Update documentation

_sources/user_guide/quick_start.md

@@ -1,3 +1,9 @@
+---
+file_format: mystnb
+kernelspec:
+  name: python3
+---
+
 # Quick Start for Users
 
 ## Instaling `mosaic`
@@ -16,19 +22,15 @@ For a developers installation guide, see the [section](Dev_install_guide) in the
 
 ### Global Mesh
 
-First we need to download a valid MPAS mesh. To do so run:
-```
-curl https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/mpas-o/EC30to60E2r3/mpaso.EC30to60E2r3.230313.nc -o mpaso.EC30to60E2r3.230313.nc
-```
-
 Then we can use `mosaic` to plot on the native mesh using `matplotlib`. For example:
-```python
+```{code-cell} ipython3
 import cartopy.crs as ccrs
 import mosaic
 import matplotlib.pyplot as plt
 import xarray as xr
 
-ds = xr.open_dataset("mpaso.EC30to60E2r3.230313.nc")
+# download and read the mesh from lcrc
+ds = mosaic.datasets.open_dataset("QU.240km")
 
 # define a map projection for our figure
 projection = ccrs.InterruptedGoodeHomolosine()
@@ -46,38 +48,29 @@ descriptor = mosaic.Descriptor(ds, projection, transform)
 
 # using the `Descriptor` object we just created, make a pseudocolor plot of
 # the "indexToCellID" variable, which is defined at cell centers.
-collection = mosaic.polypcolor(ax, descriptor, ds.indexToCellID, antialiaseds=False)
+collection = mosaic.polypcolor(ax, descriptor, ds.indexToCellID, antialiaseds=True)
 
-ax.gridlines()
 ax.coastlines()
-fig.colorbar(collection, fraction=0.1, shrink=0.5, label="Cell Index")
-
-plt.show()
+fig.colorbar(collection, fraction=0.1, shrink=0.5, label="Cell Index");
 ```
 
-![mpaso.EC30to60E2r3](images/mpaso.EC30to60E2r3.png)
-
 ### Planar Non-Periodic 
 
-First we need to download a valid MPAS mesh. To do so run:
-```
-curl https://web.lcrc.anl.gov/public/e3sm/inputdata/glc/mpasli/mpas.ais8to30km/ais_8to30km.20231222.nc -o mpasli.ais8to30km.nc
-```
-
 In this case the underlying coordinate arrays (i.e. `xCell/yCell`)
 correspond to a South Polar Stereographic projection, which is also the map projection we
 want to us. Therefore, the `projection` and the `transform` will be equivalent
 for this example. When instantiating the `mosaic.Descriptor` object we have to 
 careful to set `use_latlon=False` to ensure the `xCell`/`yCell` coordinate
 arrays are parsed (c.f. `lonCell`/`latCell`). 
 
-```python
+```{code-cell} ipython3
 import cartopy.crs as ccrs
 import mosaic
 import matplotlib.pyplot as plt
 import xarray as xr
 
-ds = xr.open_dataset("mpasli.ais8to30km.nc").squeeze()
+# download and read the mesh from lcrc
+ds = mosaic.datasets.open_dataset("mpasli.AIS8to30")
 
 # define a map projection for our figure
 projection = ccrs.SouthPolarStereo()
@@ -102,9 +95,8 @@ ax.set_extent([-180, 180, -90, -60], ccrs.PlateCarree())
 
 ax.gridlines()
 ax.coastlines()
-fig.colorbar(collection, fraction=0.1, label="Thickness [m]")
+fig.colorbar(collection, fraction=0.1, label="Thickness [m]");
 ```
-![mpasli.ais8to30km](images/mpasli.ais8to30km.png)
 
 In the case where we do not know what projection the coordinate arrays of the
 mesh correspond to we can use the `lonCell`/`latCell` coordinates and `mosaic`

_static/copybutton.css

@@ -0,0 +1,94 @@
+/* Copy buttons */
+button.copybtn {
+    position: absolute;
+    display: flex;
+    top: .3em;
+    right: .3em;
+    width: 1.7em;
+    height: 1.7em;
+	opacity: 0;
+    transition: opacity 0.3s, border .3s, background-color .3s;
+    user-select: none;
+    padding: 0;
+    border: none;
+    outline: none;
+    border-radius: 0.4em;
+    /* The colors that GitHub uses */
+    border: #1b1f2426 1px solid;
+    background-color: #f6f8fa;
+    color: #57606a;
+}
+
+button.copybtn.success {
+    border-color: #22863a;
+    color: #22863a;
+}
+
+button.copybtn svg {
+    stroke: currentColor;
+    width: 1.5em;
+    height: 1.5em;
+    padding: 0.1em;
+}
+
+div.highlight  {
+    position: relative;
+}
+
+/* Show the copybutton */
+.highlight:hover button.copybtn, button.copybtn.success {
+	opacity: 1;
+}
+
+.highlight button.copybtn:hover {
+    background-color: rgb(235, 235, 235);
+}
+
+.highlight button.copybtn:active {
+    background-color: rgb(187, 187, 187);
+}
+
+/**
+ * A minimal CSS-only tooltip copied from:
+ *   https://codepen.io/mildrenben/pen/rVBrpK
+ *
+ * To use, write HTML like the following:
+ *
+ * <p class="o-tooltip--left" data-tooltip="Hey">Short</p>
+ */
+ .o-tooltip--left {
+  position: relative;
+ }
+
+ .o-tooltip--left:after {
+    opacity: 0;
+    visibility: hidden;
+    position: absolute;
+    content: attr(data-tooltip);
+    padding: .2em;
+    font-size: .8em;
+    left: -.2em;
+    background: grey;
+    color: white;
+    white-space: nowrap;
+    z-index: 2;
+    border-radius: 2px;
+    transform: translateX(-102%) translateY(0);
+    transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1);
+}
+
+.o-tooltip--left:hover:after {
+    display: block;
+    opacity: 1;
+    visibility: visible;
+    transform: translateX(-100%) translateY(0);
+    transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1);
+    transition-delay: .5s;
+}
+
+/* By default the copy button shouldn't show up when printing a page */
+@media print {
+    button.copybtn {
+        display: none;
+    }
+}