initial test and draft of Jupyter book

.github/workflows/build_course_page.yml

@@ -0,0 +1,40 @@
+name: build-course-page
+
+# Only run this when the master branch changes
+on:
+  push:
+    branches:
+    - main
+    # If your git repository has the Jupyter Book within some-subfolder next to
+    # unrelated files, you can make this run only if a file within that specific
+    # folder has been modified.
+    #
+    # paths:
+    # - content/**
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python 3.11.11
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.11.11
+
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+    # Build the page
+    - name: Build the course page
+      run: |
+        jupyter-book build cmm_course/
+    # Push the book's HTML to github-pages
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./cmm_course/_build/html

.gitignore

@@ -1,3 +1,6 @@
+# JB builds
+cmm_course/_build/*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

cmm_course/README.md

@@ -0,0 +1,17 @@
+# Models of Memory
+
+Welcome!  This repository contains course materials for the Dartmouth graduate course on computational models of learning and memory.  The syllabus may be found [here](https://github.com/ContextLab/memory-models-course/blob/main/admin/syllabus.pdf).  Feel free to follow along with the course materials (whether you are officially enrolled in the course or just visiting!), submit comments and suggestions, etc.  An outline of the course materials, including links to lecture and discussion topics and assignments may be found [here](https://github.com/ContextLab/memory-models-course/blob/main/slides/README.md).
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/ContextLab/memory-models-course/main/admin/readme_robot.png" alt="robot" width="400"/>
+</p>
+
+## A note about this Open Course
+This course is taught as an *Open Course*, meaning that the course is designed from the ground up to be shareable and freely accessible to anyone.  All code for this course is written in [Python](https://www.python.org/) and most of the material is organized in [Jupyter notebooks](http://jupyter.org/).
+
+Feel free to follow along with this course, do the assignments, post questions and/or issues to this repository or Discord, suggest changes, etc.  However, I won't formally evaluate your submitted work unless you are a Dartmouth student who is currently enrolled.
+
+If you are a course instructor teaching overlapping material, feel free to borrow any materials used in this course!  If you directly copy (or "draw heavy inspiration from") the materials, I would appreciate a citation (e.g., a pointer to this repository).  I'd also love to hear from you about how you're using this resource!
+
+This course is a continually evolving work in progress.  I plan to update the material to keep the syllabus fresh and relevant.  By the same token, although my goal is 100% accuracy and currency, it's unlikely that I'll achieve that goal.  You should participate with the understanding that this material will likely have occasional mistakes, omissions, errors, etc.  Given this fact, one way to approach the course is to maintain an open yet critical view of the material.  If you think there's a mistake, I encourage you to bring it to my attention!
+

cmm_course/_config.yml

@@ -0,0 +1,38 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Computational memory Models
+author: Jeremy Manning
+copyright: 2025 -
+logo: https://raw.githubusercontent.com/ContextLab/memory-models-course/main/admin/readme_robot.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: false
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+sphinx:
+  config:
+    bibtex_reference_style: author_year  
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/ContextLab/memory-models-course  # Online location of your book
+  path_to_book: ccm_course  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+

cmm_course/_toc.yml

@@ -0,0 +1,13 @@
+format: jb-book
+root: README
+chapters:
+- file: instructions
+- file: admin/syllabus
+- file: slides/README
+- file: assignments/README
+  sections:
+  - file: assignments/Assignment_1:Hopfield_Networks/README
+  - file: assignments/Assignment_2:Search_of_Associative_Memory_Model/README
+  - file: assignments/Assignment_3:Context_Maintenance_and_Retrieval_Model/README
+  - file: assignments/Assignment_4:_Laplace_Temporal_Context_Model/README
+  - file: assignments/Final_Project/README

admin/syllabus.md → cmm_course/admin/syllabus.md

@@ -1,32 +1,11 @@
----
-title: "PSYC 133: Models of Memory"
-geometry: margin=1in
-header-includes:
-  - \usepackage{fontspec}
-  - \usepackage{booktabs}
-  - \setmainfont{Berkeley Mono} 
-output: pdf
----
-
-\setlength{\arrayrulewidth}{0.5mm}
-\vspace{-0.75in}
-\begin{center}
-\begin{tabular}{|p{1.25in}|p{2in}|}
-\hline
-\textbf{Meeting times}   & TBD                       \\
-\hline
-\textbf{Classroom}       & TBD                       \\
-\hline
-\textbf{Instructor}      & Dr. Jeremy R. Manning      \\
-\hline
-\textbf{Email}           & \href{mailto:[email protected]}{[email protected]} \\
-\hline
-\textbf{Office location} & 349 Moore Hall            \\
-\hline
-\textbf{Office hours}    & By appointment            \\
-\hline
-\end{tabular}
-\end{center}
+| **Field**           | **Details**                                                                 |
+|----------------------|-----------------------------------------------------------------------------|
+| **Meeting times**    | TBD                                                                         |
+| **Classroom**        | TBD                                                                         |
+| **Instructor**       | Dr. Jeremy R. Manning                                                      |
+| **Email**            | [[email protected]](mailto:[email protected])                        |
+| **Office location**  | 349 Moore Hall                                                             |
+| **Office hours**     | By appointment                                                             |
 
 ## Course Description
 Knowing how our brains organize and spontaneously retrieve memories is at the heart of understanding the basis of the ongoing internal dialog of our conscious thoughts.  Put simply, our memories make us _who we are_.  In this course, we will use readings, discussions, and hands-on demonstrations to explore historical approaches, current approaches, and hints about the "next generation" of computational (mathematical) models of learning and memory.

cmm_course/assignments/README.md

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+# Assignments
+
+Include general information about assignments here.

cmm_course/instructions.md

@@ -0,0 +1,14 @@
+# Student instructions
+
+## Overview
+We will use the following tools in this course:
+- [GitHub](https://www.github.com): used to download code and data, collaborate with other students, and submit course assignments
+- [Google Colaboratory](https://colab.research.google.com/): a Google resource we will use to write code, download data, and run analyses
+- [Discord](https://discord.com/): used to coordinate all course communication.  Use this link to join our class server:
+
+[![](https://dcbadge.vercel.app/api/server/R6kM9bjpFj)](https://discord.gg/R6kM9bjpFj)
+
+## Setup 
+1. Start by creating a free [GitHub account](https://www.github.com) if you don't already have one.  (If you already have an account, you may use it for this course.)
+2. Next, sign into the course's [Discord workspace](https://discord.gg/R6kM9bjpFj).  You can ask questions and get help with all aspects of the course via our Discord community.  You'll need to create a (free) Discord account.
+3. If you don't already have one, create a [Google account](http://google.com/).  (If you already have an account, you may use it for this course.) Make sure you can sign into Colaboratory using [this link](https://colab.research.google.com/).

slides/README.md → cmm_course/slides/README.md

@@ -1,4 +1,6 @@
-# Week 1: Introduction, Hopfield Networks
+# Course topics
+
+## Week 1: Introduction, Hopfield Networks
   - Discussions:
     - What is memory?
     - What does it mean to build a "model" of memory?
@@ -9,7 +11,7 @@
   - **Assignment 1**: [Explore Hopfield Networks](https://github.com/ContextLab/memory-models-course/tree/main/assignments/Assignment%201%3A%20Hopfield%20Networks)
 
 
-# Weeks 2--3: Free recall, Short Term and Long Term Memory
+## Weeks 2--3: Free recall, Short Term and Long Term Memory
   - Discussions:
     - free recall and memory search
     - naturalistic memory tasks
@@ -25,7 +27,7 @@
   - **Assignment 2**: [Build the Search of Associative Memory Model](https://github.com/ContextLab/memory-models-course/tree/main/assignments/Assignment%202%3A%20Search%20of%20Associative%20Memory%20Model)
 
 
-# Weeks 4--5: Temporal Context and Multi-Timescale Models
+## Weeks 4--5: Temporal Context and Multi-Timescale Models
 - Discussion: the temporal scales of memory, event boundaries, and situation models
 - Readings:
   - [Howard and Kahana (2002)](https://www.dropbox.com/scl/fi/yjnusbmoixbf4aen1mkx8/HowaKaha02.pdf?rlkey=ktt245cw09szubjnoe4cco1tz&dl=1)
@@ -40,30 +42,30 @@
   - [Brunec et al. (2018)](https://www.dropbox.com/scl/fi/1eu28rpwyp8eg2sn4fgau/BrunEtal18b.pdf?rlkey=64dnn3onc90o59fuv33peil6g&dl=1)
 - **Assignemnt 3**: [Build the Context Maintenance and Retrieval Model](https://github.com/ContextLab/memory-models-course/tree/main/assignments/Assignment%203%3A%20Context%20Maintenance%20and%20Retrieval%20Model)
 
-# Week 6--7: Laplace Transforms
+## Week 6--7: Laplace Transforms
 - Discussion: is TCM *really* multi-timescale?
 - Discussion: Introduction to the Laplace Transform (and its inverse) and its relevance to memory
 - Readings:
   - [Shankar and Howard (2012)](https://www.dropbox.com/scl/fi/cqh37rsdn11f6egdiskvf/ShanHowa12.pdf?rlkey=45qhdi5u2fmlxd4azq8is3j89&dl=1)
   - [Manning (2024)](https://www.dropbox.com/scl/fi/9amk5mlgeop0srtpwqesg/Mann23.pdf?rlkey=lc785xhq1pcjqdtarn692e21k&dl=1)
 - **Assignment 4**: [Implement the Laplace Temporal Context Model](https://github.com/ContextLab/memory-models-course/tree/main/assignments/Assignment%204%3Laplace%20Temporal%20Context%20Model)
 
-# Week 8: Biologically Inspired Network Models
+## Week 8: Biologically Inspired Network Models
 - Discussion: what does "biologically inspired" mean in practice?
 - Readings:
   - [McClelland et al. (1995)](https://imss-www.upmf-grenoble.fr/prevert/MasterICA/SpecialiteSC/FichiersPDF/Why%20there%20are%20complementary%20learning%20systems%20in%20the%20hippocampus%20and%20neocortex%20insights%20from%20th.pdf)
   - [Rumelhart et al. (1986)](http://www.cs.toronto.edu/~fritz/absps/pdp2.pdf)
   - [O'Reilly and Norman (2002)](http://www.princeton.edu/~compmem/normorei02.pdf)
   - [Schapiro et al. (2017)](https://www.dropbox.com/scl/fi/no2647c2witr2knb76gs2/SchaEtal17.pdf?rlkey=bpon63fy8g2rl3y9csabq748o&dl=1)
 
-# Week 9: Recurrent networks, LSTM networks, Transformers
+## Week 9: Recurrent networks, LSTM networks, Transformers
 - Readings:
   - [Schuster and Paliwal (1997)](https://www.dropbox.com/scl/fi/0guahq2kcbria108xyb9j/SchuPali97.pdf?rlkey=yp1a8272qhljeob68amdpxjki&dl=1)
   - [Hochreiter and Schmidhuber (1997)](https://deeplearning.cs.cmu.edu/S23/document/readings/LSTM.pdf)
   - [Radford et al. (2019)](https://insightcivic.s3.us-east-1.amazonaws.com/language-models.pdf)
     - Tutorial video: [Let's build GPT: from scratch, in code, spelled out](https://www.youtube.com/watch?v=kCc8FmEb1nY)
 - **Assignment 5**: [Final Project](https://github.com/ContextLab/memory-models-course/tree/main/assignments/Final%20Project)
 
-# Week 10: Final project presentations
+## Week 10: Final project presentations
 - Discussion: ad-hoc discussions and demos of final projects
 - **Final projects are due on the last day of class at 11:59PM Eastern Time**

environment.yml

@@ -0,0 +1,113 @@
+name: ccm_course
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - bzip2=1.0.8
+  - ca-certificates=2022.9.24
+  - libffi=3.4.2
+  - libsqlite=3.40.0
+  - libzlib=1.2.13
+  - ncurses=6.3
+  - openssl=3.0.7
+  - pip=22.3.1
+  - python=3.11.0
+  - readline=8.1.2
+  - setuptools=65.5.1
+  - tk=8.6.12
+  - tzdata=2022f
+  - wheel=0.38.4
+  - xz=5.2.6
+  - pip:
+    - accessible-pygments==0.0.5
+    - alabaster==0.7.16
+    - appnope==0.1.4
+    - asttokens==3.0.0
+    - attrs==25.3.0
+    - babel==2.17.0
+    - beautifulsoup4==4.13.3
+    - certifi==2025.1.31
+    - charset-normalizer==3.4.1
+    - click==8.1.8
+    - comm==0.2.2
+    - debugpy==1.8.13
+    - decorator==5.2.1
+    - docutils==0.21.2
+    - executing==2.2.0
+    - fastjsonschema==2.21.1
+    - greenlet==3.1.1
+    - idna==3.10
+    - imagesize==1.4.1
+    - importlib-metadata==8.6.1
+    - ipykernel==6.29.5
+    - ipython==9.0.2
+    - ipython-pygments-lexers==1.1.1
+    - jedi==0.19.2
+    - jinja2==3.1.6
+    - jsonschema==4.23.0
+    - jsonschema-specifications==2024.10.1
+    - jupyter-book==1.0.4.post1
+    - jupyter-cache==1.0.1
+    - jupyter-client==8.6.3
+    - jupyter-core==5.7.2
+    - latexcodec==3.0.0
+    - linkify-it-py==2.0.3
+    - markdown-it-py==3.0.0
+    - markupsafe==3.0.2
+    - matplotlib-inline==0.1.7
+    - mdit-py-plugins==0.4.2
+    - mdurl==0.1.2
+    - myst-nb==1.2.0
+    - myst-parser==3.0.1
+    - nbclient==0.10.2
+    - nbformat==5.10.4
+    - nest-asyncio==1.6.0
+    - packaging==24.2
+    - parso==0.8.4
+    - pexpect==4.9.0
+    - platformdirs==4.3.7
+    - prompt-toolkit==3.0.50
+    - psutil==7.0.0
+    - ptyprocess==0.7.0
+    - pure-eval==0.2.3
+    - pybtex==0.24.0
+    - pybtex-docutils==1.0.3
+    - pydata-sphinx-theme==0.15.4
+    - pygments==2.19.1
+    - python-dateutil==2.9.0.post0
+    - pyyaml==6.0.2
+    - pyzmq==26.3.0
+    - referencing==0.36.2
+    - requests==2.32.3
+    - rpds-py==0.23.1
+    - six==1.17.0
+    - snowballstemmer==2.2.0
+    - soupsieve==2.6
+    - sphinx==7.4.7
+    - sphinx-book-theme==1.1.4
+    - sphinx-comments==0.0.3
+    - sphinx-copybutton==0.5.2
+    - sphinx-design==0.6.1
+    - sphinx-external-toc==1.0.1
+    - sphinx-jupyterbook-latex==1.0.0
+    - sphinx-multitoc-numbering==0.1.3
+    - sphinx-thebe==0.3.1
+    - sphinx-togglebutton==0.3.2
+    - sphinxcontrib-applehelp==2.0.0
+    - sphinxcontrib-bibtex==2.6.3
+    - sphinxcontrib-devhelp==2.0.0
+    - sphinxcontrib-htmlhelp==2.1.0
+    - sphinxcontrib-jsmath==1.0.1
+    - sphinxcontrib-qthelp==2.0.0
+    - sphinxcontrib-serializinghtml==2.0.0
+    - sqlalchemy==2.0.39
+    - stack-data==0.6.3
+    - tabulate==0.9.0
+    - tornado==6.4.2
+    - traitlets==5.14.3
+    - typing-extensions==4.12.2
+    - uc-micro-py==1.0.3
+    - urllib3==2.3.0
+    - wcwidth==0.2.13
+    - zipp==3.21.0
+prefix: /Users/peerherholz/anaconda3/envs/ccm_course