Merge pull request #71 from BrainAnnex/dev

Dev Release Candidate 0

Author: BrainAnnex

.gitignore

@@ -131,3 +131,4 @@ dmypy.json
 /.idea
 
 # Project-specific
+/experiments/PRIVATE/

experiments/1D/diffusion/diffusion_along_gradient_1.ipynb

@@ -17,20 +17,24 @@
 # A single chemical, whose initial concentration is a mix of a bell shape and a gradient.   
 # Contrary to perhaps an intuition of a "pile sliding down a sand dune as a unit", the concentration peak
 # remains in place, and simply spreads out from there
-#
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
 
 # %%
-import set_path      # Importing this module will add the project's home directory to sys.path
+LAST_REVISED = "Nov. 12, 2024"
+LIFE123_VERSION = "1.0.0.rc.0"      # Library version this experiment is based on
+
+# %%
+#import set_path              # Using MyBinder?  Uncomment this before running the next cell!
 
 # %%
-from life123 import BioSim1D
+#import sys
+#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
+# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path   
 
-from life123 import ChemData as chem
+from life123 import BioSim1D, ChemData
 
 # %%
 # Initialize the system
-chem_data = chem(names=["A"], diffusion_rates=[10.])
+chem_data = ChemData(names=["A"], diffusion_rates=[10.])
 
 bio = BioSim1D(n_bins=200, chem_data=chem_data)
 

experiments/1D/diffusion/diffusion_along_gradient_1.py

@@ -18,23 +18,25 @@
 #
 # The system starts out with a uniform concentration.  
 # Then identical concentrations are repeatedly *injected to the left* and *drained from the right*
-#
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
 
 # %%
-import set_path      # Importing this module will add the project's home directory to sys.path
+LAST_REVISED = "Nov. 12, 2024"
+LIFE123_VERSION = "1.0.0.rc.0"      # Library version this experiment is based on
+
+# %%
+#import set_path              # Using MyBinder?  Uncomment this before running the next cell!
 
 # %%
+#import sys
+#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
+# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path   
+
 from experiments.get_notebook_info import get_notebook_basename
 
-from life123 import BioSim1D
+from life123 import BioSim1D, ChemData, GraphicLog, HtmlLog as log
 
 import plotly.express as px
 
-from life123 import ChemData as chem
-from life123 import HtmlLog as log
-from life123 import GraphicLog
-
 # %%
 # Initialize the HTML logging
 log_file = get_notebook_basename() + ".log.htm"    # Use the notebook base filename for the log file
@@ -56,7 +58,7 @@
 
 # %%
 # Initialize the system with a uniform concentration (of the only species)
-chem_data = chem(names=["A"], diffusion_rates=[0.6])
+chem_data = ChemData(names=["A"], diffusion_rates=[0.6])
 bio = BioSim1D(n_bins=9, chem_data=chem_data)
 
 bio.set_uniform_concentration(species_index=0, conc=100.)

experiments/1D/diffusion/gradient_1.ipynb

@@ -28,7 +28,7 @@
 
 from life123 import BioSim1D
 from life123 import ChemData as chem
-from life123 import MovieArray
+from life123 import CollectionArray
 from life123 import Numerical as num
 
 import numpy as np
@@ -78,7 +78,7 @@
 
 # %%
 # All the system states will get collected in this object
-history = MovieArray()
+history = CollectionArray()
 
 # %%
 # Store the initial state

experiments/1D/diffusion/gradient_1.py

@@ -34,7 +34,7 @@
 
 from life123 import BioSim1D
 from life123 import ChemData as chem
-from life123 import MovieArray
+from life123 import CollectionArray
 from life123 import Numerical as num
 
 import numpy as np
@@ -79,7 +79,7 @@
 
 # %%
 # All the system state will get collected in this object
-history = MovieArray()
+history = CollectionArray()
 
 # %%
 # Store the initial state
@@ -157,7 +157,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -215,7 +215,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -274,7 +274,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -332,7 +332,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -391,7 +391,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -448,7 +448,7 @@
 bio.inject_sine_conc(species_name="A", frequency=2, amplitude=8)
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")

experiments/1D/diffusion/validate_diffusion_1.py

@@ -29,7 +29,7 @@
 
 from life123 import BioSim1D
 from life123 import ChemData as chem
-from life123 import MovieArray
+from life123 import CollectionArray
 from life123 import Numerical as num
 
 import numpy as np
@@ -74,7 +74,7 @@
 # #### Now do 4 rounds of single-step diffusion, to collect the system state at a total of 5 time points: t0 (the initial state), plus t1, t2, t3 and t4
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")
@@ -137,7 +137,7 @@
 # #### Now do 4 rounds of single-step diffusion, to collect the system state at a total of 5 time points: t0 (the initial state), plus t1, t2, t3 and t4
 
 # %%
-history = MovieArray()   # All the system state will get collected in this object
+history = CollectionArray()   # All the system state will get collected in this object
 # Store the initial state
 arr = bio.lookup_species(species_index=0, copy=True)
 history.store(par=bio.system_time, data_snapshot=arr, caption=f"State at time {bio.system_time}")

experiments/1D/diffusion/validate_diffusion_2.py

@@ -26,21 +26,24 @@
 #
 # A LOT of plots are sent to the log file from this experiment; the reason is to compare two
 # graphic elements, "vue_curves_3" and "vue_curves_4"
-#
-# LAST REVISED: June 23, 2024 (using v. 1.0 beta34.1)
 
 # %%
-import set_path      # Importing this module will add the project's home directory to sys.path
+LAST_REVISED = "Nov. 13, 2024"
+LIFE123_VERSION = "1.0.0.rc.0"      # Library version this experiment is based on
+
+# %%
+#import set_path              # Using MyBinder?  Uncomment this before running the next cell!
 
 # %%
+#import sys
+#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
+# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path   
+
 from experiments.get_notebook_info import get_notebook_basename
 
-from life123 import BioSim1D
+from life123 import BioSim1D, ChemData, GraphicLog, HtmlLog as log
 
 import plotly.express as px
-from life123 import ChemData as chem
-from life123 import HtmlLog as log
-from life123 import GraphicLog
 
 # %%
 # Initialize the HTML logging
@@ -53,7 +56,7 @@
 
 # %%
 # Initialize the system
-chem_data = chem(names=["A", "B", "C"], diffusion_rates=[50., 50., 1.])
+chem_data = ChemData(names=["A", "B", "C"], diffusion_rates=[50., 50., 1.])