tethysplatform · swainn · Aug 24, 2024 · Jun 20, 2024 · Jun 20, 2024 · Jun 20, 2024
diff --git a/docs/README.md b/docs/README.md
@@ -11,6 +11,15 @@ cd docs
 conda env create -f docs_environment.yml
 ```
 
+## Initialize git lfs
+
+Use Git LFS to download the images:
+
+```
+git lfs install
+git lfs pull
+```
+
 ## Build Docs
 
 Activate the conda environment and build the documentation using these commands:

diff --git a/docs/conf.py b/docs/conf.py
@@ -22,6 +22,7 @@
 from django.conf import settings
 from setuptools_scm import get_version
 from sphinxawesome_theme import ThemeOptions, LinkIcon
+from sphinxawesome_theme.postprocess import Icons
 
 # Mock Dependencies
 # NOTE: No obvious way to automatically anticipate all the sub modules without
@@ -123,12 +124,18 @@ def __getattr__(cls, name):
     "tethys_layouts",
 ]
 
-settings.configure(
-    INSTALLED_APPS=installed_apps,
-    DEBUG=True,
-    SECRET_KEY="QNT5VImbg7PktTYfyXZWGwfKqOe1G3CanQWfG0zsE5HZxwHdQs",
-)
-django.setup()
+try:
+    settings.configure(
+        INSTALLED_APPS=installed_apps,
+        DEBUG=True,
+        SECRET_KEY="QNT5VImbg7PktTYfyXZWGwfKqOe1G3CanQWfG0zsE5HZxwHdQs",
+    )
+    django.setup()
+except RuntimeError as e:
+    # Ignore error if settings are already configured
+    # This can occur when using sphinx-autobuild
+    if "settings already configured" in str(e).lower():
+        pass
 
 # Sphinx extensions
 extensions = [
@@ -292,10 +299,4 @@ def __getattr__(cls, name):
 html_collapsible_definitions = True
 
 # Link icon for header links instead of pharagraph icons that are the default
-html_permalinks_icon = (
-    '<svg viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">'
-    '<path d="M3.9 12c0-1.71 1.39-3.1 3.1-3.1h4V7H7c-2.76 0-5 2.24-5 5s2.24 5 5 '
-    "5h4v-1.9H7c-1.71 0-3.1-1.39-3.1-3.1zM8 13h8v-2H8v2zm9-6h-4v1.9h4c1.71 "
-    '0 3.1 1.39 3.1 3.1s-1.39 3.1-3.1 3.1h-4V17h4c2.76 0 5-2.24 5-5s-2.24-5-5-5z">'
-    "</path></svg>"
-)
+html_permalinks_icon = Icons.permalinks_icon
diff --git a/docs/images/tutorial/advanced/Persistent_Store_Service.png b/docs/images/tutorial/advanced/Persistent_Store_Service.png
diff --git a/docs/images/tutorial/advanced/key-concepts-advanced-screenshot.png b/docs/images/tutorial/advanced/key-concepts-advanced-screenshot.png
diff --git a/docs/images/tutorial/advanced/key-concepts-beginner-screenshot.png b/docs/images/tutorial/advanced/key-concepts-beginner-screenshot.png
diff --git a/docs/images/tutorial/advanced/key-concepts-intermediate-screenshot.png b/docs/images/tutorial/advanced/key-concepts-intermediate-screenshot.png
diff --git a/docs/images/tutorial/dask/blank_home.png b/docs/images/tutorial/dask/blank_home.png
diff --git a/docs/images/tutorial/dask/blank_jobs_table.png b/docs/images/tutorial/dask/blank_jobs_table.png
diff --git a/docs/images/tutorial/dask/home_with_delayed_button.png b/docs/images/tutorial/dask/home_with_delayed_button.png
diff --git a/docs/images/tutorial/dask/home_with_distributed_button.png b/docs/images/tutorial/dask/home_with_distributed_button.png
diff --git a/docs/images/tutorial/dask/home_with_multiple_button.png b/docs/images/tutorial/dask/home_with_multiple_button.png
diff --git a/docs/images/tutorial/dask/jobs_table_with_delayed.png b/docs/images/tutorial/dask/jobs_table_with_delayed.png
diff --git a/docs/images/tutorial/dask/jobs_table_with_distributed.png b/docs/images/tutorial/dask/jobs_table_with_distributed.png
diff --git a/docs/images/tutorial/dask/jobs_table_with_multiple.png b/docs/images/tutorial/dask/jobs_table_with_multiple.png
diff --git a/docs/images/tutorial/gee/about_page.png b/docs/images/tutorial/gee/about_page.png
diff --git a/docs/images/tutorial/gee/clip_by_asset.png b/docs/images/tutorial/gee/clip_by_asset.png
diff --git a/docs/images/tutorial/gee/dataset_controls.png b/docs/images/tutorial/gee/dataset_controls.png
diff --git a/docs/images/tutorial/gee/dataset_controls_js.png b/docs/images/tutorial/gee/dataset_controls_js.png
diff --git a/docs/images/tutorial/gee/deploy_app.png b/docs/images/tutorial/gee/deploy_app.png
diff --git a/docs/images/tutorial/gee/file_upload.png b/docs/images/tutorial/gee/file_upload.png
diff --git a/docs/images/tutorial/gee/gee_intro.png b/docs/images/tutorial/gee/gee_intro.png
diff --git a/docs/images/tutorial/gee/home_page.png b/docs/images/tutorial/gee/home_page.png
diff --git a/docs/images/tutorial/gee/map_view.png b/docs/images/tutorial/gee/map_view.png
diff --git a/docs/images/tutorial/gee/plot_data.png b/docs/images/tutorial/gee/plot_data.png
diff --git a/docs/images/tutorial/gee/rest_api.png b/docs/images/tutorial/gee/rest_api.png
diff --git a/docs/images/tutorial/gee/scaffolded_app.png b/docs/images/tutorial/gee/scaffolded_app.png
diff --git a/docs/images/tutorial/gee/visualize_gee_layers.png b/docs/images/tutorial/gee/visualize_gee_layers.png
diff --git a/docs/installation/production/manual/configuration/basic/static_and_workspaces.rst b/docs/installation/production/manual/configuration/basic/static_and_workspaces.rst
@@ -83,11 +83,13 @@ The app workspaces directory is one location where all app workspaces are collec
 3. Collect the app workspaces to the ``TETHYS_WORKSPACES_ROOT`` location:
 
     .. code-block::
+
         tethys manage collectworkspaces
 
 .. tip::
 
     You can collect both the static files and the app workspaces with a single command:
 
     .. code-block::
-            tethys manage collectall
+
+        tethys manage collectall
diff --git a/docs/tethys_sdk/workspaces.rst b/docs/tethys_sdk/workspaces.rst
@@ -160,10 +160,12 @@ In the rare cases where you need to use a workspace where it is not convenient o
 .. _workspace_get_app_workspace_func:
 
 .. automethod:: tethys_apps.base.paths.get_app_workspace
+    :no-index:
 
 .. _workspace_get_user_workspace_func:
 
 .. automethod:: tethys_apps.base.paths.get_user_workspace
+    :no-index:
 
 
 Working with Workspaces

diff --git a/docs/tutorials/bokeh.rst b/docs/tutorials/bokeh.rst
@@ -4,7 +4,7 @@
 Bokeh Integration Concepts
 **************************
 
-**Last Updated:** November 2019
+**Last Updated:** July 2024
 
 This tutorial introduces ``Bokeh Server`` integration concepts for Tethys developers. Two ``bokeh`` handlers will be created to demonstrate how to link Bokeh plots or widgets to Python functions in the brackground using both a plain Bokeh approach as well as a ``Param`` approach. The topics covered include:
 
@@ -33,7 +33,7 @@ To leverage the Bokeh integration with Tethys you will need the ``bokeh`` and ``
 .. code-block:: bash
 
     # conda: conda-forge channel strongly recommended for bokeh (the erdc/label/dev channel is currently needed for bokeh-django)
-    conda install -c conda-forge -c erdc/label/dev bokeh bokeh-django
+    conda install -c conda-forge -c erdc/label/dev bokeh bokeh-django bokeh_sampledata
 
     # pip
     pip install bokeh bokeh-django
@@ -56,6 +56,7 @@ To leverage the Bokeh integration with Tethys you will need the ``bokeh`` and ``
         packages:
           - bokeh
           - bokeh_django
+          - bokeh_sampledata
 
       pip:
 
@@ -94,7 +95,7 @@ Let's use Bokeh's sea temperature sample data to create a time series plot and l
 
 This simple handler contains the logic for a time series plot of the sea surface temperature sample data provided by ``Bokeh``. The ``handler`` decorator marks this function as a handler. It auto generates a default ``controller function`` that is linked to the handler. A default template can also be used, but we specified a custom template using the ``template`` argument to the ``handler`` decorator. The ``handler`` decorator also sets up the routing. By default the route name and the URL are derived from the ``handler function`` name (in this case ``home``). For more information about the ``handler`` decorator and additional arguments that can be passed see :ref:`handler-decorator`. Since this default controller is sufficient, we don't need to create a custom controller and can just delete the ``controller.py`` file.
 
-2. Delete the ``controller.py`` file.
+2. Delete the ``controllers.py`` file.
 
 3. Clear the default ``home.html`` template and add the following code to it.
 
@@ -125,7 +126,7 @@ This is a simple Bokeh plot. We will now add the rest of the logic to make it an
 
     ...
 
-    def home_handler(document):
+    def home(document):
         df = sea_surface_temperature.copy()
         source = ColumnDataSource(data=df)
 
@@ -185,6 +186,7 @@ In this example we will build on top of the ``bokeh_tutorial`` app to demonstrat
         packages:
           - bokeh
           - bokeh_django
+          - bokeh_sampledata
           - panel
           - param
 
@@ -202,8 +204,6 @@ In this example we will build on top of the ``bokeh_tutorial`` app to demonstrat
     import numpy as np
     from bokeh.plotting import figure
 
-    ...
-
 
     class Shape(param.Parameterized):
         radius = param.Number(default=1, bounds=(0, 1))
@@ -307,9 +307,9 @@ Note that in this case we are not using a custom template, but we add the ``app_
     {% block app_navigation_items %}
       {% url tethys_app|url:'home' as home_url %}
       {% url tethys_app|url:'shapes' as shapes_url %}
-      <li class="title">Examples</li>
-      <li class="{% if request.path == home_url %}active{% endif %}"><a href="{{ home_url }}">Sea Surface</a></li>
-      <li class="{% if request.path == shapes_url %}active{% endif %}"><a href="{{ shapes_url }}">Shapes</a></li>
+      <li class="nav-item title">Examples</li>
+      <li class="nav-item"><a class="nav-link {% if request.path == home_url %}active{% endif %}" href="{{ home_url }}">Sea Surface</a></li>
+      <li class="nav-item"><a class="nav-link {% if request.path == shapes_url %}active{% endif %}" href="{{ shapes_url }}">Shapes</a></li>
     {% endblock %}
 
 If you start tethys and go to the shapes endpoint of this app you should see something like this:

diff --git a/docs/tutorials/dask.rst b/docs/tutorials/dask.rst
@@ -2,7 +2,7 @@
 Dask Tutorial
 *************
 
-**Last Updated:** May 2022
+**Last Updated:** August 2024
 
 This tutorial will walk you through the steps of working with Dask using the Tethys Platform. If you have not already installed Tethys Platform, follow the :doc:`../installation` documentation and then return.
 

diff --git a/docs/tutorials/dask/dask_delayed.rst b/docs/tutorials/dask/dask_delayed.rst
@@ -2,7 +2,7 @@
 Dask Delayed
 ************
 
-**Last Updated:** May 2022
+**Last Updated:** August 2024
 
 The ``DaskJob`` can be used with either the ``dask.delayed`` or ``dask.distributed`` APIs. The next three sections will illustrate how to use each Dask API with TethysJobs. This section will illustrate how to use the ``dask.delayed`` API with ``DaskJob`` in Tethys.
 
@@ -45,7 +45,7 @@ Modify the ``home`` controller in the :file:`controller.py` module, adding a but
                     'data-bs-placement': 'top',
                     'title': 'Dask Delayed Job'
                 },
-                href=reverse('dask_tutorial:run_job', kwargs={'job_type': 'delayed'})
+                href=App.reverse('run_job', kwargs={'job_type': 'delayed'})
             )
 
             jobs_button = Button(
@@ -77,10 +77,10 @@ Add the ``run_job`` controller to the :file:`controller.py` module as well:
             Controller for the app home page.
             """
             # Get scheduler from dask_primary setting.
-            scheduler = app.get_scheduler(name='dask_primary')
+            scheduler = App.get_scheduler(name='dask_primary')
 
             if job_type.lower() == 'delayed':
-                from tethysapp.dask_tutorial.job_functions import delayed_job
+                from .job_functions import delayed_job
 
                 # Create dask delayed object
                 delayed = delayed_job()
@@ -94,7 +94,7 @@ Add the ``run_job`` controller to the :file:`controller.py` module as well:
                 # Execute future
                 dask.execute(delayed)
 
-            return HttpResponseRedirect(reverse('dask_tutorial:jobs_table'))
+            return HttpResponseRedirect(App.reverse('jobs_table'))
 
 .. note::
 
@@ -117,13 +117,13 @@ Add the ``app_content`` block to the :file:`home.html` so that it looks like the
 
 If your tethys project does not restart on its own, you may need to do so manually by ending the server with ``ctrl+c``, and then entering the command ``tethys manage start`` again. Now when you navigate to your app page, you should see this:
 
-.. figure:: ../../images/tutorial/NewPostDaskDelayedHome.png
+.. figure:: ../../images/tutorial/dask/home_with_delayed_button.png
     :width: 900px
     :align: center
 
 Click on the ``Dask Delayed Job`` button to launch the new job type. It will submit the job and redirect to the jobs table page:
 
-.. figure:: ../../images/tutorial/NewPostDaskDelayedJobsTable.png
+.. figure:: ../../images/tutorial/dask/jobs_table_with_delayed.png
     :width: 900px
     :align: center
 

diff --git a/docs/tutorials/dask/dask_distributed.rst b/docs/tutorials/dask/dask_distributed.rst
@@ -2,7 +2,7 @@
 Dask Distributed
 ****************
 
-**Last Updated:** May 2022
+**Last Updated:** August 2024
 
 This section will illustrate how to use the ``dask.distributed`` API with ``DaskJob`` in Tethys. This example also illustrates how to use a custom process results function.
 
@@ -46,7 +46,7 @@ Modify the ``home`` controller in the :file:`controller.py` module, adding a but
                     'data-bs-placement': 'top',
                     'title': 'Dask Delayed Job'
                 },
-                href=reverse('dask_tutorial:run_job', kwargs={'job_type': 'delayed'})
+                href=App.reverse('run_job', kwargs={'job_type': 'delayed'})
             )
 
             dask_distributed_button = Button(
@@ -57,7 +57,7 @@ Modify the ``home`` controller in the :file:`controller.py` module, adding a but
                     'data-bs-placement': 'top',
                     'title': 'Dask Future Job'
                 },
-                href=reverse('dask_tutorial:run_job', kwargs={'job_type': 'distributed'})
+                href=App.reverse('run_job', kwargs={'job_type': 'distributed'})
             )
 
             jobs_button = Button(
@@ -114,7 +114,7 @@ Additionally update the ``run_job`` controller in :file:`controller.py` to look
                 try:
                     client = scheduler.client
                 except DaskJobException:
-                    return redirect(reverse('dask_tutorial:error_message'))
+                    return App.redirect(App.reverse('error_message'))
 
                 # Create future job instance
                 future = distributed_job(client)
@@ -127,7 +127,7 @@ Additionally update the ``run_job`` controller in :file:`controller.py` to look
                 dask.process_results_function = convert_to_dollar_sign
                 dask.execute(future)
 
-            return HttpResponseRedirect(reverse('dask_tutorial:jobs_table'))
+            return HttpResponseRedirect(App.reverse('jobs_table'))
 
 3. Setup HTML
 =============
@@ -149,13 +149,13 @@ Modify the ``app_content`` block in the :file:`home.html` so that it looks like
 
 If your tethys project does not restart on its own, you may need to do so manually by ending the server with ``ctrl+c``, and then entering the command ``tethys manage start`` again. Now when you navigate to your app page, you should see this:
 
-.. figure:: ../../images/tutorial/NewPostDaskDistributedHome.png
+.. figure:: ../../images/tutorial/dask/home_with_distributed_button.png
     :width: 900px
     :align: center
 
 Click on the ``Dask Distributed Job`` button to launch the new job type. It will submit the job and redirect to the jobs table page:
 
-.. figure:: ../../images/tutorial/NewPostDaskDistributedJobsTable.png
+.. figure:: ../../images/tutorial/dask/jobs_table_with_distributed.png
     :width: 900px
     :align: center