From dda9cbecacf8ec8bf8b515ea605b2a25df909a0d Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 20:33:55 -0500 Subject: [PATCH 01/12] Update Gemfile and fix some typos --- .codespell-ignore | 6 ++++++ .github/workflows/test_and_build.yml | 8 +++++--- Gemfile | 18 ++++++++++++++++-- Makefile | 4 ++-- _config.yml | 2 +- _extras/discuss.md | 4 ++-- 6 files changed, 32 insertions(+), 10 deletions(-) create mode 100644 .codespell-ignore diff --git a/.codespell-ignore b/.codespell-ignore new file mode 100644 index 00000000..79f47edb --- /dev/null +++ b/.codespell-ignore @@ -0,0 +1,6 @@ +Fram +dropse +figurestyle +hist +namd +rouge diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index 892ec2bd..03760d93 100644 --- a/.github/workflows/test_and_build.yml +++ b/.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 diff --git a/Gemfile b/Gemfile index 5714bad6..27e6eb5a 100644 --- a/Gemfile +++ b/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 --git a/Makefile b/Makefile index f451874e..3b18602b 100644 --- a/Makefile +++ b/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 diff --git a/_config.yml b/_config.yml index 7e99f937..36f9c871 100644 --- a/_config.yml +++ b/_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. diff --git a/_extras/discuss.md b/_extras/discuss.md index 352f424b..b142565e 100644 --- a/_extras/discuss.md +++ b/_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: From 278332008e01fd96ea9983edd046212b2a52bc83 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 20:52:27 -0500 Subject: [PATCH 02/12] codespell args are hard --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 3b18602b..d8add2b7 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ export SHELL = /bin/bash # Settings MAKEFILES=Makefile $(wildcard *.mk) -JEKYLL=bundle config --local set path .bundle && bundle install && bundle update && bundle exec jekyll +JEKYLL=bundle config --local set path .vendor/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 -I .codespell-ignore + codespell --skip=".bundle,.vendor,assets,*.svg" --quiet-level=2 --ignore-words=".codespell-ignore" ## ## IV. Auxililary (plumbing) commands From 39b9ad4a174dc867e28d4d5cf4ac7df196ff7511 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 20:57:04 -0500 Subject: [PATCH 03/12] cleanup crufty text from another lib --- .../modules/wrong-gcc-version.snip | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/_includes/snippets_library/Birmingham_Baskerville_slurm/modules/wrong-gcc-version.snip b/_includes/snippets_library/Birmingham_Baskerville_slurm/modules/wrong-gcc-version.snip index 23ee5df8..41dfffce 100644 --- a/_includes/snippets_library/Birmingham_Baskerville_slurm/modules/wrong-gcc-version.snip +++ b/_includes/snippets_library/Birmingham_Baskerville_slurm/modules/wrong-gcc-version.snip @@ -3,32 +3,29 @@ C/C++/Fortran compiler. Tons of software is dependent on the GCC version, and might not compile or run if the wrong version is loaded. In this case, there are few different versions: -`GCC/7.3.0-2.30 GCC/8.2.0-2.31.1 GCC/8.3.0 GCC/9.3.0` +`GCC/7.3.0 GCC/8.2.0 GCC/8.3.0 GCC/9.3.0` How do we load each copy and which copy is the default? -On SAGA and Fram we do not have default modules and we must use the full name -to load it. - ``` -{{ site.host_prompt }} module load gcc +{{ site.host_prompt }} module load GCC ``` {: .language-bash} ``` Lmod has detected the following error: The following module(s) are unknown: -"gcc" +"GCC" Please check the spelling or version number. Also try "module spider ..." It is also possible your cache file is out-of-date; it may help to try: - $ module --ignore-cache load "gcc" + $ module --ignore-cache load "GCC" ``` {: .output} To load a software module we must specify the full module name: ``` -{{ site.host_prompt }} module load GCC/8.2.0-2.31.1 +{{ site.host_prompt }} module load GCC/8.2.0 {{ site.host_prompt }} gcc --version ``` {: .language-bash} From 24d81957612e88b7a493842363e0aaa8988f3fcc Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 20:59:22 -0500 Subject: [PATCH 04/12] Use packaged codespell instead of pip --- .github/workflows/test_and_build.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index 03760d93..f8bd4318 100644 --- a/.github/workflows/test_and_build.yml +++ b/.github/workflows/test_and_build.yml @@ -12,13 +12,9 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: '3.9' - name: Install codespell run: | - python3 -m pip install codespell + sudo apt-get install codespell - name: Check spelling run: | make spellcheck From f4671befee55b64287916b9bdaac81a2df430caa Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 21:03:37 -0500 Subject: [PATCH 05/12] Create missing file --- .../parallel/one-task-jobscript.snip | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 _includes/snippets_library/Birmingham_Baskerville_slurm/parallel/one-task-jobscript.snip diff --git a/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/one-task-jobscript.snip b/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/one-task-jobscript.snip new file mode 100644 index 00000000..3ca27f07 --- /dev/null +++ b/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/one-task-jobscript.snip @@ -0,0 +1,15 @@ +``` +{{ site.remote.bash_shebang }} +{{ site.sched.comment }} {{ site.sched.flag.name }} solo-job +{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }} +{{ site.sched.comment }} -N 1 +{{ site.sched.comment }} -n 1 +{{ site.sched.comment }} --mem=3G + +# Load the computing environment we need +module load python + +# Execute the task +mpiexec amdahl +``` +{: .language-bash} From 292704b146f08e32c4d51d140f154cb60a3ffbc8 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 21:05:32 -0500 Subject: [PATCH 06/12] cache bundle --- .github/workflows/test_and_build.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index f8bd4318..062f8852 100644 --- a/.github/workflows/test_and_build.yml +++ b/.github/workflows/test_and_build.yml @@ -26,6 +26,7 @@ jobs: - uses: ruby/setup-ruby@v1 with: ruby-version: '3.0.4' + bundler-cache: true - name: Install basic requirements run: | # Need this library for nokogiri @@ -65,6 +66,7 @@ jobs: - uses: ruby/setup-ruby@v1 with: ruby-version: '3.0.4' + bundler-cache: true - name: Install basic requirements run: | # Need this library for nokogiri From f02f31786eea945111d132ace5d69047e8837563 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 21:07:54 -0500 Subject: [PATCH 07/12] missing file --- .../parallel/eight-tasks-jobscript.snip | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 _includes/snippets_library/Birmingham_Baskerville_slurm/parallel/eight-tasks-jobscript.snip diff --git a/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/eight-tasks-jobscript.snip b/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/eight-tasks-jobscript.snip new file mode 100644 index 00000000..62569a87 --- /dev/null +++ b/_includes/snippets_library/Birmingham_Baskerville_slurm/parallel/eight-tasks-jobscript.snip @@ -0,0 +1,15 @@ +``` +{{ site.remote.bash_shebang }} +{{ site.sched.comment }} {{ site.sched.flag.name }} parallel-pi +{{ site.sched.comment }} {{ site.sched.flag.queue }} {{ site.sched.queue.testing }} +{{ site.sched.comment }} -N 1 +{{ site.sched.comment }} -n 8 +{{ site.sched.comment }} --mem=3G + +# Load the computing environment we need +module load python3 + +# Execute the task +mpiexec amdahl +``` +{: .language-bash} From 30a2417f311d8c11224c121ae0daa911874fb3da Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 23:05:10 -0500 Subject: [PATCH 08/12] Overhaul markdownlint using config file --- .github/workflows/test_and_build.yml | 17 ++++- .markdownlint-cli2.yaml | 73 +++++++++++++++++++ CONTRIBUTING.md | 1 - LICENSE.md | 4 +- _episodes/11-connecting.md | 1 + _episodes/13-scheduler.md | 1 - .../modules/wrong-gcc-version.snip | 1 - .../scheduler/terminate-multiple-jobs.snip | 2 - _includes/snippets_library/README.md | 2 - 9 files changed, 88 insertions(+), 14 deletions(-) create mode 100644 .markdownlint-cli2.yaml diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index 062f8852..a802a095 100644 --- a/.github/workflows/test_and_build.yml +++ b/.github/workflows/test_and_build.yml @@ -8,16 +8,23 @@ on: - gh-pages jobs: - spellcheck: + lint_common_files: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 + - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install codespell run: | sudo apt-get install codespell - name: Check spelling run: | make spellcheck + - name: Check episode Markdown syntax + run: | + markdownlint-cli2 _episodes + - name: Check extra Markdown syntax + run: | + markdownlint-cli2 _extra check_lesson_and_build_default: runs-on: ubuntu-latest @@ -27,6 +34,7 @@ jobs: with: ruby-version: '3.0.4' bundler-cache: true + - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install basic requirements run: | # Need this library for nokogiri @@ -37,7 +45,7 @@ jobs: 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 {} \; + bundle exec mdl _episodes {} \; - name: "Check lesson for warnings" run: | make lesson-check-all @@ -67,6 +75,7 @@ jobs: with: ruby-version: '3.0.4' bundler-cache: true + - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install basic requirements run: | # Need this library for nokogiri @@ -78,6 +87,6 @@ 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" + - name: Lint snippet markdown run: | - find _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}} -name \*.snip -exec bundle exec mdl -r MD001,MD003,MD005,MD006,MD007,MD008,MD009,MD010,MD011,MD012,MD015,MD016,MD017,MD018,MD019,MD020,MD021,MD022,MD023,MD025,MD035,MD036,MD037,MD038,MD039,MD046 {} \; + markdownlint-cli2 "_includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/**/*.snip" diff --git a/.markdownlint-cli2.yaml b/.markdownlint-cli2.yaml new file mode 100644 index 00000000..7b5abfc3 --- /dev/null +++ b/.markdownlint-cli2.yaml @@ -0,0 +1,73 @@ +# markdownlint-cli2: +# - Example: +# - Rules: +--- +config: + MD001: false # heading-increment + MD002: false + MD003: true # heading-style + MD004: true # ul-style + MD005: true # list-indent + MD006: true + MD007: true # ul-indent + MD008: true + MD009: true # no-trailing-spaces + MD010: true # no-hard-tabs + MD011: true # no-reversed-links + MD012: true # no-multiple-blanks + MD013: false + MD014: false + MD015: true + MD016: true + MD017: true + 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 --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7843ea6f..466e7156 100644 --- a/CONTRIBUTING.md +++ b/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 --git a/LICENSE.md b/LICENSE.md index edbad2a1..46deb500 100644 --- a/LICENSE.md +++ b/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 --git a/_episodes/11-connecting.md b/_episodes/11-connecting.md index 9c5b9234..15f6992b 100644 --- a/_episodes/11-connecting.md +++ b/_episodes/11-connecting.md @@ -409,6 +409,7 @@ 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 diff --git a/_episodes/13-scheduler.md b/_episodes/13-scheduler.md index 98bd2d47..b75d1c0d 100644 --- a/_episodes/13-scheduler.md +++ b/_episodes/13-scheduler.md @@ -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 diff --git a/_includes/snippets_library/EPCC_Cirrus_pbs/modules/wrong-gcc-version.snip b/_includes/snippets_library/EPCC_Cirrus_pbs/modules/wrong-gcc-version.snip index 74506dcf..39f37a33 100644 --- a/_includes/snippets_library/EPCC_Cirrus_pbs/modules/wrong-gcc-version.snip +++ b/_includes/snippets_library/EPCC_Cirrus_pbs/modules/wrong-gcc-version.snip @@ -89,4 +89,3 @@ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. {: .output} This achieves the same result as unload followed by load but in a single step. - diff --git a/_includes/snippets_library/EPCC_Cirrus_pbs/scheduler/terminate-multiple-jobs.snip b/_includes/snippets_library/EPCC_Cirrus_pbs/scheduler/terminate-multiple-jobs.snip index 139597f9..e69de29b 100644 --- a/_includes/snippets_library/EPCC_Cirrus_pbs/scheduler/terminate-multiple-jobs.snip +++ b/_includes/snippets_library/EPCC_Cirrus_pbs/scheduler/terminate-multiple-jobs.snip @@ -1,2 +0,0 @@ - - diff --git a/_includes/snippets_library/README.md b/_includes/snippets_library/README.md index 56b65740..6be1cee2 100644 --- a/_includes/snippets_library/README.md +++ b/_includes/snippets_library/README.md @@ -28,5 +28,3 @@ If the naming seems counter-intuitive, please feel free to make changes locally, and file an issue of submit a pull request to fix it upstream. None of this is set in stone, and improvements are always welcome. - - From 5683b94548926f25ef9e2e3330c0b203c823864b Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 23:09:42 -0500 Subject: [PATCH 09/12] Missed a file --- reference.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/reference.md b/reference.md index 61df7f9b..09993605 100644 --- a/reference.md +++ b/reference.md @@ -9,11 +9,12 @@ title: Knowledge Base Search online for the one that fits you best, but here's some to start: * [Slurm summary](https://slurm.schedmd.com/pdfs/summary.pdf) from SchedMD -* [Torque/PBS summary]( - https://gif.biotech.iastate.edu/torque-pbs-job-management-cheat-sheet) +* [Torque/PBS + summary](https://gif.biotech.iastate.edu/torque-pbs-job-management-cheat-sheet) from Iowa State -* [Translating between Slurm and PBS]( - https://www.msi.umn.edu/slurm/pbs-conversion) from University of Minnesota +* [Translating between Slurm and + PBS](https://www.msi.umn.edu/slurm/pbs-conversion) from University of + Minnesota ### Units and Language @@ -28,10 +29,10 @@ History and common language have however mixed this notation with a different meaning. When people say "Kilobyte", they mean 1024 Bytes instead. In that spirit, a Megabyte is 1024 Kilobytes. -To address this ambiguity, the [International System of Quantities]( -https://en.wikipedia.org/wiki/International_System_of_Quantities) standardizes -the *binary* prefixes (with base of 210=1024) by the prefixes Kibi -(ki), Mebi (Mi), Gibi (Gi), etc. For more details, see +To address this ambiguity, the [International System of +Quantities](https://en.wikipedia.org/wiki/International_System_of_Quantities) +standardizes the *binary* prefixes (with base of 210=1024) by the +prefixes Kibi (ki), Mebi (Mi), Gibi (Gi), etc. For more details, see [here](https://en.wikipedia.org/wiki/Binary_prefix). ### "No such file or directory" or "symbol 0096" Errors From 2edc1a9a98e8c4086e07821052f7ccd28f623d66 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 23:17:42 -0500 Subject: [PATCH 10/12] Figuring out how GH Actions work. --- .github/workflows/test_and_build.yml | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index a802a095..58e77188 100644 --- a/.github/workflows/test_and_build.yml +++ b/.github/workflows/test_and_build.yml @@ -12,19 +12,22 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install codespell run: | 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 - run: | - markdownlint-cli2 _episodes + uses: DavidAnson/markdownlint-cli2-action@v9 + with: + globs: _episodes/*.md - name: Check extra Markdown syntax - run: | - markdownlint-cli2 _extra + uses: DavidAnson/markdownlint-cli2-action@v9 + with: + globs: _extras/*.md check_lesson_and_build_default: runs-on: ubuntu-latest @@ -34,7 +37,6 @@ jobs: with: ruby-version: '3.0.4' bundler-cache: true - - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install basic requirements run: | # Need this library for nokogiri @@ -43,9 +45,6 @@ jobs: bundle config set path '.vendor/bundle' bundle config build.nokogiri --use-system-libraries bundle install - - name: "Lint episode markdown" - run: | - bundle exec mdl _episodes {} \; - name: "Check lesson for warnings" run: | make lesson-check-all @@ -75,7 +74,6 @@ jobs: with: ruby-version: '3.0.4' bundler-cache: true - - uses: DavidAnson/markdownlint-cli2-action@v9 - name: Install basic requirements run: | # Need this library for nokogiri @@ -88,5 +86,6 @@ jobs: run: | make --always-make site HPC_JEKYLL_CONFIG=_includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/_config_options.yml - name: Lint snippet markdown - run: | - markdownlint-cli2 "_includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/**/*.snip" + uses: DavidAnson/markdownlint-cli2-action@v9 + with: + globs: _includes/snippets_library/${{matrix.HPC_JEKYLL_CONFIG}}/**/*.snip From b7250032eac95aa2aba9b0ca49f40197e199c0ad Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 23:22:53 -0500 Subject: [PATCH 11/12] Long URLs should maybe be ref-links? --- _extras/discuss.md | 9 +++------ _extras/guide.md | 3 +-- _extras/learner-prerequisites.md | 3 +-- 3 files changed, 5 insertions(+), 10 deletions(-) diff --git a/_extras/discuss.md b/_extras/discuss.md index b142565e..228f78a1 100644 --- a/_extras/discuss.md +++ b/_extras/discuss.md @@ -89,8 +89,7 @@ individual to individual! > ## Running Many Serial BLAST+ Analyses in Parallel > -> [BLAST+]( -https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) +> [BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) > finds regions of similarity between biological sequences. The program > compares nucleotide or protein sequences to sequence databases and calculates > the statistical significance. @@ -107,14 +106,12 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do > > We have prepared an example dataset that has 100 sequences to analyse > (actually this is 10 sequences repeated 10 times). This set is based on the -> [BLAST GNU Parallel example]( -https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel) +> [BLAST GNU Parallel example](https://github.com/LangilleLab/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel) > > This exercise involves: > > - Downloading and expanding the dataset to the HPC system from: -> [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz]( -> {{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz) +> [{{ site.url }}{{site.baseurl }}/files/parallel_example.tar.gz]({{ site.url }}{{site.baseurl}}/files/parallel_example.tar.gz) > - Writing a job submission script to run a single analysis using the `blast` > module and the following command: > diff --git a/_extras/guide.md b/_extras/guide.md index 80d4f28e..1f952e9c 100644 --- a/_extras/guide.md +++ b/_extras/guide.md @@ -66,8 +66,7 @@ is a great way to contribute. : *to be defined* [Supercomputer](https://en.wikipedia.org/wiki/Supercomputer) -: ["... a major scientific instrument ..."]( -https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html) +: ["... a major scientific instrument ..."](https://www.hpcnotes.com/2015/10/essential-analogies-for-hpc-advocate.html) [Workstation](https://en.wikipedia.org/wiki/Workstation) : *to be defined* diff --git a/_extras/learner-prerequisites.md b/_extras/learner-prerequisites.md index 0ec2a5fa..ba5752d9 100644 --- a/_extras/learner-prerequisites.md +++ b/_extras/learner-prerequisites.md @@ -14,8 +14,7 @@ bring all prerequisites to the course. ## Pre-Workshop Survey For a motivation of this survey type, see Greg Wilson's template in [Teaching -Tech Together]( -https://teachtogether.tech/en/index.html#s:checklists-preassess). +Tech Together](https://teachtogether.tech/en/index.html#s:checklists-preassess). ### Shell From 23e931f84be95dce4b7992cb1be0a9fb0e6a0c98 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 9 Jan 2024 23:29:25 -0500 Subject: [PATCH 12/12] Complete listing of mdl rules --- .markdownlint-cli2.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.markdownlint-cli2.yaml b/.markdownlint-cli2.yaml index 7b5abfc3..077a30a8 100644 --- a/.markdownlint-cli2.yaml +++ b/.markdownlint-cli2.yaml @@ -4,22 +4,22 @@ --- config: MD001: false # heading-increment - MD002: false + MD002: false # mdl rule undefined MD003: true # heading-style MD004: true # ul-style MD005: true # list-indent - MD006: true + MD006: false # mdl rule undefined MD007: true # ul-indent - MD008: true + 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 - MD014: false - MD015: true - MD016: true - MD017: true + 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