Update ondemand

.codespell-ignore

@@ -0,0 +1,6 @@
+Fram
+dropse
+figurestyle
+hist
+namd
+rouge

.github/workflows/test_and_build.yml

@@ -8,28 +8,35 @@ on:
       - gh-pages
 
 jobs:
-  spellcheck:
+  lint_common_files:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.7
       - name: Install codespell
         run: |
-          pip3 install codespell
+          sudo apt-get install codespell
       - name: Check spelling
         run: |
           make spellcheck
+      - name: Check top-level Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+      - name: Check episode Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _episodes/*.md
+      - name: Check extra Markdown syntax
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _extras/*.md
 
   check_lesson_and_build_default:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
+          bundler-cache: true
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri
@@ -38,9 +45,6 @@ jobs:
           bundle config set path '.vendor/bundle'
           bundle config build.nokogiri --use-system-libraries
           bundle install
-      - name: "Lint episode markdown"
-        run: |
-          find _episodes -name \*.md -exec bundle exec mdl -r MD001,MD003,MD005,MD006,MD007,MD008,MD009,MD010,MD011,MD012,MD015,MD016,MD017,MD018,MD019,MD020,MD021,MD022,MD023,MD025,MD035,MD036,MD037,MD038,MD039,MD046 {} \;
       - name: "Check lesson for warnings"
         run: |
           make lesson-check-all
@@ -56,18 +60,21 @@ jobs:
     strategy:
       matrix:
         HPC_JEKYLL_CONFIG:
+          - Birmingham_Baskerville_slurm
           - ComputeCanada_Graham_slurm
-          - EPCC_Cirrus_pbs
+          - EPCC_Cirrus_slurm
+          - HPCC_MagicCastle_slurm
+          - Magic_Castle_EESSI_slurm
           - NIST_CTCMS_slurm
           - Norway_SIGMA2_SAGA_slurm
           - UCL_Myriad_sge
-          - Magic_Castle_EESSI_slurm
           - BSU_Borah_slurm
     steps:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
+          bundler-cache: true
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri
@@ -79,6 +86,7 @@ jobs:
       - name: Check build ${{matrix.HPC_JEKYLL_CONFIG}}
         run: |
           make --always-make site HPC_JEKYLL_CONFIG=_includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/_config_options.yml
-      - name: "Lint snippet markdown"
-        run: |
-          find _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}} -name \*.snip -exec bundle exec mdl -r MD001,MD003,MD005,MD006,MD007,MD008,MD009,MD010,MD011,MD012,MD015,MD016,MD017,MD018,MD019,MD020,MD021,MD022,MD023,MD025,MD035,MD036,MD037,MD038,MD039,MD046 {} \;
+      - name: Lint snippet markdown
+        uses: DavidAnson/markdownlint-cli2-action@v9
+        with:
+          globs: _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/**/*.snip

.markdownlint-cli2.yaml

@@ -0,0 +1,73 @@
+# markdownlint-cli2:
+# - Example: <https://github.com/DavidAnson/markdownlint-cli2/blob/main/test/markdownlint-cli2-yaml-example/.markdownlint-cli2.yaml>
+# - Rules:   <https://github.com/DavidAnson/markdownlint/blob/main/README.md#rules--aliases>
+---
+config:
+  MD001: false  # heading-increment
+  MD002: false  # mdl rule undefined
+  MD003: true   # heading-style
+  MD004: true   # ul-style
+  MD005: true   # list-indent
+  MD006: false  # mdl rule undefined
+  MD007: true   # ul-indent
+  MD008: false  # mdl rule undefined
+  MD009: true   # no-trailing-spaces
+  MD010: true   # no-hard-tabs
+  MD011: true   # no-reversed-links
+  MD012: true   # no-multiple-blanks
+  MD013: false  # line-length
+  MD014: false  # commands-show-output
+  MD015: false  # mdl rule undefined
+  MD016: false  # mdl rule undefined
+  MD017: false  # mdl rule undefined
+  MD018: true   # no-missing-space-atx
+  MD019: true   # no-multiple-space-atx
+  MD020: true   # no-missing-space-closed-atx
+  MD021: true   # no-multiple-space-closed-atx
+  MD022: true   # blanks-around-headings
+  MD023: true   # heading-start-left
+  MD024: false  # no-duplicate-heading
+  MD025: true   # single-h1
+  MD026: false  # no-trailing-punctuation
+  MD027: false  # no-multiple-space-blockquote
+  MD028: false  # no-blanks-blockquote
+  MD029: true   # ol-prefix
+  MD030: true   # list-marker-space
+  MD031: false  # blanks-around-fences
+  MD032: true   # blanks-around-lists
+  MD033: false  # no-inline-html
+  MD034: true   # no-bare-urls
+  MD035: true   # hr-style
+  MD036: true   # no-emphasis-as-heading
+  MD037: true   # no-space-in-emphasis
+  MD038: true   # no-space-in-code
+  MD039: true   # no-space-in-links
+  MD040: false  # fenced-code-language
+  MD041: false  # first-line-h1
+  MD042: true   # no-empty-links
+  MD043: false  # required-headings
+  MD044: true   # proper-names
+  MD045: true   # no-alt-text
+  MD046: true   # code-block-style
+  MD047: true   # single-trailing-newline
+  MD048: true   # code-fence-style
+  MD049: false  # emphasis-style
+  MD050: false  # strong-style
+  MD051: true   # link-fragments
+  MD052: true   # reference-links-images
+  MD053: false  # link-image-reference-definitions
+  MD054: false  # link-image-style
+  MD055: true   # table-pipe-style
+  MD056: true   # table-column-count
+
+ignores:
+  - .vendor
+  - .bundle
+  - _extras/figures.md  # really HTML
+  - _includes/links.md  # just a list of links
+  - "**/*.html"
+  - "**/*.sh"
+  - "**/*.yaml"
+  - "**/*.yml"
+
+# noProgress: true

CONTRIBUTING.md

@@ -130,4 +130,3 @@ which everyone is welcome to join. You can also [reach us by email][email].
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: https://software-carpentry.org/lessons/
 [swc-site]: https://software-carpentry.org/
-

Gemfile

@@ -1,4 +1,18 @@
-source "https://rubygems.org"
-gem "github-pages", group: :jekyll_plugins
+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
+
+# Synchronize with https://pages.github.com/versions
+ruby '3.3.4'
+
+gem 'github-pages', group: :jekyll_plugins
+
+if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0')
+  gem 'webrick', '>= 1.6.1'
+end
+
 gem "kramdown-parser-gfm"
+
 gem "mdl"

LICENSE.md

@@ -1,9 +1,7 @@
 ---
-title: "Licenses"
+title: "License: CC BY 4.0"
 ---
 
-# CC BY 4.0
-
 ## Instructional Material
 
 All High Performance Computing Carpentry instructional material is

Makefile

@@ -154,7 +154,7 @@ lesson-fixme :
 
 ## spellcheck
 spellcheck:
-	codespell --skip="assets,*.svg,.vendor" --quiet-level=2  -L "dropse,figurestyle,hist,namd,rouge"
+	codespell --skip=".bundle,.vendor,assets,*.svg" --quiet-level=2 --ignore-words=".codespell-ignore"
 
 ##
 ## IV. Auxililary (plumbing) commands

_config.yml

@@ -6,14 +6,14 @@
 #------------------------------------------------------------
 
 # Cluster host and scheduler options: the defaults come from
-# Graham at Compute Canada, running Slurm. Other options can
-# be found in the library of snippets,
+# the HPC Carpentry tutorial cluster, running Slurm. Other
+# options can be found in the library of snippets,
 # `_includes/snippets_library`. To use one, replace options
 # below with those in `_config_options.yml` from the
 # library. E.g, to customise for Cirrus at EPCC, running
-# PBS, we could replace the options below with those from
+# Slurm, we could replace the options below with those from
 #
-# _includes/snippets_library/EPCC_Cirrus_pbs/_config_options.yml
+# _includes/snippets_library/EPCC_Cirrus_slurm/_config_options.yml
 #
 # If your cluster is not represented in the library, please
 # copy an existing folder, rename it, and customize for your
@@ -23,7 +23,7 @@
 snippets: "/snippets_library/BSU_Borah_slurm"
 
 local:
-  prompt: "[user@laptop ~]$"
+  prompt: "[you@laptop:~]$"
   bash_shebang: "#!/usr/bin/env bash"
 
 remote:
@@ -35,6 +35,7 @@ remote:
   homedir: "/bsuhome"
   user: "yourUsername"
   prompt: "[yourUsername@borah-login ~]$"
+  module_python3: "python/3.9.7"
   bash_shebang: "#!/usr/bin/env bash"
 
 sched:
@@ -60,16 +61,17 @@ sched:
   info: "sinfo"
   comment: "#SBATCH"
   hist: "sacct"
+  hist_filter: ""
 
 episode_order:
   - 10-hpc-intro
   - 11-connecting
   - 12-cluster
   - 13-scheduler
   - 01-break
-  - 14-modules
-  - 15-transferring-files
-  - 18-responsibility
+  - 15-modules
+  - 16-transferring-files
+  - 19-responsibility
 
 #------------------------------------------------------------
 # Values for this lesson
@@ -79,7 +81,7 @@ episode_order:
 # "swc": Software Carpentry
 # "dc":  Data Carpentry
 # "lc":  Library Carpentry
-# "cp":  Carpentries (e.g., instructor traning)
+# "cp":  Carpentries (e.g., instructor training)
 carpentry: "incubator"
 
 # Overall title for pages.

_episodes/11-connecting.md

@@ -19,17 +19,17 @@ keypoints:
 ## Secure Connections
 
 The first step in using a cluster is to establish a connection from our laptop
-to the cluster. When we are sitting at a computer, we have come to expect a 
-visual display with icons, widgets, and perhaps some windows or applications: 
-a _graphical user interface_, or GUI. Since computer clusters are remote 
-resources that we connect to over slow or intermittent interfaces (WiFi 
-and VPNs especially), it is more practical to use a _command-line interface_, 
-or CLI, to send commands as plain-text. If a command returns output, it is 
-printed as plain text as well. The commands we run today will not open a window 
+to the cluster. When we are sitting at a computer, we have come to expect a
+visual display with icons, widgets, and perhaps some windows or applications:
+a _graphical user interface_, or GUI. Since computer clusters are remote
+resources that we connect to over slow or intermittent interfaces (WiFi
+and VPNs especially), it is more practical to use a _command-line interface_,
+or CLI, to send commands as plain-text. If a command returns output, it is
+printed as plain text as well. The commands we run today will not open a window
 to show graphical results.
 
-If you have already taken The Carpentries' courses on the UNIX Shell or 
-Version Control, you have used the CLI on your _local machine_ extensively. 
+If you have already taken The Carpentries' courses on the UNIX Shell or
+Version Control, you have used the CLI on your _local machine_ extensively.
 The only leap to be made here is to open a CLI on a _remote machine_,
 while taking some precautions so that other folks on the network can't see (or
 change) the commands you're running or the results the remote machine sends
@@ -70,12 +70,12 @@ the password prompt are not displayed on the screen. Normal output will resume
 once you press `Enter`.
 
 You may have noticed that the prompt changed when you logged into the remote
-system using the terminal. This change is important because it can help you 
-distinguish on which system the commands you type will be run when you pass 
-them into the terminal. This change is also a small complication that we will 
-need to navigate throughout the workshop. Exactly what is displayed as the 
-prompt (which conventionally ends in `$`) in the terminal when it is connected 
-to the local system and the remote system will typically be different for 
+system using the terminal. This change is important because it can help you
+distinguish on which system the commands you type will be run when you pass
+them into the terminal. This change is also a small complication that we will
+need to navigate throughout the workshop. Exactly what is displayed as the
+prompt (which conventionally ends in `$`) in the terminal when it is connected
+to the local system and the remote system will typically be different for
 every user. We still need to indicate which system we are entering commands
 on though so we will adopt the following convention:
 
@@ -87,7 +87,7 @@ on though so we will adopt the following convention:
 
 ## Changing Your Password
 
-When your account is created, Research Computing assigns you a password. The 
+When your account is created, Research Computing assigns you a password. The
 first thing you should do upon logging in is change it!
 
 You can change your password by entering the `passwd` command as shown below:
@@ -105,12 +105,12 @@ the new password, and finally confirmation of the new password.
 > When prompted, enter a strong password that you will remember. There are two
 > common approaches to this:
 >
-> 1. Create a memorable passphrase with some punctuation, mixed-case and 
->    number-for-letter substitutions, 32 characters or longer. Please note 
+> 1. Create a memorable passphrase with some punctuation, mixed-case and
+>    number-for-letter substitutions, 32 characters or longer. Please note
 >    that passwords are case sensitive.
 > 2. Use a password manager and its built-in password generator with all
 >    character classes, 25 characters or longer. [KeePass][keepass] and
->    [BitWarden][bitwarden] are two good options. This is also a good option 
+>    [BitWarden][bitwarden] are two good options. This is also a good option
 >    for storing passwords.
 {: .callout}
 
@@ -157,8 +157,8 @@ scratch
 ```
 {: .output}
 
-The system administrators have configured your home directory with a link 
-(a shortcut) to a scratch space reserved for you. You can also include 
+The system administrators have configured your home directory with a link
+(a shortcut) to a scratch space reserved for you. You can also include
 hidden files in your directory listing:
 
 ```