v1.1.1 (#174)

See changelog for high level, user-facing changes.

- docker python install changes. pin watchdog version, turn off unneeded
caching.
- docker entrypoint changes. run cite process immediately, ensure no
simultaneous runs.
- first time setup fixes. don't parse config.yaml as yaml, instead
customize with string replacement to preserve key order and comments.
- add title and link fallbacks to citation component
- fix start/end markers for blog post excerpts, and remove special
characters from hidden search attribute
- change member page from col layout to float
- add multi-line option to regex_scan liquid plugin (to support
start/end marker bug above)
- add new regex_strip liquid plugin to strip all special characters from
string
- card, code, portrait, post excerpt css fixes
- fix testbed image links
- (re)include user pr template
- fix versioning workflow to correctly parse and split changelog
- add show-title and show-subtitle site config options
- include site subtitle in description meta tag

.docker/Dockerfile

@@ -16,10 +16,10 @@ RUN VERSION=$(grep -A 1 'BUNDLED WITH' Gemfile.lock | tail -n 1 | xargs); \
 RUN apt update && apt install -y python3 python3-pip
 
 # install python packages
-RUN python3 -m pip install --upgrade --requirement requirements.txt
+RUN python3 -m pip install --no-cache-dir --upgrade --requirement requirements.txt
 
 # install python package for listening for file changes
-RUN pip install "watchdog[watchmedo]"
+RUN pip install "watchdog[watchmedo]==3.0.0"
 
 # ports used by jekyll
 EXPOSE 4000

.docker/entrypoint.sh

@@ -6,19 +6,22 @@ echo ""
 ls
 echo ""
 
-# run jekyll serve in hot-reload mode.
-# rerun whenever _config.yaml changes (jekyll hot-reload doesn't work with this file).
+# run cite process
+python3 _cite/cite.py
+
+# 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' &
+    | sed "s/LiveReload address.*//g;s/0.0.0.0/localhost/g" &
 
-# run cite process.
-# rerun whenever _data files change.
+# rerun cite process whenever _data files change
 watchmedo shell-command \
     --debug-force-polling \
     --recursive \
+    --wait \
     --command="python3 _cite/cite.py" \
     --patterns="_data/sources*;_data/orcid*;_data/pubmed*;_data/google-scholar*" \

.github/user_pull_request_template.md

@@ -0,0 +1,4 @@
+This website is based on the Lab Website Template.
+See its documentation for working with this site:
+
+https://greene-lab.gitbook.io/lab-website-template-docs

.github/workflows/build-preview.yaml

@@ -21,6 +21,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 

.github/workflows/build-site.yaml

@@ -20,6 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 

.github/workflows/first-time-setup.yaml

@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 
@@ -28,9 +29,11 @@ jobs:
         with:
           ref: gh-pages
 
+      # clean slate, as if starting from orphan branch
       - name: Clear Pages branch
-        run: rm -rf * .github .gitignore
+        run: rm -rf * .*
 
+      # prevent GitHub from running Jekyll a second time after build
       - name: Make .nojekyll file
         run: touch .nojekyll
 
@@ -46,15 +49,18 @@ jobs:
       - name: Checkout main branch
         uses: actions/checkout@v3
 
-      - name: Remove unneeded files
+      - name: Remove files user doesn't need
         run: |
           rm -rf \
-            README.md \
             CHANGELOG.md \
             testbed.md \
             .github/ISSUE_TEMPLATE \
             .github/workflows/versioning.yaml \
             .github/pull_request_template.md \
+      
+      - name: Rename files
+        run: \
+          mv .github/user_pull_request_template.md .github/pull_request_template.md
 
       - name: Set vars for personalization
         run: |
@@ -73,25 +79,22 @@ jobs:
           _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
           " > README.md
 
-      - name: Install packages
-        run: yarn add yaml
-
       - name: Personalize Jekyll config for user
         uses: actions/github-script@v6
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
-            const { parse, stringify } = require("yaml");
             const file = "_config.yaml";
-            const config = parse(readFileSync(file).toString());
-            config.title = "${{ env.USER }}";
-            config.description = "${{ env.DESCRIPTION }}";
-            config.email = "contact@${{ env.USER }}.com";
-            config.github = "${{ env.USER }}";
-            config.twitter = "${{ env.USER }}";
-            config.instagram = "${{ env.USER }}";
-            config.youtube = "${{ env.USER }}";
-            writeFileSync(file, stringify(config));
+            const contents = readFileSync(file)
+              .toString()
+              .replace(/(^title: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^subtitle: ).*$/m, "$1")
+              .replace(/(^description: ).*$/m, "$1${{ env.DESCRIPTION }}")
+              .replace(/(^  email: ).*$/m, "$1contact@${{ env.USER }}.com")
+              .replace(/(^  github: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^  twitter: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^  youtube: ).*$/m, "$1${{ env.USER }}");
+            writeFileSync(file, contents);
 
       - name: Personalize homepage for user
         uses: actions/github-script@v6

.github/workflows/update-citations.yaml

@@ -28,6 +28,7 @@ jobs:
     timeout-minutes: 15
 
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 

.github/workflows/update-url.yaml

@@ -19,6 +19,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 
@@ -31,6 +32,7 @@ jobs:
       - name: Checkout branch contents
         uses: actions/checkout@v3
 
+      # update link to site in readme
       - name: Update readme
         uses: actions/github-script@v6
         with:

.github/workflows/versioning.yaml

@@ -20,6 +20,7 @@ jobs:
       github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 
@@ -54,10 +55,10 @@ jobs:
             );
             const changelog = readFileSync("pr/CHANGELOG.md")
               .toString()
-              .split(/^##?#?#?/m)
+              .split(/^## /m)
               .map((section) => {
                 const [heading, ...body] = section.split("\n");
-                return { heading, body: body.join("\n") };
+                return [heading.trim(), body.join("\n").trim()];
               });
 
             // check version
@@ -71,8 +72,8 @@ jobs:
 
             // check changelog
             const newSection = changelog.find(
-              ({ heading, body }) =>
-                heading.includes(newVersion) && heading.includes(newDate) && body.trim()
+              ([heading, body]) =>
+                heading.includes(newVersion) && heading.includes(newDate) && body
             );
             if (!newSection) throw Error("Changelog not updated or not valid");
 
@@ -83,6 +84,7 @@ jobs:
       github.event_name == 'push'
     runs-on: ubuntu-latest
     steps:
+      # for debugging
       - name: Print contexts
         uses: crazy-max/ghaction-dump-context@v1
 
@@ -106,24 +108,30 @@ jobs:
             );
             const changelog = readFileSync("CHANGELOG.md")
               .toString()
-              .split(/^##?#?#?/m)
+              .split(/^## /m)
               .map((section) => {
                 const [heading, ...body] = section.split("\n");
-                return { heading, body: body.join("\n") };
+                return [heading.trim(), body.join("\n").trim()];
               });
 
             // find changelog body for version
-            const body =
+            const [, body = ""] =
               changelog.find(
-                ({ heading }) => heading.includes(version) && heading.includes(date)
-              )?.body || "";
+                ([heading]) => heading.includes(version) && heading.includes(date)
+              ) || [];
 
             return { version, body };
 
-      - name: Create tag and GitHub release
+      - name: Create tag
+        id: tag
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          custom_tag: ${{ fromJson(steps.version.outputs.result).version }}
+
+      - name: Create GitHub release
         uses: ncipollo/release-action@v1
         with:
-          commit: ${{ github.ref }}
-          tag: v${{ fromJson(steps.version.outputs.result).version }}
-          name: v${{ fromJson(steps.version.outputs.result).version }}
+          tag: ${{ fromJson(steps.version.outputs.result).version }}
+          name: ${{ fromJson(steps.version.outputs.result).version }}
           body: ${{ fromJson(steps.version.outputs.result).body }}

CHANGELOG.md

@@ -2,6 +2,23 @@
 
 Reference: common-changelog.org
 
+## 1.1.1 - 2023-04-06
+
+### Changed
+
+- Change member profile page from col layout to float.
+- Fix first time setup. Preserve config formatting and comments.
+- Improve Docker cite process behavior.
+- Fix post excerpt component start/end markers and special search attr chars.
+- Fix misc CSS.
+
+### Added
+
+- Add show-title and show-subtitle site config options.
+- Include site subtitle in description meta tag.
+- Add user pull request template.
+- Add title and link fallbacks to citation component.
+
 ## 1.1.0 - 2023-03-17
 
 Add alert component, Docker support, accessibility fixes.

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.1.0
-date-released: 2023-03-17
+version: 1.1.1
+date-released: 2023-04-06
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_cite/cite.py

@@ -1,3 +1,7 @@
+"""
+cite process to convert sources and metasources into full citations
+"""
+
 from importlib import import_module
 from pathlib import Path
 from dotenv import load_dotenv
@@ -85,11 +89,11 @@
 
 # merge sources with matching (non-blank) ids
 for a in range(0, len(sources)):
-    id = sources[a].get("id")
-    if not id:
+    _id = sources[a].get("id")
+    if not _id:
         continue
     for b in range(a + 1, len(sources)):
-        if sources[b].get("id") == id:
+        if sources[b].get("id") == _id:
             sources[a].update(sources[b])
             sources[b] = {}
 sources = [entry for entry in sources if entry]
@@ -113,15 +117,15 @@
     citation = {}
 
     # source id
-    id = source.get("id", "").strip()
+    _id = source.get("id", "").strip()
 
     # Manubot doesn't work without an id
-    if id:
+    if _id:
         log("Using Manubot to generate citation", 1)
 
         try:
             # run Manubot and set citation
-            citation = cite_with_manubot(source)
+            citation = cite_with_manubot(_id)
 
         except Exception as e:
             # if manually-entered source, throw error on cite failure

_cite/plugins/google-scholar.py

@@ -42,15 +42,14 @@ def query():
     for work in response:
 
         # create source
-        source = {}
-
-        # format source fields
-        source["id"] = work.get("citation_id", "")
-        source["title"] = work.get("title", "")
-        source["authors"] = list(map(str.strip, work.get("authors", "").split(",")))
-        source["publisher"] = work.get("publication", "")
-        source["date"] = work.get("year", "") + "-01-01"
-        source["link"] = work.get("link", "")
+        source = {
+            "id": work.get("citation_id", ""),
+            "title": work.get("title", ""),
+            "authors": list(map(str.strip, work.get("authors", "").split(","))),
+            "publisher": work.get("publication", ""),
+            "date": work.get("year", "") + "-01-01",
+            "link": work.get("link", ""),
+        }
 
         # copy fields from entry to source
         source.update(entry)

_cite/util.py

@@ -1,3 +1,7 @@
+"""
+utility functions for cite process and plugins
+"""
+
 import subprocess
 import json
 import yaml
@@ -64,7 +68,7 @@ def list_of_dicts(data):
     check if data is list of dicts
     """
 
-    return type(data) == list and all(type(entry) == dict for entry in data)
+    return isinstance(data, list) and all(isinstance(entry, dict) for entry in data)
 
 
 def format_date(date):
@@ -144,17 +148,14 @@ def save_data(path, data):
 
 @log_cache
 @cache.memoize(name="manubot", expire=90 * (60 * 60 * 24))
-def cite_with_manubot(source):
+def cite_with_manubot(_id):
     """
-    generate citation data for source with Manubot
+    generate citation data for source id with Manubot
     """
 
-    # source id
-    id = source.get("id")
-
     # run Manubot
     try:
-        commands = ["manubot", "cite", id, "--log-level=WARNING"]
+        commands = ["manubot", "cite", _id, "--log-level=WARNING"]
         output = subprocess.Popen(commands, stdout=subprocess.PIPE).communicate()
     except Exception as e:
         log(e, 3)
@@ -170,7 +171,7 @@ def cite_with_manubot(source):
     citation = {}
 
     # original id
-    citation["id"] = id
+    citation["id"] = _id
 
     # title
     citation["title"] = manubot.get("title", "")