support molecule-based data types🌽 (#384)

src/simmate/command_line/base_command.py

@@ -85,9 +85,12 @@ def run_server():
 
     logging.info("Setting up local test server...")
     subprocess.run(
-        "django-admin runserver --settings=simmate.configuration.django.settings",
+        "django-admin runserver --settings=simmate.configuration.django.settings --insecure",
         shell=True,
     )
+    # BUG: we added the "--insecure" flag in order to serve static files with
+    # the DEBUG=False mode turned on. This makes the file serving slower though.
+    #   https://stackoverflow.com/questions/5836674/
 
 
 @simmate_app.command()

src/simmate/database/base_data_types/base.py

@@ -764,6 +764,7 @@ def from_toolkit(cls, as_dict: bool = False, **kwargs):
         all_data.pop("migration_images", None)
         all_data.pop("band_structure", None)
         all_data.pop("density_of_states", None)
+        all_data.pop("molecule", None)
 
         for parent in parents:
             # Skip the parent class if it doesn't directly inherit from the

src/simmate/database/utilities.py

@@ -63,7 +63,6 @@ def reset_database(apps_to_migrate=APPS_TO_MIGRATE, use_prebuilt=False):
         # django so that we can close everything down easily.
         import psycopg2
 
-        logging.info("Connecting to database")
         # Setup Postgres connection
         connection = psycopg2.connect(
             host=DATABASES["default"]["HOST"],
@@ -79,9 +78,12 @@ def reset_database(apps_to_migrate=APPS_TO_MIGRATE, use_prebuilt=False):
         cursor = connection.cursor()
 
         # Build out database extensions and tables
-        logging.info("Deleting database & building an empty one")
         db_name = DATABASES["default"]["NAME"]
-        cursor.execute(f"DROP DATABASE IF EXISTS {db_name} WITH (FORCE);")
+        cursor.execute(f"DROP DATABASE IF EXISTS {db_name};")
+        # BUG: if others are connected I could add 'WITH (FORCE)' above.
+        # For now, I don't use this but should consider adding it for convenience.
+        # I think this is buggy with older versions of postgres (like RDkit),
+        # so I hold off on this for now.
         cursor.execute(f"CREATE DATABASE {db_name};")
 
         # Make the changes to the database persistent
@@ -90,7 +92,6 @@ def reset_database(apps_to_migrate=APPS_TO_MIGRATE, use_prebuilt=False):
         # Close communication with the database
         cursor.close()
         connection.close()
-        logging.info("Empty database established.")
 
     elif not using_sqlite and not using_postgres:
         logging.warning(
@@ -106,7 +107,13 @@ def reset_database(apps_to_migrate=APPS_TO_MIGRATE, use_prebuilt=False):
             continue
 
         migration_dir = Path(app_config.path) / "migrations"
-        if migration_dir.exists():
+        # BUG: I need a good way to avoid deleting initial migrations that
+        # do things like register extensions.
+        # Maybe have these migrations listed as 0000_setup.py and then delete
+        # everything after?
+        # Maybe skip folders that contain a 0001_setup.py?
+        skip_deletes = ["rdkit", "datasets"]
+        if migration_dir.exists() and migration_dir.parent.name not in skip_deletes:
             shutil.rmtree(migration_dir)
             continue
 

src/simmate/website/core/urls.py

@@ -1,10 +1,48 @@
 # -*- coding: utf-8 -*-
 
+import importlib
+
 from django.contrib import admin
 from django.urls import include, path
 
+from simmate.configuration.django.settings import SIMMATE_APPS
 from simmate.website.core import views
 
+
+def get_app_urls():
+    # First let's find our custom simmate apps that supply a 'urls' module. We
+    # want to automatically make these avaialable in the web UI.
+
+    extra_url_paths = []
+
+    for app_name in SIMMATE_APPS:
+        # This section of code is copied from...
+        #   simmate.workflows.utilities.get_all_workflows
+        # Consider making another util.
+        config_modulename = ".".join(app_name.split(".")[:-1])
+        config_name = app_name.split(".")[-1]
+        config_module = importlib.import_module(config_modulename)
+        config = getattr(config_module, config_name)
+        app_path = config.name
+        simple_name = app_path.split(".")[-1]
+
+        # check if there is a urls module in the app
+        #   stackoverflow.com/questions/14050281
+        urls_found = importlib.util.find_spec(f"{app_path}.urls") is not None
+
+        if urls_found:
+            new_path = path(
+                route=f"apps/{simple_name}/",
+                # set the namespace so that we can easily look up app urls
+                #   https://stackoverflow.com/questions/48608894
+                view=include((f"{app_path}.urls", simple_name), namespace=simple_name),
+                name=simple_name,
+            )
+            extra_url_paths.append(new_path)
+
+    return extra_url_paths
+
+
 urlpatterns = [
     #
     # This is the path to the homepage (just simmate.org)
@@ -62,4 +100,8 @@
     path(route="extras/", view=views.extras, name="extras"),
     path(route="contact/", view=views.contact, name="contact"),
     path(route="about/", view=views.about, name="about"),
+    #
+    # Custom Simmate apps (if present)
+    path(route="apps/", view=views.apps, name="apps"),
+    *get_app_urls(),
 ]

src/simmate/website/core/views.py

@@ -1,9 +1,12 @@
 # -*- coding: utf-8 -*-
 
+import importlib
+
 from django.contrib.auth.decorators import login_required
 from django.db.models import F
 from django.shortcuts import render
 
+from simmate.configuration.django.settings import SIMMATE_APPS
 from simmate.database.third_parties import (
     AflowStructure,
     CodStructure,
@@ -108,6 +111,31 @@ def home(request):
     return render(request, template, context)
 
 
+def apps(request):
+    ################
+    # This section of code is copied from...
+    #   simmate.web.core.urls
+    # Consider making another util. I might want a SimmateConfig class that
+    # subclasses Django app's Config class. Add things like "learn-more" links
+    # and short descriptions
+    extra_apps = []
+    for app_name in SIMMATE_APPS:
+        config_modulename = ".".join(app_name.split(".")[:-1])
+        config_name = app_name.split(".")[-1]
+        config_module = importlib.import_module(config_modulename)
+        config = getattr(config_module, config_name)
+        app_path = config.name
+        simple_name = app_path.split(".")[-1]
+        urls_found = importlib.util.find_spec(f"{app_path}.urls") is not None
+        if urls_found:
+            extra_apps.append(simple_name)
+            # TODO: maybe grab a short description too?
+    ################
+    context = {"extra_apps": extra_apps}
+    template = "core_components/apps.html"
+    return render(request, template, context)
+
+
 def extras(request):
     context = {}
     template = "core_components/extras.html"

src/simmate/website/templates/core_components/apps.html

@@ -0,0 +1,46 @@
+{% extends "core_components/site_base.html" %}
+
+{% block tabtitle %}
+Simmate
+{% endblock %}
+
+{% block banner %}
+{% include "core_components/header.html"%}
+{% endblock %}
+
+
+{% block body %}
+
+<!-- Header -->
+<section class="pt-5 jumbotron text-center">
+    <div class="container">
+        <h1 class="jumbotron-heading">Apps</h1>
+        <p class="lead text-muted">Additional apps, plugins, & dashboards made with Simmate.</p>
+    </div>
+</section>
+
+<div class="row">
+
+    {% for app_name in extra_apps %}
+    <div class="col-md-4">
+        <div class="card" style="width: 25rem;">
+            <div class="card-body">
+                <h5 class="card-title">{{ app_name }}</h5>
+                <p class="card-text">
+                    ~~ an example description for this new app ~~
+                </p>
+
+                <a role="button" class="btn btn-primary btn-sm"
+                    href="#" target="_blank">
+                    Learn More...</a>
+                <a role="button" class="btn btn-primary btn-sm"
+                    href="{{ app_name }}">
+                    Try it out!</a>
+            </div>
+        </div>
+    </div>
+    {% endfor %}
+
+</div>
+
+{% endblock %}

src/simmate/website/templates/core_components/sidebar.html

@@ -29,6 +29,13 @@
         </li>
         -->
 
+        <li id="apps" class="side-nav-item">
+            <a href="{% url 'apps' %}" class="side-nav-link">
+                <i class="uil-apps"></i>
+                <span> Apps </span>
+            </a>
+        </li>
+
         <li id="workflows" class="side-nav-item">
             <a href="{% url 'workflows' %}" class="side-nav-link">
                 <i class="uil-sitemap"></i>