{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Setting up computing resources" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "nbsphinx": "hidden", "tags": [] }, "outputs": [], "source": [ "# Colab setup ------------------\n", "import os, sys, subprocess\n", "if \"google.colab\" in sys.modules:\n", " cmd = \"pip install --upgrade watermark\"\n", " process = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n", " stdout, stderr = process.communicate()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this lesson you will set up a Python computing environment for scientific computing on your own computer and also learn a bit about Google Colab, a cloud service for running Jupyter notebooks.\n", "\n", "It is advantageous to learn how to set up a Python distribution and manage packages on your own machine, as each person can have different needs. That said, [Google Colab](https://colab.research.google.com/) is a nice, free resource to run Jupyter Notebooks on Google's computers without any local installations necessary." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setting up Google Colab\n", "\n", "In order to use Google Colab, you must have a Google account. Caltech students and employees have an account through Caltech's G Suite. Many of you may have a personal Google account, usually set up for things like GMail, YouTube, etc. For your work in this class, **use your Caltech account.** This will facilitate collaboration with your teammates in the course, as well as with course staff.\n", "\n", "Many of you probably use your personal Google account on your machine, so it can get annoying to log in and out of it. A trick that I find useful is to use one browser, e.g., Safari or Microsoft Edge, for your personal use, web browsing, etc., and a different browser for your scientific work, including the work in this class. Google Colab are most tested for Chrome, Firefox, and Safari (in fact JupyterLab, which you will use on your own machine, only supports these three browsers).\n", "\n", "Once you have either logged out of all of your personal accounts or have a different browser open, you can launch a Colab notebook by simply navigating to [https://colab.research.google.com/](https://colab.research.google.com/). Alternatively, you can click the \"Launch in Colab\" badge at the top right of this page, and you will launch this notebook in Colab. That badge will appear in the top right of all pages in the course content generated from notebooks." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Watchouts when using Colab\n", "\n", "If you do run a notebook in Colab, you are doing your computing on one of Google's computers via a virtual machine. You get two CPU cores and limited (about 12 GB, but it varies) RAM. You can also get GPUs and TPUs (Google's tensor processing units), but we will not use those in this course. The computing resources should be enough for all of our calculations this term (though you will need more computing power in the sequel of this course). However, there are some limitations you should be aware of.\n", "\n", "- If your notebook is idle for too long, you will get disconnected from your notebook. \"Idle\" means that cells are not being edited or executed. The idle timeout varies depending on the load on Google's computers; I find that I almost always get disconnected if idle for an hour.\n", "- Your virtual machine will disconnect if it is being used for too long. It typically will only available for 12 hours before disconnecting, though times can vary, again based on load.\n", "\n", "These limitations are in place so that Google can offer Colab for free. If you want more cores, longer timeouts, etc., you might want to check out [Colab Pro](https://colab.research.google.com/signup). However, the free tier should work well for you in the course. You can of course always run on your own machine, and in fact are encouraged to do so.\n", "\n", "There are additional software-specific watchouts when using Colab.\n", "\n", "- Colab does not allow for full functionality of [Bokeh](http://bokeh.pydata.org/) apps that we will use when we do dashboarding. \n", "- Colab instances have specific software installed, so you will need to install anything else you need in your notebook. This is not a major burden, and is discussed in the next section.\n", "\n", "\n", "I recommend reading the [Colab FAQs](https://research.google.com/colaboratory/faq.html) for more information about Colab." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Software in Colab\n", "\n", "When you launch a Google Colab notebook, much of the software we will use in class is already installed. It is not always the latest version of the software, however. In fact, as of mid-September 2023, Colab is running Python 3.10, whereas you will run Python 3.11 on your machine through your Anaconda installation. Nonetheless, most (but not all) of the analyses we do for this class will work just fine in Colab. We will make every effort to let you know when Colab will not be able to handle activities in class, the most important example being some dashboarding applications.\n", "\n", "Because the notebooks in Colab have software preinstalled, and no more, you will often need to install software before you can run the rest of the code in a notebook. To enable this, when necessary, in the first code cell of each notebook in this class, we will have the following code (or a variant thereof depending on what is needed or if the default installations of Colab change). Running this code will not affect running your notebook on your local machine; the same notebook will work on your local machine or on Colab.\n", "\n", "```python\n", "# Colab setup ------------------\n", "import os, sys, subprocess\n", "if \"google.colab\" in sys.modules:\n", " cmd = \"pip install --upgrade iqplot bebi103 watermark\"\n", " process = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n", " stdout, stderr = process.communicate()\n", " data_path = \"https://s3.amazonaws.com/bebi103.caltech.edu/data/\"\n", "else:\n", " data_path = \"../data/\"\n", "# ------------------------------\n", "```\n", "\n", "In addition to installing the necessary software on a Colab instance, this also sets the relative path to data sets we will use in the course. When running in Colab, the data set is fetched from cloud storage on [AWS](https://aws.amazon.com). When running on your local machine for homeworks, the path to the data is one directory up from where you are working.\n", "\n", "In most notebooks, the Colab and data path setup code cells are hidden in the HTML rendering to avoid clutter, but will be present when you download the notebooks." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Collaborating with Colab\n", "\n", "If you want to collaborate with another student or with the course staff on a notebook, you can click \"Share\" on the top right corner of the Colab window and choose with whom and how (the defaults are fine) you want to share.\n", "\n", "When we talk about Git in a future lesson, we will discuss Colab's GitHub support, which will be necessary for version control and submitting and sharing your homework." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Installation on your own machine\n", "\n", "We now proceed to discuss installation of the necessary software on your own machine. Before we get into that, there are some preliminaries for Windows users." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Windows users: Install Git and Chrome or Firefox\n", "\n", "We will be using [JupyterLab](https://jupyterlab.readthedocs.io/en/stable/) in this course. It is browser-based, and Chrome, Firefox, and Safari are supported. Microsoft Edge is **not**. Therefore, if you are a Windows user, you need to be sure you have either Chrome of Firefox installed.\n", "\n", "Git is natively installed on Macs. For Windows users, you need to install Git by itself. You can do this by following the instructions [here](https://gitforwindows.org)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Downloading and installing Anaconda\n", "\n", "If you already have Anaconda installed on your machine, you can skip this step.\n", "\n", "Downloading and installing Anaconda is simple. \n", "\n", "1. Go to the [Anaconda's download page](https://www.anaconda.com/download) and click the Download button.\n", "2. Follow the on-screen instructions for installation. While doing so, be sure that Anaconda is installed in your home directory (which is the default), not in root.\n", "\n", "That's it! After you do that, you will have a functioning Python distribution." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Install node.js\n", "\n", "[node.js](https://nodejs.org/) is a platform that enables you to run JavaScript outside of the browser. We will not use it directly, but it needs to be installed for some of the more sophisticated JupyterLab functionality. Install node.js by downloading the appropriate installer for your machine [here](https://nodejs.org/en/download/)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setting up a conda environment\n", "\n", "I have created a conda environment for use in this class. You can download the YML specification for the environment:\n", "\n", "> [Download bebi103.yml](https://raw.githubusercontent.com/bebi103a/bebi103a.github.io/main/_static/bebi103.yml)\n", "\n", "You can set up and activate the environment on the command line or by using the Anaconda Navigator, which should be installed with Anaconda. You can do either of the two options, (a) or (b), below." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### a) Activating from the command line\n", "\n", "To set up your conda environment from the command line, navigate to the directory where you saved the `bebi103.yml` file. Then, on the command line, enter\n", "\n", " conda env create -f bebi103.yml\n", "\n", "This should build the environment for you (it may take several minutes). To then activate the environment, enter\n", "\n", " conda activate bebi103\n", "\n", "on the command line." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### b) Activating using the Anaconda Navigator\n", "\n", "If you are using macOS, Anaconda Navigator will be available in your `Applications` menu. If you are using Windows, you can launch Anaconda Navigator from the Start menu.\n", "\n", "When the Navigator window opens, select `Environments` on the left menu pane. Upon selecting `Environments`, you will see a pane immediately to the right of the `Home/Environments/Learning/Community` pane with a `Search Environments` window at the top. At the bottom of that pane, click `Import`. In the window that pops up, click on the folder icon under `Local drive`. Find the `bebi103.yml` file you just downloaded. Click `Import`. It may take some time for the environment to be imported and built." ] }, { "cell_type": "markdown", "metadata": { "jp-MarkdownHeadingCollapsed": true }, "source": [ "## Launching JupyterLab\n", "\n", "You can alternatively launch JupyterLab via the Anaconda Navigator or via your operating system's terminal program (Terminal on macOS and PowerShell on Windows). If you wish to launch using the latter (which I prefer), skip to the next section.\n", "\n", "In the Anaconda Navigator, click `Home` on the left pane. To the right, you will have a pane from which you can launch JupyterLab. On the top of the right pane, you will see two pulldown menus separated by the word \"on.\" Be sure you select `bebi103` on the right pulldown menu. This ensures that you are using the environment you just set up.\n", "\n", "**You need to make sure you are using the pol_stats environment whenever you launch JupyterLab during the workshop.**\n", "\n", "You should see a card for JupyterLab. Do not confuse this with Notebook; you want to launch JupyterLab. Click Launch on the JupyterLab card. This will launch JupyterLab in your default browser." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Launching JupyterLab from the command line\n", "\n", "While launching JupyterLab from the Anaconda Navigator is fine, I generally prefer to launch it from the command line on my own machine. If you are on a Mac, open the `Terminal` program. You can do this hitting `Command + space bar` and searching for \"terminal.\" Using Windows, you should launch PowerShell. You can do this by hitting `Windows + R` and typing \"powershell\" in the text box.\n", "\n", "Once you have a terminal or PowerShell window open, you will have a prompt. At the prompt, type\n", "\n", " conda activate bebi103\n", "\n", "This will ensure you are using the bebi103 environment you just created.\n", "\n", "**You need to make sure you are using the bebi103 environment whenever you launch JupyterLab, so you should do conda activate bebi103 each time you open a terminal.**\n", "\n", "Now that you have activated the bebi103 environment, you can launch JupyterLab by typing\n", "\n", " jupyter lab\n", "\n", "on the command line. You will have an instance of JupyterLab running in your default browser. If you want to specify the browser, you can, for example, type\n", "\n", " jupyter lab --browser=firefox\n", "\n", "on the command line.\n", "\n", "It is up to you if you want to launch JupyterLab from the Anaconda Navigator or command line." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Checking your distribution\n", "We'll now run a quick test to make sure things are working properly. We will make a quick plot that requires some of the scientific libraries we will use.\n", "\n", "Use the JupyterLab launcher (you can get a new launcher by clicking on the `+` icon on the left pane of your JupyterLab window) to launch a notebook. In the first cell (the box next to the `[ ]:` prompt), paste the code below. To run the code, press `Shift+Enter` while the cursor is active inside the cell. You should see a plot that looks like the one below. If you do, you have a functioning Python environment for scientific computing!\n", "\n", "You can also test this in Colab (and it should work with no problems)." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " const force = true;\n", "\n", " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", "const JS_MIME_TYPE = 'application/javascript';\n", " const HTML_MIME_TYPE = 'text/html';\n", " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " const CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " const script = document.createElement(\"script\");\n", " node.appendChild(script);\n", " }\n", "\n", " /**\n", " * Handle when an output is cleared or removed\n", " */\n", " function handleClearOutput(event, handle) {\n", " const cell = handle.cell;\n", "\n", " const id = cell.output_area._bokeh_element_id;\n", " const server_id = cell.output_area._bokeh_server_id;\n", " // Clean up Bokeh references\n", " if (id != null && id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", "\n", " if (server_id !== undefined) {\n", " // Clean up Bokeh references\n", " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", " cell.notebook.kernel.execute(cmd_clean, {\n", " iopub: {\n", " output: function(msg) {\n", " const id = msg.content.text.trim();\n", " if (id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", " }\n", " }\n", " });\n", " // Destroy server and session\n", " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd_destroy);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " const output_area = handle.output_area;\n", " const output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", "\n", " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", " // store reference to embed id on output_area\n", " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " }\n", " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " const bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " const script_attrs = bk_div.children[0].attributes;\n", " for (let i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", " }\n", "\n", " function register_renderer(events, OutputArea) {\n", "\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " const toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[toinsert.length - 1]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " /* Handle when an output is cleared or removed */\n", " events.on('clear_output.CodeCell', handleClearOutput);\n", " events.on('delete.Cell', handleClearOutput);\n", "\n", " /* Handle when a new output is added */\n", " events.on('output_added.OutputArea', handleAddOutput);\n", "\n", " /**\n", " * Register the mime type and append_mime function with output_area\n", " */\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " /* Is output safe? */\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " const events = require('base/js/events');\n", " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " const NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " const el = document.getElementById(\"b8e7c069-b385-4558-8966-c814d1649498\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.debug(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(css_urls, js_urls, callback) {\n", " if (css_urls == null) css_urls = [];\n", " if (js_urls == null) js_urls = [];\n", "\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", "\n", " function on_load() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", " run_callbacks()\n", " }\n", " }\n", "\n", " function on_error(url) {\n", " console.error(\"failed to load \" + url);\n", " }\n", "\n", " for (let i = 0; i < css_urls.length; i++) {\n", " const url = css_urls[i];\n", " const element = document.createElement(\"link\");\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.rel = \"stylesheet\";\n", " element.type = \"text/css\";\n", " element.href = url;\n", " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", " document.body.appendChild(element);\n", " }\n", "\n", " for (let i = 0; i < js_urls.length; i++) {\n", " const url = js_urls[i];\n", " const element = document.createElement('script');\n", " element.onload = on_load;\n", " element.onerror = on_error.bind(null, url);\n", " element.async = false;\n", " element.src = url;\n", " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.head.appendChild(element);\n", " }\n", " };\n", "\n", " function inject_raw_css(css) {\n", " const element = document.createElement(\"style\");\n", " element.appendChild(document.createTextNode(css));\n", " document.body.appendChild(element);\n", " }\n", "\n", " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.2.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.2.1.min.js\"];\n", " const css_urls = [];\n", "\n", " const inline_js = [ function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", "function(Bokeh) {\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " if (root.Bokeh !== undefined || force === true) {\n", " for (let i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }\n", "if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " const cell = $(document.getElementById(\"b8e7c069-b385-4558-8966-c814d1649498\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(css_urls, js_urls, function() {\n", " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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103 a\",\"text_align\":\"center\",\"x\":0,\"y\":0}}]}}]}};\n", " const render_items = [{\"docid\":\"b0b30c54-2c9e-4832-bd05-219995c1673f\",\"roots\":{\"p1001\":\"f962b716-779d-4458-91c8-151df5a21cf7\"},\"root_ids\":[\"p1001\"]}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p1001" } }, "output_type": "display_data" } ], "source": [ "import numpy as np\n", "import bokeh.plotting\n", "import bokeh.io\n", "\n", "bokeh.io.output_notebook()\n", "\n", "# Generate plotting values\n", "t = np.linspace(0, 2*np.pi, 200)\n", "x = 16 * np.sin(t)**3\n", "y = 13 * np.cos(t) - 5 * np.cos(2*t) - 2 * np.cos(3*t) - np.cos(4*t)\n", "\n", "p = bokeh.plotting.figure(height=250, width=275)\n", "p.line(x, y, color='red', line_width=3)\n", "text = bokeh.models.Label(x=0, y=0, text='BE/Bi 103 a', text_align='center')\n", "p.add_layout(text)\n", "\n", "bokeh.io.show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Computing environment" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Python implementation: CPython\n", "Python version : 3.11.5\n", "IPython version : 8.15.0\n", "\n", "numpy : 1.24.3\n", "bokeh : 3.2.1\n", "jupyterlab: 4.0.6\n", "\n" ] } ], "source": [ "%load_ext watermark\n", "%watermark -v -p numpy,bokeh,jupyterlab" ] } ], "metadata": { "anaconda-cloud": {}, "jupytext": { "target_format": "ipynb,auto:percent" }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.5" } }, "nbformat": 4, "nbformat_minor": 4 }