[WIP] Ecosystem registry infrastructure

README_ecosystem_plugins.md

@@ -0,0 +1,56 @@
+# Managing the ecosystem catalog
+
+A subset of this website is devoted to providing a catalog of software that
+makes up the broader Open Free Energy ecosystem. This is intended to be a
+central clearinghouse where users can find different modular tools that can be
+plugged into an Open Free Energy workflow. This page documents that part of the
+website.
+
+## Adding a new catalog entry
+
+External contributors are most likely to want to add a new catalog entry,
+representing some useful code that they have created and wish to share. Adding
+new entries is intended to be as easy as possible.
+
+Basically, all you need to do is fork and clone this repo, and add a new item
+under the `_ecosystem/` directory. This will be a Markdown file with YAML
+frontmatter.  Copy the `_ecosystem/_defaults.md` file to get a template that
+you can work from.
+
+Add that file in a branch on your fork, and make a pull request to have your
+new entry added to the catalog!
+
+NOTE: Each ecosystem catalog entry should fit into exactly one category. If
+you've created a package that involves tools from multiple categories, please
+create multiple catalog entries. One pull request may contain as many catalog
+entries as you would like to add.
+
+## Customizing ecosystem configuration
+
+The general idea  here is that catalog entries represent different "categories"
+of object, with the objects within a category being modular replacements for
+each other. As an example, "protocol" is one of the categories for Open Free
+Energy.
+
+Details of the ecosystem configuration are in the `_config.yaml` for the site.
+In particular, custom configuration the ecosystem tools are under the
+`ecosystem_catalog` top-level heading. This allows you to change, e.g., the
+allowed categories.
+
+Some aspects of configuration are based on Jekyll's standard configuration
+tools. In particular, note that `ecosystem` is one the Jekyll `collections`,
+and note that we can set the default layout for ecosystem entries within the
+standard `defaults` configuration heading.
+
+## Changing the presentation of catalog entries
+
+Catalog entries are shown in two different styles:
+
+1. Full-page mode, where a full web page is dedicated to each entry. This is
+   intended to provide sufficient details for a reader to learn more about the
+   entry. You can customize this mode in `_layouts/ecosystem-entry.html`. 
+2. Summary mode, where a brief summary of each entry is provided, e.g., as part
+   of a list of other catalog entries. You can customize this mode in
+   `_includes/ecosystem-summary.html`.
+
+You can, of course, always create a custom page that loops over the 

_config.yml

@@ -32,6 +32,14 @@ collections:
   projects:
   jobs:
     output: true
+  ecosystem:
+    output: true
+
+ecosystem_catalog:
+  category_labels:
+    atommapper: "Atom Mappers"
+    networkplanner: "Network Planners"
+    protocol: "Protocols"
 
 paginate: 10
 paginate_path: "/news/:num/"
@@ -60,6 +68,11 @@ defaults:
       type: "jobs"
     values:
       layout: "job"
+  - scope:
+      path: ""
+      type: "ecosystem"
+    values:
+      layout: "ecosystem-entry"
   - scope:
       path: ""
     values:

_ecosystem/_default.md

@@ -0,0 +1,19 @@
+---
+name: <NAME OF ENTRY>
+category: <CATEGORY>
+developers: <DEVELOPERS AS A STRING>
+source: <URL FOR SOURCE CODE>
+license: <STRING NAME OF LICENSE>
+summary: >-
+  <ADD SUMMARY HERE>
+
+### FOLLOWING ARE OPTIONAL
+# docs: <URL FOR DOCUMENTATION>
+# contact: <EMAIL FOR CONTACT>
+# publications:
+#   - <LIST OF DOI>
+# thumbnail:
+#   src: <URL FOR THUMBNAIL IMAGE>
+#   alt: <ALT TEXT FOR THUMBNAIL>
+---
+<FREE FORM LONG DESCRIPTION HERE>

_ecosystem/example.md

@@ -0,0 +1,11 @@
+---
+name: An example plugin
+category: atommapper
+developers: Those cool cats at OpenFE
+source: https://github.com/openfreeenergy/openfreeenergy.github.io
+license: MIT
+summary: >-
+  An awesome OpenFE plugin
+---
+
+Now let me tell you all the awesome details about this plugin.

_ecosystem/example2.md

@@ -0,0 +1,11 @@
+---
+name: Another example plugin
+category: protocol
+developers: more cool cats at OpenFE
+source: https://github.com/openfreeenergy/openfreeenergy.github.io
+license: MIT
+summary: >-
+  A protocol plugin
+---
+
+

_ecosystem/kartograf.md

@@ -0,0 +1,13 @@
+---
+name: Kartograf
+category: atommapper
+developers: Ben Ries and other OpenFE people
+source: https://github.com/openfreeenergy/kartograf
+license: MIT
+summary: >-
+  Kartograf is a 3D-first atom mapper. This allows it to avoid some problems,
+  particularly those around chirality, that can occur with 2D mappers (e.g.,
+  those focused on common substructure.) Ben can expand this a little if he wants.
+---
+
+This is where Ben should write a lot more detail about Kartograf.

_ecosystem/lomap-mapper.md

@@ -0,0 +1,36 @@
+---
+name: LOMAP Atom Mapper
+category: atommapper
+developers: Mobley Lab and Open Free Energy
+source: https://github.com/openfreeenergy/Lomap
+license: MIT
+summary: >-
+  The LOMAP atom mapper is based on a maximum common substructure approach to
+  detemine the mapping between two ligands.
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Elit duis tristique sollicitudin
+nibh sit amet. Vitae auctor eu augue ut lectus. Sit amet dictum sit amet justo
+donec enim diam. Id venenatis a condimentum vitae sapien pellentesque habitant
+morbi. Ut eu sem integer vitae justo eget magna fermentum iaculis. Vel orci
+porta non pulvinar neque laoreet suspendisse interdum. Curabitur vitae nunc sed
+velit. Id aliquet risus feugiat in ante metus dictum at. Venenatis cras sed
+felis eget velit aliquet sagittis id. Nibh sed pulvinar proin gravida
+hendrerit. Eget nullam non nisi est. Viverra maecenas accumsan lacus vel
+facilisis volutpat est velit egestas. Lectus vestibulum mattis ullamcorper
+velit sed. Pellentesque elit ullamcorper dignissim cras tincidunt lobortis
+feugiat. Dolor sed viverra ipsum nunc aliquet bibendum enim.
+
+Morbi non arcu risus quis varius quam quisque id. Dui sapien eget mi proin sed.
+Nunc vel risus commodo viverra maecenas accumsan lacus. Condimentum mattis
+pellentesque id nibh tortor id aliquet lectus. In metus vulputate eu
+scelerisque felis imperdiet proin. Id velit ut tortor pretium viverra
+suspendisse potenti. Ut pharetra sit amet aliquam id. In fermentum et
+sollicitudin ac orci phasellus egestas tellus. Ultricies mi eget mauris
+pharetra. Nunc id cursus metus aliquam. Nunc non blandit massa enim nec dui
+nunc mattis. Mattis aliquam faucibus purus in massa tempor nec feugiat nisl.
+Lacus sed turpis tincidunt id aliquet risus feugiat in ante. Nisl purus in
+mollis nunc sed. In hac habitasse platea dictumst quisque sagittis. Neque
+ornare aenean euismod elementum nisi quis eleifend. Vel quam elementum pulvinar
+etiam non quam lacus suspendisse.

_includes/ecosystem-summary.html

@@ -0,0 +1,24 @@
+{% comment %}
+This is the include file for a catalog entry summary card. Style can be done
+in SASS/CSS. In this implementation, there's a paragraph for the entry
+name (which links to the entry's full page), a paragraph for the developers,
+a paramgraph for the entry's summary, and a list of bullet points for the
+license and anything else we might want to add to the summary.
+{% endcomment %}
+
+<div class="ecosystemSummary" id="ecosystem-{{ include.entry.name }}">
+    <p class="ecosystemSummaryTitle">
+        <a href="{{ include.entry.url }}">{{ include.entry.name }}</a>
+    </p>
+    <p class="ecosystemSummaryAuthor">
+        {{ include.entry.developers }}
+    </p>
+    <p class="ecosystemSummarySummary">
+        {{ include.entry.summary }}
+    </p>
+    <!-- TODO: add this in later, once there are more things to include
+    <ul class="ecosystemSummaryExtras">
+        <li>{{ include.entry.license }}</li>
+    </ul>
+    -->
+</div>

_layouts/ecosystem-entry.html

@@ -0,0 +1,32 @@
+---
+layout: page
+---
+
+<div class="ecosystemEntry">
+
+<!-- TODO: this should probably be converted to an HTML5 <aside> -->
+<div class="ecosystemDetailsBox">
+<dl>
+    <dt>Developers</dt>
+    <dd class="ecosystemEntryDevelopers">{{ page.developers }}</dd>
+    <dt>Source code</dt>
+    <!-- TODO: extract GitHub links to make prettier -->
+    <dd class="ecosystemEntrySourceCode">
+        <a href="{{ page.source }}">{{ page.source }}</a>
+    </dd>
+    <dt>License</dt>
+    <dd class="ecosystemEntryLicense">
+        {{ page.license }}
+    </dd> <!-- TODO: link known licenses -->
+</dl>
+{{ page.summary | markdownify }}
+</div>
+
+<p><span class="ecosystemCategoryLabel">
+    {% assign label = site.ecosystem_catalog.category_labels[page.category] %}
+    {{ label | upcase }}
+</span></p>
+
+{{ page.content | markdownify }}
+
+</div>

_sass/customizations.scss

@@ -105,3 +105,97 @@ code {
 }
 
 
+// for the ecosystem summary entries (e.g., ecosystem.html)
+ul.ecosystemSummaryList {
+    display: flex;
+    flex-flow: row wrap;
+    gap: 10px;
+}
+
+li.ecosystemSummaryItem {
+    display: inline-block;
+    flex: 0 0 45%;
+    vertical-align: top;
+    border: 1px solid var(--other-blue);
+    padding: 1ex;
+    box-shadow: 2px 2px 2px var(--beastly-grey);
+}
+
+div.ecosystemSummary {
+    float: left;
+    margin-bottom: 0px;
+    margin-block-start: 0px;
+    height: 100%;
+}
+
+.ecosystemSummary p {
+    margin-bottom: 10px;
+    line-height: normal;
+}
+
+p.ecosystemSummaryTitle {
+    font-size: 1.0em;
+    font-weight: 600;
+    margin-top: 5px;
+}
+
+p.ecosystemSummaryAuthor {
+    font-size: 0.5em;
+    font-weight: 300;
+}
+
+p.ecosystemSummarySummary {
+    font-size: 0.8em;
+    font-weight: 300;
+    line-height: 1.1em;
+}
+
+ul.ecosystemSummaryExtras {
+    font-size: 0.5em;
+    font-weight: 300;
+}
+
+ul.ecosystemSummaryExtras li {
+    display: inline-block;
+}
+
+// switch to 1-column layout for mobile
+@media screen and (max-width: 639px) {
+    ul.ecosystemSummaryList {
+        flex-flow: column nowrap;
+    }
+}
+
+
+// for the ecosystem entries (individual pages)
+.ecosystemEntry {
+    overflow: auto;
+}
+
+div.ecosystemDetailsBox {
+    width: 45%;
+    float: right;
+    color: var(--beastly-grey);
+    border: 1px solid var(--other-blue);
+    padding: 1ex;
+    margin: 1ex;
+}
+
+div.ecosystemDetailsBox dd.ecosystemEntrySourceCode {
+    // if URL for source is too long, use ellipsis
+    overflow: hidden;
+    white-space: nowrap;
+    text-overflow: ellipsis;
+}
+
+div.ecosystemDetailsBox p {
+    font-size: 1.0em;
+}
+
+@media screen and (max-width: 639px) {
+    div.ecosystemDetailsBox {
+        width: 90%;
+        float: left;
+    }
+
+}

ecosystem.html

@@ -0,0 +1,22 @@
+---
+title: Ecosystem
+permalink: /ecosystem/
+description: >-
+  Other tools in the OpenFE ecosystem.
+---
+
+{% assign grouped = site.ecosystem | group_by:"category" %}
+{% for category in site.ecosystem_catalog.category_labels %}
+<h3>{{ category[1] }}</h3>
+  {% assign cat_plugins = grouped | where: "name", category[0] %}
+  {% comment %}
+  There can only be one object in grouped with the appropriate name, so we
+  take cat_plugins[0]. We loop over them as li (as opposed to creating a
+  structure of divs) because that's better for screenreaders.
+  {% endcomment %}
+  <ul class="ecosystemSummaryList">
+    {% for plugin in cat_plugins[0].items %}
+    <li class="ecosystemSummaryItem">{% include ecosystem-summary.html entry=plugin %}</li>
+    {% endfor %}
+  </ul>
+{% endfor %}