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+
\ No newline at end of file
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diff --git a/theme2/SF100/commandline-slides.md b/theme2/SF100/commandline-slides.md
deleted file mode 100644
index 01f6e73..0000000
--- a/theme2/SF100/commandline-slides.md
+++ /dev/null
@@ -1,62 +0,0 @@
----
-title: "Commmandline and Scripting"
-# author: "Sajith Sasidharan"
-date: last-modified
-format:
- revealjs:
- theme: default
- output-file: commandline-slides-revealjs.html
- beamer:
- # aspectratio: 32
- # navigation: horizontal
- theme: default
----
-
-# Linux
-
-## The command line
-
-# The shell
-
-## Bash
-
-## Environment variables
-
-# Files and directories
-
-## Directory navigation
-
-## Wildcards
-
-## The current working directory
-
-## Fun facts about file names
-
-## Standard input, output, and error
-
-## I/O redirection
-
-## Pipes
-
-## Symbolic links
-
-# Users and Groups
-
-## Permissions and ownership
-
-## Changing permissions
-
-
-# Processes
-
-## Background and foreground processes
-
-## Terminating processes
-
-## Signals
-
-# Text editors
-
-# Shell Scripting
-
-# Terminal multiplexers
diff --git a/theme2/SF100/linux-commandline-scripting.md b/theme2/SF100/linux-commandline-scripting.md
index cc9bf4a..d09cf7d 100644
--- a/theme2/SF100/linux-commandline-scripting.md
+++ b/theme2/SF100/linux-commandline-scripting.md
@@ -1,4 +1,10 @@
-# Linux, Command Line, and Scripting
+---
+title: "Linux, Command Line, and Scripting"
+date: "2024-05-08"
+date-modified: last-modified
+aliases:
+ - "/theme2/SF100/"
+---
The following notes assume that you are all set up to use your
accounts on the CLASSE Linux systems.
@@ -21,8 +27,8 @@ systems.
Slides accompanying these notes are available in [HTML][html-slides]
and [PDF][pdf-slides] formats.
-[html-slides]: commandline-slides-revealjs.html
-[pdf-slides]: commandline-slides.pdf
+[html-slides]: slides.html
+[pdf-slides]: slides.pdf
:::
@@ -733,7 +739,7 @@ What if you want to discard `stdout` completely? You can redirect it
to the special file `/dev/null`:
```{.bash}
-[ssasidharan@lnx201 ~]$ ls -l >> ls-output.txt
+[ssasidharan@lnx201 ~]$ ls -l > /dev/null
```
If you want to append `stdout` to a file instead of overwriting it,
diff --git a/theme2/SF100/slides.css b/theme2/SF100/slides.css
new file mode 100644
index 0000000..241da68
--- /dev/null
+++ b/theme2/SF100/slides.css
@@ -0,0 +1,13 @@
+#org-logos {
+ display: flex;
+ align-items: center;
+ justify-content: center;
+}
+
+#org-logos img {
+ float: left;
+ width: 200px;
+ object-fit: cover;
+ display: inline-block;
+ margin: 0 20px 0 0;
+}
diff --git a/theme2/SF100/slides.md b/theme2/SF100/slides.md
new file mode 100644
index 0000000..b38b6d0
--- /dev/null
+++ b/theme2/SF100/slides.md
@@ -0,0 +1,490 @@
+---
+title: "The commmand-line"
+subtitle: "X-CITE 2024 workshop"
+# author: "Sajith Sasidharan"
+date: last-modified
+format:
+ revealjs:
+ theme: default
+ # output-file: commandline-slides-revealjs.html
+ footer: |
+
+
+ Supported by the NSF awards
+ [OAC-2320373](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2320373),
+ [OAC-2320374](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2320374),
+ and
+ [OAC-2320375](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2320375).
+
+ logo: ../../images/x-cite-logo-2.png
+
+ template-partials:
+ - title-slide.html
+ css:
+ - slides.css
+
+ pptx:
+ theme: default
+ slide-level: 2
+ reference-doc: ../../assets/reference.pptx
+
+ beamer:
+ # aspectratio: 32
+ # navigation: horizontal
+ theme: default
+ slide-level: 2
+ # logo: ../../images/x-cite-logo-2.png
+---
+
+# Preliminaries
+
+Getting into CLASSE Linux systems
+
+## Assumptions
+
+- You have your CLASSE accounts set up.
+ - Talk to CLASSE staff otherwise!
+
+- Options:
+
+ - Use ssh
+ - Use NoMachine
+ - Use JupyterLab
+
+
+## Use SSH
+
+
+
+`ssh ${username}@lnx201.classe.cornell.edu`
+
+
+## Use NoMachine
+
+
+
+
+
+
+## Use JupyterLab
+
+
+
+
+
+
+# Linux, command line, etc.
+
+## Linux
+
+- A popular operating system.
+ - (Actually an OS kernel, plus userland from various other projects.
+ But those are details...)
+- Unix-like, which traces back to 1969, therefore has accumulated
+ quirks.
+ - Expect "hysterical raisins".
+
+## `lnx201`
+
+- The Linux host we'll be using is `lnx201.classe.cornell.edu`.
+- Runs a **distribution** called Scientific Linux.
+- Good enough for general use.
+- Do not run anything resource heavy on `lnx201`.
+
+
+## The command line
+
+
+
+- You will type **commands** in a **shell**, hint
+ {{}} key, and then things happen.
+
+
+
+
+## Commands
+
+- Commands are either **programs** or **shell builtins**.
+- Use one of these commands to read documentation:
+
+ - `man ${command}`
+ - `info ${command}`
+ - or `${command} --help` (sometimes!)
+
+## The shell
+
+- A program that accepts commands, and passes those commands to the OS
+ to execute.
+- A popular shell is `bash`, which is the default on `lnx201`.
+
+
+## Bash
+
+- "Bourne-again shell"
+ - Based on an earlier Bourne shell, thus the "again".
+ - Developed by the [GNU project][gnu].
+ - On `lnx201`, `/bin/bash` is the program.
+- For documentation: `info bash` or `man bash`.
+
+[gnu]: http://gnu.org/
+
+
+
+
+# Files and directories
+
+Unix slogan: Everything is a file!
+
+
+## Directory navigation
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ tree -d -L 1 /
+/
+├── bin -> usr/bin
+├── boot
+├── cdat
+├── cifs
+├── cvmfs
+├── dev
+├── etc
+├── home
+├── lib -> usr/lib
+├── lib64 -> usr/lib64
+├── media
+├── misc
+├── mnt
+├── net
+├── nfs
+├── opt
+├── proc
+├── root
+├── run
+├── sbin -> usr/sbin
+├── srv
+├── sys
+├── tmp
+├── usr
+└── var
+
+25 directories
+```
+
+## Your home directory
+
+- You have a "home" directory.
+- Usually `/home/$USER`
+ - Also `$HOME`
+- You can write your files and create directories here.
+
+
+
+
+## The current working directory
+
+"Wherever you go, there you are"
+
+- At any time in the shell, you are "inside" a single directory,
+ called the **current working directory**.
+- When you log in, your current work will be `/home/${username}`.
+- You will use `cd` (change directory) to move around.
+- Use the command `pwd` to find where you are.
+
+
+## Absolute and relative paths
+
+- **Absolute path names** begin with the root directory, `/`.
+ - Example: `/home/ssasidharan/Documents/hello.txt`
+
+- **Relative paths** start with the working directory.
+ - Example: `./Documents/hello.txt` (or just `Documents/hello.txt`)
+ when I'm in my home directory.
+
+## Fun facts about file names
+
+- Names that begin with "." are "hidden".
+ - Omitted from directory listing when you do `ls`.
+
+- `.` and `..` are special directory names.
+ - `.` stands for the current directory.
+ - `..` stands for the directory above the current directory.
+
+
+## More fun facts about file names
+
+- File and directory names are case sensitive.
+ - (Depends on filesystem, but that is a detail.)
+- Better to avoid spaces in file names, because they are a hassle.
+ - Use `_` (underscore character) instead (example: `file_name`), or
+ CamelCase (example: `FileName`).
+
+## Wildcards
+
+Some characters are given special treatment:
+
+- `*` matches any set of characters.
+
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls /usr/bin/ab*
+/usr/bin/ab /usr/bin/abs2rel
+```
+
+- `?` matches any one character.
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls /usr/bin/?abc*
+/usr/bin/kabc2mutt /usr/bin/kabcclient
+```
+
+
+## Standard input, output, and error
+
+- Input is read from **standard input** (or `stdin`).
+- Output is written to **standard output** (or `stdout`).
+- Error messages are written to **standard error** (or `stderr`).
+
+::: {.callout-note}
+
+They are files too: `/dev/stdin`, `/dev/stdout`, and `/dev/stderr`.
+
+:::
+
+## I/O redirection
+
+You can redirect `stdout` to a file with `>` operator:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls -l > ls-output.txt
+```
+
+Or append with `>>`:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls -l >> ls-output.txt
+```
+
+To direct a file to a programs input, use `<` operator:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ cat < sonnet18.txt
+Shall I compare thee to a summer’s day?
+```
+
+
+## Pipes
+
+- Using the `|` ("pipe") operator, you can "chain" programs such that
+one programs output is another programs input:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls -l /bin/ | less
+```
+
+- You can create longer pipes:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ls /bin /sbin | sort | uniq | wc
+ 4289 4288 46820
+```
+
+
+
+
+# Users and Groups
+
+## You belong (to groups)
+
+Your account belongs to several groups:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ id
+uid=63499(ssasidharan) gid=262(chess) groups=262(chess),750(classeuser)
+[ssasidharan@lnx201 ~]$ groups
+chess classeuser
+```
+
+## Permissions and ownership
+
+Do a "long" file listing (with `ls -l`) and behold:
+
+```{.bash}
+$ ls -l
+total 8
+drwxr-xr-x 2 ssasidharan chess 44 May 8 10:42 bin
+drwxr-xr-x 2 ssasidharan chess 144 Mar 12 00:27 CLASSE_shortcuts
+drwxr-xr-x 2 ssasidharan chess 52 Apr 2 00:27 Desktop
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Documents
+lrwxrwxrwx 1 ssasidharan chess 31 Mar 26 15:21 Downloads -> /cdat/tem/ssasidharan/Downloads
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Music
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Pictures
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Public
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Templates
+drwxr-xr-x 2 ssasidharan chess 28 Apr 2 00:27 Videos
+```
+
+What do those characters mean?
+
+
+## Changing permissions
+
+- Use `chmod` command to change file mode bits (the first column in
+ the previous listing).
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ chmod +x test.sh
+[ssasidharan@lnx201 ~]$ ls -l test.sh
+-rwxr-xr-x 1 ssasidharan chess 0 Mar 28 13:39 test.sh
+[ssasidharan@lnx201 ~]$ chmod -x test.sh
+[ssasidharan@lnx201 ~]$ ls -l test.sh
+-rw-r--r-- 1 ssasidharan chess 0 Mar 28 13:39 test.sh
+```
+
+- Use `chown` and `chgrp` commands to change owner and group (the
+ third and fourth columns in the previous listing).
+ - Probably not immediately useful; just know that they exist.
+
+
+# Processes
+
+## Listing processes
+
+- List running processes using `ps` command:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ ps
+ PID TTY TIME CMD
+ 694411 pts/81 00:00:00 ps
+3479688 pts/81 00:00:00 bash
+```
+
+The four columns:
+
+- `PID` is process id.
+- `TTY` is the terminal associated with the process.
+- `TIME` is the elapsed CPU time for the process.
+- `CMD` is the command that created the process.
+
+
+(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.
+- Background processes, well, run in the background. Send things to
+ the background with `&`:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ sleep 100 &
+[1] 949751
+```
+
+- Bring a background process to foreground using `fg` command, and
+terminate it using {{}}:
+
+```{.bash}
+[ssasidharan@lnx201 ~]$ fg 2
+sleep 100
+^C
+```
+
+## Terminating processes
+
+- `kill PID` command to end one process.
+- `killall` command to end many processes
+
+
+
+# Other tools of the trade
+
+## Text editors
+
+Many choices! Use:
+
+- Emacs
+- Vim
+- Nano
+- JupyterLab
+
+
+## Terminal multiplexers
+
+
+
+
+# Shell scripts
+
+## Hello world!
+
+```{.bash filename=hello.sh code-line-numbers="true"}
+#! /bin/bash
+
+# A simple script.
+
+echo "Hello $USER!"
+```
+
+- Make the thing executable with `chmod +x hello.sh`
+- Run the thing with `./hello.sh`
+
+## Other things
+
+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
+
+BUT
+
+- This is another topic, not really in scope of this presentation
+- We're likely out of time anyway
+
+
+# Some resources
+
+# A cheat sheet
+
+[{height=600}](cheat-sheet.png)
+
+
+# Resources elsewhere
+
+- [Shell Tools and Scripting][missing] module of MIT "The Missing
+ Semester of Your CS Education" class.
+- [The Linux Command Line, A Complete Introduction][tlcl] by William
+ E. Shotts, Jr. The book is freely available under a Creative
+ 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.
+
+
+# Fin!
+
+[missing]: https://missing.csail.mit.edu/2020/shell-tools/
+[tlcl]: http://linuxcommand.org/tlcl.php
+[tupe]: https://archive.org/details/UNIXProgrammingEnvironment
diff --git a/theme2/SF100/title-slide.html b/theme2/SF100/title-slide.html
new file mode 100644
index 0000000..ed87dfa
--- /dev/null
+++ b/theme2/SF100/title-slide.html
@@ -0,0 +1,22 @@
+
+
+ 
+ 
+