Merge branch 'main' of github.com:stochss/gillespy2 into develop

Author: briandrawert

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#     - requirements: docs/requirements.txt

docs/getting_started/basic_usage/basic_usage.rst

@@ -55,7 +55,7 @@ In GillesPy2, a model is expressed as an object.  Components, such as the reacti
         model.add_reaction([r_c, r_d])
 
         # Set the timespan for the simulation.
-        tspan = gillespy2.TimeSpan.linspace(0, 100, 101)
+        tspan = gillespy2.TimeSpan.linspace(t=100, num_points=101)
         model.timespan(tspan)
         return model
 
@@ -126,7 +126,7 @@ First, let's define a simple model to use in this example.
         model.add_reaction([r1,r2,r3])
 
         # Set the timespan for the simulation.
-        tspan = gillespy2.TimeSpan.linspace(0, 600, 601)
+        tspan = gillespy2.TimeSpan.linspace(t=600, num_points=601)
         model.timespan(tspan)
         return model
 

docs/tutorials/tut_toggle_switch/tut_toggle_switch.rst

@@ -42,7 +42,7 @@ Next, we define a model. This is a model based on a publication by Gardner et al
                    rate=mu)
      model.add_reaction([cu, cv, du, dv])
 
-     tspan = gillespy2.TimeSpan.linspace(0, 100, 101)
+     tspan = gillespy2.TimeSpan.linspace(t=100, num_points=101)
      model.timespan(tspan)
      return model