UBC-DSCI · trevorcampbell · Sep 13, 2023 · Sep 12, 2023 · Sep 12, 2023 · Sep 12, 2023
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,5 @@ source/*.py
 *.swp
 *.swo
 source/__pycache__
+.local/
+.viminfo
diff --git a/Dockerfile b/Dockerfile
@@ -24,6 +24,9 @@ RUN pip install numpy jinja2 pandas"<2.1" altair">=5.1.1" "vegafusion[embed]" vl
 # TODO: remove this once scikit-learn 1.4.x or beyond releases and is incorporated into jupyter/scipy-notebook
 RUN pip install -U git+https://github.com/scikit-learn/scikit-learn.git@main
 
+# install plotly for 3d figures
+RUN pip install plotly
+
 # disable warnings that pollute build logs; seems to be related to the update to python 3.11
 # https://discourse.jupyter.org/t/debugger-warning-it-seems-that-frozen-modules-are-being-used-python-3-11-0/16544/12
 ENV PYDEVD_DISABLE_FILE_VALIDATION=1

diff --git a/build_html.sh b/build_html.sh
@@ -1,2 +1,2 @@
 chmod -R o+w source/
-docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230831171718ddf538 /bin/bash -c "jupyter-book build source"
+docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230913180510589822 /bin/bash -c "jupyter-book build source"
diff --git a/build_pdf.sh b/build_pdf.sh
@@ -1,2 +1,2 @@
 chmod -R o+w source/
-docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230831171718ddf538 /bin/bash -c "export BOOK_BUILD_TYPE='PDF'; jupyter-book build source --builder pdflatex"
+docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230913180510589822 /bin/bash -c "export BOOK_BUILD_TYPE='PDF'; jupyter-book build source --builder pdflatex"
@@ -78,6 +78,8 @@ sphinx:
   local_extensions: # A list of local extensions to load by sphinx specified by "name: path" items
   config: # key-value pairs to directly over-ride the Sphinx configuration
     bibtex_reference_style: author_year
+    html_js_files:
+    - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
   html_context:
     default_mode: light
 

@@ -14,11 +14,12 @@ kernelspec:
 
 ```{code-cell} ipython3
 :tags: [remove-cell]
-
 from chapter_preamble import *
 from IPython.display import HTML
 from sklearn.metrics.pairwise import euclidean_distances
 import numpy as np
+import plotly.express as px
+import plotly.graph_objects as go
 ```
 
 (classification1)=
@@ -781,7 +782,7 @@ for idx in min_5_idx:
 ```
 
 ```{code-cell} ipython3
-:tags: [remove-cell]
+:tags: [remove-input]
 
 fig = px.scatter_3d(
     perim_concav_with_new_point_df4,
@@ -828,13 +829,7 @@ for neighbor_df in neighbor_df_list:
 # tight layout
 fig.update_layout(margin=dict(l=0, r=0, b=0, t=1), template="plotly_white")
 
-plot(fig, filename="img/classification1/fig05-more.html", auto_open=False)
-```
-
-```{code-cell} ipython3
-:tags: [remove-input]
-
-display(HTML("img/classification1/fig05-more.html"))
+glue("fig:05-more", fig)
 ```
 
 ```{figure} data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7

@@ -20,6 +20,8 @@ kernelspec:
 
 from chapter_preamble import *
 from IPython.display import HTML
+import plotly.express as px
+import plotly.graph_objects as go
 ```
 
 ## Overview
@@ -1083,7 +1085,7 @@ time the predictions are a surface in 3D space, instead of a line in 2D space, a
 predictors instead of 1.
 
 ```{code-cell} ipython3
-:tags: [remove-cell]
+:tags: [remove-input]
 
 # create a prediction pt grid
 xvals = np.linspace(
@@ -1096,7 +1098,7 @@ xygrid = np.array(np.meshgrid(xvals, yvals)).reshape(2, -1).T
 xygrid = pd.DataFrame(xygrid, columns=["sqft", "beds"])
 
 # add prediction
-knnPredGrid = sacr_pipeline_mult.predict(xygrid)
+knnPredGrid = sacr_fit.predict(xygrid)
 
 fig = px.scatter_3d(
     sacramento_train,
@@ -1125,13 +1127,7 @@ fig.update_layout(
     template="plotly_white",
 )
 
-plot(fig, filename="img/regression1/fig07-knn-mult-viz.html", auto_open=False)
-```
-
-```{code-cell} ipython3
-:tags: [remove-input]
-
-display(HTML("img/regression1/fig07-knn-mult-viz.html"))
+glue("fig:07-knn-mult-viz", fig)
 ```
 
 ```{figure} data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7

@@ -21,6 +21,8 @@ kernelspec:
 from chapter_preamble import *
 from IPython.display import HTML
 import numpy as np
+import plotly.express as px
+import plotly.graph_objects as go
 ```
 
 ## Overview
@@ -751,7 +753,7 @@ In the case of two predictors, we can plot the predictions made by our linear re
 shown in {numref}`fig:08-3DlinReg`.
 
 ```{code-cell} ipython3
-:tags: [remove-cell]
+:tags: [remove-input]
 
 # create a prediction pt grid
 xvals = np.linspace(
@@ -793,13 +795,7 @@ fig.update_layout(
     template="plotly_white",
 )
 
-plot(fig, filename="img/regression2/fig08-3DlinReg.html", auto_open=False)
-```
-
-```{code-cell} ipython3
-:tags: [remove-input]
-
-display(HTML("img/regression2/fig08-3DlinReg.html"))
+glue("fig:08-3DlinReg", fig)
 ```
 
 ```{figure} data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,3 +9,5 @@ source/*.py @@
     *.swp
     *.swo
     source/__pycache__
+    .local/
+    .viminfo