v1.1.0

.docker/Dockerfile

@@ -0,0 +1,30 @@
+# start with official ruby docker image as base
+FROM ruby:3.1.2
+
+# set working directory within container
+WORKDIR /usr/src/app
+
+# pull in ruby (jekyll) and python (cite process) package info
+COPY Gemfile Gemfile.lock _cite/requirements.txt ./
+
+# install ruby packages
+RUN VERSION=$(grep -A 1 'BUNDLED WITH' Gemfile.lock | tail -n 1 | xargs); \
+    gem install bundler --version ${VERSION} && \
+    bundle _${VERSION}_ install
+
+# install python
+RUN apt update && apt install -y python3 python3-pip
+
+# install python packages
+RUN python3 -m pip install --upgrade --requirement requirements.txt
+
+# install python package for listening for file changes
+RUN pip install "watchdog[watchmedo]"
+
+# ports used by jekyll
+EXPOSE 4000
+EXPOSE 35729
+
+# run jekyll and cite process
+COPY .docker/entrypoint.sh /var
+CMD [ "/var/entrypoint.sh" ]

.docker/entrypoint.sh

@@ -0,0 +1,24 @@
+#! /bin/bash
+
+# print folder contents for debugging
+echo "Contents:"
+echo ""
+ls
+echo ""
+
+# run jekyll serve in hot-reload mode.
+# rerun whenever _config.yaml changes (jekyll hot-reload doesn't work with this file).
+watchmedo auto-restart \
+    --debug-force-polling \
+    --patterns="_config.yaml" \
+    --signal SIGTERM \
+    -- bundle exec jekyll serve --open-url --force_polling --livereload --trace --host=0.0.0.0 \
+    | sed 's/0.0.0.0/localhost/g' &
+
+# run cite process.
+# rerun whenever _data files change.
+watchmedo shell-command \
+    --debug-force-polling \
+    --recursive \
+    --command="python3 _cite/cite.py" \
+    --patterns="_data/sources*;_data/orcid*;_data/pubmed*;_data/google-scholar*" \

.docker/run.sh

@@ -0,0 +1,37 @@
+#! /bin/bash
+
+# name of image
+IMAGE=lab-website-renderer:latest
+
+# name of running container
+CONTAINER=lab-website-renderer
+
+# choose platform flag
+PLATFORM=""
+
+# default vars
+DOCKER_RUN="docker run"
+WORKING_DIR=$(pwd)
+
+# fix windows faux linux shells/tools
+if [[ $OSTYPE == msys* ]] || [[ $OSTYPE == cygwin* ]]; then
+    DOCKER_RUN="winpty docker run"
+    WORKING_DIR=$(cmd //c cd)
+fi
+
+# build docker image
+docker build ${PLATFORM} \
+    --tag ${IMAGE} \
+    --file ./.docker/Dockerfile . && \
+
+# run built docker image
+${DOCKER_RUN} ${PLATFORM} \
+    --name ${CONTAINER} \
+    --init \
+    --rm \
+    --interactive \
+    --tty \
+    --publish 4000:4000 \
+    --publish 35729:35729 \
+    --volume "${WORKING_DIR}:/usr/src/app" \
+    ${IMAGE} "$@"

.github/pull_request_template.md

@@ -6,8 +6,8 @@ You are about to open this pull request against THE TEMPLATE ITSELF. You probabl
 
 FOR THE TEMPLATE MAINTAINER(S)
 
-Checklist:
+New template version checklist:
 
-- [ ] I have updated CITATION and CHANGELOG.
+- [ ] I have updated CITATION and CHANGELOG as appropriate.
 - [ ] I have updated lab-website-template-docs as appropriate.
 - [ ] I have checked the testbed as appropriate.

.github/workflows/build-preview.yaml

@@ -47,7 +47,7 @@ jobs:
       - name: Build preview version of site
         if: github.event.action != 'closed'
         run: |
-          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
 
       - name: Commit preview to Pages branch
         uses: rossjrw/pr-preview-action@v1

.github/workflows/build-site.yaml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Build live version of site
         run: |
-          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
 
       - name: Commit live site to Pages branch
         uses: JamesIves/github-pages-deploy-action@v4

.github/workflows/versioning.yaml

@@ -57,7 +57,7 @@ jobs:
               .split(/^##?#?#?/m)
               .map((section) => {
                 const [heading, ...body] = section.split("\n");
-                return [heading.trim(), body.join("\n").trim()];
+                return { heading, body: body.join("\n") };
               });
 
             // check version
@@ -71,8 +71,8 @@ jobs:
 
             // check changelog
             const newSection = changelog.find(
-              ([heading, body]) =>
-                heading.includes(newVersion) && heading.includes(newDate) && body
+              ({ heading, body }) =>
+                heading.includes(newVersion) && heading.includes(newDate) && body.trim()
             );
             if (!newSection) throw Error("Changelog not updated or not valid");
 
@@ -109,27 +109,21 @@ jobs:
               .split(/^##?#?#?/m)
               .map((section) => {
                 const [heading, ...body] = section.split("\n");
-                return [heading.trim(), body.join("\n").trim()];
+                return { heading, body: body.join("\n") };
               });
 
             // find changelog body for version
             const body =
               changelog.find(
-                ([heading]) => heading.includes(version) && heading.includes(date)
+                ({ heading }) => heading.includes(version) && heading.includes(date)
               )?.body || "";
 
             return { version, body };
 
-      - name: Create a tag
-        id: tag
-        uses: mathieudutour/[email protected]
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          custom_tag: ${{ fromJson(steps.version.outputs.result).version }}
-
-      - name: Create a GitHub release
+      - name: Create tag and GitHub release
         uses: ncipollo/release-action@v1
         with:
-          tag: ${{ fromJson(steps.version.outputs.result).version }}
-          name: ${{ fromJson(steps.version.outputs.result).version }}
+          commit: ${{ github.ref }}
+          tag: v${{ fromJson(steps.version.outputs.result).version }}
+          name: v${{ fromJson(steps.version.outputs.result).version }}
           body: ${{ fromJson(steps.version.outputs.result).body }}

CHANGELOG.md

@@ -2,6 +2,25 @@
 
 Reference: common-changelog.org
 
+## 1.1.0 - 2023-03-17
+
+Add alert component, Docker support, accessibility fixes.
+
+### Changed
+
+- Fix Lighthouse accessibility issues.
+- De-href components when link isn't provided (no hand cursor icon on hover or nav on click).
+- In search script, limit highlights by total count instead of char length.
+- Grid and link style tweaks.
+- Take ORCID icon from Font Awesome.
+- Misc bug fixes in tags script, float component.
+
+### Added
+
+- Add Docker configuration and scripts for local previewing.
+- Add alert component and types.
+- Role icon in portrait component hoisted to top left.
+
 ## 1.0.0 - 2023-02-28
 
 First official release.

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.0.0
-date-released: 2023-02-28
+version: 1.1.0
+date-released: 2023-03-17
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

Gemfile.lock

@@ -10,9 +10,11 @@ GEM
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
     ffi (1.15.5)
+    ffi (1.15.5-x64-mingw-ucrt)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
     google-protobuf (3.22.0-arm64-darwin)
+    google-protobuf (3.22.0-x64-mingw-ucrt)
     http_parser.rb (0.8.0)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
@@ -59,6 +61,10 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
+    mini_portile2 (2.8.1)
+    nokogiri (1.13.10)
+      mini_portile2 (~> 2.8.0)
+      racc (~> 1.4)
     nokogiri (1.13.10-arm64-darwin)
       racc (~> 1.4)
     pathutil (0.16.2)
@@ -75,6 +81,8 @@ GEM
     safe_yaml (1.0.5)
     sass-embedded (1.58.3-arm64-darwin)
       google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x64-mingw-ucrt)
+      google-protobuf (~> 3.21)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     unicode-display_width (2.4.2)
@@ -85,6 +93,7 @@ PLATFORMS
   linux
   universal-darwin-21
   universal-darwin-22
+  x64-mingw-ucrt
   x64-mingw32
   x64-unknown
   x86_64-linux
@@ -99,4 +108,4 @@ DEPENDENCIES
   webrick (~> 1.7)
 
 BUNDLED WITH
-   2.4.7
+  2.4.7

README.md

@@ -8,7 +8,7 @@ Spend less time worrying about managing a website and citations, and more time r
 
 👇👇 **Get Started** 👇👇
 
-[**📚 Documentation 📚**](https://greene-lab.gitbook.io/lab-website-template-docs)
+[**Documentation**](https://greene-lab.gitbook.io/lab-website-template-docs)
 
 ## Key Features
 

_config.yaml

@@ -12,7 +12,6 @@ links:
   google-scholar: ETJoidYAAAAJ
   github: your-lab
   twitter: YourLabHandle
-  instagram: YourLabHandle
   youtube: YourLabChannel
 
 ### jekyll settings

_data/citations.yaml

@@ -54,8 +54,8 @@
   plugin: sources.py
   file: sources.yaml
   type: paper
-  description: Lorem ipsum _dolor sit amet_, consectetur adipiscing elit, sed do eiusmod
-    tempor incididunt ut labore et dolore magna aliqua.
+  description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed
+    do eiusmod tempor incididunt ut labore et dolore magna aliqua.
   image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2
   buttons:
   - type: manubot

_data/sources.yaml

@@ -1,6 +1,6 @@
 - id: doi:10.1371/journal.pcbi.1007128
   type: paper
-  description: Lorem ipsum _dolor sit amet_, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+  description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
   date: 2020-12-4
   image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2
   buttons:

_data/types.yaml

@@ -73,7 +73,7 @@ search:
 # social media
 
 orcid:
-  icon: orcid.svg
+  icon: fa-brands fa-orcid
   text: ORCID
   tooltip: ORCID
   link: https://orcid.org/$VALUE
@@ -120,6 +120,32 @@ linkedin:
   tooltip: LinkedIn
   link: https://www.linkedin.com/in/$VALUE
 
+# alerts
+
+tip:
+  icon: fa-solid fa-lightbulb
+  color: "#d946ef"
+
+help:
+  icon: fa-solid fa-circle-question
+  color: "#6366f1"
+
+info:
+  icon: fa-solid fa-circle-info
+  color: "#0ea5e9"
+
+success:
+  icon: fa-solid fa-circle-check
+  color: "#22c55e"
+
+warning:
+  icon: fa-solid fa-circle-exclamation
+  color: "#F59E0B"
+
+error:
+  icon: fa-solid fa-ban
+  color: "#ef4444"
+
 # publications
 
 paper:

_includes/alert.html

@@ -0,0 +1,10 @@
+{% assign color = site.data.types[include.type].color | default: "#808080" %}
+<div class="alert" style="--color: {{ color }}">
+  {% assign icon = site.data.types[include.type].icon
+    | default: "fa-solid fa-circle-info"
+  %}
+  {% include icon.html icon=icon %}
+  <div class="alert-content">
+    {{ include.content | markdownify }}
+  </div>
+</div>

_includes/button.html

@@ -9,12 +9,11 @@
       {% if button.tooltip %}
         data-tooltip="{{ button.tooltip }}"
       {% endif %}
-      {% if include.style %}
-        data-style="{{ include.style }}"
-      {% endif %}
+      data-style="{{ include.style }}"
       {% if include.flip %}
         data-flip
       {% endif %}
+      aria-label="{{ button.tooltip | default: button.icon | default: "button" }}"
     >
       {% include icon.html icon=button.icon %}
       {% if button.text and button.text != "" %}