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update-documentation #293

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Jan 27, 2025
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update-documentation #293

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9020f9e
updated usage.md with more indepth documentation
ymahlich Jan 13, 2025
9a4c24b
updates to index.md
ymahlich Jan 14, 2025
5ad6421
test use of html tags for code blocks
ymahlich Jan 23, 2025
128fbdd
added test
ymahlich Jan 23, 2025
faafd4b
revert changes
ymahlich Jan 23, 2025
69a1e90
updated css
ymahlich Jan 23, 2025
7a7452e
css update to distinguish inline code and code blocks
ymahlich Jan 26, 2025
2cf7cad
fix padding of inline code and x-overflow scrolling behaviour of code…
ymahlich Jan 27, 2025
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90 changes: 83 additions & 7 deletions docs/assets/css/style.css
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Expand Up @@ -139,15 +139,26 @@ body {
box-shadow: 0px 2px 4px rgba(0, 0, 0, 0.05);
}

code {
/* inline code */
code.highlighter-rouge{
background: white;
border: 1px solid #ccc;
padding: 2.5px;

}

/* code block */
div.highlighter-rouge {
background-color: white;
width: 60%;
border: 1px solid #ccc;
padding: 2.5px;
padding: 2.5px;
overflow-x: auto;

}

/* pre > code.language-bash {
/*
pre > code.language-bash {
background-color: white;
width: 60%;
border: 1px solid #ccc;
Expand All @@ -162,7 +173,8 @@ pre > code.language-python {
display: block;
overflow-x: auto;
border: 1px solid #ccc;
} */
}
*/
/*
.hamburger {
display: none;
Expand Down Expand Up @@ -230,7 +242,7 @@ pre > code.language-python {
*/


.code-box {
.code-box {
background-color: white;
border: 1px solid #ccc;
font-family: monospace; /* Gives the text a code-like appearance */
Expand All @@ -247,7 +259,7 @@ pre > code.language-python {

.flex-container {
display: flex;
justify-content: space-around; /* Or use 'center' if you prefer */
justify-content: space-around; /* Or use 'center' if you ffer */
align-items: center;
flex-wrap: wrap; /* Allows items to wrap onto the next line on smaller screens */
width: 100%;
Expand Down Expand Up @@ -476,4 +488,68 @@ th {
font-size: 16px;
}

}
}

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60 changes: 40 additions & 20 deletions docs/index.md
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Expand Up @@ -7,42 +7,62 @@ title: CoderData

<!-- # Cancer Omics and Drug Experiment Response Data (`coderdata`) Python Package -->

### Introduction
## Introduction
CoderData is a cancer benchmark data package developed in Python and R.
There are two aspects of this package, the backend build section and the user facing python package.
The build section is a github workflow that generates four cancer datasets in a format that is easy for users and algorithms to ingest.
The python package allows users to easily download the data, load it into python and reformat it as desired.

### Installation and Usage
##### Bash / Command Line
## Installation and Usage
### Installation

To install coderdata, simply run the following command in your terminal:
Assuming `python>=3.9` is installed on the system, simply run the following command in the terminal to install the most recent release of the coderdata API:

```bash
pip install coderdata
$ pip install coderdata
```

##### Bash / Command line
To download datasets, simply run the following command in your terminal. Remove the prefix argument if you'd like to install all datasets.
### Bash / Command line
A full list of available datasets can be retrieved via:
```sh
$ coderdata --list
```

To download datasets, simply run the following command in your terminal substituting `<DATASET>` with the desired dataset (e.g. `beataml`). To download all datasets use `--name all`.

```bash
coderdata download --prefix hcmi
$ coderdata download --name <DATASET>
```

##### Python
To download, load, and call datasets in python, simply run the following commands.

<div class="code-box">
<p>import coderdata as cd </p>
<p>cd.download_data_by_prefix('hcmi')</p>
<p>hcmi_data = cd.DatasetLoader('hcmi')</p>
<p>hcmi_data.transcriptomics</p>
</div>
### Python

To download, load, and call datasets in python, simply run the following commands.

```python
>>> import coderdata as cd
>>> cd.download(name='beataml')
>>> beataml = cd.load('beataml')
>>> beataml.experiments
source improve_sample_id improve_drug_id study time time_unit dose_response_metric dose_response_value
0 synapse 3907 SMI_11123 BeatAML 72 hrs fit_auc 0.0564
1 synapse 3907 SMI_11211 BeatAML 72 hrs fit_auc 0.9621
2 synapse 3907 SMI_12192 BeatAML 72 hrs fit_auc 0.1691
3 synapse 3907 SMI_12254 BeatAML 72 hrs fit_auc 0.4245
4 synapse 3907 SMI_12469 BeatAML 72 hrs fit_auc 0.7397
... ... ... ... ... ... ... ... ...
233775 synapse 3626 SMI_7110 BeatAML 72 hrs dss 0.0000
233776 synapse 3626 SMI_7590 BeatAML 72 hrs dss 0.0000
233777 synapse 3626 SMI_8159 BeatAML 72 hrs dss 0.1946
233778 synapse 3626 SMI_8724 BeatAML 72 hrs dss 0.0000
233779 synapse 3626 SMI_987 BeatAML 72 hrs dss 0.7165

[233780 rows x 8 columns]
```

View our [Usage](pages/usage.md) page for full instructions.
For more indepth instructions view our [Usage](pages/usage.md) page.


### Datasets
## Datasets

<table>
<thead>
Expand Down Expand Up @@ -171,7 +191,7 @@ View our [Usage](pages/usage.md) page for full instructions.
</div> -->


### Data Overview
## Data Overview

<div class="flex-container">
<div class="flex-item">
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