Merge branch 'main' into update-robotics-course

AccelerationConsortium · Oct 21, 2024 · 2b2316e · 2b2316e
2 parents 6d2dccb + 6c09db7
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diff --git a/docs/conf.py b/docs/conf.py
@@ -154,6 +154,7 @@
     "1.4-hardware-software-communication.ipynb",  # MicroPython code
     "1.4.1-onboard-led-temp.ipynb",  # assumes a MCU is actively receiving
     "1.5-data-logging.ipynb",  # MicroPython code
+    "1.5.1-aws-lambda-read.ipynb",  # just not tested
     "2.*",  # TODO: Bayes opt notebooks
     "3.*",  # TODO: Robotics notebooks
     "4.*",  # TODO: Software dev notebooks

diff --git a/docs/course-data.yaml b/docs/course-data.yaml
@@ -227,7 +227,7 @@ data-science:
   description: "Unleash the power of data science in the realm of self-driving laboratories. This remote, asynchronous course empowers you to apply data science concepts to materials discovery tasks. You'll create Bayesian optimization scripts, explore advanced optimization topics, and adapt templates to create an advanced optimization setup for a materials discovery task. Topics will include multi-objective, constrained, high-dimensional, multi-fidelity, batch, asynchronous, and domain-aware Bayesian optimization. Additionally, you'll learn to share your findings by uploading datasets to a data repository, creating benchmark models, and hosting models on data science platforms."
   media_command: "![](./images/ax-repo/bo_1d_opt.gif)"
   media_caption: "*Animation of 1D Bayesian Optimization: A Gaussian Process surrogate model can be used with an acquisition function to seamlessly transition from exploration to optimization in noisy settings. Source: [https://ax.dev/docs/bayesopt.html](https://ax.dev/docs/bayesopt.html)*"
-  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }}"
+  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }} (Course 1: Hello World)"
   learning_outcomes:
     - "Describe and categorize a materials discovery task using data science language and concepts"
     - "Customize a Bayesian optimization script to systematically identify the optimal chocolate chip cookie recipe, demonstrating practical application of optimization techniques"
@@ -431,7 +431,7 @@ robotics:
   description: "Embark on a journey into the world of robotics and automation for self-driving laboratories. This asynchronous, remote course equips you with the skills to control peristaltic pumps, linear actuators, automated liquid handlers, and solid dispensers using a microcontroller, a motor driver, and a workflow orchestration package. You'll also learn to control mobile cobots and perform spatial referencing and ID recognition via computer vision. The course will conclude with a solid sample transfer workflow using a multi-axis robot. Remotely accessible resources will be provided as necessary."
   media_command: "<video width='100%' controls autoplay muted><source src='./../../_static/ac-website/robot-loop.mp4' type='video/mp4'>Your browser does not support the video tag.</video>"
   media_caption: "Self-driving lab robotic platforms. 1. ADA at the University of British Columbia (C. Berlinguette, J. Hein, A. Aspuru-Guzik); 2. Artificial Chemist (M. Abolhasani, NC State University); 3. Robotically reconfigurable flow chemistry platform (C. Coley, MIT); 4. Chemputer (L. Cronin, University of Glasgow); 5. Mobile robot chemist (A. Cooper, University of Liverpool). Source: [https://acceleration.utoronto.ca/maps](https://acceleration.utoronto.ca/maps)"
-  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }}"
+  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }} (Course 1: Hello  World)"
   # I am also thinking about adding: **This course requires physical hardware and a 2.4 GHz WPA-2 wireless network**. If you do not have the hardware, you will need to purchase the physical hardware associated with “Introduction to AI for Discovery using Self-driving Labs” and the the [required components](https://github.com/ac-rad/digital-pipette) for the “Digital Pipette”, replacing the 6V DC power supply with the correct style for your country (e.g., European type C), if necessary. If you do not have the required wireless network, you can use a mobile hotspot in extended compatibility mode or a SIM-enabled router (see [recommendations](https://github.com/sparks-baird/self-driving-lab-demo/discussions/83) for more information).
   learning_outcomes:
     - "Design and execute software to manage a peristaltic pump's operations using a microcontroller and motor driver, demonstrating application and integration skills"
@@ -499,6 +499,7 @@ robotics:
         - "Perform liquid transfer between vials with an automated liquid handler (Science Jubilee and OT-2)"
 
     - module_name: "3.4 Mobile robotics"
+      tutorial_file: 3.4-mobile-robotics.md
       topics:
         - "ROS"
         - "Isaac Sim"
@@ -510,6 +511,7 @@ robotics:
         - "Define asynchrony in the context of hardware control for automonous laboratories"
 
     - module_name: "3.5 Computer vision"
+      tutorial_file: 3.5-computer-vision.md
       topics:
         - "OpenCV"
         - "AprilTags"
@@ -518,6 +520,7 @@ robotics:
         - "Use a motorized microscope and OpenCV to search for regions of interest in a sample"
 
     - module_name: "3.6 Solid sample transfer"
+      tutorial_file: 3.6-solid-sample-transfer.md
       topics:
         - "Workflow orchestration"
         - "ROS"
@@ -536,7 +539,7 @@ software-dev:
   description: "Elevate your software development skills in the context of self-driving laboratories. This asynchronous, remote course introduces software development concepts and best practices and productivity tools such as integrated development environments (IDEs) with VS Code, unit testing with pytest, continuous integration via GitHub actions, and documentation creation using Sphinx and Read the Docs. You'll also learn to deploy materials discovery campaigns on cloud servers or dedicated hardware and run offline simulations using cloud hosting."
   media_command: ""
   media_caption: ""
-  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }}"
+  recommended_prerequisites: "The **recommended prerequisite** for this course is {{ hello-world }} (Course 1: Hello World)"
   learning_outcomes:
     - "Enumerate and explain software development best practices along with their corresponding benefits, demonstrating understanding and recall"
     - "Identify and evaluate various productivity tools for developers, highlighting how they enhance efficiency, to demonstrate analytical and selection skill"
@@ -556,22 +559,39 @@ software-dev:
   course_assessments_and_grading_schema: "{{ courses.hello-world.course_assessments_and_grading_schema }}"
   developers:
     - "Sterling Baird, PhD Materials Science and Engineering (Acceleration Consortium)"
+    - "Sissi Feng, PhD Electrical and Computer Engineering (Acceleration Consortium)"
   module_note: "Each module is intended to take approximately 3-4 hours, assuming that the recommended prerequisites have been met."
   modules:
-    - module_name: "Deep dive into Git and GitHub"
+    - module_name: "4.0 Orientation"
+      tutorial_file: 4.0-orientation.md
+      topics:
+        - "Git"
+        - "GitHub"
+        - "Version control"
+        - "GitHub Classroom"
+        - "Codespaces"
+      learning_outcomes:
+        - "Describe the purpose of Git and GitHub"
+        - "Create a GitHub account and a repository"
+        - "Commit, push, and pull changes"
+        - "Run a unit test and fix a simple Python function"
+        - "Define continuous integration"
+    - module_name: "4.1 Deep dive into Git and GitHub"
+      tutorial_file: 4.1-github-deep-dive.md
       topics:
         - "GitHub issues"
         - "Pull requests"
         - "Collaborative coding"
         - "Branches"
         - "Merge conflicts"
-        - "Project management"
+        # - "Project management"
       learning_outcomes:
         - "Open a GitHub issue on a repository"
         - "Create a new branch"
         - "Merge a GitHub pull request"
         - "Resolve a merge conflict"
-    - module_name: "Setting up VS Code"
+    - module_name: "4.2 Setting up VS Code"
+      tutorial_file: 4.2-vscode-setup.md
       topics:
         - "IDEs"
         - "Miniconda"
@@ -586,7 +606,8 @@ software-dev:
         - "Set up VS Code"
         - "Install Miniconda"
         - "Install VS Code extensions"
-    - module_name: "Debugging in VS Code"
+    - module_name: "4.3 Debugging in VS Code"
+      tutorial_file: 4.3-vscode-debugging.md
       topics:
         - "Print statements"
         - "Setting breakpoints"
@@ -601,7 +622,8 @@ software-dev:
         - "Step through code"
         - "Use the debug console"
         - "Set up debug configurations"
-    - module_name: "Unit testing"
+    - module_name: "4.4 Unit testing"
+      tutorial_file: 4.4-unit-testing.md
       topics:
         - "pytest"
         - "Test result interpretation"
@@ -617,7 +639,8 @@ software-dev:
     # Coding best practices? (e.g., modularity, readability, PEP8, object-oriented programming, etc.)
     # Linting and code formatting? (e.g., black, flake8, isort, etc., especially VS Code Extensions)
     # VS Code extensions? (e.g., Python, Jupyter, Git, etc.)
-    - module_name: "Automated documentation"
+    - module_name: "4.5 Automated docs"
+      tutorial_file: 4.5-automated-docs.md
       topics:
         - "Markdown"
         - "Documentation as code"
@@ -631,7 +654,8 @@ software-dev:
         - "Set up a readthedocs account and publish a readthedocs page"
       tutorial:
         - "GitHub-flavored Markdown tutorial"
-    - module_name: "Continuous integration (CI)"
+    - module_name: "4.6 Continuous integration"
+      tutorial_file: 4.6-continuous-integration.md
       topics:
         - "Continuous integration"
         - "GitHub actions"
@@ -641,7 +665,8 @@ software-dev:
         - "Explain the purpose of continuous integration"
         - "Set up a GitHub actions workflow"
         - "Run unit tests and documentation builds on GitHub actions"
-    - module_name: "Project templates"
+    - module_name: "4.7 Project templates"
+      tutorial_file: 4.7-project-templates.md
       topics:
         - "PyScaffold"
         - "Cookiecutter"
@@ -655,7 +680,8 @@ software-dev:
         - "Add project content"
         - "Publish a Python package to PyPI"
         - "Outline the key benefits of dependency management during software development"
-    - module_name: "Launching a free cloud server"
+    - module_name: "4.8 Launching a free cloud server"
+      tutorial_file: 4.8-cloud-server.md
       topics:
         - "Serverless computing"
         - "PythonAnywhere"
@@ -666,7 +692,8 @@ software-dev:
         - "Use a container"
         - "Create a container"
         - "Deploy a materials discovery campaign on a cloud server"
-    - module_name: "On-demand cloud simulations"
+    - module_name: "4.9 On-demand cloud simulations"
+      tutorial_file: 4.9-cloud-simulations.md
       topics:
         - "Cloud computing"
         - "Setting up an AWS account"

diff --git a/docs/courses/data-science/2.0-orientation.md b/docs/courses/data-science/2.0-orientation.md
@@ -23,7 +23,7 @@ https://q.utoronto.ca/courses/370068/quizzes/398746
 You will record your GitHub username and GitHub Classroom Student Identifier, which will be used later in the course. You can refer back to these quiz answers if you forget. See below for information on these two.
 
 ```{warning}
-Your GitHub Classroom Student Identifier is not necessary the same between each course. If the same GitHub Classroom Student Identifier from a previous course is still available, you may select that one. Please keep track of which one corresponds to which course to avoid confusion.
+Your GitHub Classroom Student Identifier is not necessarily the same between each course. If the same GitHub Classroom Student Identifier from a previous course is still available, you may select that one. Please keep track of which one corresponds to which course to avoid confusion.
 ```
 
 ### GitHub Account
@@ -110,7 +110,7 @@ If you're not eligible, you may consider a paid subscription (~$10 USD/month). I
 
 ## 📄 Python Refresher Assignment
 
-Optionally, you may try out the [Python refresher assignment](https://classroom.github.com/a/TvdgHvvu). This is ungraded.
+Optionally, you may try out the [Python refresher assignment](https://classroom.github.com/a/M4fCrpTp). This is ungraded.
 
 ## ➰ Bayesian Optimization Refresher
 

diff --git a/docs/courses/data-science/2.6-benchmarking.md b/docs/courses/data-science/2.6-benchmarking.md
@@ -108,3 +108,11 @@ https://q.utoronto.ca/courses/370068/assignments/1327560
 :::
 
 ::::
+
+## Course Completion
+
+For those who have completed the course, thank you for your participation, and congratulations! 🥳
+
+Once you have completed all the modules, fill out the [Certificate of Completion Request form](https://learn.utoronto.ca/help/forms-and-applications/confirmation-completion-request) through the School of Continuing Studies to receive your microcredential. This process may take up to 4-6 weeks. As a reminder, 70% is the required threshold to pass.
+
+Please also consider filling out [the final course evaluation form](https://forms.office.com/r/gssTGHhuUz) listed on your course syllabus as well as [the learner equity survey](https://redcap.utoronto.ca/surveys/?s=77R3YNHDHX3TKRLD).
diff --git a/docs/courses/hello-world/1.0-orientation.md b/docs/courses/hello-world/1.0-orientation.md
@@ -140,7 +140,7 @@ If you're not eligible, you may consider a paid subscription (~$10 USD/month). I
 
 ## Python Refresher Assignment
 
-Optionally, you may try out the [Python refresher assignment](https://classroom.github.com/a/oDMoonRK). This is ungraded.
+Optionally, you may try out the [Python refresher assignment](https://classroom.github.com/a/eBPVY0Yg). This is ungraded.
 
 ## Syllabus
 

diff --git a/docs/courses/hello-world/1.1-running-the-demo.md b/docs/courses/hello-world/1.1-running-the-demo.md
@@ -76,10 +76,6 @@ https://q.utoronto.ca/courses/351407/assignments/1286925?display=full_width
 
 ## 📄 Assignment
 
-```{warning}
-The Data API is now deprecated (as of 2024-09-10). While the end of life for the Data API is 2025-09-30, the Data API can no longer be enabled for users/database for which it's not already enabled. If you already have it enabled for a particular instance, it should work until the end-of-life date. See https://github.com/AccelerationConsortium/ac-microcourses/issues/45 for context. We are working quickly to adjust the tutorials and assignments based on this change. This also affects the fifth module and the final module.
-```
-
 A partial walkthrough of the assignment is shown below. If you get stuck, refer back to the build instructions manuscript and the [AC Microcourses Hello World GitHub discussions](https://github.com/AccelerationConsortium/ac-microcourses/discussions/categories/hello-world).
 
 <video width="700" height="394" controls>

diff --git a/docs/courses/hello-world/1.2-blink-and-read.md b/docs/courses/hello-world/1.2-blink-and-read.md
@@ -86,7 +86,7 @@ print(T)
 
 **I2C (Inter-Integrated Circuit)**: I2C is a communication protocol used for connecting and exchanging data between electronic components on a circuit board or between different devices. It stands for Inter-Integrated Circuit and allows multiple digital devices to communicate with each other using a common set of wires, typically two (SDA for data and SCL for clock), making it useful for connecting sensors, displays, and other peripherals in a simple and standardized way.
 
-**RGB Color Values**: In the context of RGB color representation, 0 to 255 refers to the range of values for each of the three color channels: Red (R), Green (G), and Blue (B). Each channel can have a value between 0 (no intensity) and 255 (maximum intensity), allowing for a total of 256 different levels of intensity for each color. By combining different levels of intensity for these three channels, you can create a wide range of colors by specifying how much red, green, and blue are mixed together. For example, RGB(255, 0, 0) represents full red, RGB(0, 255, 0) represents full green, and RGB(0, 0, 255) represents full blue. Mixing these channels in different proportions produces various colors in the RGB color space.
+**RGB Color Values**: In the context of RGB color representation, 0 to 255 refers to the range of values for each of the three color channels: Red (`R`), Green (`G`), and Blue (`B`). Each channel can have a value between 0 (no intensity) and 255 (maximum intensity), allowing for a total of 256 different levels of intensity for each color. By combining different levels of intensity for these three channels, you can create a wide range of colors by specifying how much red, green, and blue are mixed together. For example, RGB(255, 0, 0) represents full red, RGB(0, 255, 0) represents full green, and RGB(0, 0, 255) represents full blue. Mixing these channels in different proportions produces various colors in the RGB color space.
 
 **Spectrophotometer**: A spectrophotometer is a scientific instrument used to measure the intensity of light at different wavelengths in a sample. It works by passing a beam of light through the sample and measuring how much light is absorbed or transmitted. Spectrophotometers are commonly used in chemistry, biology, and physics to analyze the concentration of substances in a solution, study the properties of materials, and determine the color or composition of samples by measuring their absorption or emission spectra.