Add example scripts.

Author: JoeZiminski

docs/source/pages/examples/acquisition-script.md

@@ -1,57 +1,51 @@
 :html_theme.sidebar_secondary.remove:
 
-```bash
-
-#!/bin/bash
-
-# Ensure Bash is loaded
-source ~/.bashrc
-
-echo "Starting script..."
-micromamba activate datashuttle-env
-echo "Micromamba environment activated."
-
-
-# Change to the appropriate directory (modify as needed)
-cd ~/datashuttle
-
-# Run the Python script
-python3 - <<EOF
-print("Python script started...")
-from datashuttle import DataShuttle
-import os
-
-# Define the projects directory
-projects_dir = "/mnt/ceph/_projects"
-
-# Get the list of projects
-project_list = os.listdir(projects_dir)
-
-# Dictionary to store error messages
-error_messages = {}
-
-# Iterate through projects and validate
-for p in project_list:
-    project_path = os.path.join(projects_dir, p)
-    if os.path.isdir(project_path):  # Only process directories
-        project = DataShuttle(p)
-        # project.make_config_file(local_path=project_path)
-        try:
-            errors = project.validate_project("rawdata", display_mode="print", strict_mode=True)
-            error_messages[p] = errors if errors else "No errors"
-        except Exception as e:
-            error_messages[p] = f"Validation failed: {e}"
-
-# Save log file
-log_file = "project_validation.txt"
-with open(log_file, "w") as f:
-    for project, message in error_messages.items():
-        f.write(f"{project}: {message}\n")
-
-# Optional: Print summary of error messages
-for project, message in error_messages.items():
-    print(f"{project}: {message}")
-EOF
-
-echo "Python script executed."
+# Acquisition Script
+
+
+
+```python
+def get_file_path():
+
+    # get your project
+    project = DataShuttle("social_sleaping")
+
+    # create a prompt to enter the ID number
+    # (which we will use to get the subject number)
+    id_number = input("Enter ID number: ")
+    sub = ID_DICT.get(id_number)
+
+    # get your session number and create a new folder
+    # for the session you are about to record.
+    # the function get_next_ses() normally checks for the next session
+    # if you are recording for a new subject you can use it as well to create
+    # the first session folder for this subject.
+    session = project.get_next_ses(top_level_folder="rawdata",
+                                   sub=f"sub-{sub}_id-{id_number}")
+
+    # create the folders
+    created_folders = project.create_folders(
+        top_level_folder="rawdata",
+        sub_names=f"sub-{sub}_id-{id_number}",
+        ses_names=f"{session}_@DATETIME@",
+        datatype=["behav"]
+    )
+    # create a prompt to enter the experiment information and
+    # conspecific ID for social experiments.
+    # (this is only important for the video file name and might not be
+    # relevant for you.)
+    exp_number = input("Enter Experiment condition: ")
+    comsp_id = input("Enter Conspecific ID: ")
+
+    # print the start of your acquisition
+    start = datetime.now()
+    print(datetime.now())
+    # create the video file name
+    file_name_video_1 = f"{exp_number}_{comsp_id}.avi"
+
+    # create the path to the video file
+    file_path1 = created_folders['behav'][0] / file_name_video_1
+    file_path1.touch()
+
+    return file_path1
 ```

docs/source/pages/examples/index.md

@@ -9,7 +9,7 @@
 
 
 :::{grid-item-card} {fas}`desktop;sd-text-primary` Acquisition Script
-:link: validate
+:link: acquisition-script
 :link-type: doc
 :class-img-top: tutorial-link-image
 
@@ -18,7 +18,7 @@
 
 
 :::{grid-item-card} {fas}`desktop;sd-text-primary` Validate A Labs Projects
-:link: validate
+:link: lab-project-checker
 :link-type: doc
 :class-img-top: tutorial-link-image
 

docs/source/pages/examples/lab-project-checker.md

@@ -1,47 +1,60 @@
 :html_theme.sidebar_secondary.remove:
 
-```python
-def get_file_path():
-
-    # get your project
-    project = DataShuttle("social_sleaping")
-
-    # create a prompt to enter the ID number
-    # (which we will use to get the subject number)
-    id_number = input("Enter ID number: ")
-    sub = ID_DICT.get(id_number)
-
-    # get your session number and create a new folder
-    # for the session you are about to record.
-    # the function get_next_ses() normally checks for the next session
-    # if you are recording for a new subject you can use it as well to create
-    # the first session folder for this subject.
-    session = project.get_next_ses(top_level_folder="rawdata",
-                                   sub=f"sub-{sub}_id-{id_number}")
-
-    # create the folders
-    created_folders = project.create_folders(
-        top_level_folder="rawdata",
-        sub_names=f"sub-{sub}_id-{id_number}",
-        ses_names=f"{session}_@DATETIME@",
-        datatype=["behav"]
-    )
-    # create a prompt to enter the experiment information and
-    # conspecific ID for social experiments.
-    # (this is only important for the video file name and might not be
-    # relevant for you.)
-    exp_number = input("Enter Experiment condition: ")
-    comsp_id = input("Enter Conspecific ID: ")
-
-    # print the start of your acquisition
-    start = datetime.now()
-    print(datetime.now())
-    # create the video file name
-    file_name_video_1 = f"{exp_number}_{comsp_id}.avi"
-
-    # create the path to the video file
-    file_path1 = created_folders['behav'][0] / file_name_video_1
-    file_path1.touch()
-
-    return file_path1
+# Validating a Labs' projects
+
+
+```bash
+
+#!/bin/bash
+
+# Ensure Bash is loaded
+source ~/.bashrc
+
+echo "Starting script..."
+micromamba activate datashuttle-env
+echo "Micromamba environment activated."
+
+
+# Change to the appropriate directory (modify as needed)
+cd ~/datashuttle
+
+# Run the Python script
+python3 - <<EOF
+print("Python script started...")
+from datashuttle import DataShuttle
+import os
+
+# Define the projects directory
+projects_dir = "/mnt/ceph/_projects"
+
+# Get the list of projects
+project_list = os.listdir(projects_dir)
+
+# Dictionary to store error messages
+error_messages = {}
+
+# Iterate through projects and validate
+for p in project_list:
+    project_path = os.path.join(projects_dir, p)
+    if os.path.isdir(project_path):  # Only process directories
+        project = DataShuttle(p)
+        # project.make_config_file(local_path=project_path)
+        try:
+            errors = project.validate_project("rawdata", display_mode="print", strict_mode=True)
+            error_messages[p] = errors if errors else "No errors"
+        except Exception as e:
+            error_messages[p] = f"Validation failed: {e}"
+
+# Save log file
+log_file = "project_validation.txt"
+with open(log_file, "w") as f:
+    for project, message in error_messages.items():
+        f.write(f"{project}: {message}\n")
+
+# Optional: Print summary of error messages
+for project, message in error_messages.items():
+    print(f"{project}: {message}")
+EOF
+
+echo "Python script executed."
 ```