organize content

shifted around some things

getting_started.md

@@ -297,6 +297,47 @@ USERNAME@HOSTNAME    # Username and server address to login to
 ```
 You can then open your notebook server in your favorite web browser by navigating to http://127.0.0.1:8888/lab.
 
+````{dropdown} Optional
+## Configuring JupyterLab for HTTPS
+### Make jupyter password and `certfile` directory
+```bash
+mkdir -p ~/.jupyter/certfiles
+jupyter lab --generate-config
+jupyter lab password 
+```
+### Create your private (.key) and public key (.pem)
+Make sure to replace `HOSTNAME` with the machine you are on (i.e. z014).
+```bash
+openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
+  -keyout ~/.jupyter/certfiles/jupyter.key \
+  -out ~/.jupyter/certfiles/jupyter.pem \
+  -subj "/CN=HOSTNAME"
+chmod 600 ~/.jupyter/certfiles/jupyter.key
+```
+### Add config options to your `jupyter_server_conifg.py`
+Make sure to replace `HOSTNAME` with the machine you are on (i.e. z014) and `USERNAME` with your username.
+```python
+c.ServerApp.certfile = '/Users/USERNAME/.jupyter/certfiles/jupyter.pem'
+c.ServerApp.keyfile = '/Users/USERNAME/.jupyter/certfiles/jupyter.key'
+c.ServerApp.ip = 'HOSTNAME'
+c.ServerApp.port = 8888
+c.ServerApp.allow_remote_access = True
+c.ServerApp.password_required = True
+c.ServerApp.config_file = '/Users/USERNAME/.jupyter/jupyter_server_config.json'
+c.ServerApp.notebook_dir = '/data/GROUP/USERNAME'
+```
+Now start jupyter lab using your preferred method. [See Getting Started](getting_started.md) if you are unsure. Navigate to `https://127.0.0.1:8888/lab`. If this is you first time doing this, your browser may return a self-signed certificate warning. Ignore this error, and connect to the url. Now you can login using the password you made at the beginning.
+
+Defining our config options in `jupyter_server_config.py` allows you be less declarative when starting jupyter in the terminal. For example, when using singularity we can start jupyter lab with:
+```bash
+singularity exec --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics jupyter lab
+```
+As opposed to:
+```bash
+singularity exec --writable -B /data,/zata /zata/zippy/$(whoami)/bin/bioinformatics jupyter lab --port=8888 --ip=HOSTNAME --no-browser --notebook-dir=/data/GROUP/$(whoami)
+```
+````
+
 ## Common issues with JupyterLab
 ### Unable to delete files
 This is an issue that has come up before. To fix, you first need to find you jupyter config file. It will most likely be located at `/home/USERNAME/.jupyter`. First, change into that directory:

learning_resources.md

@@ -12,24 +12,31 @@ While there are many ways to go about this, here are some suggestions on how to
 
 Once you have a handle on the basics, I strongly advise moving on to learning specific python libraries (i.e. numpy, pandas, tensorflow, pytorch, etc). While continuing to gain proficiency in python itself is good, most of the work in our lab will exclusively involve certain libraries which have their own learning curves.
 > [DataCamp](https://app.datacamp.com/) is a great place to start learning these libraries (ask Zhiping for access), but as before -- chose whatever learning material best suits you!
+
 ## Command Line Basics
 First start with learning the basics of Linux [here](https://linuxjourney.com/). I suggest only completing the "Grasshopper" courses, as these cover most of what you need to know. After you've gotten a good grasp of the basics, then move on to learning bash scripting [here](https://exercism.org/tracks/bash). While bash scripting is useful, know when to grab for fully-featured programming language as you requirements become more complex.
 > [Bash Cheatsheet](https://devhints.io/bash)
+
 ## CLI Text Editor
 Sometime you may need to quickly edit a config file or make changes to you .bashrc file. In these cases, the quickest way is almost always to use a CLI text editor. 
+
 ### `vim`
 `vim` has more functionality and configurability. However, it notoriously has a steep learning curve. Here is [a good tutorial](https://github.com/iggredible/Learn-Vim/blob/master/ch00_read_this_first.md) if you are interested.
+
 ### A Quick `vim` Tutorial
+
 #### Basic Navigation
 - `h/j/k/l` - Move cursor left/down/up/right 
 - `w/b` - Jump forward/backward by word
 - `0/$` - Move to start/end of line
 - `gg/G` - Go to first/last line
+
 #### Modes
 - `i` - Enter insert mode before cursor
 - `a` - Enter insert mode after cursor
 - `ESC` or `CTRL+[` - Return to normal mode
 - `v` - Enter visual mode for selection
+
 #### Essential Commands
 - `:w` - Save file
 - `:q` - Quit (`:q!` to force quit without saving)
@@ -39,6 +46,7 @@ Sometime you may need to quickly edit a config file or make changes to you .bash
 - `dd` - Delete line
 - `yy` - Copy line
 - `p` - Paste after cursor
+
 #### Text Operations
 - `x` - Delete character
 - `dw` - Delete word
@@ -48,7 +56,9 @@ Sometime you may need to quickly edit a config file or make changes to you .bash
 - `:%s/old/new/g` - Replace all occurrences
 
 You can find a more in-depth tutorial [here](https://github.com/iggredible/Learn-Vim/blob/master/ch00_read_this_first.md) if you are interested.
+
 ## Version Control
+
 ### Git
 The official Git documentation includes a tutorial [here](https://git-scm.com/docs/gittutorial).
 

myst.yml

@@ -9,9 +9,8 @@ project:
   github: https://github.com/weng-lab/zlabwiki
   id: 8965acc4-b9cd-4f25-a3f5-2ca202b40f79
   toc:
-    # Auto-generated by `myst init --write-toc`
     - file: root.md
     - file: getting_started.md
-    - file: computing_resources.md
+    - file: software_tools.md
     - file: learning_resources.md