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results=FALSE and results='hide' both not working as expected for python code chunks #2379

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dmca-glasgow opened this issue Oct 31, 2024 · 2 comments
Open
3 tasks done

results=FALSE and results='hide' both not working as expected for python code chunks #2379

dmca-glasgow opened this issue Oct 31, 2024 · 2 comments

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@dmca-glasgow
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dmca-glasgow commented Oct 31, 2024 •
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With the following RMarkdown:

```{python results=FALSE}
from sklearn.datasets import load_digits
from sklearn.model_selection import train_test_split
X,y = load_digits(return_X_y=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33)
from sklearn.neighbors import KNeighborsClassifier
model = KNeighborsClassifier(n_neighbors=3)
model.fit(X_train, y_train)
```

Although I have set results=FALSE (or results='hide'), the resulting Markdown still includes the results from python, and isn't marked as knitr-output but {=html}:

``` python
from sklearn.datasets import load_digits
from sklearn.model_selection import train_test_split
X,y = load_digits(return_X_y=True)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33)
from sklearn.neighbors import KNeighborsClassifier
model = KNeighborsClassifier(n_neighbors=3)
model.fit(X_train, y_train)
```

```{=html}
<style>#sk-container-id-1 {
  /* Definition of color scheme common for light and dark mode */
  --sklearn-color-text: black;
  --sklearn-color-line: gray;
  /* Definition of color scheme for unfitted estimators */
  --sklearn-color-unfitted-level-0: #fff5e6;
  --sklearn-color-unfitted-level-1: #f6e4d2;
  --sklearn-color-unfitted-level-2: #ffe0b3;
  --sklearn-color-unfitted-level-3: chocolate;
  /* Definition of color scheme for fitted estimators */
  --sklearn-color-fitted-level-0: #f0f8ff;
  --sklearn-color-fitted-level-1: #d4ebff;
  --sklearn-color-fitted-level-2: #b3dbfd;
  --sklearn-color-fitted-level-3: cornflowerblue;

  /* Specific color for light theme */
  --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));
  --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, white)));
  --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, black)));
  --sklearn-color-icon: #696969;

  @media (prefers-color-scheme: dark) {
    /* Redefinition of color scheme for dark theme */
    --sklearn-color-text-on-default-background: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));
    --sklearn-color-background: var(--sg-background-color, var(--theme-background, var(--jp-layout-color0, #111)));
    --sklearn-color-border-box: var(--sg-text-color, var(--theme-code-foreground, var(--jp-content-font-color1, white)));
    --sklearn-color-icon: #878787;
  }
}

#sk-container-id-1 {
  color: var(--sklearn-color-text);
}

#sk-container-id-1 pre {
  padding: 0;
}

#sk-container-id-1 input.sk-hidden--visually {
  border: 0;
  clip: rect(1px 1px 1px 1px);
  clip: rect(1px, 1px, 1px, 1px);
  height: 1px;
  margin: -1px;
  overflow: hidden;
  padding: 0;
  position: absolute;
  width: 1px;
}

#sk-container-id-1 div.sk-dashed-wrapped {
  border: 1px dashed var(--sklearn-color-line);
  margin: 0 0.4em 0.5em 0.4em;
  box-sizing: border-box;
  padding-bottom: 0.4em;
  background-color: var(--sklearn-color-background);
}

#sk-container-id-1 div.sk-container {
  /* jupyter's `normalize.less` sets `[hidden] { display: none; }`
     but bootstrap.min.css set `[hidden] { display: none !important; }`
     so we also need the `!important` here to be able to override the
     default hidden behavior on the sphinx rendered scikit-learn.org.
     See: https://github.com/scikit-learn/scikit-learn/issues/21755 */
  display: inline-block !important;
  position: relative;
}

#sk-container-id-1 div.sk-text-repr-fallback {
  display: none;
}

div.sk-parallel-item,
div.sk-serial,
div.sk-item {
  /* draw centered vertical line to link estimators */
  background-image: linear-gradient(var(--sklearn-color-text-on-default-background), var(--sklearn-color-text-on-default-background));
  background-size: 2px 100%;
  background-repeat: no-repeat;
  background-position: center center;
}

/* Parallel-specific style estimator block */

#sk-container-id-1 div.sk-parallel-item::after {
  content: "";
  width: 100%;
  border-bottom: 2px solid var(--sklearn-color-text-on-default-background);
  flex-grow: 1;
}

#sk-container-id-1 div.sk-parallel {
  display: flex;
  align-items: stretch;
  justify-content: center;
  background-color: var(--sklearn-color-background);
  position: relative;
}

#sk-container-id-1 div.sk-parallel-item {
  display: flex;
  flex-direction: column;
}

#sk-container-id-1 div.sk-parallel-item:first-child::after {
  align-self: flex-end;
  width: 50%;
}

#sk-container-id-1 div.sk-parallel-item:last-child::after {
  align-self: flex-start;
  width: 50%;
}

#sk-container-id-1 div.sk-parallel-item:only-child::after {
  width: 0;
}

/* Serial-specific style estimator block */

#sk-container-id-1 div.sk-serial {
  display: flex;
  flex-direction: column;
  align-items: center;
  background-color: var(--sklearn-color-background);
  padding-right: 1em;
  padding-left: 1em;
}


/* Toggleable style: style used for estimator/Pipeline/ColumnTransformer box that is
clickable and can be expanded/collapsed.
- Pipeline and ColumnTransformer use this feature and define the default style
- Estimators will overwrite some part of the style using the `sk-estimator` class
*/

/* Pipeline and ColumnTransformer style (default) */

#sk-container-id-1 div.sk-toggleable {
  /* Default theme specific background. It is overwritten whether we have a
  specific estimator or a Pipeline/ColumnTransformer */
  background-color: var(--sklearn-color-background);
}

/* Toggleable label */
#sk-container-id-1 label.sk-toggleable__label {
  cursor: pointer;
  display: block;
  width: 100%;
  margin-bottom: 0;
  padding: 0.5em;
  box-sizing: border-box;
  text-align: center;
}

#sk-container-id-1 label.sk-toggleable__label-arrow:before {
  /* Arrow on the left of the label */
  content: "▸";
  float: left;
  margin-right: 0.25em;
  color: var(--sklearn-color-icon);
}

#sk-container-id-1 label.sk-toggleable__label-arrow:hover:before {
  color: var(--sklearn-color-text);
}

/* Toggleable content - dropdown */

#sk-container-id-1 div.sk-toggleable__content {
  max-height: 0;
  max-width: 0;
  overflow: hidden;
  text-align: left;
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-0);
}

#sk-container-id-1 div.sk-toggleable__content.fitted {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-0);
}

#sk-container-id-1 div.sk-toggleable__content pre {
  margin: 0.2em;
  border-radius: 0.25em;
  color: var(--sklearn-color-text);
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-0);
}

#sk-container-id-1 div.sk-toggleable__content.fitted pre {
  /* unfitted */
  background-color: var(--sklearn-color-fitted-level-0);
}

#sk-container-id-1 input.sk-toggleable__control:checked~div.sk-toggleable__content {
  /* Expand drop-down */
  max-height: 200px;
  max-width: 100%;
  overflow: auto;
}

#sk-container-id-1 input.sk-toggleable__control:checked~label.sk-toggleable__label-arrow:before {
  content: "▾";
}

/* Pipeline/ColumnTransformer-specific style */

#sk-container-id-1 div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {
  color: var(--sklearn-color-text);
  background-color: var(--sklearn-color-unfitted-level-2);
}

#sk-container-id-1 div.sk-label.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {
  background-color: var(--sklearn-color-fitted-level-2);
}

/* Estimator-specific style */

/* Colorize estimator box */
#sk-container-id-1 div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-2);
}

r-id-1 div.sk-estimator.fitted input.sk-toggleable__control:checked~label.sk-toggleable__label {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-2);
}

#sk-container-id-1 div.sk-label label.sk-toggleable__label,
#sk-container-id-1 div.sk-label label {
  /* The background is the default theme color */
  color: var(--sklearn-color-text-on-default-background);
}

/* On hover, darken the color of the background */
#sk-container-id-1 div.sk-label:hover label.sk-toggleable__label {
  color: var(--sklearn-color-text);
  background-color: var(--sklearn-color-unfitted-level-2);
}

/* Label box, darken color on hover, fitted */
#sk-container-id-1 div.sk-label.fitted:hover label.sk-toggleable__label.fitted {
  color: var(--sklearn-color-text);
  background-color: var(--sklearn-color-fitted-level-2);
}

/* Estimator label */

#sk-container-id-1 div.sk-label label {
  font-family: monospace;
  font-weight: bold;
  display: inline-block;
  line-height: 1.2em;
}

#sk-container-id-1 div.sk-label-container {
  text-align: center;
}

/* Estimator-specific */
#sk-container-id-1 div.sk-estimator {
  font-family: monospace;
  border: 1px dotted var(--sklearn-color-border-box);
  border-radius: 0.25em;
  box-sizing: border-box;
  margin-bottom: 0.5em;
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-0);
}

#sk-container-id-1 div.sk-estimator.fitted {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-0);
}

/* on hover */
#sk-container-id-1 div.sk-estimator:hover {
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-2);
}

#sk-container-id-1 div.sk-estimator.fitted:hover {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-2);
}

/* Specification for estimator info (e.g. "i" and "?") */

/* Common style for "i" and "?" */

.sk-estimator-doc-link,
a:link.sk-estimator-doc-link,
a:visited.sk-estimator-doc-link {
  float: right;
  font-size: smaller;
  line-height: 1em;
  font-family: monospace;
  background-color: var(--sklearn-color-background);
  border-radius: 1em;
  height: 1em;
  width: 1em;
  text-decoration: none !important;
  margin-left: 1ex;
  /* unfitted */
  border: var(--sklearn-color-unfitted-level-1) 1pt solid;
  color: var(--sklearn-color-unfitted-level-1);
}

.sk-estimator-doc-link.fitted,
a:link.sk-estimator-doc-link.fitted,
a:visited.sk-estimator-doc-link.fitted {
  /* fitted */
  border: var(--sklearn-color-fitted-level-1) 1pt solid;
  color: var(--sklearn-color-fitted-level-1);
}

/* On hover */
div.sk-estimator:hover .sk-estimator-doc-link:hover,
.sk-estimator-doc-link:hover,
div.sk-label-container:hover .sk-estimator-doc-link:hover,
.sk-estimator-doc-link:hover {
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-3);
  color: var(--sklearn-color-background);
  text-decoration: none;
}

div.sk-estimator.fitted:hover .sk-estimator-doc-link.fitted:hover,
.sk-estimator-doc-link.fitted:hover,
div.sk-label-container:hover .sk-estimator-doc-link.fitted:hover,
.sk-estimator-doc-link.fitted:hover {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-3);
  color: var(--sklearn-color-background);
  text-decoration: none;
}

/* Span, style for the box shown on hovering the info icon */
.sk-estimator-doc-link span {
  display: none;
  z-index: 9999;
  position: relative;
  font-weight: normal;
  right: .2ex;
  padding: .5ex;
  margin: .5ex;
  width: min-content;
  min-width: 20ex;
  max-width: 50ex;
  color: var(--sklearn-color-text);
  box-shadow: 2pt 2pt 4pt #999;
  /* unfitted */
  background: var(--sklearn-color-unfitted-level-0);
  border: .5pt solid var(--sklearn-color-unfitted-level-3);
}

.sk-estimator-doc-link.fitted span {
  /* fitted */
  background: var(--sklearn-color-fitted-level-0);
  border: var(--sklearn-color-fitted-level-3);
}

.sk-estimator-doc-link:hover span {
  display: block;
}

/* "?"-specific style due to the `<a>` HTML tag */

#sk-container-id-1 a.estimator_doc_link {
  float: right;
  font-size: 1rem;
  line-height: 1em;
  font-family: monospace;
  background-color: var(--sklearn-color-background);
  border-radius: 1rem;
  height: 1rem;
  width: 1rem;
  text-decoration: none;
  /* unfitted */
  color: var(--sklearn-color-unfitted-level-1);
  border: var(--sklearn-color-unfitted-level-1) 1pt solid;
}

#sk-container-id-1 a.estimator_doc_link.fitted {
  /* fitted */
  border: var(--sklearn-color-fitted-level-1) 1pt solid;
  color: var(--sklearn-color-fitted-level-1);
}

/* On hover */
#sk-container-id-1 a.estimator_doc_link:hover {
  /* unfitted */
  background-color: var(--sklearn-color-unfitted-level-3);
  color: var(--sklearn-color-background);
  text-decoration: none;
}

#sk-container-id-1 a.estimator_doc_link.fitted:hover {
  /* fitted */
  background-color: var(--sklearn-color-fitted-level-3);
}
</style><div id="sk-container-id-1" class="sk-top-container"><div class="sk-text-repr-fallback"><pre>KNeighborsClassifier(n_neighbors=3)</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class="sk-container" hidden><div class="sk-item"><div class="sk-estimator fitted sk-toggleable"><input class="sk-toggleable__control sk-hidden--visually" id="sk-estimator-id-1" type="checkbox" checked><label for="sk-estimator-id-1" class="sk-toggleable__label fitted sk-toggleable__label-arrow fitted">&nbsp;&nbsp;KNeighborsClassifier<a class="sk-estimator-doc-link fitted" rel="noreferrer" target="_blank" href="https://scikit-learn.org/1.5/modules/generated/sklearn.neighbors.KNeighborsClassifier.html">?<span>Documentation for KNeighborsClassifier</span></a><span class="sk-estimator-doc-link fitted">i<span>Fitted</span></span></label><div class="sk-toggleable__content fitted"><pre>KNeighborsClassifier(n_neighbors=3)</pre></div> </div></div></div></div>
```

Rscript -e "xfun::session_info('knitr')"                      
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin23.2.0 (64-bit)
Running under: macOS 15.0.1

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  evaluate_1.0.1  graphics_4.3.3  grDevices_4.3.3 highr_0.11     
  knitr_1.48      methods_4.3.3   stats_4.3.3     tools_4.3.3    
  utils_4.3.3     xfun_0.48       yaml_2.3.10

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@dmca-glasgow
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We have found a fix for this by prepending:

```{python echo=FALSE}
import sklearn
sklearn.set_config(display="text")
```

I guess ideally, this should be automatically configured when using knitr.

@cderv
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cderv commented Nov 5, 2024

I believe the handling of knitr ooutput for python cell is done by reticulate engine directly.

This is the engine handling the knitr option, and deciding what to output for knitr to insert in the document.

I would open the issue there. Unless this is related to existing one like

So this will be solved in reticulate

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@cderv @dmca-glasgow