Merge pull request #66 from BrainAnnex/dev

beta 36

Author: BrainAnnex

experiments/reactions_single_compartment/cascade_2_a.ipynb

@@ -15,7 +15,7 @@
     "\n",
     "**Background**: please see experiments `cascade_1` and `mystery_reaction_1`\n",
     "\n",
-    "LAST REVISED: June 14, 2024 (using v. 1.0 beta33)"
+    "LAST REVISED: June 23, 2024 (using v. 1.0 beta36)"
    ]
   },
   {
@@ -47,8 +47,8 @@
    "source": [
     "from experiments.get_notebook_info import get_notebook_basename\n",
     "\n",
-    "from src.modules.reactions.uniform_compartment import UniformCompartment\n",
-    "from src.modules.visualization.plotly_helper import PlotlyHelper"
+    "from life123 import UniformCompartment\n",
+    "from life123.visualization.plotly_helper import PlotlyHelper"
    ]
   },
   {

experiments/reactions_single_compartment/cascade_2_a.py

@@ -23,7 +23,7 @@
 #
 # **Background**: please see experiments `cascade_1` and `mystery_reaction_1`
 #
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
+# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)
 
 # %%
 import set_path      # Importing this module will add the project's home directory to sys.path

experiments/reactions_single_compartment/cascade_2_b.ipynb

@@ -14,7 +14,7 @@
     "\n",
     "**Background**: please see experiment `cascade_2_a`  \n",
     "\n",
-    "LAST REVISED: June 14, 2024 (using v. 1.0 beta33)"
+    "LAST REVISED: June 23, 2024 (using v. 1.0 beta36)"
    ]
   },
   {
@@ -46,8 +46,8 @@
    "source": [
     "from experiments.get_notebook_info import get_notebook_basename\n",
     "\n",
-    "from src.modules.reactions.uniform_compartment import UniformCompartment\n",
-    "from src.modules.visualization.plotly_helper import PlotlyHelper"
+    "from life123 import UniformCompartment\n",
+    "from life123.visualization.plotly_helper import PlotlyHelper"
    ]
   },
   {

experiments/reactions_single_compartment/cascade_2_b.py

@@ -22,7 +22,7 @@
 #
 # **Background**: please see experiment `cascade_2_a`  
 #
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
+# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)
 
 # %%
 import set_path      # Importing this module will add the project's home directory to sys.path

experiments/reactions_single_compartment/cascade_2_c.ipynb

@@ -14,7 +14,7 @@
     "\n",
     "**Background**: please see experiment `cascade_2_b`  \n",
     "\n",
-    "LAST REVISED: June 14, 2024 (using v. 1.0 beta33)"
+    "LAST REVISED: June 23, 2024 (using v. 1.0 beta36)"
    ]
   },
   {
@@ -46,8 +46,8 @@
    "source": [
     "from experiments.get_notebook_info import get_notebook_basename\n",
     "\n",
-    "from src.modules.reactions.uniform_compartment import UniformCompartment\n",
-    "from src.modules.visualization.plotly_helper import PlotlyHelper"
+    "from life123 import UniformCompartment\n",
+    "from life123.visualization.plotly_helper import PlotlyHelper"
    ]
   },
   {

experiments/reactions_single_compartment/cascade_2_c.py

@@ -22,7 +22,7 @@
 #
 # **Background**: please see experiment `cascade_2_b`  
 #
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
+# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)
 
 # %%
 import set_path      # Importing this module will add the project's home directory to sys.path

experiments/reactions_single_compartment/cycles_1.ipynb

@@ -13,7 +13,7 @@
     "\n",
     "All 1st-order kinetics.    \n",
     "\n",
-    "LAST REVISED: June 10, 2024 (using v. 1.0 beta33)"
+    "LAST REVISED: June 23, 2024 (using v. 1.0 beta36)"
    ]
   },
   {
@@ -45,11 +45,11 @@
    "source": [
     "from experiments.get_notebook_info import get_notebook_basename\n",
     "\n",
-    "from src.modules.chemicals.chem_data import ChemData\n",
-    "from src.modules.reactions.uniform_compartment import UniformCompartment\n",
-    "from src.modules.numerical.numerical import Numerical as num\n",
+    "from life123 import ChemData\n",
+    "from life123 import UniformCompartment\n",
+    "from life123 import Numerical as num\n",
     "\n",
-    "from src.modules.visualization.graphic_log import GraphicLog"
+    "from life123 import GraphicLog"
    ]
   },
   {

experiments/reactions_single_compartment/cycles_1.py

@@ -22,7 +22,7 @@
 #
 # All 1st-order kinetics.    
 #
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
+# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)
 
 # %%
 import set_path      # Importing this module will add the project's home directory to sys.path

experiments/reactions_single_compartment/down_regulate_1.ipynb

@@ -18,7 +18,7 @@
     "\n",
     "All reactions are 1st order, mostly forward.  Taken to equilibrium.\n",
     "\n",
-    "LAST REVISED: June 12, 2024 (using v. 1.0 beta33)"
+    "LAST REVISED: June 23, 2024 (using v. 1.0 beta36)"
    ]
   },
   {
@@ -69,11 +69,11 @@
    "source": [
     "from experiments.get_notebook_info import get_notebook_basename\n",
     "\n",
-    "from src.modules.chemicals.chem_data import ChemData as chem\n",
-    "from src.modules.reactions.uniform_compartment import UniformCompartment\n",
+    "from life123 import ChemData as chem\n",
+    "from life123 import UniformCompartment\n",
     "\n",
     "import plotly.express as px\n",
-    "from src.modules.visualization.graphic_log import GraphicLog"
+    "from life123 import GraphicLog"
    ]
   },
   {

experiments/reactions_single_compartment/down_regulate_1.py

@@ -26,7 +26,7 @@
 #
 # All reactions are 1st order, mostly forward.  Taken to equilibrium.
 #
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
+# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)
 
 # %% [markdown]
 # ## Bathtub analogy: