Merge pull request #32 from UCL-ARC/cdkharris/big-merge

Cdkharris/big merge

Author: dpshelio

Diff for: .codespell-ignore

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

Diff for: .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: actions/setup-ruby@v1
+      - 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
@@ -56,17 +60,20 @@ 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
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-ruby@v1
+      - 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
@@ -78,6 +85,7 @@ 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

Diff for: .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

Diff for: 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/
-

Diff for: 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 '>=3.0.4'
+
+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"

Diff for: 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

Diff for: 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

Diff for: _config.yml

@@ -6,24 +6,25 @@
 #------------------------------------------------------------
 
 # 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
 # installation. Remember to keep the leading slash on the
 # `snippets` variable below!
+
 # UCL, University College London: Myriad + SGE
 snippets: "/snippets_library/UCL_Myriad_sge"
 
 local:
-  prompt: "[user@laptop ~]$"
+  prompt: "[you@laptop:~]$"
   bash_shebang: "#!/usr/bin/env bash"
 
 remote:
@@ -70,11 +71,12 @@ episode_order:
   - 11-connecting
   - 12-cluster
   - 13-scheduler
-  - 14-modules
-  - 15-transferring-files
-  - 16-parallel
-  - 17-resources
-  - 18-responsibility
+  - 14-environment-variables
+  - 15-modules
+  - 16-transferring-files
+  - 17-parallel
+  - 18-resources
+  - 19-responsibility
 
 #------------------------------------------------------------
 # Values for this lesson
@@ -84,7 +86,7 @@ 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.

Diff for: _episodes/11-connecting.md

@@ -47,7 +47,7 @@ SSH clients are usually command-line tools, where you provide the remote
 machine address as the only required argument. If your username on the remote
 system differs from what you use locally, you must provide that as well. If
 your SSH client has a graphical front-end, such as PuTTY or MobaXterm, you will
-7set these arguments before clicking "connect." From the terminal, you'll write
+set these arguments before clicking "connect." From the terminal, you'll write
 something like `ssh userName@hostname`, where the argument is just like an
 email address: the "@" symbol is used to separate the personal ID from the
 address of the remote machine.
@@ -300,7 +300,9 @@ See the [PuTTY documentation][putty-agent].
 ### Transfer Your Public Key
 
 {% if site.remote.portal %}
-Visit {{ site.remote.portal }} to upload your SSH public key.
+Visit [{{ site.remote.portal }}]({{ site.remote.portal }}) to upload your SSH
+public key. (Remember, it's the one ending in `.pub`!)
+
 {% else %}
 Use the **s**ecure **c**o**p**y tool to send your public key to the cluster.
 
@@ -309,7 +311,7 @@ Use the **s**ecure **c**o**p**y tool to send your public key to the cluster.
 ```
 {: .language-bash}
 
-{% include {{ site.snippets }}/ssh-key-instructions.snip %}
+{% include {{ site.snippets }}/login/ssh-key-instructions.snip %}
 
 {% endif %}
 
@@ -319,7 +321,7 @@ Go ahead and open your terminal or graphical SSH client, then log in to the
 cluster. Replace `{{ site.remote.user }}` with your username or the one
 supplied by the instructors.
 
-{% include {{ site.snippets }}/login-instructions.snip %}
+{% include {{ site.snippets }}/login/login-instructions.snip %}
 
 ```
 {{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
@@ -411,6 +413,8 @@ the other files, or files like them: `.bashrc` is a shell configuration file,
 which you can edit with your preferences; and `.ssh` is a directory storing SSH
 keys and a record of authorized connections.
 
+{% unless site.remote.portal %}
+
 ### Install Your SSH Key
 
 > ## There May Be a Better Way
@@ -454,6 +458,7 @@ password for your SSH key.
 {{ site.local.prompt }} ssh {{ site.remote.user }}@{{ site.remote.login }}
 ```
 {: .language-bash}
+{% endunless %}
 
 {% include links.md %}
 

Diff for: _episodes/12-cluster.md

@@ -81,8 +81,7 @@ dev   lib   opt    run   srv      usr
 
 The "{{ site.remote.homedir | replace: "/", "" }}" directory is the one where
 we generally want to keep all of our files. Other folders on a UNIX OS contain
-system files, and get modified and changed as you install new software or
-upgrade your OS.
+system files and change as you install new software or upgrade your OS.
 
 > ## Using HPC filesystems
 >

Diff for: _episodes/13-scheduler.md

@@ -130,7 +130,7 @@ status, we check the queue using the command
 > nothing was printed to the terminal.
 >
 > Cluster job output is typically redirected to a file in the directory you
-> launched it from. Use `ls` to find and read the file.
+> launched it from. Use `ls` to find and `cat` to read the file.
 {: .discussion}
 
 ## Customising a Job
@@ -181,7 +181,6 @@ Submit the job and monitor its status:
 
 Fantastic, we've successfully changed the name of our job!
 
-
 ### Resource Requests
 
 What about more important changes, such as the number of cores and memory for
@@ -219,7 +218,7 @@ later episode of this lesson.
 > >
 > > ```
 > > {{ site.remote.bash_shebang }}
-> > {{ site.sched.comment }} {{ site.sched.flag.time }} 00:01 # timeout in HH:MM
+> > {{ site.sched.comment }} {{ site.sched.flag.time }}00:01:00 # timeout in HH:MM
 > >
 > > echo -n "This script is running on "
 > > sleep 20 # time in seconds
@@ -236,8 +235,6 @@ later episode of this lesson.
 > {: .solution}
 {: .challenge}
 
-{% include {{ site.snippets }}/scheduler/print-sched-variables.snip %}
-
 Resource requests are typically binding. If you exceed them, your job will be
 killed. Let's use wall time as an example. We will request 1 minute of
 wall time, and attempt to run a job for two minutes.
@@ -328,4 +325,4 @@ can run these types of tasks as a one-off with `{{ site.sched.interactive }}`.
 {% include links.md %}
 
 [fshs]: https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
-[hisat]: https://ccb.jhu.edu/software/hisat2/index.shtml
+[hisat]: https://daehwankimlab.github.io/hisat2/