Merge pull request #2 from RuiApostolo/gh-pages

Updated course for 2023-01-17

CODE_OF_CONDUCT.md

@@ -8,4 +8,6 @@ we pledge to follow the [Carpentry Code of Conduct][coc].
 Instances of abusive, harassing, or otherwise unacceptable behavior
 may be reported by following our [reporting guidelines][coc-reporting].
 
+Participants are required to abide by the [ARCHER2 Training Code of Conduct][archer2-tcoc].
+
 {% include links.md %}

CONTRIBUTING.md

@@ -55,7 +55,7 @@ and to meet some of our community members.
 2.  If you wish to change the example lesson,
     please work in <https://github.com/carpentries/lesson-example>,
     which documents the format of our lessons
-    and can be viewed at <https://carpentries.github.io/lesson-example>.
+    and can be viewed [here][lesson-example].
 
 3.  If you wish to change the template used for workshop websites,
     please work in <https://github.com/carpentries/workshop-template>.
@@ -65,7 +65,7 @@ and to meet some of our community members.
 
 4.  If you wish to change CSS style files, tools,
     or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
-    please work in <https://github.com/carpentries/styles>.
+    please work in [styles][styles].
 
 ## What to Contribute
 
@@ -120,19 +120,4 @@ your clone of the originating `gh-pages` branch.
 Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
 repository for reference while revising.
 
-[email]: mailto:[email protected]
-[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
-[dc-lessons]: http://datacarpentry.org/lessons/
-[dc-site]: http://datacarpentry.org/
-[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[github]: https://github.com
-[github-flow]: https://guides.github.com/introduction/flow/
-[github-join]: https://github.com/join
-[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
-[issues]: https://guides.github.com/features/issues/
-[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
-[c-site]: https://carpentries.org/
-[lc-site]: https://librarycarpentry.org/
-[lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry
+{% include links.md %}

LICENSE.md

@@ -3,6 +3,7 @@ layout: page
 title: "Licences"
 root: .
 ---
+
 ### Context
 This is not an official lesson of the Carpentries, however the licencing approach that the Carpentries take is ideal, so much of the material below resembles the Carpentries' documentation, where this is appropriate.
 

README.md

@@ -1,14 +1,7 @@
-
-
 # ARCHER2 Advanced use of LAMMPS (31 March 2022)
 
-
-
 ## Course timetable
 
 This is a one-day advanced use of LAMMPS course.
 
-The rendered course is available at https://epcced.github.io/20220421_GROMACS_introduction/
-
-
-
+The rendered course is available at TODO

_episodes/00-connecting.md

@@ -8,62 +8,60 @@ objectives:
 - "Understand how to connect to ARCHER2."
 keypoints:
 - "ARCHER2's login address is `login.archer2.ac.uk`."
+- "You have to change the default text password the first time you log in"
+- "MFA is mandatory in ARCHER2"
 ---
 
-## Puspose
+## Purpose
 
-Attendees of this course will get access to the ARCHER2 HPC facility. You will
-have the ability to request an account and to login to ARCHER2 before the
-course begins. If you are not able to login, you can come to this pre-session
-where the instructors will help make sure you can login to ARCHER2.
+Attendees of this course will get access to the ARCHER2 HPC facility.
+You will have the ability to request an account and to login to ARCHER2 before the course begins.
+If you are not able to login, you can come to this pre-session where the instructors will help make sure you can login to ARCHER2.
 
-Note that if you are not able to login to ARCHER2 and do not attend this 
-session, you may struggle to run the course excercises as these were designed 
-to run on ARCHER2 specifically.
+Note that if you are not able to login to ARCHER2, and do not attend this session,
+you may struggle to run the course exercises as these were designed to run on ARCHER2 specifically.
 
 ## Connecting using SSH
 
 The ARCHER2 login address is
 
-```
+```bash
 login.archer2.ac.uk
 ```
-{: .language-bash}
 
-Access to ARCHER2 is via SSH using **both** a password and a passphrase-protected SSH key pair.
+Access to ARCHER2 is via SSH using **both** a time-based one time password (TOTP) and a passphrase-protected SSH key pair.
 
 ## Passwords and password policy
 
-When you first get an ARCHER2 account, you will get a single-use password from the 
-SAFE which you will be asked to change to a password of your choice. Your chosen 
-password must have the required complexity as specified in the
-[ARCHER2 Password Policy](https://www.archer2.ac.uk/about/policies/passwords_usernames.html).
+When you first get an ARCHER2 account, you will get a single-use password from the SAFE which you will be asked to change to a password of your choice.
+Your chosen  password must have the required complexity as specified in the [ARCHER2 Password Policy][archer2-password].
 
-The password policy has been chosen to allow users to use both complex, shorter passwords and
-long, but comparatively simple passwords. For example, passwords in the style of both
-`LA10!£lsty` and `horsebatterystaple` would be supported.
+The password policy has been chosen to allow users to use both complex, shorter passwords and long, but comparatively simple passwords.
+For example, passwords in the style of both `LA10!£lsty` and `horsebatterystaple` would be supported.
 
 ## SSH keys
 
-As well as password access, users are required to add the public part of an SSH key pair to access ARCHER2.
-The public part of the key pair is associated with your account using the SAFE web interface.
-See the ARCHER2 User and Best Practice Guide for information on how to create SSH key pairs
-and associate them with your account:
+As well as password access, users are required to add the public part of an SSH key pair to access ARCHER2. The public part of the key pair is associated with your account using the SAFE web interface.
+See the ARCHER2 User and Best Practice Guide for information on how to create SSH key pairs and associate them with your account:
+
+* [Connecting to ARCHER2][archer2-connecting].
 
-* [Connecting to ARCHER2](https://docs.archer2.ac.uk/user-guide/connecting/)
+## TOTP/MFA
+
+ARCHER2 accounts are now required to use timed one-time passwords (TOTP), as part of a multi-factor authorisation (MFA) system.
+Instructions on how to add MFA authentication to a machine account on SAFE can be found [here][safe-machine-mfa].
 
 ## Data transfer services: scp, rsync, Globus Online
 
-ARCHER2 supports a number of different data transfer mechanisms. The one you choose depends
-on the amount and structure of the data you want to transfer and where you want to transfer
-the data to. The three main options are:
+ARCHER2 supports a number of different data transfer mechanisms.
+The one you choose depends on the amount and structure of the data you want to transfer and where you want to transfer the data to.
+The three main options are:
 
-* `scp`: The standard way to transfer small to medium amounts of data off ARCHER2 to any other location
+* `scp`: The standard way to transfer small to medium amounts of data off ARCHER2 to any other location.
 * `rsync`: Used if you need to keep small to medium datasets synchronised between two different locations
 
 More information on data transfer mechanisms can be found in the ARCHER2 User and Best Practice Guide:
 
-* [Data management and transfer](https://docs.archer2.ac.uk/user-guide/data/)
+* [Data management and transfer][archer2-data].
 
 {% include links.md %}
-

_episodes/01-welcome.md

@@ -9,55 +9,43 @@ questions:
 objectives:
 - "Understand how this course works, how I can get help and how I can give feedback."
 keypoints:
-- "We should all understand and follow the [ARCHER2 Code of Conduct](https://www.archer2.ac.uk/training/code-of-conduct/) to ensure this course is conducted in the best teaching environment."
+- "We should all understand and follow the [ARCHER2 Code of Conduct][archer2-tcoc] to ensure this course is conducted in the best teaching environment."
 - "The course will be flexible to best meet the learning needs of the attendees."
 - "Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees."
 ---
 
 ## Course structure and method
 
-Rather than having separate lectures and practical sessions, this course is taught following
-[The Carpentries methodology](https://carpentries.org) where we all work together through material
-learning key skills and information throughout the course. Typically, this follows the method of
-the instructor demonstrating and then the attendees doing along with the instructor.
+Rather than having separate lectures and practical sessions, this course is taught following [The Carpentries methodology][c-site],
+where we all work together through material learning key skills and information throughout the course.
+Typically, this follows the method of the instructor demonstrating and then the attendees doing along with the instructor.
 
-There are many helpers available to assist you and to answer any questions you may have as we
-work through the material together. You should also feel free to ask questions of the instructor
-whenever you like. The instructor will also provide many opportunities to pause and ask questions.
+There are many helpers available to assist you and to answer any questions you may have as we work through the material together.
+You should also feel free to ask questions of the instructor whenever you like.
+The instructor will also provide many opportunities to pause and ask questions.
 
-We will also make use of a shared collaborative document - the *etherpad*. You will find a link
-to this collaborative document on the course page. We will use it for a number of different purposes,
-for example, it may be used during exercises and instructors and helpers may put useful information
-or links in the etherpad that help or expand on the material being taught. If you have useful
-information to share with the class then please do add it to the etherpad. At the end of the course,
-we take a copy of the information in the etherpad, remove any personally-identifiable information 
-and post this on the course archive page so you should always be able to come back and find any
-information you found useful.
+We will also make use of a shared collaborative document - the *etherpad*.
+You will find a link to this collaborative document on the course page.
+We will use it for a number of different purposes, for example,
+it may be used during exercises and instructors and helpers may put useful information,
+or links in the etherpad that help or expand on the material being taught.
+If you have useful information to share with the class then please do add it to the etherpad.
+At the end of the course, we take a copy of the information in the etherpad,
+remove any personally-identifiable information,
+and post this on the course archive page so you should always be able to come back and find any information you found useful.
 
 ## Feedback
 
-Feedback is integral to how we approach training both during and after the course. In particular, we
-use informal and structured feedback activities during the course to ensure we tailor the pace and
-content appropriately for the attendees and feedback after the course to help us improve our training
-for the future.
-
-You will be issued with red and green "stickies" (or shown how to use their virtual equivalent for 
-online courses) to allow you give the instructor and helpers quick visual feedback on how you
-are getting on with the pace and the content of the course. If you are comfortable with the 
-pace/content then you should place your green sticky on the back of your laptop; if you are stuck,
-have questions, or are struggling with the pace/content then you should place the red sticky on
-the back of your laptop and a helper will come and speak to you. The instructor may also ask you
-to use the stickies in other, specific situations.
-
-At the lunch break (and end of days for multi-day courses) we will also run a quick feedback
-activity to gauge how the course is matching onto attendees requirements. Instructors and helpers
-will review this feedback over lunch (or overnight) and provide a summary of what we found at the
-start of the next session and, potentially, how the upcoming materiel/schedule will be changed
-to address the feedback.
-
-Finally, you will be provided with the opportunity to provide feedback on the course after it has
-finished. We welcome all this feedback, both good and bad, as this information in key to allow
-us to continually improve the training we offer.
+Feedback is integral to how we approach training both during and after the course.
+In particular, we use informal and structured feedback activities during the course to ensure we tailor the pace and content appropriately for the attendees,
+and feedback after the course to help us improve our training for the future.
 
-{% include links.md %}
+If you are not comfortable with the pace/content then you can use the reaction function of the collaborate session.
+
+At the lunch break (and end of days for multi-day courses) we will also run a quick feedback activity to gauge how the course is matching onto attendees requirements.
+Instructors and helpers will review this feedback over lunch and provide a summary of what we found at the start of the next session and, potentially, how the upcoming materiel/schedule will be changed to address the feedback.
 
+Finally, you will be provided with the opportunity to provide feedback on the course after it has finished.
+We welcome all this feedback, both good and bad, as this information in key to allow us to continually improve the training we offer.
+
+{% include links.md %}