Updating the program

Author: gvegayon

_quarto.yml

@@ -0,0 +1,69 @@
+project:
+  type: book
+  output-dir: _book
+
+book:
+  title: "PHS 7045: Advanced Programming"
+  page-navigation: true
+  chapters:
+    - index.qmd
+    - part: "01 Git"
+      chapters:
+        - 01-git/slides.qmd
+        - 01-git/lab.qmd
+        - 01-git/hello-world.qmd
+        - 01-git/quarto.qmd
+    - part: "02 Essentials"
+      chapters:
+        - 02-essentials/slides.qmd
+        - 02-essentials/lab.qmd
+        - 02-essentials/01-essentialsSimulations.qmd
+    - part: "03 Debugging And Profiling"
+      chapters:
+        - 03-debugging-and-profiling/slides.qmd
+        - 03-debugging-and-profiling/lab.qmd
+    - part: "04 More Functions And Data Table"
+      chapters:
+        - 04-more-functions-and-datatable/slides.qmd
+        - 04-more-functions-and-datatable/lab.qmd
+        - 04-more-functions-and-datatable/homework.qmd
+    - part: "05 Cpp"
+      chapters:
+        - 05-cpp/slides.qmd
+        - 05-cpp/lab.qmd
+    - part: "06 Rcpp"
+      chapters:
+        - 06-rcpp/slides.qmd
+        - 06-rcpp/lab.qmd
+        - 06-rcpp/02-vectorizing-rcpp.qmd
+    - part: "07 Parallel Computing"
+      chapters:
+        - 07-parallel-computing/slides.qmd
+        - 07-parallel-computing/lab.qmd
+    - part: "09 Midterm"
+      chapters:
+        - 09-midterm/homework.qmd
+    - part: "10 Slurm Practice"
+      chapters:
+        - 10-slurm-practice/lab.qmd
+        - 10-slurm-practice/04-slurm.qmd
+    - part: "11 Slurm Week 1"
+      chapters:
+        - 11-slurm-week1/slides.qmd
+    - part: "12 Slurm Week 2"
+      chapters:
+        - 12-slurm-week2/slides.qmd
+        - 12-slurm-week2/12-slurm-hw.qmd
+    - part: "13 Rpkgs I"
+      chapters:
+        - 13-rpkgs-i/slides.qmd
+        - 13-rpkgs-i/lab.qmd
+    - part: "15 Autoreport"
+      chapters:
+        - 15-autoreport/slides.qmd
+        - 15-autoreport/README.qmd
+
+format:
+  html:
+    toc: true
+    number-sections: false

index.qmd

@@ -0,0 +1,5 @@
+---
+title: "PHS 7045: Advanced Programming"
+---
+
+{{< include _course-home.qmd >}}

pages.csv

@@ -1,37 +1,37 @@
-date,week,session,name,issue,link_text,link,source,extra
-8/25/26,1,Lecture,Intro classes AI (George),,"slides",01-git/slides.html,01-git/slides.qmd,
-8/27/26,1,Lab,How to use AI in the class (George),,"slides",01-git/slides.html,01-git/slides.qmd,
-9/1/26,2,Lecture,Intro to Git (Mui),,"slides",01-git/slides.html,01-git/slides.qmd,
-9/3/26,2,Lab,Intro to classes (Mui),,"lab",01-git/lab.html,01-git/lab.qmd,"+ [quarto](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/quarto.html) ([source](01-git/quarto.qmd))"
-9/8/26,2,Lecture,Functions and data.table,,"slides",04-more-functions-and-datatable/slides.html,04-more-functions-and-datatable/slides.qmd,"+ 02-essentials/slides.qmd"
-9/10/26,2,Lab,Functions and data.table,,"lab",04-more-functions-and-datatable/lab.html,04-more-functions-and-datatable/lab.qmd,"+ [Homework 2](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/homework.html) ([source](04-more-functions-and-datatable/homework.qmd))"
-9/15/26,3,Lecture,Debugging and profiling,,"slides",03-debugging-and-profiling/slides.html,03-debugging-and-profiling/slides.qmd,
-9/17/26,3,Lab,Debugging and profiling,,"lab",03-debugging-and-profiling/lab.html,03-debugging-and-profiling/lab.qmd,
-9/22/26,4,Lecture,Functions and data.table,,"slides",04-more-functions-and-datatable/slides.html,04-more-functions-and-datatable/slides.qmd,
-9/24/26,4,Lab,Functions and data.table,,"lab",04-more-functions-and-datatable/lab.html,04-more-functions-and-datatable/lab.qmd,""
-9/29/26,5,Lecture,Introduction to C++,,"slides",05-cpp/slides.html,05-cpp/slides.qmd,
-10/1/26,5,Lab,Introduction to C++,,"lab",05-cpp/lab.html,05-cpp/lab.qmd,
-10/6/26,6,Lecture,C++ in R,,"slides",06-rcpp/slides.html,06-rcpp/slides.qmd,
-10/8/26,6,Lab,C++ in R,,"lab",06-rcpp/lab.html,06-rcpp/lab.qmd,"Deliver a paragraph in abstract mode describing their projects for the midterm."
-10/13/26,7,Break,Fall Break,,,,,
-10/15/26,7,Break,Fall Break,,,,,
-10/20/26,8,Lecture,Parallel Computing,,"slides",07-parallel-computing/slides.html,07-parallel-computing/slides.qmd,
-10/22/26,8,Lab,Parallel Computing,,"lab",07-parallel-computing/lab.html,07-parallel-computing/lab.qmd,
-10/27/26,9,Lecture,Midterm project,,,,,
-10/29/26,9,Presentations,Midterm project,,"Homework 3",09-midterm/homework.html,09-midterm/homework.qmd,
-11/3/26,10,Lecture,UofU's CHPC,,"CHPC overview",10-chpc-week/chpc_overview.pdf,,"[Linux slides](10-chpc-week/IntroLinux-RClass.pdf), [using R slides](10-chpc-week/using_r_at_chpc.pdf), [Slurm slides](10-chpc-week/RClass-Slurm.pdf)"
-11/5/26,10,Lab,Slurm practice,,"lab",10-slurm-practice/lab.html,10-slurm-practice/lab.qmd,
-11/10/26,11,Lecture,Slurm,,"slides",11-slurm-week1/slides.html,11-slurm-week1/slides.qmd,
-11/12/26,11,Lab,Slurm,,,,,"+ Homework 4 (Slurm)"
-11/17/26,12,Lecture,More practice with slurm,,"slides",12-slurm-week2/slides.html,12-slurm-week2/slides.qmd,
-11/19/26,12,Lab,More practice with slurm,,"Homework 4",12-slurm-week2/12-slurm-hw.html,12-slurm-week2/12-slurm-hw.qmd,
-11/24/26,13,Lecture,R packages I,,"slides",13-rpkgs-i/slides.html,13-rpkgs-i/slides.qmd,
-11/26/26,13,Lab,R packages I,,"lab",13-rpkgs-i/lab.html,13-rpkgs-i/lab.qmd,
-12/1/26,14,Lecture,R packages II,,,,,
-12/3/26,14,Off,Thanksgiving recess,,,,,
-12/8/26,15,Lecture,Automatic Reports with GitHub Actions,,"slides",15-autoreport/slides.html,15-autoreport/slides.qmd,
-12/10/26,15,Lab,R packages II,,,,,
-12/15/26,16,Hybrid,Final Prep (Hackathon),,,,,
-12/17/26,16,Hybrid,Final Prep (Hackathon),,,,,
-12/22/26,17,Package,Final,,,,,
-12/24/26,17,Talk,Final,,Requirements,https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/02-final.html,,
+date,week,session,name,issue,link_text,link,source,extra,notes,who
+8/25/26,1,Lecture,Intro classes AI,,slides,01-git/slides.html,01-git/slides.qmd,,,George
+8/27/26,1,Lab,How to use AI in the class,,slides,01-git/slides.html,01-git/slides.qmd,,,George
+9/1/26,2,Lecture,Intro to Git,,slides,01-git/slides.html,01-git/slides.qmd,,,Mui
+9/3/26,2,Lab,Intro to classes,,lab,01-git/lab.html,01-git/lab.qmd,+ [quarto](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/quarto.html) ([source](01-git/quarto.qmd)),,Mui
+9/8/26,2,Lecture,Functional programming,,slides,04-more-functions-and-datatable/slides.html,04-more-functions-and-datatable/slides.qmd,#NAME?,,Mui
+9/10/26,2,Lab,Functional programming,,lab,04-more-functions-and-datatable/lab.html,04-more-functions-and-datatable/lab.qmd,+ [Homework 2](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/homework.html) ([source](04-more-functions-and-datatable/homework.qmd)),,Mui
+9/15/26,3,Lecture,Debugging and profiling,,slides,03-debugging-and-profiling/slides.html,03-debugging-and-profiling/slides.qmd,,Mui out,George
+9/17/26,3,Lab,Debugging and profiling,,lab,03-debugging-and-profiling/lab.html,03-debugging-and-profiling/lab.qmd,,Mui out,George
+9/22/26,4,Lecture,Introduction to C++,,slides,05-cpp/slides.html,05-cpp/slides.qmd,,,Mui
+9/24/26,4,Lab,Introduction to C++,,lab,05-cpp/lab.html,05-cpp/lab.qmd,,,Mui
+9/29/26,5,Lecture,C++ in R,,slides,06-rcpp/slides.html,06-rcpp/slides.qmd,,,George
+10/1/26,5,Lab,C++ in R,,lab,06-rcpp/lab.html,06-rcpp/lab.qmd,Deliver a paragraph in abstract mode describing their projects for the midterm.,,George
+10/6/26,6,Lecture,Parallel Computing,,slides,07-parallel-computing/slides.html,07-parallel-computing/slides.qmd,,,George
+10/8/26,6,Lab,Parallel Computing,,lab,07-parallel-computing/lab.html,07-parallel-computing/lab.qmd,,,George
+10/13/26,7,Break,Fall Break,,,,,,,
+10/15/26,7,Break,Fall Break,,,,,,,
+10/20/26,8,Lecture and Lab,Bonus Track 1: More on AI,,,,,,,"Mui, George"
+10/22/26,8,Lecture and Lab,Bunus Track 2: Ollama,,,,,,,"Mui, George"
+10/27/26,9,Lecture,Midterm project,,,,,,,"Mui, George"
+10/29/26,9,Lab,Midterm project,,Homework 3,09-midterm/homework.html,09-midterm/homework.qmd,,,"Mui, George"
+11/3/26,10,Lecture and Lab,UofU's CHPC intro,,CHPC overview,10-chpc-week/chpc_overview.pdf,,"[Linux slides](10-chpc-week/IntroLinux-RClass.pdf), [using R slides](10-chpc-week/using_r_at_chpc.pdf), [Slurm slides](10-chpc-week/RClass-Slurm.pdf)",,CHPC
+11/5/26,10,Lecture and Lab,UofU's CHPC coding agents,,lab,10-slurm-practice/lab.html,10-slurm-practice/lab.qmd,,,CHPC
+11/10/26,11,Lecture,Slurm,,slides,11-slurm-week1/slides.html,11-slurm-week1/slides.qmd,,,Mui
+11/12/26,11,Lab,More practice with slurm,,slides,12-slurm-week2/slides.html,12-slurm-week2/slides.qmd,,,George
+11/17/26,12,Lecture,R packages I,,slides,13-rpkgs-i/slides.html,13-rpkgs-i/slides.qmd,,Mui out,George
+11/19/26,12,Lab,R packages I,,lab,13-rpkgs-i/lab.html,13-rpkgs-i/lab.qmd,,Mui out,George
+11/24/26,13,Lecture,TBD,,,,,,,Mui
+11/26/26,13,Lab,Thanksgiving recess,,,,,,,
+12/1/26,14,Lecture,Automatic Reports with GitHub Actions,,slides,15-autoreport/slides.html,15-autoreport/slides.qmd,,,George
+12/3/26,14,Off,TBD,,,,,,,Mui
+12/8/26,15,Lecture,Final Prep (Hackathon),,,,,,,"Mui, George"
+12/10/26,15,Lab,Final Prep (Hackathon),,,,,,,"Mui, George"
+12/15/26,16,Lecture,Final,,,,,,,"Mui, George"
+12/17/26,16,Lecture,Final,,Requirements,https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/02-final.html,,,,"Mui, George"
+,,,,,,,,,,
+,,,,,,,,,,