Started obsoleting and eliminating the substeps option

general code cleanup, including elimination of obsolete pytests
Removed argument `snapshots` from reaction_step_orchestrator()

Author: BrainAnnex

README.md

@@ -1,4 +1,4 @@
-### VERSION 1.0-beta25
+### VERSION 1.0-beta26_IN_PROGRESS
 
 
 

experiments/reactions_single_compartment/up_regulate_3.ipynb

@@ -13,7 +13,7 @@
     "Invoking [Le Chatelier's principle](https://www.chemguide.co.uk/physical/equilibria/lechatelier.html), it can be seen that, starting from equilibrium, when [U] goes up, so does [S]; and when [S] goes up, so does [X].   \n",
     "Conversely, when [U] goes down, so does [S]; and when [S] goes down, so does [X].   \n",
     "\n",
-    "This experiment is a counterpart of `up_regulate_2`, with \"upstream\" rather than \"downstream\" reactions.\n",
+    "This experiment is a counterpart of experiment `up_regulate_2`, with \"upstream\" rather than \"downstream\" reactions.\n",
     "\n",
     "Note: numerical errors in the same reactions (with the same initial conditions) is explored in the experiment \"large_time_steps_2\"\n",
     "\n",

experiments/reactions_single_compartment/up_regulate_3.py

@@ -22,7 +22,7 @@
 # Invoking [Le Chatelier's principle](https://www.chemguide.co.uk/physical/equilibria/lechatelier.html), it can be seen that, starting from equilibrium, when [U] goes up, so does [S]; and when [S] goes up, so does [X].   
 # Conversely, when [U] goes down, so does [S]; and when [S] goes down, so does [X].   
 #
-# This experiment is a counterpart of `up_regulate_2`, with "upstream" rather than "downstream" reactions.
+# This experiment is a counterpart of experiment `up_regulate_2`, with "upstream" rather than "downstream" reactions.
 #
 # Note: numerical errors in the same reactions (with the same initial conditions) is explored in the experiment "large_time_steps_2"
 #