Merge pull request #6 from AccelerationConsortium/dev

flowchart, wording, images

Author: sgbaird

.pre-commit-config.yaml

@@ -6,6 +6,7 @@ repos:
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
+    args: ['--maxkb=2000']
   - id: check-ast
   - id: check-json
   - id: check-merge-conflict

CONTRIBUTING.md

@@ -335,6 +335,91 @@ on [PyPI], the following steps can be used to release a new version for
     to collectively create software are general and can be applied to all sorts
     of environments, including private companies and proprietary code bases.
 
+### Updating the Clickable SVG
+
+The SVG is created using PowerPoint (select all objects, right click, save as picture -> change file format to SVG) and saved to `course-flowchart.svg`. Note that I put 99% transparent white boxes in front of the locations I want to be clickable. Kind of hacky, but with minimal effect. To make it easier to identify objects, these can be renamed either in PowerPoint or in Inkscape.
+
+After opening the SVG file in Inkscape:
+1. click on the mostly transparent rectangle object (might need to double click)
+2. right click and select "Link Properties.." (or create link)
+3. Insert the absolute or relative link into the href field
+  - `courses/hello-world/overview.html`
+  - `courses/data-science/overview.html`
+  - `courses/robotics/overview.html`
+  - `courses/software-dev/overview.html`
+  - `courses/capstone/overview.html`
+4. Save
+5. Open the SVG file (i.e., raw code) in a text editor such as VS Code
+6. Replace:
+
+```html
+   width="XXXX"
+   height="YYYY"
+```
+
+
+with the following:
+
+```html
+   viewBox="0 0 XXXX YYYY"
+   width="100%"
+   height="100%"
+```
+
+For example, replace:
+
+```html
+   width="2965"
+   height="1876"
+```
+
+with:
+
+```html
+   viewBox="0 0 2965 1876"
+   width="100%"
+   height="100%"
+```
+
+1. To add a hover fill effect, add the following to each of the transparent rectangles:
+
+```html
+         onmouseover="evt.target.setAttribute('fill', 'blue'); evt.target.setAttribute('fill-opacity', '0.25');"
+         onmouseout="evt.target.setAttribute('fill', 'white'); evt.target.setAttribute('fill-opacity', '0.01');"
+```
+
+For example, replace:
+
+```html
+       xlink:href="courses/data-science/overview.html"><rect
+         x="1909"
+         y="690"
+         width="388"
+         height="389"
+         fill="#FFFFFF"
+         fill-opacity="0.0117647"
+         id="rect85" /></a><a
+```
+
+with the following:
+
+```html
+       xlink:href="courses/data-science/overview.html"><rect
+         x="1909"
+         y="690"
+         width="388"
+         height="389"
+         fill="#FFFFFF"
+         fill-opacity="0.0117647"
+         onmouseover="evt.target.setAttribute('fill', 'blue'); evt.target.setAttribute('fill-opacity', '0.25');"
+         onmouseout="evt.target.setAttribute('fill', 'white'); evt.target.setAttribute('fill-opacity', '0.01');"
+         id="rect85" /></a><a
+```
+8. Save, build docs to verify, and commit/push to GitHub.
+
+You can search for `hello-world`, `data-science`, etc. to find corresponding locations.
+
+See also https://app.screencast.com/yIypgQZ22BO83 and https://stackoverflow.com/questions/39203857/scaling-svg-produced-with-inkscape
 
 [black]: https://pypi.org/project/black/
 [commonmark]: https://commonmark.org/
@@ -367,5 +452,5 @@ on [PyPI], the following steps can be used to release a new version for
 ```{todo} Please review and change the following definitions:
 ```
 
-[repository]: https://github.com/<USERNAME>/ac-microcourses
-[issue tracker]: https://github.com/<USERNAME>/ac-microcourses/issues
+[repository]: https://github.com/AccelerationConsortium/ac-microcourses
+[issue tracker]: https://github.com/AccelerationConsortium/ac-microcourses/issues

docs/_images/clslab-light-abstract.png

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2022 sgbaird
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docs/_images/mqtt-workflow.png

@@ -0,0 +1,7 @@
+Various content taken from https://github.com/sparks-baird/self-driving-lab-demo.
+
+For provenance:
+grid vs. random vs. bayesian: https://github.com/sparks-baird/self-driving-lab-demo/blob/7b9a2a9bc4a5079b03907ffd5c758094217d3872/notebooks/3.1-random-vs-grid-vs-bayesian.ipynb
+
+Star protocols as used in:
+> Baird, S. G.; Sparks, T. D. Building a “Hello World” for Self-Driving Labs: The Closed-Loop Spectroscopy Lab Light-Mixing Demo. STAR Protocols 2023, 4 (2), 102329. https://doi.org/10.1016/j.xpro.2023.102329.

docs/_images/sdl-demo/LICENSE.txt

@@ -9,7 +9,7 @@ Here, we provide details for the five core microcourses, including title, descri
 ```
 
 ```{raw} html
-:file: course-flowchart-viewbox.svg
+:file: course-flowchart.svg
 ```
 
 <!-- <div align="center">

docs/_images/sdl-demo/README.md

@@ -87,6 +87,65 @@
 templates_path = ["_templates"]
 
 
+# # Specify the root directory
+# root_dir = 'courses'
+
+# # Initialize the dictionary
+# nbsphinx_thumbnails = {}
+
+# # Walk through the directory
+# for dirpath, dirnames, filenames in os.walk(root_dir):
+#     for filename in filenames:
+#         # Check if the file is a notebook
+#         if filename.endswith('.ipynb'):
+#             # Construct the key by removing the root directory and the file extension
+#             key = os.path.join(dirpath, filename)[len(root_dir)+1:-len('.ipynb')]
+#             # Construct the value by replacing the slashes with dashes and adding the directory and extension
+#             value = '_static/' + key.replace('/', '-') + '.png'
+#             # Add the key-value pair to the dictionary
+#             nbsphinx_thumbnails[key] = value
+
+# # Print the dictionary
+# print("nbsphinx_thumbnails = ", nbsphinx_thumbnails)
+
+# nbsphinx_thumbnails = {
+#     "courses/hello-world/1.1-running-the-demo": "_static/1.1-running-the-demo.png",
+#     ...
+# }
+
+nbsphinx_thumbnails = {
+    "courses/hello-world/1.1-running-the-demo": "../../_images/sdl-demo/star-protocols-graphical-abstract.png",
+    "courses/hello-world/1.2-blink-and-read": "../../_images/sdl-demo/green-led.jpg",
+    "courses/hello-world/1.3-bayesian-optimization": "../../_images/sdl-demo/grid-vs-random-vs-bayesian.png",
+    "courses/hello-world/1.4-hardware-software-communication": "../../_images/mqtt-workflow.png",
+    "courses/hello-world/1.5-logging-data": "../../_images/1.5-logging-data.png",
+    "courses/hello-world/1.6-piecing-the-modules-together": "../../_images/1.6-piecing-the-modules-together.png",
+    "courses/hello-world/1.7-convert-to-a-lab-sensor-system": "../../_images/1.7-convert-to-a-lab-sensor-system.png",
+    "courses/data-science/2.1-gentle-intro-bayesian": "../../_images/2.1-gentle-intro-bayesian.png",
+    "courses/data-science/2.2-multi-objective-opt": "../../_images/2.2-multi-objective-opt.png",
+    "courses/data-science/2.3-constrained-opt": "../../_images/2.3-constrained-opt.png",
+    "courses/data-science/2.4-high-dimensional-opt": "../../_images/2.4-high-dimensional-opt.png",
+    "courses/data-science/2.5-multi-fidelity-opt": "../../_images/2.5-multi-fidelity-opt.png",
+    "courses/data-science/2.6-predefined-candidates": "../../_images/2.6-predefined-candidates.png",
+    "courses/data-science/2.7-benchmarks": "../../_images/2.7-benchmarks.png",
+    "courses/robotics/3.1-pumps-and-pipettes": "../../_images/3.1-pumps-and-pipettes.png",
+    "courses/robotics/3.2-liquid-handlers": "../../_images/3.2-liquid-handlers.png",
+    "courses/robotics/3.3-mobile-robotics": "../../_images/3.3-mobile-robotics.png",
+    "courses/robotics/3.4-computer-vision": "../../_images/3.4-computer-vision.png",
+    "courses/robotics/3.5-solid-sample-transfer": "../../_images/3.5-solid-sample-transfer.png",
+    "courses/software-dev/4.1-vscode-setup": "../../_images/4.1-vscode-setup.png",
+    "courses/software-dev/4.2-vscode-debugging": "../../_images/4.2-vscode-debugging.png",
+    "courses/software-dev/4.3-unit-testing": "../../_images/4.3-unit-testing.png",
+    "courses/software-dev/4.4-automated-docs": "../../_images/4.4-automated-docs.png",
+    "courses/software-dev/4.5-continuous-integration": "../../_images/4.5-continuous-integration.png",
+    "courses/software-dev/4.6-project-templates": "../../_images/4.6-project-templates.png",
+    "courses/software-dev/4.7-cloud-servers": "../../_images/4.7-cloud-servers.png",
+    "courses/software-dev/4.8-cloud-computing": "../../_images/4.8-cloud-computing.png",
+    "courses/capstone/5.1-project-proposal": "../../_images/5.1-project-proposal.png",
+    "courses/capstone/5.2-design-and-execution": "../../_images/5.2-design-and-execution.png",
+    "courses/capstone/5.3-dissemination": "../../_images/5.3-dissemination.png",
+}
+
 # Enable markdown
 extensions.append("myst_parser")
 

docs/_images/sdl-demo/clslab-light-orthographic.png

@@ -5,13 +5,17 @@
 If you've already completed the [Certificate Overview](certificate-framework.md), you're ready to dive into the course content! If not, we recommend you start there.
 
 ## 🚀 Getting Started
-As [mentioned in the overview](/courses/hello-world/overview.md), each course is comprised of modules, where the typical structure for each module is:
+As [mentioned in the overview](/courses/hello-world/overview.md), each course is comprised of modules, where each module typically has three components:
 
-1. A guided notebook tutorial (ungraded)
-2. A standalone notebook assignment (graded)
-3. A mini project (graded)
 
-To familarize yourself with the assignment structure and to keep everyone on the same page, complete the[🔗 GitHub starter tutorial](https://github.com/AC-Classroom/github-starter-course).
+|  | Component | Points |
+|---|-------------------|--------|
+| 1. | 🧭 Guided tutorial | 0 |
+| 2. | 📓 Notebook assignment | 5 |
+| 3. | 🛠️ Mini project | 10 |
+
+
+These courses are integrated with coding exercises via GitHub Classroom. To familarize yourself with the assignment structure and keep everyone on the same page, complete the [🔗 GitHub starter tutorial](https://github.com/AC-Classroom/github-starter-course).
 
 <!-- If you've reached this point, and you're wondering what a self-driving lab is in the first place, watch [▶️ "The Future of Chemistry is Self-driving"](). *TODO: Video needs to be edited and uploaded to YouTube. Add this as an embedded iframe perhaps* -->
 
@@ -80,6 +84,10 @@ courses/software-dev/4.8-cloud-computing.ipynb
 
 ## 🏢 Capstone Project at the AC Training Lab
 
+```{note}
+🔑 Due to the intensive nature of this in-person course and to maximize value to the participants, completion of the previous four courses are mandatory.
+```
+
 ```{include} courses/capstone/description.md
 ```