Merge pull request #55 from RSEToolkit/ns-rse/54-further-linting

Lints existing code base with pre-commit & markdownlint-cli2
RSEToolkit · Oct 19, 2023 · f454216 · f454216
2 parents 94f347f + 130019d
commit f454216
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Showing 44 changed files with 235 additions and 145 deletions.
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,6 @@
+# This file ignores the blame associated with the listed commits from being shown
+# The initial use is to prevent blame associated with linting giving a false impression of who wrote the code.
+
+# Linting of README.md and all_documents.
+67ce492384b52461123daefa740c0d90a2d044c5
+4a45bdfe8e8dbba40d8d8df35bba0a6e67328c9a
diff --git a/.github/workflows/jekyll.yaml b/.github/workflows/jekyll.yaml
@@ -62,4 +62,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v1
diff --git a/.gitignore b/.gitignore
@@ -4,4 +4,8 @@ _site
 .jekyll-metadata
 vendor
 # temporary spreadsheet files
-.~lock.*
+.~lock.*
+
+# Emacs temp files
+\#*
+*~
diff --git a/.markdownlint-cli2.yaml b/.markdownlint-cli2.yaml
@@ -14,5 +14,9 @@ globs:
   - "**/*.md"
   - "**/*.markdown"
 
+# Ignores
+ignores:
+  - "*.svg"
+
 # Fix any fixable errors
 fix: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0  # Use the ref you want to point at
+    rev: v4.5.0  # Use the ref you want to point at
     hooks:
       - id: trailing-whitespace
         types: [yaml, markdown]

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -10,12 +10,12 @@ GEM
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
     eventmachine (1.2.7-x64-mingw32)
-    ffi (1.16.1)
-    ffi (1.16.1-x64-mingw32)
+    ffi (1.16.3)
+    ffi (1.16.3-x64-mingw32)
     forwardable-extended (2.6.0)
-    google-protobuf (3.23.4-arm64-darwin)
-    google-protobuf (3.23.4-x64-mingw32)
-    google-protobuf (3.23.4-x86_64-linux)
+    google-protobuf (3.24.4-arm64-darwin)
+    google-protobuf (3.24.4-x64-mingw32)
+    google-protobuf (3.24.4-x86_64-linux)
     http_parser.rb (0.8.0)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
@@ -64,18 +64,18 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.6)
-    rouge (3.30.0)
+    rouge (4.1.3)
     safe_yaml (1.0.5)
-    sass-embedded (1.58.3)
-      google-protobuf (~> 3.21)
-      rake (>= 10.0.0)
+    sass-embedded (1.69.4)
+      google-protobuf (~> 3.23)
+      rake (>= 13.0.0)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     tzinfo-data (1.2023.3)
       tzinfo (>= 1.0.0)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     wdm (0.1.1)
     webrick (1.8.1)
 

diff --git a/LICENSE.md b/LICENSE.md
diff --git a/_data/resources.csv b/_data/resources.csv
@@ -105,4 +105,4 @@ Id,Name,Authors,Citation,FirstAuthor,Journal,PublicationYear,CreateDate,PMCID,NI
 19158119,Bronchial epithelial cells cultured from clinically stable lung allograft patients promote the development of macrophages from monocytes rather than dendritic cells,"Ward C, Eger K, Diboll J, Jones D, Haniffa MA, Brodlie M, Fisher A, Lordan JL, Corris PA, Hilkens CM.",Thorax. 2009 May;64(5):430-5. doi: 10.1136/thx.2008.104067. Epub 2009 Jan 21.,Ward C,Thorax,2009,2009/01/23,PMC2669498,,10.1136/thx.2008.104067
 34262047,Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity,"Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE; Human Cell Atlas Lung Biological Network.",Nat Commun. 2021 Jul 14;12(1):4314. doi: 10.1038/s41467-021-24467-0.,Bui LT,Nat Commun,2021,2021/07/15,PMC8280215,,10.1038/s41467-021-24467-0
 16901329,Painful leg ulcers and a rash in a patient with polycythaemia rubra vera. Diagnosis: hydroxyurea-induced leg ulceration and dermatomyositis-like skin changes,"Haniffa MA, Speight EL.",Clin Exp Dermatol. 2006 Sep;31(5):733-4. doi: 10.1111/j.1365-2230.2006.02193.x.,Haniffa MA,Clin Exp Dermatol,2006,2006/08/12,,,10.1111/j.1365-2230.2006.02193.x
-11507311,Aortoenteric fistula complicating an infected aortic graft: diagnosis by leukocyte scintigraphy,"Ganatra RH, Haniffa MA, Hawthorne AB, Rees JI.",Clin Nucl Med. 2001 Sep;26(9):800-1. doi: 10.1097/00003072-200109000-00022.,Ganatra RH,Clin Nucl Med,2001,2001/08/17,,,10.1097/00003072-200109000-00022
+11507311,Aortoenteric fistula complicating an infected aortic graft: diagnosis by leukocyte scintigraphy,"Ganatra RH, Haniffa MA, Hawthorne AB, Rees JI.",Clin Nucl Med. 2001 Sep;26(9):800-1. doi: 10.1097/00003072-200109000-00022.,Ganatra RH,Clin Nucl Med,2001,2001/08/17,,,10.1097/00003072-200109000-00022
diff --git a/_data/resources_list.csv b/_data/resources_list.csv
@@ -42,4 +42,4 @@ Interactive Data Tools,https://millennialcities.com/interactive-data-tools/,"Int
 Righting Software: A Method for System and Project Design,https://www.amazon.co.uk/Righting-Software-Juval-L%C3%B6wy/dp/0136524036,,,,"technical",,,
 "quality (poor, medium, good)",https://carpentries-incubator.github.io/git-novice-branch-pr/,,,,"technical",,,
 Workflows with Python and Git,https://carpentries-incubator.github.io/swc-ext-python/,,,,"technical",,,
-Real Python,https://realpython.com,"Extensive collection of Python-related guides and tutorials, for all levels. Some require a subscritpionl, but most of them all free. ","-","programming, python","technical",,,
+Real Python,https://realpython.com,"Extensive collection of Python-related guides and tutorials, for all levels. Some require a subscritpionl, but most of them all free. ","-","programming, python","technical",,,
diff --git a/_data/skills.json b/_data/skills.json
@@ -63,4 +63,4 @@
         "Peer science communication",
         "Content and knowledge management"
     ]
-}
+}
diff --git a/_includes/footer.html b/_includes/footer.html
@@ -120,4 +120,4 @@ <h6 class="text-sm">Legal</h6>
       </div>
     </div>
   </div>
-</footer>
+</footer>
diff --git a/_includes/head.html b/_includes/head.html
@@ -21,4 +21,4 @@
   {%- if jekyll.environment == 'production' and site.google_analytics -%}
   {%- include google-analytics.html -%}
   {%- endif -%}
-</head>
+</head>
diff --git a/_includes/header.html b/_includes/header.html
@@ -63,4 +63,4 @@ <h1 class="text-white">Research Software<br />Competencies Toolkit</h1>
             </div>
         </div>
     </header>
-    {% endif %}
+    {% endif %}
diff --git a/_layouts/default.html b/_layouts/default.html
@@ -13,4 +13,4 @@
   <script src="{{ '/assets/js/core/material-kit.min.js?v=3.0.4' | relative_url }}" type="text/javascript"></script>
 </body>
 
-</html>
+</html>
diff --git a/_layouts/page.html b/_layouts/page.html
@@ -16,4 +16,4 @@ <h3>{{ page.title }}</h3>
       {{ content }}
     </div>
   </div>
-</div>
+</div>
diff --git a/about.md b/about.md
@@ -3,49 +3,69 @@ layout: page
 title: "About the project"
 category: Project
 ---
-RSE Competencies Toolkit is a resource to support RSEs (Research Software Engineers) in tracking and managing their professional development. It is currently in the early stages of development and we welcome contributions and feedback.
+RSE Competencies Toolkit is a resource to support RSEs (Research Software Engineers) in tracking and managing their
+professional development. It is currently in the early stages of development and we welcome contributions and feedback.
 
-Note that, while we've focussed on RSE during the early stages of development, this tool can be used for any roles. We plan to extend this to other research roles and welcome contributions and collaboration from anyone working in research, broadly defined.
+Note that, while we've focussed on RSE during the early stages of development, this tool can be used for any roles. We
+plan to extend this to other research roles and welcome contributions and collaboration from anyone working in research,
+broadly defined.
 
 RSE Competencies Toolkit comprises:
 
-* An RSE competency framework, outlining a structured set of skills that are useful when working as an RSE, with examples of how these skills can be demonstrated at different levels of experience. Not all RSEs will or need to have all skills at all levels.
+* An RSE competency framework, outlining a structured set of skills that are useful when working as an RSE, with
+  examples of how these skills can be demonstrated at different levels of experience. Not all RSEs will or need to have
+  all skills at all levels.
 * A curated set of training resources, linked to the skills and levels from the competency framework.
 * A tool to visualise and compare different competency profiles.
 
 RSE Competencies Toolkit aims to support the following uses:
 
 * Recording and visualising your competency profile as an individual RSE
-* Comparing competency profiles across a group of RSEs (e.g. to show the commonalities and variety across RSEs doing the same role at the same level at the same organisation, or comparing across organisations)
+* Comparing competency profiles across a group of RSEs (e.g. to show the commonalities and variety across RSEs doing the
+  same role at the same level at the same organisation, or comparing across organisations)
 * Find high-quality training resources to improve skills in a particular competency
-* Define aspirational competency profiles, illustrate the gap to your current profile and highlight training resources that could help bridge that gap.
+* Define aspirational competency profiles, illustrate the gap to your current profile and highlight training resources
+  that could help bridge that gap.
 
 ### Get in touch
 
-* Join our Slack channel in the UK RSE Workspace ([#rse-competencies-toolkit](https://ukrse.slack.com/archives/C05CY0YFWEL))
-* Join our Google Groups group ([groups.google.com/g/rse-competencies-toolkit](https://groups.google.com/g/rse-competencies-toolkit))
-* Star us on Github ([github.com/RSEToolkit/rse-competencies-toolkit](https://github.com/RSEToolkit/rse-competencies-toolkit/issues))
+* Join our Slack channel in the UK RSE Workspace
+  ([#rse-competencies-toolkit](https://ukrse.slack.com/archives/C05CY0YFWEL))
+* Join our Google Groups group
+  ([groups.google.com/g/rse-competencies-toolkit](https://groups.google.com/g/rse-competencies-toolkit))
+* Star us on Github
+  ([github.com/RSEToolkit/rse-competencies-toolkit](https://github.com/RSEToolkit/rse-competencies-toolkit/issues))
 
 ### Support the project
 
-If you would like to contribute, we welcome all [contributions on a range of topics](https://github.com/RSEToolkit/rse-competencies-toolkit/tree/main#support-needed). Please also check the following list of [Issues on the Github repository](https://github.com/RSEToolkit/rse-competencies-toolkit/issues) for ways to help.
+If you would like to contribute, we welcome all [contributions on a range of
+topics](https://github.com/RSEToolkit/rse-competencies-toolkit/tree/main#support-needed). Please also check the
+following list of [Issues on the Github repository](https://github.com/RSEToolkit/rse-competencies-toolkit/issues) for
+ways to help.
 
 ### Important links
 
-In this early stage of the project, we have several working documents. The following documents have been used for community discussions and development.
+In this early stage of the project, we have several working documents. The following documents have been used for
+community discussions and development.
 
-**Active collaborative documents**
+#### Active collaborative documents
 
-* [Collaborative meeting notes (Google Docs)](https://docs.google.com/document/d/1D1RhtnZ9CTTkSaornYE3l3I1JAqZfEWiiW8nADV9kEw/edit?usp=sharing)
-* [Slide deck (Google Slides)](https://docs.google.com/presentation/d/10jG8FYFAyKD8FI_MNo9RTqFUHg4A9e5jB_iHpA_Ut3A/edit?usp=sharing)
+* [Collaborative meeting notes (Google
+  Docs)](https://docs.google.com/document/d/1D1RhtnZ9CTTkSaornYE3l3I1JAqZfEWiiW8nADV9kEw/edit?usp=sharing)
+* [Slide deck (Google
+  Slides)](https://docs.google.com/presentation/d/10jG8FYFAyKD8FI_MNo9RTqFUHg4A9e5jB_iHpA_Ut3A/edit?usp=sharing)
 
-**Working documents for the framework**
+#### Working documents for the framework
 
-* [Skills framework (Google Docs)](https://docs.google.com/spreadsheets/d/1M8f9luJrc3w4rz4lD-cEpJUfi6qigh9PBk7Fm5sq_jQ/edit?usp=sharing)
+* [Skills framework (Google
+  Docs)](https://docs.google.com/spreadsheets/d/1M8f9luJrc3w4rz4lD-cEpJUfi6qigh9PBk7Fm5sq_jQ/edit?usp=sharing)
 * [Skills framework (JSON)](https://github.com/RSEToolkit/rse-competencies-toolkit/blob/main/_data/skills.json)
-* [Resources for professional development (Google Sheets)](https://docs.google.com/spreadsheets/d/1bHagH4hibAlPJ1inuaZMu-0tmNtjXoJeVPzGFwwWh0U/edit?usp=sharing)
-* [Skill levels (Google Docs)](https://docs.google.com/document/d/1syrY4gyaAcNuONK0ANUiHgHcbJ3P9RoqSjy57AjUsuM/edit#heading=h.nlkwx70wrmf)
+* [Resources for professional development (Google
+  Sheets)](https://docs.google.com/spreadsheets/d/1bHagH4hibAlPJ1inuaZMu-0tmNtjXoJeVPzGFwwWh0U/edit?usp=sharing)
+* [Skill levels (Google
+  Docs)](https://docs.google.com/document/d/1syrY4gyaAcNuONK0ANUiHgHcbJ3P9RoqSjy57AjUsuM/edit#heading=h.nlkwx70wrmf)
 
-**Notes from community sessions and engagement**
+#### Notes from community sessions and engagement
 
-* [Notes from RSECon23 Unconference sessions (Google Docs)](https://docs.google.com/document/d/1BTShiFZ7tYu5TcYa5xb5WGoxL_CD69qSVX_h1qrsuG8/edit?usp=sharing)
+* [Notes from RSECon23 Unconference sessions (Google
+  Docs)](https://docs.google.com/document/d/1BTShiFZ7tYu5TcYa5xb5WGoxL_CD69qSVX_h1qrsuG8/edit?usp=sharing)
diff --git a/assets/css/material-kit.css b/assets/css/material-kit.css
@@ -27933,4 +27933,4 @@ pre[class*="language-"] {
   }
 }
 
-/*# sourceMappingURL=kit-free.css.map */
+/*# sourceMappingURL=kit-free.css.map */
diff --git a/assets/css/material-kit.css.map b/assets/css/material-kit.css.map
diff --git a/assets/css/material-kit.min.css b/assets/css/material-kit.min.css
diff --git a/assets/css/nucleo-icons.css b/assets/css/nucleo-icons.css
@@ -594,4 +594,4 @@ License - nucleoapp.com/license/
 }
 
 
-/* all icon font classes list here */
+/* all icon font classes list here */
diff --git a/assets/css/nucleo-svg.css b/assets/css/nucleo-svg.css
@@ -132,4 +132,4 @@ Stroke effects - Nucleo outline icons
   -ms-transform: translateX(0.5px) translateY(0.5px);
   -o-transform: translateX(0.5px) translateY(0.5px);
   transform: translateX(0.5px) translateY(0.5px);
-}
+}
diff --git a/assets/img/down-arrow-white.svg b/assets/img/down-arrow-white.svg
diff --git a/assets/img/down-arrow.svg b/assets/img/down-arrow.svg
diff --git a/assets/img/logos/gray-logos/logo-apple.svg b/assets/img/logos/gray-logos/logo-apple.svg
diff --git a/assets/img/logos/gray-logos/logo-coinbase.svg b/assets/img/logos/gray-logos/logo-coinbase.svg