changes

.gitignore

@@ -1,7 +1,7 @@
 **.DS_Store
 
 # temp jupyter notebook used for quarto jupyter execution
-.quarto_ipynb
+**.quarto_ipynb
 
 /.quarto/
 _site/

DESCRIPTION_temp

@@ -0,0 +1,4 @@
+# notes for package we installed
+
+- RMarkdown
+- here

Makefile

@@ -8,6 +8,7 @@ render:
 
 setup_python_venv:
 	pip freeze | xargs pip uninstall -y
+	pip install --upgrade pip
 	pip install -r requirements.txt
 	pip freeze > requirements_snapshot.txt
 

_quarto.yml

@@ -1,9 +1,27 @@
 project:
   type: website
+  preview:
+    port: 54321
+    browser: true
 
 website:
   title: "DSCI 521: Computing Platforms for Data Science"
+  site-url: https://ubc-mds.github.io/DSCI_521_platforms-dsci_book/
+  issue-url: https://github.com/UBC-MDS/DSCI_521_platforms-dsci_book/issues/new
+  repo-actions: [edit, source, issue]
+  google-analytics: "G-1RNLL8GPXK"
+  open-graph: true
+  twitter-card: true
+  page-navigation: true
+  bread-crumbs: true
+  search:
+    show-item-context: true
+    type: overlay
   navbar:
+    right:
+      - icon: github
+        href: https://github.com/UBC-MDS/DSCI_521_platforms-dsci_book
+        aria-label: GitHub
     left:
       - href: index.qmd
         text: Home
@@ -16,27 +34,52 @@ website:
     style: "docked"
     search: true
     contents:
-      - text: "Lecture 0a: JupyterLab Orientation"
-        href: lectures/0-jupyterlab-orientation-intro.qmd
-      - text: "Lecture 0b: RStudio Orientation"
-        href: lectures/0-rstudio-orientation-intro.qmd
-      - text: "Lecture 1: Introduction to MDS software and Bash"
-        href: lectures/1-MDStools-bash-filesystem.qmd
-      - text: "Lecture 2: Introduction to version control with Git and GitHub"
-        href: lectures/2-git-github-ssh-basic-workflow.qmd
-      - text: "Lecture 3: Getting grovy with Git and GitHub"
-        href: lectures/3-git-history-merge-conflicts-stash.qmd
-      - text: "Lecture 4: Introduction to Quarto and Github Pages"
-        href: lectures/4-quarto_github_pages.qmd
-      - text: "Lecture 5: Dynamic documents: from markdown to Rmarkdown documents"
-        href: lectures/5-rstudio-projects-notebooks.qmd
-      - text: "Lecture 6: Quarto, RMarkdown, and Jupyter Slides"
-        href: lectures/6-rmarkdown-quarto-slides-ghpages.qmd
-      - text: "Lecture 7: Virtual environments"
-        href: lectures/7-virtual-environments.qmd
-      - text: "Lecture 8: Organization of Data Science projects and some useful tools"
-        href: lectures/8-regex-filenames-project-organization.qmd
 
+      - section: "Orientation"
+        contents:
+          - text: "Lecture 0a: JupyterLab Orientation"
+            href: lectures/0-jupyterlab-orientation-intro.qmd
+          - text: "Lecture 0b: RStudio Orientation"
+            href: lectures/0-rstudio-orientation-intro.qmd
+
+      - section: "Lectures"
+        contents:
+          - text: "Lecture 1: Introduction to MDS software and Bash"
+            href: lectures/1-MDStools-bash-filesystem.qmd
+
+          - text: "Lecture 2: Introduction to version control with Git and GitHub"
+            href: lectures/2-git-github-ssh-basic-workflow.qmd
+
+          - text: "Lecture 3: Git: History, Conflicts, and Ignores"
+            href: lectures/3-git-history-merge-conflicts-stash.qmd
+
+          - text: "Lecture 4: Introduction to Quarto and Github Pages"
+            href: lectures/4-quarto_github_pages.qmd
+
+          - text: "Lecture 5: RStudio Projects and Literate Programming Documents"
+            href: lectures/5-rstudio-projects-notebooks.qmd
+
+          - text: "Lecture 6: Quarto, RMarkdown, and Jupyter Slides"
+            href: lectures/6-rmarkdown-quarto-slides-ghpages.qmd
+
+          - text: "Lecture 7a: Virtual environments: conda"
+            href: lectures/7a-virtual-environments-conda.qmd
+          - text: "Lecture 7b: Virtual environments: renv"
+            href: lectures/7b-virtual-environments-renv.qmd
+
+          - text: "Lecture 8a: Organization of Data Science projects"
+            href: lectures/8-regex-filenames-project-organization.qmd
+          - text: "Lecture 8b: Introduction to Regular Expressions (RegEx)"
+            href: lectures/8b-regex.qmd
+
+      - section: "Appendix"
+        contents:
+          - text: "Git Configuration"
+            href: appendix/git_config.qmd
+          - text: "RStudio Configuration"
+            href: appendix/rstudio_config.qmd
+          - text: "Semantic Line Breaks"
+            href: appendix/semantic_line_breaks.qmd
 
 format:
   html:

appendix/git_config.qmd

@@ -0,0 +1,90 @@
+---
+title: "Git Configuration"
+---
+
+A short list of commands for git setup from the installation instructions
+and other settings to get goit working from the course
+
+Configure your git commit messages (User and Email)
+
+Use your email for github.com (not ubc github)
+
+```
+git config --global user.name ""
+git config --global user.email ""
+```
+
+SSH keys
+
+```
+sudo systemctl enable teamviewerd
+```
+
+Edit `~/.ssh/config`
+
+::: {.panel-tabset}
+
+## MacOS + *nix
+
+```
+Host github.com
+  AddKeysToAgent yes
+  UseKeychain yes
+  IdentityFile ~/.ssh/id_ed25519
+
+Host github.ubc.ca
+  AddKeysToAgent yes
+  UseKeychain yes
+  IdentityFile ~/.ssh/id_ed25519
+```
+
+
+## Git Bash (Windows)
+
+```
+Host github.com
+  AddKeysToAgent yes
+  IdentityFile ~/.ssh/id_ed25519
+
+Host github.ubc.ca
+  AddKeysToAgent yes
+  IdentityFile ~/.ssh/id_ed25519
+```
+:::
+
+
+Use your `~/.ssh/id_ed25519.pub` file and copy paste the contents to register your SSH key
+in **BOTH** the `github.com` and `github.ubc.ca` repositories
+
+## Git pull merge option
+
+If you push and try to pull with changes in the repote,
+you need to tell git how to reconsize the differences
+
+You may see this
+
+```
+hint: You have divergent branches and need to specify how to reconcile them.
+hint: You can do so by running one of the following commands sometime before
+hint: your next pull:
+hint:
+hint:   git config pull.rebase false  # merge
+hint:   git config pull.rebase true   # rebase
+hint:   git config pull.ff only       # fast-forward only
+hint:
+hint: You can replace "git config" with "git config --global" to set a default
+hint: preference for all repositories. You can also pass --rebase, --no-rebase,
+hint: or --ff-only on the command line to override the configured default per
+hint: invocation.
+fatal: Need to specify how to reconcile divergent branches.
+```
+
+We will use the old git default setting of `rebase false` (the first option).
+
+You can do this as a repo specific setting or as a global setting (add a `--global` flag)
+like you did with `user.name` and `user.email`
+
+- Repo setting: `git config pull.rebase false`
+- Global: `git config --global pull.rebase false`
+
+THen you can `pull` again, where you may or may not see a merge conflict.

appendix/rstudio_config.qmd

@@ -0,0 +1,39 @@
+---
+title: "RStudio Configuration"
+---
+
+## Global Setup
+
+In the `Tools` > `Global Options` > `General` Tab,
+you want to uncheck the boxes that open previous files and projects,
+and also make sure that no `.RData` is saved when you quit RStudio,
+and to never save the `.RData`
+(this prevents RStudio from loading up previous data when you open it,
+it does not refer to its ability to load and save data as you use it).
+
+![](../lectures/img/rstudio-global_options-general.png)
+
+## LaTeX and XeLaTeX
+
+In the `Sweave` option
+
+change the `Sweave` option to `Knitr`,
+and `pdflatex` to `xelatex`.
+
+
+
+
+## Code snippets
+
+As we started to type `for` above,
+the code completion popped up
+and the first entry said "snippet",
+what is that?
+A code snippet is a text macro,
+which means that you can type a short string of characters
+to insert a template or snippet of text by pressing <kbd>TAB</kbd>.
+You can see all the default snippets
+and define your own by going to
+`Tools -> Global options -> Code -> Edit snippets`.
+Snippets are available anywhere in RStudio,
+not just in R Markdown documents.

appendix/semantic_line_breaks.qmd

@@ -0,0 +1,75 @@
+---
+title: "Semantic Line Breaks"
+---
+
+> Most documents go through several versions (always more than you expected) before they are finally finished. Accordingly, you should do whatever possible to make the job of changing them easy.
+>
+> First, when you do the purely mechanical operations of typing, type so subsequent editing will be easy. Start each sentence on a new line. Make lines short, and break lines at natural places, such as after commas and semicolons, rather than randomly. Since most people change documents by rewriting phrases and adding, deleting and rearranging sentences, these precautions simplify any editing you have to do later.
+>
+> — Brian W. Kernighan, 1974 [9]
+
+
+Semantic line breaks utilize how markdown treats line breaks and tries to combine it
+with regular prose text.
+You can read more about semantic line breaks here: <https://sembr.org/>
+
+Here are examples of how it works with markdown syntax
+
+
+```markdown
+this is a very long line that has over 80 characterslasdfja asldfja sljf lsd jflkadjsf
+```
+
+is rendered as:
+
+this is a very long line that has over 80 characterslasdfja asldfja sljf lsd jflkadjsf
+
+
+```markdown
+this is a very long line that has
+over 80 characterslasdfja asldfja
+sljf lsd jflkadjsf
+```
+
+is rendered as:
+
+this is a very long line that has
+over 80 characterslasdfja asldfja
+sljf lsd jflkadjsf
+
+
+### Add a line break
+
+Markdown allows 2 spaces at the end of a line for a line break
+
+```markdown
+this is a very long line that has<br/>
+over 80 characterslasdfja asldfja<br/>
+sljf lsd jflkadjsf
+```
+
+this is a very long line that has<br/>
+over 80 characterslasdfja asldfja<br/>
+sljf lsd jflkadjsf
+
+Markdown also allows 2 spaces at the end of a line for a line break.
+THis may not work with many text editor options that strip trailing white space
+
+
+### Add an empty line for a paragraph break
+
+```markdown
+this is a very long line that has
+
+over 80 characterslasdfja asldfja
+
+sljf lsd jflkadjsf
+```
+
+Rendered as:
+
+this is a very long line that has
+
+over 80 characterslasdfja asldfja
+
+sljf lsd jflkadjsf

learning_objectives/lo-ch-05.qmd

@@ -1,7 +1,7 @@
-1. Create RProjects in Rstudio using `here` to define robust file paths.
-2. Detect the basic components of a dynamic document in Jupyter Notebooks and in R Markdown
-3. Explain markdown usage in relation to dynamic documents
-4. Differentiate between code chunks and code cells in Rmarkdown and Jupyter Notebooks.
-5. Select appropiate code chunk options for RMarkdown.
-6. Use semantic line breaks for version control files
-7. Specify metadata in the YAML header block
+1. Create RProjects in RStudio using `here` to define robust file paths.
+2. Detect the basic components of a dynamic document in Jupyter Notebooks and in R Markdown.
+3. Explain markdown usage in relation to dynamic documents.
+4. Differentiate between code chunks and code cells in RMarkdown and Jupyter Notebooks.
+5. Select appropriate code chunk options for RMarkdown.
+6. Use semantic line breaks for version control files.
+7. Specify metadata in the YAML header block.

learning_objectives/lo-ch-06.qmd

@@ -1,4 +1,4 @@
-1. Understand how Quarto extend RMarkdown documents functionalities.
+1. Understand how Quarto extend R Markdown documents functionalities.
 2. Explore different data science products to communicate your results: slides, blogs and books.
 3. Create slides using Jupyter Notebook and Quarto slides with `reveal.js`
 4. Create a Jupyter Book and a Quarto books.

lectures/0-jupyterlab-orientation-intro.qmd

@@ -7,6 +7,8 @@ jupyter: python3
 
 {{< include ../learning_objectives/lo-ch-00.qmd >}}
 
+**Platform in focus** Jupyter Lab
+
 ## What is JupyterLab
 
 The most rudimentary interaction with programming languages

lectures/0-rstudio-orientation-intro.qmd

@@ -6,6 +6,8 @@ title: "RStudio Orientation"
 
 {{< include ../learning_objectives/lo-ch-00-rstudio.qmd >}}
 
+**Platform in focus** RStudio IDE
+
 ## What is RStudio
 
 RStudio is another integrated development environment (IDE),
@@ -38,7 +40,7 @@ you can run RStudio as a desktop application.
 
 ## RStudio Panes
 
-RStudio follows a "four-pane datascience" IDE view:
+RStudio follows a "four-pane data science" IDE view:
 
 1. Editor: Where you will type your code and work with other source documents
 2. Environment: Contains the variables in your current session

lectures/1-MDStools-bash-filesystem.qmd

@@ -7,6 +7,8 @@ jupyter: python3
 
 {{< include ../learning_objectives/lo-ch-01.qmd >}}
 
+**Platform in focus** BASH
+
 ## Introduction
 
 Welcome to Computer Platforms in Data Science!
@@ -360,7 +362,7 @@ Which command would move you to the parent directory?
 
 ```
 A. cd .
-B. cd .. 
+B. cd ..
 C. cd ~
 D. cd
 ```