[WIP] Ecosystem registry infrastructure

README_ecosystem_plugins.md

@@ -0,0 +1,49 @@
+# 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!
+
+## 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 (cards), 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`.

_config.yml

@@ -32,6 +32,21 @@ collections:
   projects:
   jobs:
     output: true
+  ecosystem:
+    output: true
+
+ecosystem_catalog:
+  collection: "ecosystem"
+  categories:
+    # name is the name used in YAML; label is the natural language label
+    - name: "atommappers"
+      label: "Atom Mappers"
+    - name: "scorers"
+      label: "Mapping Scorers"
+    - name: "networkplanners"
+      label: "Network Planners"
+    - name: "protocols"
+      label: "Protocols"
 
 paginate: 10
 paginate_path: "/news/:num/"
@@ -60,6 +75,11 @@ defaults:
       type: "jobs"
     values:
       layout: "job"
+  - scope:
+      path: ""
+      type: "ecosystem"
+    values:
+      layout: "ecosystem-entry"
   - scope:
       path: ""
     values:

_ecosystem/_default.md

@@ -0,0 +1,47 @@
+---
+name: <NAME OF ENTRY>
+developers: <DEVELOPERS AS A STRING>
+source: <URL FOR SOURCE CODE>
+license: <STRING NAME OF LICENSE>
+### SELECT THE TYPES OF PLUGINS YOU PROVIDE
+# atommappers:
+# - name: <NAME OF FIRST PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# - name: <NAME OF NEXT PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# networkplanners:
+# - name: <NAME OF FIRST PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# - name: <NAME OF NEXT PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# scorers:
+# - name: <NAME OF FIRST PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# - name: <NAME OF NEXT PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# protocols:
+# - name: <NAME OF FIRST PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+# - name: <NAME OF NEXT PLUGIN>
+#   description: >-
+#     <BRIEF DESCRIPTION OF PLUGIN>
+
+### FOLLOWING ARE OPTIONAL
+# docs: <URL FOR DOCUMENTATION>
+# contact: <EMAIL FOR CONTACT> (not used)
+# conda-forge: <INSTALL NAME FOR CONDA-FORGE>
+# pypi: <INSTALL NAME FOR PYPI>
+# publications:
+#   - <LIST OF DOI>
+# thumbnail: (not used)
+#   src: <URL FOR THUMBNAIL IMAGE>
+#   alt: <ALT TEXT FOR THUMBNAIL>
+---
+<FREE FORM LONG DESCRIPTION HERE>

_ecosystem/example.md

@@ -0,0 +1,12 @@
+---
+title: An example plugin
+developers: Those cool cats at OpenFE
+source: https://github.com/openfreeenergy/openfreeenergy.github.io
+license: MIT
+atommappers:
+  - name: Example
+    description: >-
+      An awesome OpenFE plugin
+---
+
+Now let me tell you all the awesome details about this plugin.

_ecosystem/example2.md

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

_ecosystem/kartograf.md

@@ -0,0 +1,15 @@
+---
+title: Kartograf
+developers: Ben Ries and other OpenFE people
+source: https://github.com/openfreeenergy/kartograf
+license: MIT
+atommappers:
+  - name: KartografAtomMapper
+    description: >-
+      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.md

@@ -0,0 +1,42 @@
+---
+title: LOMAP
+developers: Mobley Lab and Open Free Energy
+source: https://github.com/openfreeenergy/Lomap
+conda-forge: lomap2
+license: MIT
+atommappers:
+  - name: LomapAtomMapper
+    description: >-
+      The LOMAP atom mapper is based on a maximum common substructure approach
+      to detemine the mapping between two ligands.
+networkplanners:
+  - name: LomapNetworkPlanner
+    description: >-
+      lorem ipsum
+---
+
+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 +1,29 @@
+{% comment %}
+This is the include file for a catalog entry summary card. Style can be done
+in SASS/CSS. 
+
+This `include` takes `package` and `plugin` arguments.
+{% endcomment %}
+
+<div class="ecosystemSummary" id="ecosystem-{{ include.plugin.name }}">
+    <h1>
+        <a href="{{ include.project.url }}">{{ include.plugin.name }}</a>
+    </h1>
+    <address class="ecosystemSummaryAuthor">
+        {{ include.project.developers }}
+        <br />
+        <span class="part-of-project">
+        Part of <a href="{{ include.project.url }}">
+            {{ include.project.title }}
+        </a>
+        </span>
+    </address>
+    <div class="ecosystemSummarySummary">
+        {{ include.plugin.description | markdownify }}
+    </div>
+    <!-- TODO: add this in later, once there are more things to include
+    <ul class="ecosystemSummaryExtras">
+        <li>{{ include.package.license }}</li>
+    </ul>
+    -->
+</div>

_layouts/ecosystem-entry.html

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+---
+layout: page
+---
+
+<div class="ecosystemEntry">
+
+<aside class="ecosystemDetailsBox">
+<dl>
+    <dt>Developers</dt>
+    <dd class="ecosystemEntryDevelopers">{{ page.developers }}</dd>
+    <!-- TODO: add contact link (obfuscate?) -->
+    <dt>Source code</dt>
+    <!-- TODO: extract GitHub links to make prettier -->
+    <dd class="ecosystemEntryLink">
+        <a href="{{ page.source }}">{{ page.source }}</a>
+    </dd>
+    {% if page.docs %}
+    <dt>Documentation</dt>
+    <dd class="ecosystemEntryLink">
+        <a href="{{ page.docs }}">{{ page.docs }}</a>
+    </dd>
+    {% endif %}
+    {% if page.conda-forge or page.pypi %}
+    <dt>Installation</dt>
+    <dd class="ecosystemEntryInstallation">
+        <ul>
+            {% if page.conda-forge %}
+            <li>
+            <kbd>mamba install -c conda-forge {{ page.conda-forge }}</kbd>
+            </li>
+            {% endif %}
+            {% if page.pypi %}
+            <li>
+            <kbd>python -m pip install {{ page.pypi }}</kbd>
+            </li>
+            {% endif %}
+        </ul>
+    </dd>
+    {% endif %}
+    <dt>License</dt>
+    <dd class="ecosystemEntryLicense">
+        {{ page.license }}
+    </dd> <!-- TODO: link known licenses -->
+    <dt>Plugins</dt>
+    <dd class="ecosystemEntryPlugins">
+        <ul>
+            {% for category in site.ecosystem_catalog.categories %}
+            {% for plugin in page[category.name] %}
+            <li>{{ plugin.name }}</li>
+            {% endfor %}
+            {% endfor %}
+        </ul>
+    </dd>
+    {% if page.publications %}
+    <dt>Publications</dt>
+    <dd class="ecosystemEntryPublications">
+        <ul>
+            {% for pub in page.publications %}
+            <li><a href="{{ pub }}">{{ pub }}</a></li>
+            {% endfor %}
+        </ul>
+    </dd>
+    {% endif %}
+</dl>
+</aside>
+
+<ul class="ecosystemCategoryTag">
+  {% for category in site.ecosystem_catalog.categories %}
+    {% if page[category.name] %}
+      <li>{{ category.label | upcase }}</li>
+    {% endif %}
+  {% endfor %}
+</ul>
+
+{{ page.content | markdownify }}
+
+</div>