fix links in setup

Author: hschellman

_includes/setup.toc.md

@@ -7,24 +7,22 @@
 - [Step 2: Getting accounts](#step-2-getting-accounts)
    - [With FNAL](#with-fnal)
    - [With CERN](#with-cern)
-- [Step 3: Mission setup (rest of this page)](#step-3-mission-setup-(rest-of-this-page))
-- [Basic setup on your computer](#basic-setup-on-your-computer)
-- [Kerberos business](#kerberos-business)
-- [ssh-in](#ssh-in)
-- [Get a clean shell](#get-a-clean-shell)
-- [Software setup](#software-setup)
+- [Step 3: Mission setup](#step-3-mission-setup)
+   - [Basic setup on your computer](#basic-setup-on-your-computer)
+   - [Kerberos business](#kerberos-business)
+   - [ssh-in](#ssh-in)
+   - [Get a clean shell](#get-a-clean-shell)
+- [Step 4. Software setup](#step-4.-software-setup)
    - [SL7 version](#sl7-version)
-   - [Caveats for later](#caveats-for-later)
+   - [SL7 Caveats for batch submission](#sl7-caveats-for-batch-submission)
    - [Alma9 version](#alma9-version)
-   - [Caveats for later](#caveats-for-later)
-- [4.2 Setting up DUNE software - Alma9 version](#4.2-setting-up-dune-software---alma9-version)
-   - [Caveats](#caveats)
-- [Exercise! (For SL7 - it's easy)](#exercise!-(for-sl7---it's-easy))
-- [Exercise! (For AL9 - it's easy)](#exercise!-(for-al9---it's-easy))
-- [Getting setup for streaming and grid access](#getting-setup-for-streaming-and-grid-access)
-   - [Tokens method <a name="tokens"></a>](#tokens)
+   - [Alma9 Caveats](#alma9-caveats)
+- [Step 5. Exercises](#step-5.-exercises)
+   - [Exercise! (For SL7 - it's easy)](#exercise!-(for-sl7---it's-easy))
+   - [Exercise! (For AL9 - it's easy)](#exercise!-(for-al9---it's-easy))
+- [Step 6. Getting authentication for streaming and grid access](#step-6.-getting-authentication-for-streaming-and-grid-access)
+   - [Tokens method](#tokens-method)
       - [Get and store your token](#get-and-store-your-token)
-      - [2. Tell the system where your token is](#2.-tell-the-system-where-your-token-is)
 - [Set up on CERN machines](#set-up-on-cern-machines)
    - [Setup in Alma9](#setup-in-alma9)
    - [For SL7](#for-sl7)

setup.md

@@ -65,7 +65,7 @@ See [lxplus documentation](#lxplus) for information about using lxplus.
 If you have trouble getting access, please reach out to the training team several days ahead of time.  Some issues take some time to resolve.  Please do not put this off.  We cannot help you the day of the tutorial as we are busy doing the tutorial.  
 
 
-## Step 3: Mission setup (rest of this page)
+## Step 3: Mission setup
 
 
 
@@ -84,15 +84,15 @@ Also check out our [Computing FAQ](https://github.com/orgs/DUNE/projects/19/view
 
 
 
-## Basic setup on your computer
+### Basic setup on your computer
 
 [Computer Setup]({{ site.baseurl }}/ComputerSetup) goes through how to find a terminal and set up xwindows on MacOS and Windows.  You can skip this if already familiar with doing that. 
 
 > ## Note
 > The instructions directly below are for FNAL accounts. If you do not have a valid FNAL account but a CERN one, go at the bottom of this page to the [Setup on CERN machines](#Setup) section.
 {: .challenge}
 
-## Kerberos business
+### Kerberos business
 
 <!--**STEP 1**: DUNE Membership
 To follow the tutorial, you must be on the DUNE Collaboration member list. You can check if you are on it [here][dune-collaboration]. If you are not, talk to your Institutional Board representative to get on it.
@@ -203,7 +203,7 @@ Check out the DUNE FAQ for a long list of possible error messages and suggested
 
 [DUNE FAQ][DUNE FAQ]
 
-## ssh-in
+### ssh-in
 **What is it?** SSH stands for Secure SHell. It uses an encrypted protocol used for connecting to remote machines and it works with Kerberos tickets when configured to do so. The configuration is done in your local file in your home directory:
 
 ~~~
@@ -240,7 +240,7 @@ ssh username@dunegpvmXX.fnal.gov
 where XX is a number from 01 to 15. 
 If you experience long delays in loading programs or graphical output, you can try connecting with VNC. More info: [Using VNC Connections on the dunegpvms][dunegpvm-vnc].  Please remember to shut down your VNC connection at least once/week - the machines can get overrun by zombies. 
 
-## Get a clean shell
+### Get a clean shell
 To run DUNE software, it is necessary to have a 'clean login'. What is meant by clean here? If you work on other experiment(s), you may have some environment variables defined (for NOvA, MINERvA, MicroBooNE). Theses may conflict with the DUNE environment ones.
 
 Two ways to clean your shell once on a DUNE machine:
@@ -287,7 +287,7 @@ A simpler solution would be to rename your login scripts (for instance .bashrc a
 {: .callout}
 
 
-## Software setup
+## Step 4. Software setup
 ### SL7 version
 
 
@@ -298,7 +298,7 @@ To set up your environment in SL7, the commands are:
 Log into a DUNE machine running Alma9
 
 
-> ### Launch an SL7 container
+> #### Launch an SL7 container
 > 
 > > ## gpvm apptainer
 > > ~~~
@@ -337,7 +337,7 @@ Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/
 {: .output}
 
 
-> ### See if ROOT works
+> #### See if ROOT works
 >
 > > ## Try testing ROOT to make certain things are working
 > > ~~~
@@ -348,18 +348,19 @@ Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/
 > > You should see a plot that updates and then terminates.  You may need to `export DISPLAY=0:0`.
 > {: .solution}
 {: .challenge}
-<!-- 
 
-### Caveats for later
+### SL7 Caveats for batch submission
+
+We haven't covered batch submission yet but ....
 
 > ## Note: You cannot submit basic grid jobs from the Container
-> You cannot submit jobsub jobs from the Container - you need to open a separate window. In that window do the minimal [Alma9](#4.2-alma9-version) setup above and submit your jobs from that window. 
+> You cannot submit jobsub jobs from the Container - you need to open a separate window. In that window do the minimal [Alma9](#alma9-version) setup below and submit your jobs from that window. 
 >
->You may need to print your submit command to the screen or a file to do so if your submission is done from a script that uses ups. 
+>You may need to print your submit command to the screen or a file to do so if your submission is done from a script running on SL7.
 
 {: .callout} 
 
--->
+
 ### Alma9 version
 
 <!-- Try testing ROOT to make certain things are working
@@ -375,12 +376,12 @@ root -l -q $ROOTSYS/tutorials/dataframe/df013_InspectAnalysis.C
 
 You should see a plot that updates and then terminates.   You may need to `export DISPLAY=0:0` .
 
-### Caveats for later
+    ### Caveats for later
 
 You cannot submit jobs from the Container - you need to open a separate window, not do the apptainer and submit your jobs from that window. 
 
 
-## 4.2 Setting up DUNE software - Alma9 version
+          ## 4.2 Setting up DUNE software - Alma9 version
 -->
 
 We are moving to the Alma9 version of unix.  Not all DUNE code has been ported yet but if you are doing basic root analysis work, try it out. 
@@ -422,7 +423,7 @@ Here is how you set up basic DUNE software on Alma 9. We are using the super-com
 {: .callout}
 
 
-### Caveats
+### Alma9 Caveats
 
 We don't have a full ability to rebuild DUNE Software packages such as LArSoft using Spack yet.  We will be adding more functionality soon.  Unless you are doing simple ROOT based analysis you will need to use the [SL7 Container](#sl7-version) method for now. 
 
@@ -462,9 +463,9 @@ We don't have a full ability to rebuild DUNE Software packages such as LArSoft u
 
 
 
+## Step 5. Exercises
 
-
-## Exercise! (For SL7 - it's easy)
+### Exercise! (For SL7 - it's easy)
 This exercise will help organizers see if you reached this step or need help.
 
 1) Start in your home area `cd ~` on the DUNE machine (normally CERN or FNAL) and create the file ```dune_presetup_2025_sl7.sh```.  
@@ -508,7 +509,7 @@ date >& /exp/dune/app/users/${USER}/my_first_login.txt
 {: .language-bash}
 4) With the above, we will check if you reach this point. However we want to tailor this tutorial to your preferences as much as possible. We will let you decide which animals you would like to see in future material, between: "puppy", "cat", "squirrel", "sloth", "unicorn pegasus llama" (or "prefer not to say" of course). Write your desired option on the second line of the file you just created above.
 
-## Exercise! (For AL9 - it's easy)
+### Exercise! (For AL9 - it's easy)
 This exercise will help organizers see if you reached this step or need help.
 
 1) Start in your home area `cd ~` on the DUNE machine (normally CERN or FNAL) and create the file ```dune_presetup_2025_al9.sh```.  
@@ -543,7 +544,7 @@ date >& /exp/dune/app/users/${USER}/my_first_login.txt
 > If you experience difficulties, please ask for help in the Slack channel [#computing-training-basics](https://dunescience.slack.com/archives/C02TJDHUQPR).  Please mention in your message this is about the Setup step 5. Thanks!
 {: .challenge}
 
-## Getting setup for streaming and grid access
+## Step 6. Getting authentication for streaming and grid access
 In addition to your kerberos access, you need to be in the DUNE VO (Virtual Organization) to access to global DUNE resources. This is necessary in particular to stream data and submit jobs to the grid. If you are on the DUNE collaboration list and have a Fermilab ID you should have been added automatically to the DUNE VO.
 
 <!-- To check if you are on the VO, two commands. The kx509 gets a certificate from your kerberos ticket. On a DUNE machine, type:
@@ -608,7 +609,7 @@ With this done, you should be able to submit jobs and access remote DUNE storage
 
  -->
 
-### Tokens method <a name="tokens"></a>
+### Tokens method 
 
 We have moved from proxies to tokens for authentication as of 2025.
 
@@ -653,7 +654,7 @@ Storing condor credentials for dune
 
 you should only have to do the web thing once/month
 
-#### 2. Tell the system where your token is
+    #### 2. Tell the system where your token is
 
 
 ~~~
@@ -722,7 +723,7 @@ Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/
 
 ### Getting authentication for data access
 
-If you have a Fermilab account already, get a token as described in [tokens](#tokens)
+If you have a Fermilab account already, get a token as described in [tokens](#tokens-method)