Add jekyll-remote-include gem and citation resources for tskit

hossam26644 · benjeffery · benjeffery · commit de244fca3d29 · 2025-07-14T13:55:13.000+01:00
added citation_url and citation_md (and removed some trailing white spaces)

citation page

citation page added to navbar

citation upper case

split citation to a software-citation file

Update _includes/software-citation.html

Co-authored-by: Ben Jeffery &lt;ben.jeffery@gmail.com&gt;
diff --git a/Gemfile b/Gemfile
@@ -20,6 +20,8 @@ gem "minima", "~> 2.0"
 # If you have any plugins, put them here!
 group :jekyll_plugins do
   gem "jekyll-feed", "~> 0.6"
+  gem 'jekyll-remote-include', :github => 'netrics/jekyll-remote-include'
+
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,3 +1,9 @@
+GIT
+  remote: https://github.com/netrics/jekyll-remote-include.git
+  revision: 39ae1a1744c8837d5ee64b11c5f982304ea940e5
+  specs:
+    jekyll-remote-include (1.0.2)
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -103,6 +109,7 @@ DEPENDENCIES
   jekyll-feed (~> 0.6)
   jekyll-font-awesome-sass
   jekyll-redirect-from
+  jekyll-remote-include!
   jekyll-theme-cayman
   jekyll-timeago
   minima (~> 2.0)
diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -63,6 +63,9 @@
                 <li class="nav__item">
                     <a href="{{ '/news' | relative_url }}" class=" nav__item__link">News</a>
                 </li>
+                <li class="nav__item">
+                    <a href="{{ '/citation' | relative_url }}" class=" nav__item__link">Citation</a>
+                </li>
                 <li class="nav__item">
                     <a href="{{ '/community' | relative_url }}" class=" nav__item__link">Community</a>
                 </li>
diff --git a/_includes/software-citation.html b/_includes/software-citation.html
@@ -0,0 +1,17 @@
+<div class="col-md-12">
+  <details style="border-radius: 6px; padding: 0.5em; background-color: #03303E; margin-bottom: 0.5em;">
+    <summary style="cursor: pointer; font-family: 'rothwood'">{{ app.title }}</summary>
+
+    {% if app.citation_md %}
+      {% capture citation_md %}
+        {% remote_include app.citation_md %}
+      {% endcapture %}
+      <div style="margin-top: 1em; font-size: 13px;">
+        {{ citation_md | replace: "(sec_citation)=", "" | replace: "(citation)=", "" | markdownify }}
+      </div>
+    {% endif %}
+
+    <p>Citation details for {{ app.title }} can be found at: <a href="{{ app.citation_url }}">{{ app.citation_url }}</a></p>
+  </details>
+</div>
+
diff --git a/_software/msprime.md b/_software/msprime.md
@@ -3,8 +3,8 @@ layout: software-page
 title: msprime
 name: msprime
 #Uncomment to override automatic values
-#description: 
-#repo_url: 
+#description:
+#repo_url:
 gh_org: tskit-dev
 docs_url: https://tskit.dev/msprime/docs/
 category: simulate
@@ -14,16 +14,18 @@ logo: https://raw.githubusercontent.com/tskit-dev/administrative/main/logos/svg/
 priority: 2
 code_snippet: |2
   ts = msprime.sim_ancestry(
-      samples=10, 
-      recombination_rate=1e-4, 
+      samples=10,
+      recombination_rate=1e-4,
       sequence_length=1e6
   )
   ts = msprime.sim_mutations(ts, rate=1e-6)
 redirect_from:
   - /msprime/
+citation_url: https://tskit.dev/msprime/docs/stable/CITATION.html
+citation_md: https://raw.githubusercontent.com/tskit-dev/msprime/refs/heads/main/CITATION.md
 ---
 
-Msprime is a Python package that simulates ancestral histories and 
+Msprime is a Python package that simulates ancestral histories and
 DNA sequence data. Msprime uses backwards-in-time "coalescent" models
-which allows it to simulate data very efficiently; however, it 
+which allows it to simulate data very efficiently; however, it
 is not as flexible as forwards-in-time simulators like SLiM or fwdpy11.
diff --git a/_software/pyslim.md b/_software/pyslim.md
@@ -3,20 +3,21 @@ layout: software-page
 title: pyslim
 name: pyslim
 #Uncomment to override automatic values
-#description: 
-#repo_url: 
+#description:
+#repo_url:
 gh_org: tskit-dev
 docs_url: https://tskit.dev/pyslim/docs/stable
 category: analyse
 python_package: pyslim
 priority: 12
 code_snippet: |2
   rts = pyslim.recapitate(
-      ts, 
+      ts,
       ancestral_Ne=10000
   )
 redirect_from:
   - /pyslim/
+citation_url: https://zenodo.org/records/8205346
 ---
 
 pyslim is a small python package to help analyse and manipulate tree sequences
diff --git a/_software/tsbrowse.md b/_software/tsbrowse.md
@@ -3,8 +3,8 @@ layout: software-page
 title: tsbrowse
 name: tsbrowse
 #Uncomment to override automatic values
-#description: 
-#repo_url: 
+#description:
+#repo_url:
 gh_org: tskit-dev
 docs_url: https://tskit.dev/tsbrowse/docs/
 category: analyse
@@ -15,6 +15,7 @@ code_snippet: |2
   python -m tsbrowse serve example.tsbrowse
 redirect_from:
   - /tsbrowse/
+citation_url: https://doi.org/10.1101/2025.04.23.649987
 ---
 
 tsbrowse is a Python package that creates a webapp for exploration of the data model
diff --git a/_software/tsdate.md b/_software/tsdate.md
@@ -7,11 +7,12 @@ docs_url: https://tskit.dev/tsdate/docs/stable/
 publication: https://doi.org/10.1126/science.abi8264
 category: infer
 python_package: tsdate
-logo: https://raw.githubusercontent.com/tskit-dev/administrative/main/logos/svg/tsdate/Tskit_tsdate_logo_on_black_no_background.eps.svg                                       
+logo: https://raw.githubusercontent.com/tskit-dev/administrative/main/logos/svg/tsdate/Tskit_tsdate_logo_on_black_no_background.eps.svg
 priority: 4
 code_snippet: |2
   dated_ts = tsdate.date(inferred_ts, mutation_rate=1e-8)
 redirect_from:
   - /tsdate/
+citation_url: https://tskit.dev/tsdate/docs/stable/#citing
 ---
-Tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence. 
+Tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence.
diff --git a/_software/tsinfer.md b/_software/tsinfer.md
@@ -16,6 +16,9 @@ code_snippet: |2
   ts = tsinfer.infer(sample_data)
 redirect_from:
   - /tsinfer/
+citation_url: https://tskit.dev/tsinfer/docs/stable/CITATION.html
+citation_md: https://raw.githubusercontent.com/tskit-dev/tsinfer/refs/heads/main/CITATION.md
+
 ---
 ``Tsinfer`` is a Python package to infer a tree sequence from large
 quantities of phased DNA sequence data, for example in a VCF file
diff --git a/_software/tskit.md b/_software/tskit.md
@@ -13,8 +13,10 @@ code_snippet: |2
   afs = ts.allele_frequency_spectrum()
 redirect_from:
   - /tskit/
+citation_url: https://tskit.dev/tskit/docs/stable/citation.html
+citation_md: https://raw.githubusercontent.com/tskit-dev/tskit/refs/heads/main/docs/citation.md
 ---
 The tskit library provides the underlying functionality used to load, examine, and
 manipulate tree sequences, including efficient methods for calculating genetic statistics.
-It often forms part of an installation of other software packages such as 
+It often forms part of an installation of other software packages such as
 msprime, SLiM, fwdpp, and tsinfer.
diff --git a/_software/tstrait.md b/_software/tstrait.md
@@ -3,8 +3,8 @@ layout: software-page
 title: tstrait
 name: tstrait
 #Uncomment to override automatic values
-#description: 
-#repo_url: 
+#description:
+#repo_url:
 gh_org: tskit-dev
 docs_url: https://tskit.dev/tstrait/docs/
 publication: https://doi.org/10.1093/bioinformatics/btae334
@@ -21,6 +21,8 @@ code_snippet: |2
   )
 redirect_from:
   - /tstrait/
+citation_url: https://tskit.dev/tstrait/docs/stable/citation.html
+citation_md: https://raw.githubusercontent.com/tskit-dev/tstrait/refs/heads/main/docs/citation.md
 ---
 
 tstrait is a Python package to simulate quantitative traits from a given
diff --git a/citations.html b/citations.html
@@ -0,0 +1,23 @@
+---
+layout: page
+title: Citation
+description: A list of the citation resources for different tskit ecosystem software.
+permalink: /citation/
+---
+
+{% assign sorted_apps = site.software | sort: "priority" %}
+{% assign filtered_apps = sorted_apps | where: "gh_org", "tskit-dev" %}
+
+{% assign page_apps = filtered_apps %}
+<section class="section section--cards section--cards--type-3">
+  <div class="container">
+    <div class="row">
+      <div class="col-md-12">
+        <h2 class="section__heading">How to cite tskit-dev software</h2>
+      </div>
+    </div>
+    {% for app in page_apps %}
+        {% include software-citation.html app=app %}
+    {% endfor %}
+  </div>
+</section>
