingHandler</a>): Ingestion to recording_process table for an imaging recording. Get all FOVs (TIFF stacks) for the recording and assign a new job for each one with corresponding parameters fetched from selection done in automation GUI.
 **AcquiredTiff populate function** in (<a href="https://github.com/BrainCOGS/U19-pipeline_python/blob/master/u19_pipeline/imaging_pipeline.py">Imaging pipeline</a>): Auxiliar script to call **populate_Imaging_AcquiredTiff** script in MATLAB.
 + **populate_Imaging_AcquiredTiff** in (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/scripts/populate_Imaging_AcquiredTiff.m">populate_Imaging_AcquiredTiff</a>): Population calls to:
-1. **u19_imaging_pipeline.AcquiredTiff**: Each recording is divided into Tiff Splits (e.g. Mesoscope recordings contain multiple tiff stacks that will be processed independently). (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/AcquiredTiff.m">Code here</a>)
-2. **u19_imaging_pipeline.SyncImagingBehavior**: Find correspondence between virtual reality frame in the behavior experiment and Calcium Imaging frame in recording.
-(<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/SyncImagingBehavior.m">Code here</a>)
+  1. **u19_imaging_pipeline.AcquiredTiff**: Each recording is divided into Tiff Splits (e.g. Mesoscope recordings contain multiple tiff stacks that will be processed independently). (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/AcquiredTiff.m">Code here</a>)
+  2. **u19_imaging_pipeline.SyncImagingBehavior**: Find correspondence between virtual reality frame in the behavior experiment and Calcium Imaging frame in recording.
+  (<a href="https://github.com/BrainCOGS/U19-pipeline-matlab/blob/master/schemas/%2Bimaging_pipeline/SyncImagingBehavior.m">Code here</a>)