Generated new pyscript files

notebooks/py_scripts/00-data-download-optional.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
 #     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
 #     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c

notebooks/py_scripts/01-configure.py

@@ -5,10 +5,11 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
-#     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
-#     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
+#     display_name: Python 3.9.12 ('elementsPractice')
+#     language: python
+#     name: python3
 # ---
 
 # # Configure DataJoint connection to the database
@@ -22,13 +23,10 @@
 # + As a convention, we set the configuration up in the root directory of the `workflow-calcium-imaging` package and always start importing DataJoint and pipeline modules from there.
 
 import os
-if os.path.basename(os.getcwd()) == 'notebooks':
-    os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 
 pwd
 
-import datajoint as dj
-
 # ## Configure database host address and credentials
 #
 # Now let's set up the host, user and password in the `dj.config` global variable
@@ -50,9 +48,10 @@
 #
 # + Giving a prefix to schema could help on the configuration of privilege settings. For example, if we set prefix `neuro_`, every schema created with the current workflow will start with `neuro_`, e.g. `neuro_lab`, `neuro_subject`, `neuro_imaging` etc.
 #
-# + The prefix could be configurated as follows in `dj.config`:
+# + The prefix could be configurated in `dj.config` as follows. CodeBook users should keep their username as the prefix for schema for declaration permissions.
 
-dj.config['custom'] = {'database.prefix': 'neuro_'}
+username_as_prefix = dj.config["database.user"] + "_"
+dj.config["custom"] = {"database.prefix": username_as_prefix}
 
 # ### Root directories for raw calcium imaging data and processed results
 #

notebooks/py_scripts/02-workflow-structure-optional.py

@@ -6,10 +6,11 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
-#     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
-#     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
+#     display_name: Python 3.9.12 ('elementsPractice')
+#     language: python
+#     name: python3
 # ---
 
 # # Introduction to the workflow structure
@@ -25,7 +26,7 @@
 # To load the local configuration, we will change the directory to the package root.
 
 import os
-os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 
 # ## Schemas and tables
 #

notebooks/py_scripts/03-process.py

@@ -5,10 +5,11 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
-#     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
-#     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
+#     display_name: Python 3.9.12 ('elementsPractice')
+#     language: python
+#     name: python3
 # ---
 
 # # Interactively run workflow calcium imaging
@@ -26,13 +27,14 @@
 # Let's change the directory to the package root directory to load the local configuration (`dj_local_conf.json`).
 
 import os
-os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 import numpy as np
 
 # ## `Pipeline.py`
 #
 # + This script `activates` the DataJoint `elements` and declares other required tables.
 
+import datajoint as dj
 from workflow_calcium_imaging.pipeline import *
 
 # ## Schema diagrams

notebooks/py_scripts/04-automate-optional.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
 #     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
 #     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
@@ -18,7 +18,7 @@
 # -
 
 import os
-os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 import numpy as np
 from workflow_calcium_imaging.pipeline import lab, subject, session, scan, imaging
 

notebooks/py_scripts/05-explore.py

@@ -5,18 +5,19 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
-#     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
-#     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
+#     display_name: Python 3.9.12 ('elementsPractice')
+#     language: python
+#     name: python3
 # ---
 
 # # DataJoint Workflow Calcium Imaging
 #
 # + This notebook will describe the steps for interacting with the data ingested into `workflow-calcium-imaging`.  
 
 import os
-os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 
 # +
 import datajoint as dj

notebooks/py_scripts/06-drop-optional.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
 #     display_name: 'Python 3.7.9 64-bit (''workflow-calcium-imaging'': conda)'
 #     name: python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c
@@ -20,7 +20,7 @@
 # Change into the parent directory to find the `dj_local_conf.json` file. 
 
 import os
-os.chdir('..')
+if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..")
 
 from workflow_calcium_imaging.pipeline import *
 

notebooks/py_scripts/07-downstream-analysis-optional.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.13.7
+#       jupytext_version: 1.14.1
 #   kernelspec:
 #     display_name: venv-nwb
 #     language: python
@@ -169,7 +169,7 @@
 
 analysis.ActivityAlignment()
 
-# The `AlignedTrialActivity` part table captures aligned traces for each alignment and trial condition specified in the master table.
+# The `AlignedTrialActivity` part table captures aligned traces fore each alignment and trial condition specified in the master table.
 
 analysis.ActivityAlignment.AlignedTrialActivity()