minor updates to notes and a working environment

README.md

@@ -63,6 +63,12 @@ Alternatively, use the faster [`libmamba` solver](https://conda.github.io/conda-
 conda env create -f environment.yml --solver=libmamba
 ```
 
+If users are experiencing issues with plots NOT displaying in jupyter notebooks once a cell is executed, then we recommend using the `environment_working.yml` file. We have noticed that later versions of some libraries might be creating a conflict, but we have not been able to track down the root cause since no warnings/errors are given when the plot does NOT display:
+
+```shell
+conda env create -f environment_working.yml --solver=libmamba
+```
+
 Activate the environment using the instructions printed by conda after the environment is created successfully.
 
 To update your environment to the latest versions of dependencies and/or add additional dependencies to your environment (by first editting [`environment.yml`](environment.yml)), run the following command:

examples/03_coupling_riverine_NSM_modules_(1_runSimulation).ipynb

@@ -38,9 +38,9 @@
     "\n",
     "The initial condition concentrations throughout the domain for these state variables are set to the same values as the upstream boundary condition except for Ap within the oxbow lake cells which are set to 200 mg/L.\n",
     "\n",
-    "We simulate this scenario over the course of two full days, using solar radiation data from Arizona in part to compute Ap growth which helps to show off the impacts of NSMI.\n",
+    "We simulate this scenario over the course of one full day, using solar radiation data from Arizona in part to compute Ap growth which helps to show off the impacts of NSMI.\n",
     "\n",
-    "At this time, every state variable (including the ones that are turned off) needs to have boundary conditions and initial conditions set for the NSMI model to initialize. The appropriate files with place holder values have been added to the simulation directory for this use. Also, it was noticed that CBOD has no on/off switch at this time and is also being computed during the simulation. The CBOD boundary and initial conditions are set to a constant 1 mg/L everywhere both temporally and spatially.\n",
+    "At this time, every state variable (including the ones that are turned off) needs to have boundary conditions and initial conditions set for the NSMI model to initialize. The appropriate files, including for state variables switched off, have been added to the simulation directory for this use. It should be noted that place holder values were used for these switched off variables, and the user should modify the values if alternative simulations with these state variables switched on are executed. Since the Clearwater-riverine library was use to initialize the state variables in Clearwater-modules and the code in this notebook intentionally did not pass any information regarding the switched off state variables back to \"riverine\", the saved results from this model simulaltion will also have results for the turned off state variables, but they are only being advected/diffused and are essentially acting as tracers.\n",
     "\n",
     "### Data Availability\n",
     "All data required run this notebook is available at this [Google Drive](https://drive.google.com/drive/folders/19uCjAJPZh4g6r1ZWzk1D_B8jZGluSc4N?usp=drive_link). Please download the entire folder and place it in the `data_temp` folder of this repository to run the rest of the notebook."
@@ -19749,7 +19749,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,