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<p class="pf0"><span class="cf0">This section is designed to expand users’ understanding of the basics of using Python code in </span><span class="cf0">Jupyter</span><span class="cf0"> Notebooks via </span><span class="cf0">JupyterLab</span><span class="cf0">. The topics covered will be:</span></p>
<ul>
<ul>
<li><span class="cf0">How to run (execute) a </span><span class="cf0">Jupyter</span><span class="cf0"> Notebook cell</span></li>
<li><span class="cf0">The different types of </span><span class="cf0">Jupyter</span><span class="cf0"> Notebook cells</span></li>
<li><span class="cf0">Stopping a process or restarting a </span><span class="cf0">Jupyter</span><span class="cf0"> Notebook</span></li>
</ul>
</ul>
</div>
</div>
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<h3 class="pf0"><strong><span class="cf0">1.3.2.1 Running (executing) a cell</span></strong></h3>
<p class="pf0"><span class="cf0">Jupyter</span><span class="cf0"> Notebooks allow code to be separated into sections that can be executed independent of one another. These sections are called <strong>cells</strong>.</span></p>
<p class="pf0"><span class="cf0">Python code is written into individual cells that can be executed by placing the cursor in the cell and typing <code><span style="color: #339966;">Shift-Enter</span></code> on the keyboard or selecting the </span><strong><span class="cf1">►</span></strong><span class="cf0"><strong> “run”</strong> button in the ribbon at the top of the notebook. These options will run a single cell at a time.</span></p>
<p class="pf0"><span class="cf0"><img height="87" width="650" src="/assets/courseware/v1/06a2e46768bb89d1b1a53f79005f0298/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image56.png" alt="Crop health" /></span></p>
<p class="pf0"></p>
<p class="pf0"><span class="cf0">If you wish to auto-run all cells in a notebook, navigate to the “<strong>Run</strong>” tab of the menu bar at the top of </span><span class="cf0">JupyterLab</span><span class="cf0"> and select “<strong>Run All Cells</strong>” (or the option that best suits your needs). When you run a cell, you are executing that cell’s content. Any output produced from </span><span style="font-size: 1em;">running the cell will appear directly below it.</span></p>
<p class="pf0"><span style="font-size: 1em;"><img height="315" width="436" src="/assets/courseware/v1/0a4c995a9fdf57db296f3a9bc33a3078/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image57.png" alt="Running" /></span></p>
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require(['/static/js/dateutil_factory.be68acdff619.js?raw'], function () {
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<p class="pf0"><span class="cf0">Cells are identified as either Code, Markdown, or Raw. This designation can be changed using the ribbon at the top of the notebook. </span></p>
<p class="pf0"></p>
<h3><strong><span class="cf0">1.3.3.1 Code cells</span></strong></h3>
<p class="pf0"><span class="cf0">All code operations are performed in Code cells. Code cells can be used to edit and write new code, and perform tasks like loading data, plotting data and running analyses.</span></p>
<p><span class="cf0">In the previous session, you copied the </span><code><span class="cf0" style="color: #ff0000;">Crop_health.ipynb</span></code><span class="cf0"> notebook. In your copy of the </span><code><span class="cf0" style="color: #ff0000;">Crop_health.ipynb</span></code><span class="cf0"> notebook, click on the cell that looks like:<br />______________________________________________________________<br /></span></p>
<p dir="ltr" style="line-height: 1.7999999999999998; margin-top: 10pt; margin-bottom: 0pt;"><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #37474f; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">%matplotlib</span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1c1c1c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #37474f; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">inline</span></p>
<p dir="ltr" style="line-height: 1.7999999999999998; margin-top: 10pt; margin-bottom: 0pt;"><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1967d2; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">import</span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1c1c1c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #37474f; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">datacube</span></p>
<p dir="ltr" style="line-height: 1.7999999999999998; margin-top: 10pt; margin-bottom: 0pt;"><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1967d2; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">from</span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1c1c1c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #37474f; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">deafrica_tools.app.crophealth</span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1c1c1c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1967d2; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">import</span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #1c1c1c; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="font-size: 9pt; font-family: 'Roboto Mono',monospace; color: #37474f; background-color: transparent; font-weight: 400; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">load_crophealth_data</span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #1967d2; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;">from</span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #1c1c1c; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;"> </span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #37474f; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;">deafrica_tools.app.crophealth</span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #1c1c1c; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;"> </span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #1967d2; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;">import</span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #1c1c1c; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;"> </span><span style="background-color: transparent; font-size: 9pt; font-family: 'Roboto Mono', monospace; color: #37474f; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; font-variant-emoji: normal; vertical-align: baseline; white-space-collapse: preserve;">run_crophealth_app</span></p>
<p><span class="cf0">______________________________________________________________</span></p>
<p class="pf0"></p>
<p class="pf0">You will see that the ribbon at the top of the notebook describes it as a Code Cell.</p>
<p class="pf0"><span class="cf0"><img height="159" width="652" src="/assets/courseware/v1/4f18b1b50af230af55030ccae2b425b5/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image58.png" alt="Crop health" /></span></p>
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<h3 class="pf0"><strong>1.3.3.2 Markdown cells</strong></h3>
<p class="pf0"><span class="cf0">In your copy of the </span><code><span class="cf0" style="color: #ff0000;">Crop_health.ipynb</span></code><span class="cf0"> notebook, double click on the cell that looks like:</span></p>
<p class="pf0"><span class="cf0"><img height="225" width="653" src="/assets/courseware/v1/21d40286a7eba89e2a16975ac6f6bad2/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image59.png" alt="Notebook" /></span></p>
<p class="pf0"></p>
<p class="pf0"><span class="cf0">The cell format has changed to allow for editing. Note that the ribbon at the top of the notebook describes this as a Markdown cell.</span></p>
<p class="pf0"><span class="cf0"><img height="281" width="653" src="/assets/courseware/v1/cbcd8e79a50f5cfea37cbaba1076b0ab/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image60.png" alt="Image" /></span></p>
<p class="pf0"><span class="cf0">Run this cell (<code><span style="color: #339966;">Shift-Enter</span></code>) to return the formatted version.</span></p>
<p class="pf0"><span class="cf0"><strong>Markdown cells</strong> provide the narrative to a notebook. They are used for text and are useful to describe the code operations in the following cells. To see some of the formatting options for text in a Markdown cell, navigate to the “Help” tab of the menu bar at the top of </span><span class="cf0">JupyterLab</span><span class="cf0"> and select “Markdown Reference”. Here you will see a wide range of text formatting options including headings, dot points, italics, hyperlinking and creating tables.</span></p>
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<h3 class="pf0"><strong>1.3.3.3 Raw cells</strong></h3>
<p class="pf0"><span class="cf0">Information in <strong>Raw cells</strong> is stored in the notebook metadata and can be used to render different code formats into HTML or LaTeX. There are a range of available Raw cell formats that differ depending on how they are to be rendered. For the purposes of this beginner’s guide, raw cells are rarely used by the authors and not required for most notebook users.</span></p>
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<h3 class="pf0"><strong><span class="cf0">1.3.3.4 Cell status</span></strong></h3>
<p class="pf0"><span class="cf0">The <code><span style="color: #339966;">[ ]</span></code>: symbol to the left of each Code cell describes the state of the cell:</span></p>
<ul>
<li><code style="background-color: #ffffff;"><span style="color: #339966;">[ ]</span></code>: means that the cell has not been run yet.</li>
<li><code style="background-color: #ffffff;"><span style="color: #339966;">[*]</span></code>: means that the cell is currently running.</li>
<li><code style="background-color: #ffffff;"><span style="color: #339966;">[1]</span></code>: means that the cell has finished running and was the first cell run.</li>
</ul>
<p class="pf0"><span class="cf0">The number indicates the order that the cells were run in.</span></p>
<p><span class="cf0"><strong>Note:</strong> You can also tell whether a cell is currently executing in a </span><span class="cf0">Jupyter</span><span class="cf0"> notebook by inspecting the small circle in the top-right of the window. The circle will turn grey </span><span style="font-size: 1em;">(“<strong>Kernel busy</strong>”) when the cell is running, and return to empty (“Kernel idle”) when the process is complete.</span></p>
<p></p>
<p></p>
<p></p>
<p class="pf0"><span style="font-size: 1em;"><img height="30" width="662" src="/assets/courseware/v1/05e01d6b5b8cc28ca1c1a871033fe756/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image61.png" alt="Image" /></span></p>
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<p><span class="cf0">Sometimes it can be useful to stop a cell execution before it finishes (e.g. if a process is taking too long to complete, or if you realise you need to modify some code before running the cell). To interrupt a cell execution, you can click the </span><span class="cf1">■</span><span class="cf0"> “stop” button in the ribbon above the notebook, or select “Interrupt Kernel” from the Kernel menu.</span></p>
<p><span class="cf0"><img height="80" width="657" src="/assets/courseware/v1/11da97341b82f43efdde2385c45c1002/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image62.png" alt="Image" /></span></p>
<p>or </p>
<p><img height="371" width="650" src="/assets/courseware/v1/30188ecf29df095da47224dfd9ba2a7e/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image63.png" alt="Image" /><br /><br /></p>
<p><span class="cf0"><strong>NOTE:</strong> If the approach above does not work (e.g. if the notebook has frozen or refuses to respond), you can also try restarting the entire notebook. To do this, navigate to the “Kernel” tab of the menu bar, then select “Restart Kernel”. Alternatively, click the </span><span class="cf1">↻ </span><span class="cf2"></span><span style="font-size: 1em;">“Restart the kernel” button in the ribbon above the notebook.</span></p>
<p><span style="font-size: 1em;"><img height="123" width="659" src="/assets/courseware/v1/0e206ae895ed9a180c067461f595e99e/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image64.png" alt="Image" /></span></p>
<p>Restarting a notebook can also be useful for testing whether your code will work correctly the first time a new user tries to run the notebook. To restart and then run every cell in a notebook, navigate to the “Kernel” tab, then select “Restart and Run All Cells”.</p>
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<p><span class="cf0">To create a new notebook of your own, first use </span><span class="cf0">JupyterLab’s</span><span class="cf0"> file browser to navigate to the directory you would like the notebook to be created in (if the file browser is not visible, re-open it by clicking on the </span><span class="cf1">📁</span><span class="cf0"> “File browser” icon at the top-left of the screen). </span></p>
<p><span class="cf0"><img height="128" width="390" src="/assets/courseware/v1/b7e2c97933f408c9685dea23fbe904b9/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image73.png" alt="Image" /></span></p>
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<p class="pf0"><span class="cf0">Once you have navigated to your desired location, press the </span><span class="cf1">✚</span><span class="cf0"> “New Launcher” button above the browser. </span></p>
<p class="pf0"><span class="cf0"><img height="157" width="426" src="/assets/courseware/v1/9226f1429d2f63a93cf1a46a308c9eb4/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image74.png" alt="Image" /></span></p>
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<p class="pf0"><span class="cf0">This will bring up </span><span class="cf0">JupyterLab’s</span><span class="cf0"> “Launcher” page which allows you to launch a range of new files or utilities. Below the heading “Notebook”, click the large “Python 3” button. This will create a new notebook entitled “</span><span class="cf0">Untitled.ipynb</span><span class="cf0">” in your directory.</span></p>
<p class="pf0"><span class="cf0"><img height="342" width="563" src="/assets/courseware/v1/313ccbfb0809599556259ac4993257bc/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image75.png" alt="Image" /></span></p>
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<p class="pf0"><span class="cf0">To rename this notebook to something more useful, right-click on it in the file browser and select “Rename”. Alternatively, click on the notebook in the file browser and then hit ‘F2’ on your keyboard.</span></p>
<p class="pf0"><span class="cf0"><img height="621" width="486" src="/assets/courseware/v1/d7cae13c2d69e3a2a254ae2bb334a138/asset-v1:digitalearthafrica+DEA101+2021+type@asset+block/Image77.png" alt="Image" /></span></p>
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