Merge branch 'main' into doc/cheatsheet

README.md

@@ -37,7 +37,7 @@ Check out tutorials and documentation at
 
 ## Example
 
-The following example demonstrates how to use AutoRA to automate the process of model discovery, experimental design, and data collection. 
+The following basic example demonstrates how to use AutoRA to automate the process of model discovery, experimental design, and data collection. 
 
 The discovery problem is defined by a single independent variable $x \in [0, 2 \pi]$ and dependent variable $y$.
 The experiment amounts to a simple sine wave, $y = \sin(x)$, which is the model we are trying to discover.
@@ -127,18 +127,17 @@ for i in range(5):
     print('\n')
 ```
 
+If you are curious about how to apply AutoRA to real-world discovery problems, you can find use case examples of AutoRA in the [Use Case Tutorials](https://autoresearch.github.io/autora/examples/) section of the documentation.
 
 ## Contributions
 
 We welcome contributions to the AutoRA project. Please refer to the [contributor guide](https://autoresearch.github.io/autora/contribute/) for more information. Also, feel free to ask any questions or provide any feedback regarding core contributions on the [AutoRA forum](https://github.com/orgs/AutoResearch/discussions/). 
 
 ## About
 
-This project is in active development by 
-the [Autonomous Empirical Research Group](http://empiricalresearch.ai), 
-in collaboration with the [Center for Computation and Visualization at Brown University](https://ccv.brown.edu).
+This project is in active development by the [Autonomous Empirical Research Group](https://musslick.github.io/AER_website/Research.html).
 
-The development of this package is supported by Schmidt Science Fellows, in partnership with the Rhodes Trust, as well as the Carney BRAINSTORM program at Brown University.
+The development of this package was supported by [Schmidt Science Fellows](https://schmidtsciencefellows.org/), in partnership with the Rhodes Trust, as well as the [Carney BRAINSTORM program](https://ccbs.carney.brown.edu/brainstorm) at Brown University. The development of auxiliary packages for AutoRA, such as `autodoc`, is supported by [Schmidt Sciences, LLC. and the Virtual Institute for Scientific Software (VISS)](https://www.schmidtsciences.org/viss/). The AutoRA package was developed using computational resources and services at the [Center for Computation and Visualization at Brown University](https://ccv.brown.edu).
 
 
 ## Read More

docs/contribute/index.md

@@ -15,14 +15,14 @@ Child packages are generally maintained by individual contributors. The parent p
 *core* packages, is maintained by the [Autonomous Empirical Research Group](https://musslick.github.io/AER_website/Team.html), 
 as well as external contributors.
 
-![image](../img/package_overview.png)
+![image](../img/contributor_model.png)
 
 [`autora`](https://github.com/autoresearch/autora) is the parent package which end users are expected to install. The
 parent depends on core packages, such as [`autora-core`](https://github.com/autoresearch/autora-core) and
 [`autora-synthetic`](https://github.com/autoresearch/autora-synthetic). It also includes vetted modules (child packages) as optional dependencies which users can choose 
 to install. 
 
-You may contribute to any of the core packages or develop your own module as a stand-alone package (see below).    
+You may contribute to any of the core packages or develop your own module as a stand-alone child package (see below).    
 
 
 ## Style Guide

docs/examples/closed-loop-bandit-task/init_autora.md

@@ -37,7 +37,7 @@ The AutoRA workflow (specifically the `autora-firebase-runner` and `autora-proli
 - Click on ``Service accounts``.
 ![service_account.png](../img/service_account.png)
 - Having ``Node.js`` selected, click ``Generate a new private key``. This should generate a json file that you can download.
-- Open the file `autora_workflow.py` in the `research_hub`-folder and navigate to the part of the code that contains a placeholder for the credentials. It should look like this
+- Open the file `autora_workflow.py` in the `researcher_hub`-folder and navigate to the part of the code that contains a placeholder for the credentials. It should look like this
 ```python
 firebase_credentials = {
     "type": "type",

docs/examples/closed-loop-bandit-task/setup.md

@@ -7,7 +7,7 @@ First, we need to set up our local AutoRA project.
 ## Create Repository
 To ease the setup process for this example, we provide a template repository that contains all the necessary files and configurations. 
 
-Simply visit the following repository on GitHub: https://github.com/AutoResearch/autora-closed-loop-firebase-prolific-bandit-task
+Simply visit the following repository on GitHub: [https://github.com/AutoResearch/autora-closed-loop-firebase-prolific-bandit-task](https://github.com/AutoResearch/autora-closed-loop-firebase-prolific-bandit-task)
 
 Next, click on the green "Use this template" button to create a new repository in your account.
 ![use_template.png](../img/use_template.png)
@@ -75,6 +75,9 @@ npm install -g firebase-tools
 
 We will use this package to deploy our firebase functions for storing data.
 
+!!! hint
+    If you encounter any issues with the installation, make sure that you have the necessary permissions to install packages on your system. You may need to run the commands with `sudo` or as an administrator.
+
 ## Set Up Project Folder with Coockiecutter
 
 To establish an online closed-loop for AutoRA, there are two key components that need to be configured:
@@ -120,6 +123,9 @@ You should now have the following project structure:
 
 ![project_structure.png](../img/project_structure.png)
 
+!!! hint
+    If you encounter any issues with the cookiecutter setup, make sure that you have the necessary permissions to install packages on your system. You may need to run the commands with `sudo` or as an administrator.
+
 [Next: Set up Firebase to host our experiment.](firebase.md)
 
 

docs/examples/closed-loop-bandit-task/testingzone.md

@@ -77,7 +77,7 @@ firebase init
   9. Don't overwrite the index.html file if the question pops up.
 
 ## Install jsPsych
-- Next, we install jsPsych (still within the testing_zone folder):
+- Next, we install jsPsych (still within the ``testing_zone`` folder):
 ```shell
 npm install [email protected]
 ```

docs/examples/closed-loop-basic/init_autora.md

@@ -33,7 +33,7 @@ The AutoRA workflow (specifically the `autora-firebase-runner`) will need access
 - Click on ``Service accounts``.
 ![service_account.png](../img/service_account.png)
 - Having ``Node.js`` selected, click ``Generate a new private key``. This should generate a json file that you can download.
-- Open the file `autora_workflow.py` in the `research_hub`-folder and navigate to the part of the code that contains a placeholder for the credentials. It should look like this
+- Open the file `autora_workflow.py` in the `researcher_hub`-folder and navigate to the part of the code that contains a placeholder for the credentials. It should look like this
 ```python
 firebase_credentials = {
     "type": "type",

docs/examples/closed-loop-basic/notebooks/sweetbean.ipynb

@@ -116,6 +116,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from sweetbean.sequence import Block\n",
+    "\n",
     "# create a list of instruction stimuli for the instruction block\n",
     "introduction_list = [introduction_welcome,\n",
     "                      introduction_pictures,\n",
@@ -255,7 +257,7 @@
    "source": [
     "## Experiment Block Sequence\n",
     "\n",
-    "Now that we have specified all of our experiment blocks, we put them together into an experiment. The function below compiles the experiment and converts it into a html file."
+    "Now that we have specified all of our experiment blocks, we put them together into an experiment. The function below compiles the experiment and converts it into an html file."
    ]
   },
   {
@@ -386,8 +388,7 @@
  ],
  "metadata": {
   "colab": {
-   "provenance": [],
-   "toc_visible": true
+   "provenance": []
   },
   "kernelspec": {
    "display_name": "Python 3",

docs/examples/closed-loop-basic/setup.md

@@ -77,6 +77,9 @@ npm install -g firebase-tools
 
 We will use this package to deploy our firebase functions for storing data.
 
+!!! hint
+    If you encounter any issues with the installation, make sure that you have the necessary permissions to install packages on your system. You may need to run the commands with `sudo` or as an administrator.
+
 ## Set Up Project Folder with Coockiecutter
 
 To establish an online closed-loop for AutoRA, there are two key components that need to be configured:
@@ -122,6 +125,9 @@ python -m cookiecutter https://github.com/AutoResearch/autora-user-cookiecutter
 
 ![project_structure.png](../img/project_structure.png)
 
+!!! hint
+    If you encounter any issues with the cookiecutter setup, make sure that you have the necessary permissions to install packages on your system. You may need to run the commands with `sudo` or as an administrator.
+
 ## Next Steps
 
 [Next: Set up Firebase to host our experiment.](firebase.md)

docs/examples/closed-loop-basic/testingzone.md

@@ -81,7 +81,7 @@ firebase init
   9. Don't overwrite the index.html file if the question pops up.
 
 ## Install jspsych
-- Next, we install jspsych (still within the testing_zone folder):
+- Next, we install jspsych (still within the ``testing_zone`` folder):
 ```shell
 npm install [email protected]
 ```

docs/experiment-runner/behavioral/example.md

@@ -0,0 +1,3 @@
+# Example: Closed-Loop Behavioral Study
+
+For a detailed example of setting up a closed-loop behavioral study with an online experiment, see the [Basic Closed-Loop Psychophysics Study](../../examples/closed-loop-basic/index.md).

docs/experiment-runner/behavioral/index.md

@@ -0,0 +1,8 @@
+# Online Experiments To Collect AutoRA Observations
+
+AutoRA provides functionality for running closed-loop behavioral studies with online experiments. This functionality allows researchers to set up websites that integrate with AutoRA workflows. These websites allow observations gathered from participants online.
+
+![System Overview](../../examples//img/system_overview.png)
+
+To enable this functionality, AutoRA can interface with databases, such as Firebase for hosting the website and storing data. In addition, AutoRA can recruit participants through platforms like Prolific.
+

docs/index.md

@@ -67,6 +67,6 @@ Once you are familiar with the basics, you can explore the [Use Case Tutorials](
 
 This project is in active development by the [Autonomous Empirical Research Group](https://musslick.github.io/AER_website/Research.html).
 
-The development of this package was supported by Schmidt Science Fellows, in partnership with the Rhodes Trust, as well as the [Carney BRAINSTORM program](https://ccbs.carney.brown.edu/brainstorm) at Brown University. The development of auxiliary packages for AutoRA, such as `autodoc`, is supported by [Schmidt Sciences, LLC. and the Virtual Institute for Scientific Software (VISS)](https://www.schmidtsciences.org/viss/). The AutoRA package was developed using computational resources and services at the [Center for Computation and Visualization at Brown University](https://ccv.brown.edu).
+The development of this package was supported by [Schmidt Science Fellows](https://schmidtsciencefellows.org/), in partnership with the Rhodes Trust, as well as the [Carney BRAINSTORM program](https://ccbs.carney.brown.edu/brainstorm) at Brown University. The development of auxiliary packages for AutoRA, such as `autodoc`, is supported by [Schmidt Sciences, LLC. and the Virtual Institute for Scientific Software (VISS)](https://www.schmidtsciences.org/viss/). The AutoRA package was developed using computational resources and services at the [Center for Computation and Visualization at Brown University](https://ccv.brown.edu).
 
 

docs/installation.md

@@ -49,9 +49,9 @@ In using AutoRA, it is helpful to be aware of its structure, which is described
 
 ``autora`` is organized into one "parent" and many "child" packages.
 
-![image](img/package_overview.png)
+![image](img/contributor_model.png)
 
-The ``autora`` "parent" package depends on core packages, such as [`autora-core`](https://github.com/autoresearch/autora-core), [`autora-workflow`](https://github.com/autoresearch/autora-workflow), and [`autora-synthetic`](https://github.com/autoresearch/autora-synthetic), which are automatically installed with ``autora``. 
+The ``autora`` "parent" package depends on core packages, such as [`autora-core`](https://github.com/autoresearch/autora-core) and [`autora-synthetic`](https://github.com/autoresearch/autora-synthetic), which are automatically installed with ``autora``. 
 
 However, the ``autora`` ecosystem also includes vetted modules (child packages) as **optional dependencies** which users can choose to install. Below, we provide a list of all optional dependencies that are currently vetted by the ``autora`` core team.
 
@@ -62,7 +62,7 @@ To install any (combination) of optional dependencies, users should run the rele
 pip install -U "autora[desired-dependency]"
 ```
 
-For example, to install one of the [Theorists](theorist/index.md), such as the Bayesian Machine Scientist (BMS), a user should run:
+For example, to install one of the [Theorists](theorist/index.md), such as the Bayesian Machine Scientist (BMS) from the package `autora-theorist-bms`, a user should run:
 
 ```shell
 pip install -U "autora[theorist-bms]"