Update Gemfile and fix some typos

Author: Trevor Keller

.codespell-ignore

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

.github/workflows/test_and_build.yml

@@ -29,7 +29,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri
@@ -56,17 +56,19 @@ jobs:
     strategy:
       matrix:
         HPC_JEKYLL_CONFIG:
+          - Birmingham_Baskerville_slurm
           - ComputeCanada_Graham_slurm
           - EPCC_Cirrus_pbs
+          - 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: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0.4'
       - name: Install basic requirements
         run: |
           # Need this library for nokogiri

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"

Makefile

@@ -6,7 +6,7 @@ export SHELL = /bin/bash
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=bundle config --local set path .vendor/bundle && bundle install && bundle update && bundle exec jekyll
+JEKYLL=bundle config --local set path .bundle && bundle install && bundle update && bundle exec jekyll
 HPC_JEKYLL_CONFIG?=
 PARSER=bin/markdown_ast.rb
 DST=_site
@@ -154,7 +154,7 @@ lesson-fixme :
 
 ## spellcheck
 spellcheck:
-	codespell --skip="assets,*.svg,.vendor" --quiet-level=2  -L "dropse,figurestyle,hist,namd,rouge"
+	codespell --skip="assets,*.svg,.vendor" --quiet-level=2 -I .codespell-ignore
 
 ##
 ## IV. Auxililary (plumbing) commands

_config.yml

@@ -94,7 +94,7 @@ 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.

_extras/discuss.md

@@ -82,7 +82,7 @@ individual to individual!
 >
 > - Vary the number of threads used per process
 > - Reduce the number of cores used per node
-> - Allow the calculation to use Symmetric Mutithreading (SMT) if enabled
+> - Allow the calculation to use Symmetric Multithreading (SMT) if enabled
 >
 > Please ask for more information on these options from a helper!
 {: .challenge}
@@ -95,7 +95,7 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do
 > compares nucleotide or protein sequences to sequence databases and calculates
 > the statistical significance.
 >
-> In this exercise, you should use what you have learnt so far to set up a way
+> In this exercise, you should use what you have learned so far to set up a way
 > to run multiple serial BLAST+ analyses in parallel. There are many different
 > ways to do this that can be used on their own or in combination. Some ideas
 > include: