Merge pull request #10 from MetExplore/development

Prepare for 0.9.0-alpha.4

.github/workflows/deploy-mkdocs.yml

@@ -17,7 +17,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install flake8 pytest
-          python -m pip install mkdocs-material mkdocstrings
+          python -m pip install mkdocs-material mkdocstrings mkdocs-minify-plugin
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           
       - name: Set up Python 3.7

docs/overrides/main.html

@@ -24,23 +24,27 @@
 {% endblock %}
 
 {% block scripts %}
-	<script src="{{ 'assets/javascripts/bundle.716f8af4.min.js' | url }}"></script>
-	{% for path in config["extra_javascript"] %}
-		<script src="{{ path | url }}"></script>
-	{% endfor %}
+  {{ super() }}
 	<script src="https://cdn.jsdelivr.net/npm/cookieconsent@3/build/cookieconsent.min.js" data-cfasync="false"></script>
 	<script>
 		window.cookieconsent.initialise({
-		  "palette": {
+			"palette": {
 			"popup": {
-			  "background": "#edeff5",
-			  "text": "#838391"
+				"background": "#edeff5",
+				"text": "#838391"
 			},
 			"button": {
-			  "background": "#4b81e8"
+				"background": "#4b81e8"
+			}
 			}
-		  }
 		});
 	</script>
 {% endblock %}
 
+{% block outdated %}
+  You're not viewing the latest version.
+  <a href="{{ '../' ~ base_url }}"> 
+
+    <strong>Click here to go to latest.</strong>
+  </a>
+{% endblock %}

examples/introduction_example.py

@@ -30,4 +30,7 @@
         # Get continuos vars (fluxes) and binary vars
         .get_values())
 
-print("Number of reactions with non-zero flux:", sum(abs(V) > 1e-8))
+print("Number of reactions with an absolute flux value above 1e-8:", sum(abs(V) > 1e-8))
+print("Active reactions:", sum(1 if activity == 1 else 0 for activity in model.variables.indicator_rxn_activity))
+print("Inconsistencies:", sum(1 if activity != activity else 0 for activity in model.variables.indicator_rxn_activity))
+print("Solver status:", model.get_solver_status())