Merge pull request #180 from ContextLab/feature/setup-script

Add CDL development environment setup scripts

Author: jeremymanning

compile.sh

@@ -4,4 +4,4 @@ latex -interaction=nonstopmode -halt-on-error lab_manual
 latex -interaction=nonstopmode -halt-on-error lab_manual
 latex -interaction=nonstopmode -halt-on-error lab_manual
 pdflatex -interaction=nonstopmode -halt-on-error lab_manual
-rm *.log *.aux *.fdb_latexmk *.fls *.idx *.ilg *.ind *.out *.bbl *.blg *.run.xml
+rm -f *.log *.aux *.fdb_latexmk *.fls *.idx *.ilg *.ind *.out *.bbl *.blg *.run.xml

lab_manual.pdf

@@ -6,6 +6,8 @@
 % This template has been downloaded from:
 % http://www.LaTeXTemplates.com
 %
+% Updated 2024-12-07: Added development environment setup section
+%
 % License:
 % CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
 %
@@ -864,6 +866,52 @@ \subsection{Authorship guidelines}
 feel you don't have the appropriate account type, please communicate
 your concerns to \director.
 
+\newthought{Setting up your development environment}
+\label{sec:dev-environment}
+
+\noindent To ensure all lab members have consistent development environments,
+we provide an automated setup script. The script installs standard applications
+and creates a Python environment with all necessary packages for lab research.
+
+\marginnote{\texttt{TASK:} Run the CDL setup script on your computer
+  by following the instructions below. Verify that all installations
+  complete successfully.}
+
+\textbf{To run the setup script:}
+
+\textit{On macOS or Linux:}
+\begin{verbatim}
+curl -fsSL https://raw.githubusercontent.com/
+  ContextLab/lab-manual/master/scripts/setup.sh | bash
+\end{verbatim}
+
+\textit{On Windows (PowerShell as Administrator):}
+\begin{verbatim}
+irm https://raw.githubusercontent.com/ContextLab/
+  lab-manual/master/scripts/setup.ps1 | iex
+\end{verbatim}
+
+\textbf{What the script installs:}
+\begin{itemize}
+\item \textbf{Applications:} Slack, VS Code, \LaTeX~distribution, Git, Dropbox
+\item \textbf{Python environment:} Miniconda with the \texttt{cdl} conda environment
+\item \textbf{Python packages:} NumPy, Pandas, PyTorch, Transformers, HyperTools,
+  Quail, timecorr, supereeg, and other lab-standard packages
+\end{itemize}
+
+\noindent After installation, activate the CDL environment with:
+\begin{verbatim}
+conda activate cdl
+\end{verbatim}
+
+\textbf{Getting help with setup issues:}
+\begin{itemize}
+\item For software or hardware issues: email \href{mailto:[email protected]}{[email protected]}
+\item For lab-specific issues: reach out to \director~via Slack or email
+\item For non-urgent questions or general interest problems:
+  file an issue at \url{https://github.com/ContextLab/lab-manual/issues}
+\end{itemize}
+
 \newthought{CITI training}
 
 \noindent Our lab studies human memory,
@@ -1966,6 +2014,10 @@ \chapter{Checklist and signature page}
   have also recompiled the PDF of the lab manual by running
   \texttt{pdflatex} \textbf{twice}, and have ensured that (a) the PDF compiled
   without errors, and (b) the table of contents was generated correctly.
+  \item I have run the CDL setup script (described in the
+  \hyperref[sec:dev-environment]{Setting up your development environment}
+  section) and verified that my development environment is correctly
+  configured.
   \item I have access to the following lab calendars:
     Contextual Dynamics Lab, Out of lab, CDL Resources, DHMC Meetings (if
     applicable), and PBS department events.

lab_manual.tex

@@ -0,0 +1,91 @@
+# CDL Conda Environment
+# Contextual Dynamics Laboratory, Dartmouth College
+#
+# This environment includes all packages needed for CDL research.
+#
+# To create this environment:
+#   conda env create -f cdl-environment.yml
+#
+# To update an existing environment:
+#   conda env update -n cdl -f cdl-environment.yml --prune
+#
+# To activate:
+#   conda activate cdl
+#
+
+name: cdl
+channels:
+  - conda-forge
+  - pytorch
+  - defaults
+
+dependencies:
+  # Python version
+  - python=3.11
+
+  # Core scientific computing
+  - numpy>=1.24
+  - scipy>=1.11
+  - pandas>=2.0
+  - polars>=0.19
+
+  # Visualization
+  - matplotlib>=3.7
+  - seaborn>=0.12
+
+  # Machine learning
+  - scikit-learn>=1.3
+
+  # PyTorch - will install appropriate version for platform (CPU/CUDA/MPS)
+  - pytorch>=2.0
+  - torchvision>=0.15
+  - torchaudio>=2.0
+
+  # Jupyter
+  - jupyter
+  - jupyterlab
+  - ipykernel
+  - ipywidgets
+
+  # Interactive plotting
+  - ipympl
+
+  # Utilities
+  - requests>=2.28
+  - tqdm
+  - joblib
+  - h5py
+  - pyyaml
+
+  # Development tools
+  - pytest
+  - pytest-cov
+
+  # Neuroimaging (lightweight dependencies)
+  - nibabel
+  - nilearn
+
+  # pip-installed packages
+  - pip
+  - pip:
+    # Dimensionality reduction
+    - umap-learn>=0.5
+
+    # Transformers and HuggingFace
+    - transformers>=4.30
+    - diffusers>=0.21
+    - datasets>=2.14
+    - huggingface-hub>=0.17
+    - accelerate>=0.24
+
+    # CDL packages
+    - hypertools>=0.8
+    - quail>=0.2
+    - timecorr>=0.1
+    - supereeg>=0.2
+
+    # Data storage
+    - deepdish>=0.3
+
+    # PPCA for hypertools
+    - ppca>=0.0.4