trim out duplicates

Author: hschellman

_config.yml

@@ -11,7 +11,7 @@
 carpentry: "dune"
 
 # Overall title for pages.
-title: "Computing Basics for DUNE - Late 2024 edition"
+title: "Batch Computing Basics for DUNE - 2025 transition edition"
 
 # Life cycle stage of the lesson
 # See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html

_episodes/01-introduction.md

@@ -28,9 +28,7 @@ The May 2023 DUNE computing training spanned two days: [Indico site](https://ind
 
 --> 
 
-This is a short 3 hour version of the basics.  We will be adding/offering additional tutorials.  An important one that is coming soon is:
-
-[The LArSoft tutorial at CERN, February 3-7, 2025](https://indico.cern.ch/event/1461779/) password on the [tutorials page](https://wiki.dunescience.org/wiki/Computing_tutorials)
+This is a short 3 hour version of the basics.  We will be adding/offering additional tutorials. 
 
 [Also check out the longer list of DUNE computing tutorials](https://wiki.dunescience.org/wiki/Computing_tutorials) (collaborators only)
 
@@ -48,7 +46,7 @@ A similar session from May 2022 was captured for your asynchronous review.
 
 ## Basic setup reminder
 
-You should have gone through the [setup sequence]({{ site.baseurl }}/setup)
+You should have gone through the [setup sequence](https://dune.github.io/computing-basics/setup)
 
 As a reminder you need to choose between running on sl7 in a container or al9.  You do NOT want to mix them.
 
@@ -62,11 +60,11 @@ source mysetup7.sh
 Here are some example scripts that do most of the setups explained in this tutorial.  You need to store these in your home area, source them every time you log in, and possibly update them as code versions evolve. 
 
 
-- [SL7 setup]({{ site.baseurl }}/sl7_setup)
+- [SL7 setup](https://dune.github.io/computing-basics/sl7_setup)
 
-- [AL9 setup]({{ site.baseurl }}/al9_setup)
+- [AL9 setup](https://dune.github.io/computing-basics/al9_setup)
 
-> ## If you run into problems, check out the [Common Error Messages]({{ site.baseurl }}/ErrorMessages) page and the [FAQ page](https://github.com/orgs/DUNE/projects/19/)
+> ## If you run into problems, check out the [Common Error Messages](https://dune.github.io/computing-basics/ErrorMessages) page and the [FAQ page](https://github.com/orgs/DUNE/projects/19/)
 > if that doesn't help, use Slack to ask us about the problem - there is always a new one cropping up.
 {: .challenge} 
 
@@ -95,7 +93,7 @@ Here are some example scripts that do most of the setups explained in this tutor
 There will be live documents linked from [Indico][indico-event-link] for each [Zoom][zoom-link] session. You can write questions there, anonymously or not, and experts will reply. The chat on Zoom can quickly saturate so this is a more convenient solution and proved very successful at the previous training. We will collect all questions and release a Q&A after the event.
 -->
 
-You must be on the DUNE Collaboration member list and have a valid FNAL or CERN account. See the old [Indico Requirement page][indico-event-requirements] for more information. Windows users are invited to review the [Windows Setup page]({{ site.baseurl }}/Windows.html).
+You must be on the DUNE Collaboration member list and have a valid FNAL or CERN account. See the old [Indico Requirement page][indico-event-requirements] for more information. Windows users are invited to review the [Windows Setup page](https://dune.github.io/computing-basics/Windows.html).
 
 You should join the DUNE Slack instance and look in [#computing-training-basics](https://dunescience.slack.com/archives/C02TJDHUQPR) for help with this tutorial
 

_episodes/02-submit-jobs-w-justin.md

@@ -5,20 +5,20 @@ exercises: 0
 questions:
 - How to submit realistic grid jobs with JustIn
 objectives:  
-- Demonstrate use of JustIn for job submission with more complicated setups.
+- Demonstrate use of [justIn](https://dunejustin.fnal.gov) for job submission with more complicated setups.
 keypoints:
 - Always, always, always prestage input datasets. No exceptions.
 ---
 
-#  PLEASE USE THE NEW JUSTIN SYSTEM INSTEAD OF POMS
+#  PLEASE USE THE NEW [justIn](https://dunejustin.fnal.gov) SYSTEM INSTEAD OF POMS
 
-__The JustIn Tutorial is currently in docdb at: [JustIn Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145)__
+__The [justIn](https://dunejustin.fnal.gov) Tutorial is currently in docdb at: [JustIn Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145)__
 
-The JustIn system is describe in detail at: 
+The [justIn](https://dunejustin.fnal.gov) system is describe in detail at: 
 
-__[JustIn Home](https://justin.dune.hep.ac.uk/dashboard/)__
+__[JustIn Home](https://dunejustin.fnal.gov/dashboard/)__
 
-__[JustIn Docs](https://justin.dune.hep.ac.uk/docs/)__
+__[JustIn Docs](https://dunejustin.fnal.gov/docs/)__
 
 
 > ## Note More documentation coming soon

_episodes/03.2-UPS.md

@@ -13,7 +13,7 @@ keypoints:
 - #### `bash: setup: command not found`
 
   setup is a UPS command.  You need to be running in the Apptainer and setup the DUNE ups system - check out the instructions in [SL7 setup]
-  ({{ site.baseurl }}/sl7_setup)
+  (https://dune.github.io/computing-basics/sl7_setup)
 
 
 - #### `SyntaxError: future feature annotations is not defined` 

_episodes/03.3-cvmfs.md

@@ -4,8 +4,8 @@
 ## [Computing Basics](https://dune.github.io/computing-basics/)
 A starting point for new DUNE people.  How to log in, access disk and run basic jobs at FNAL and CERN.
 
-## [The Justin Workflow System](https://justin.dune.hep.ac.uk/docs/)
-How to use the Justin Workflow system to submit jobs and access data.  [Metacat/Rucio/Justin Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145) has step by step instructions.
+## [The Justin Workflow System](https://dunejustin.fnal.gov/docs/)
+How to use the [justIn](https://dunejustin.fnal.gov) Workflow system to submit jobs and access data.  [Metacat/Rucio/Justin Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145) has step by step instructions.
 
 ## [LArTPC Reconstruction Training](https://indico.ph.ed.ac.uk/event/268/)
 Annual training on LArTPC reconstruction and simulation methods.

_extras/Common-Error-Messages.md

@@ -5,20 +5,20 @@ exercises: 0
 questions:
 - How to submit realistic grid jobs with JustIn
 objectives:  
-- Demonstrate use of JustIn for job submission with more complicated setups.
+- Demonstrate use of [justIn](https://dunejustin.fnal.gov) for job submission with more complicated setups.
 keypoints:
 - Always, always, always prestage input datasets. No exceptions.
 ---
 
-#  PLEASE USE THE NEW JUSTIN SYSTEM INSTEAD OF POMS
+#  PLEASE USE THE NEW [justIn](https://dunejustin.fnal.gov) SYSTEM INSTEAD OF POMS
 
-__The JustIn Tutorial is currently in docdb at: [JustIn Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145)__
+__The [justIn](https://dunejustin.fnal.gov) Tutorial is currently in docdb at: [JustIn Tutorial](https://docs.dunescience.org/cgi-bin/sso/RetrieveFile?docid=30145)__
 
-The JustIn system is described in detail at: 
+The [justIn](https://dunejustin.fnal.gov) system is described in detail at: 
 
-__[JustIn Home](https://justin.dune.hep.ac.uk/dashboard/)__
+__[JustIn Home](https://dunejustin.fnal.gov/dashboard/)__
 
-__[JustIn Docs](https://justin.dune.hep.ac.uk/docs/)__
+__[JustIn Docs](https://dunejustin.fnal.gov/docs/)__
 
 
 > ## Note More documentation coming soon
@@ -209,7 +209,7 @@ A given file can also be searched and visualized from the WEB interface
 
 - is the new workflow system replacing POMS
 - It can be used to process several input  files by submitting batch jobs  on the grid 
-- justIN is a workflow system that processes data by satisfying  the requirements of data location/data catalog, rapid code distribution service
+- [justIn](https://dunejustin.fnal.gov) is a workflow system that processes data by satisfying  the requirements of data location/data catalog, rapid code distribution service
 and job submission to the grid.
 
 justIN ties together:
@@ -371,7 +371,7 @@ The scary preload is to allow `xroot` to read `hdf5` files.
 $ USERF=$USER
 $ FNALURL='https://fndcadoor.fnal.gov:2880/dune/scratch/users'
 $ justinsimple-workflow --mql"files from fardet-hd:fardet-hd__fd_mc_2023a_reco2__full-reconstructed__v09_81_00d02__standard_reco2_dune10kt_nu_1x2x6__prodgenie_nu_dune10kt_1x2x6__out1__validation skip 5 limit 5 ordered " --jobscriptsubmit_ana.jobscript--rss-mb 4000 --output-pattern '*_ana_*.root:$FNALURL/$USERF"
-'You can look at your job status by using justIN dashboard https://justin.dune.hep.ac.uk/dashboard/?method=list-workflows
+'You can look at your job status by using [justIn](https://dunejustin.fnal.gov) dashboard https://dunejustin.fnal.gov/dashboard/?method=list-workflows
 
 
 
@@ -541,7 +541,7 @@ justintime
 Links
 MetacatWEB interface:    https://metacat.fnal.gov:9443/dune_meta_prod/app/auth/login
 
-justIN: https://justin.dune.hep.ac.uk/docs/
+justIN: https://dunejustin.fnal.gov/docs/
 
 Slack channels:  #workflow