From b540c2d5c1065399b1a26100e94fc0fd5ac68df7 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 21:35:15 -0400
Subject: [PATCH 01/16] Add SF100 slide authors

---
 theme2/SF100/slides.css | 4 ++++
 theme2/SF100/slides.md  | 7 +++++++
 2 files changed, 11 insertions(+)

diff --git a/theme2/SF100/slides.css b/theme2/SF100/slides.css
index d21de85..14372fe 100644
--- a/theme2/SF100/slides.css
+++ b/theme2/SF100/slides.css
@@ -13,3 +13,7 @@
     display: inline-block;
     margin: 0 20px 0 0;
 }
+
+#title-slide .author {
+    font-size: x-large;
+}
diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 90c5342..0b5a74a 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -4,6 +4,13 @@ subtitle: "Linux, command line, scripting"
 # author: "X-CITE 2024 workshop"
 # subtitle: "X-CITE 2024 workshop"
 # author: "Sajith Sasidharan"
+
+author:
+  - name: Anirban Mandal, Erik Scott, Sajith Sasidharan (RENCI, UNC Chapel Hill)
+  - name: Ewa Deelman, Karan Vahi, Mats Rynge (ISI, USC)
+  - name: Matthew Miller, Werner Sun, Peter Ko, Kelly Nygren, Keara Soloway, Rolf Verberg (CHESS, Cornell)
+  - name: Brandon Sorge (IUPUI)
+
 date: 2024-06-05
 
 code-annotations: hover

From 0963a4a0bcb436bddadbd72045b70ce7c5bf43be Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 21:39:11 -0400
Subject: [PATCH 02/16] Hide the date for now

That authors list needs some breathing room
---
 theme2/SF100/slides.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 0b5a74a..2072c44 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -11,7 +11,7 @@ author:
   - name: Matthew Miller, Werner Sun, Peter Ko, Kelly Nygren, Keara Soloway, Rolf Verberg (CHESS, Cornell)
   - name: Brandon Sorge (IUPUI)
 
-date: 2024-06-05
+# date: 2024-06-05
 
 code-annotations: hover
 

From 24aa0e55dca33c5952b029a581f15c960f870aa3 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 21:42:21 -0400
Subject: [PATCH 03/16] Add preliminary bullets

---
 theme2/SF100/slides.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 2072c44..279875f 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -43,7 +43,10 @@ format:
 
 # Preliminaries
 
-Getting into CLASSE Linux systems
+- Who are you people?
+- <https://xcitecourse.org/theme2/sf100/>
+- Getting into CLASSE Linux systems
+
 
 ## Assumptions
 

From caec2ee19c2540841ce9051b46c01d9fa442f05c Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 21:45:24 -0400
Subject: [PATCH 04/16] Add notes under preliminaries

---
 theme2/SF100/slides.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 279875f..ce0ffff 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -47,6 +47,17 @@ format:
 - <https://xcitecourse.org/theme2/sf100/>
 - Getting into CLASSE Linux systems
 
+::: {.notes}
+
+- I do not have a good idea about the audience of this workshop.  What
+  is your background?
+- Do you know how to launch a terminal?
+- Do you know use ssh?
+- Do you use JupyterLab?
+- Do you use command line?  
+- Do you use Windows, macOS, or Linux?
+
+:::
 
 ## Assumptions
 

From 617b09609c47b2423ec3f029d55ca80b898938ca Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 21:50:39 -0400
Subject: [PATCH 05/16] What are paths?

---
 theme2/SF100/slides.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index ce0ffff..d223bc1 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -264,7 +264,7 @@ Unix slogan: Everything is a file!
 ::: {.notes}
 
 - Directories and files are organized in a tree like structure.
-- Well, and inverted tree.
+- Well, an inverted tree, maybe.
 - At the bottom (or top?), you have the "/" directory.
 
 :::
@@ -316,6 +316,8 @@ Unix slogan: Everything is a file!
 
 ## Absolute and relative paths
 
+File/folder names are also referred to as **paths**.
+
 - **Absolute path names** begin with the root directory, `/`.
    - Example: `/home/ssasidharan/Documents/hello.txt`
 

From 07bfb4051fdfefc3fba2080acc9294065648ef46 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:03:48 -0400
Subject: [PATCH 06/16] List some helpful commands

---
 theme2/SF100/slides.md | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index d223bc1..9eec7ca 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -227,6 +227,20 @@ of macOS, fish, ksh, etc.
 Unix slogan: Everything is a file!
 
 
+## Some helpful commands {.smaller .scrollable}
+
+| Command | Task                                                      | Example Syntax                  |
+|---------|-----------------------------------------------------------|---------------------------------|
+| `ls`    | list the files in a directory                             | `ls [/tmp]`                     |
+| `cd`    | move into a directory                                     | `cd [/tmp]`                     |
+| `pwd`   | show cuurent working directory                            | `pwd`                           |
+| `cp`    | copy a file to another filename or into another directory | `cp [file.txt] [/tmp/file.txt]` |
+| `mv`    | rename or move a file into another directory              | `mv [file.txt] [file1.txt]`     |
+| `rm`    | delete a file                                             | `rm [file.txt]`                 |
+| `mkdir` | create a directory                                        | `mkdir [dir]`                   |
+| `rm -r` | remove a directory                                        | `rm -r [dir]`                   |
+
+
 ## Directory navigation
 
 ```{.bash}
@@ -328,7 +342,7 @@ File/folder names are also referred to as **paths**.
 ## Some fun facts about file names
 
 - Names that begin with "." are "hidden".
-  - Omitted from directory listing when you do `ls`.
+  - They are omitted from directory listing when you do `ls`.
   - Do `ls -a` (or `ls --all`) to list them.
 
 - `.` and `..` are special directory names.

From 5bb8279bf8e9a248464901fd1bb84bbbd33a016a Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:04:14 -0400
Subject: [PATCH 07/16] Remove commented cruft

---
 theme2/SF100/slides.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 9eec7ca..e1c409b 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -220,8 +220,6 @@ of macOS, fish, ksh, etc.
 
 :::
 
-<!-- ## Environment variables -->
-
 # Files and directories
 
 Unix slogan: Everything is a file!

From 07de2c5281e724c36b4e0862283e7f69df2b72dc Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:11:49 -0400
Subject: [PATCH 08/16] Mention shell history and completion

---
 theme2/SF100/slides.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index e1c409b..14cf8f1 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -220,6 +220,16 @@ of macOS, fish, ksh, etc.
 
 :::
 
+## Bash niceties: history and completion
+
+- You do not have to re-type commands that you have used in the past!
+  - Use {{<kbd up>}} and {{<kbd down>}} arrow keys to go back and forth
+  in your command history.
+  - Use {{<kbd Ctrl-R>}} (Control+R) to "search" command history.
+  - Use `history` command to list your shell history.
+- Use {{<kbd tab>}} key for command completion, after typing a few
+  characters.
+
 # Files and directories
 
 Unix slogan: Everything is a file!

From 1dcfb0f2e66a27bedd1b351cd7ebb0eacf7b3433 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:12:32 -0400
Subject: [PATCH 09/16] Omit the wise quote

---
 theme2/SF100/slides.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 14cf8f1..ef79de5 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -323,7 +323,7 @@ Unix slogan: Everything is a file!
 
 ## The current working directory
 
-"Wherever you go, there you are"
+<!-- "Wherever you go, there you are" -->
 
 - At any time in the shell, you are "inside" a single directory,
   called the **current working directory**.

From 48360f99c327212ba2d3d5cfd8024898576ed9c5 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:14:37 -0400
Subject: [PATCH 10/16] Re-title

---
 theme2/SF100/slides.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index ef79de5..88efa8c 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -358,7 +358,7 @@ File/folder names are also referred to as **paths**.
   - `..` stands for the directory above the current directory.
   
   
-## More fun facts about file names
+## Some more fun facts about file names
   
 - File and directory names are case sensitive.
   - Depends on filesystem, but that is a detail.

From 2cebd971a762cba466c578bdc9c0ea65c8aa1b96 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:16:16 -0400
Subject: [PATCH 11/16] Make a note of top/htop

---
 theme2/SF100/slides.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 88efa8c..871c9b9 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -524,14 +524,17 @@ The four columns:
 - `TIME` is the elapsed CPU time for the process.
 - `CMD` is the command that created the process.
 
+::: {.notes}
 
 (Also see: `top` and `htop`.)
 
+:::
+
 ## Background and foreground processes
 
 - Some processes run in the foreground:
    - They read input, write output, etc.
-   - Attached to a terminal.
+   - They are "attached" to a terminal.
 - Background processes, well, run in the background.  Send things to
   the background with `&`:
 

From 0f651579e6d646440d71b726468bc276fa86dd27 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:21:55 -0400
Subject: [PATCH 12/16] Make a note about what you can kill

---
 theme2/SF100/slides.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 871c9b9..195aaed 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -530,7 +530,7 @@ The four columns:
 
 :::
 
-## Background and foreground processes
+## Background and foreground processes {.smaller}
 
 - Some processes run in the foreground:
    - They read input, write output, etc.
@@ -555,7 +555,8 @@ sleep 100
 ## Terminating processes
 
 - `kill PID` command to end one process.
-- `killall` command to end many processes
+- `killall` command to end many processes.
+  - You can't `kill` other user's processes.
 
 <!--
 

From a5ffc105f63cdcbfe95a04d48f7ed62462b58f6d Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:27:03 -0400
Subject: [PATCH 13/16] Update commands

---
 theme2/SF100/slides.md | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 195aaed..95f9b15 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -237,16 +237,17 @@ Unix slogan: Everything is a file!
 
 ## Some helpful commands {.smaller .scrollable}
 
-| Command | Task                                                      | Example Syntax                  |
-|---------|-----------------------------------------------------------|---------------------------------|
-| `ls`    | list the files in a directory                             | `ls [/tmp]`                     |
-| `cd`    | move into a directory                                     | `cd [/tmp]`                     |
-| `pwd`   | show cuurent working directory                            | `pwd`                           |
-| `cp`    | copy a file to another filename or into another directory | `cp [file.txt] [/tmp/file.txt]` |
-| `mv`    | rename or move a file into another directory              | `mv [file.txt] [file1.txt]`     |
-| `rm`    | delete a file                                             | `rm [file.txt]`                 |
-| `mkdir` | create a directory                                        | `mkdir [dir]`                   |
-| `rm -r` | remove a directory                                        | `rm -r [dir]`                   |
+| Command | Task                                                                        | Example Syntax                  |
+|---------|-----------------------------------------------------------------------------|---------------------------------|
+| `ls`    | list the files in a directory                                               | `ls [/tmp]`                     |
+| `cd`    | move into a directory                                                       | `cd [/tmp]`                     |
+| `pwd`   | show curent working directory                                               | `pwd`                           |
+| `cp`    | copy a file to into another directory, or make a copy with a different name | `cp [file.txt] [/tmp/file.txt]` |
+| `cp -r` | copy a folder to into another directory                                     | `cp [file.txt] [/tmp/file.txt]` |
+| `mv`    | rename or move a file into another directory                                | `mv [file.txt] [file1.txt]`     |
+| `rm`    | delete a file                                                               | `rm [file.txt]`                 |
+| `mkdir` | create a directory                                                          | `mkdir [dir]`                   |
+| `rm -r` | remove a directory, recursively                                             | `rm -r [dir]`                   |
 
 
 ## Directory navigation

From de95ed28b167f46bdade38c7a540f446a12a3fc0 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:31:04 -0400
Subject: [PATCH 14/16] Add notes

---
 theme2/SF100/slides.md | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 95f9b15..77811d5 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -654,8 +654,8 @@ BUT
   Commons license, and contains a good discussion about shell
   scripting.
 - [The Unix Programming Environment][tupe] by Brian W. Kernighan and
-  Rob Pike.  Good old classic, still useful.  Places things in a
-  historical context.
+  Rob Pike.  Old classic, still useful.  Places things in a historical
+  context.
 - [Shell Tools and Scripting][missing] module of MIT "The Missing
   Semester of Your CS Education" class.
 
@@ -669,3 +669,10 @@ BUT
 <https://xcitecourse.org/theme2/sf100/>
 
 Contributions are welcome!
+
+::: {.notes}
+
+- Report issues!
+- Send your pull requests!
+
+:::

From 7082807b014f7bcc0ebed2bc87d2fddf49883a68 Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:35:20 -0400
Subject: [PATCH 15/16] Update extra notes about scripting

---
 theme2/SF100/slides.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index 77811d5..cc34bae 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -615,15 +615,15 @@ echo "Hello $USER!"   # <3>
 
 Bash supports a programming language with:
 
-- Conditionals (with `if` statements)
-- Loops (with `for` and `while` statements)
-- Et cetera
-- Take a peek at `/etc/bashrc` for a taste
+- `if` statements
+- `for`, `while`, `until` statements
+- functions
+- et cetera.
+- Take a peek at `/etc/bashrc` and `$HOME/.bashrc` for a taste
 
 BUT
 
-- This is another topic, not really in scope of this presentation
-- We're likely out of time anyway
+- This is not really in scope of this presentation.
 
 
 ## Demo maybe? {visibility="hidden"}

From becc672265b93c2090654de08b435f3cde2e8a1f Mon Sep 17 00:00:00 2001
From: Sajith Sasidharan <sajith@renci.org>
Date: Tue, 4 Jun 2024 22:41:30 -0400
Subject: [PATCH 16/16] Add a note about the big bad internet

---
 theme2/SF100/slides.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
index cc34bae..f5e22b1 100644
--- a/theme2/SF100/slides.md
+++ b/theme2/SF100/slides.md
@@ -664,6 +664,13 @@ BUT
 [tupe]: https://archive.org/details/UNIXProgrammingEnvironment
 
 
+# Other resources 
+
+- The Internet is pretty great. Use it.
+- However: DO NOT trust everything you read on the Internet.
+  - Do not copy and paste commands from the Internet indiscriminately.
+  - Understand how things work, and then use it.
+
 # Fin!
 
 <https://xcitecourse.org/theme2/sf100/>