Docs: change instructions to use jupyter notebook to instead suggest …

…jupyter lab
flatironinstitute · Aug 8, 2024 · cd61a86 · cd61a86
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diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ Create a working directory called `caiman_data` that includes code samples and r
 Go into the working directory you created in Step 2, and open a Jupyter notebook:
 
     cd <your home>/caiman_data/
-    jupyter notebook 
+    jupyter lab
 
 Jupyter will open. Navigate to demos/notebooks/ and click on `demo_pipeline.ipynb` to get started with a demo.
 

diff --git a/demos/notebooks/demo_OnACID_mesoscope.ipynb b/demos/notebooks/demo_OnACID_mesoscope.ipynb
@@ -189,7 +189,7 @@
     "Now inspect the components extracted by OnACID. Note that if single pass was used then several components would be non-zero only for the part of the time interval indicating that they were detected online by OnACID.\n",
     "\n",
     "Note that if you get data rate error you can start Jupyter notebooks using:\n",
-    "'jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10'"
+    "'jupyter lab --ZMQChannelsWebsocketConnection.iopub_data_rate_limit=1.0e10'"
    ]
   },
   {

diff --git a/demos/notebooks/demo_Ring_CNN.ipynb b/demos/notebooks/demo_Ring_CNN.ipynb
@@ -278,7 +278,7 @@
     "Now inspect the components extracted by OnACID. Note that if single pass was used then several components would be non-zero only for the part of the time interval indicating that they were detected online by OnACID.\n",
     "\n",
     "Note that if you get data rate error you can start Jupyter notebooks using:\n",
-    "'jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10'"
+    "'jupyter lab --ZMQChannelsWebsocketConnection.iopub_data_rate_limit=1.0e10'"
    ]
   },
   {

diff --git a/demos/notebooks/demo_pipeline.ipynb b/demos/notebooks/demo_pipeline.ipynb
@@ -842,7 +842,7 @@
     "Note this is just an initial result, which will contain many false positives, which is to be expected. The main concern to watch for here is whether you have lots of false *negatives* (has the algorithm missed neurons?). False negatives are hard to fix later, so if you have an unacceptable number, be sure to go back and re-run CNMF with new parameters.\n",
     "\n",
     "> If you get a data rate error with any notebook plotting commmands, can start your notebook using     \n",
-    "`jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10`"
+    "`jupyter lab --ZMQChannelsWebsocketConnection.iopub_data_rate_limit=1.0e10`"
    ]
   },
   {

diff --git a/docs/source/Getting_Started.rst b/docs/source/Getting_Started.rst
@@ -10,11 +10,10 @@ Demos
 
    .. code:: bash
 
-          jupyter notebook --NotebookApp.iopub_data_rate_limit=1.0e10
+          jupyter lab --ZMQChannelsWebsocketConnection.iopub_data_rate_limit=1.0e10
 
-   and select the notebook from within Jupyter’s browser. The argument
-   ``--NotebookApp.iopub_data_rate_limit=1.0e10`` will prevent any
-   memory issues while plotting on a notebook.
+   and select the notebook from within Jupyter’s browser. The argument provided
+   will prevent any output from being lost while using a notebook
 
 -  demo files are also found in the demos/general subfolder. We suggest
    trying demo_pipeline.py first as it contains most of the tasks