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For 392 | the avoidance of doubt, this paragraph does not form part of the 393 | public licenses. 394 | 395 | Creative Commons may be contacted at creativecommons.org. 396 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![CC BY 4.0][cc-by-shield]][cc-by] 2 | 3 | This work is licensed under a 4 | [Creative Commons Attribution 4.0 International License][cc-by]. 5 | [![CC BY 4.0][cc-by-image]][cc-by] 6 | 7 | [cc-by]: http://creativecommons.org/licenses/by/4.0/ 8 | [cc-by-image]: https://i.creativecommons.org/l/by/4.0/88x31.png 9 | [cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg 10 | 11 | # codingForChemists 12 | Resources for and by the #codingForChemists Discord community! 13 | If you are interested in joining the community, please contact me directly through [my website](https://supersciencegrl.co.uk). 14 | 15 | ### Put your spin on the repo! 16 | - Submit a [**pull request**](https://github.com/supersciencegrl/codingForChemists/pulls) to submit your content to be added to the repo. Content should be suitable for beginner or intermediate-level coders, and aimed at chemists 17 | - The [**Issues**](https://github.com/supersciencegrl/codingForChemists/issues) tab is our wish list. Please submit things you want to see here, or point (with sufficient detail) to any problems in our published content 18 | - Very little in this repo will have been made by me [supersciencegrl](https://github.com/supersciencegrl/)! 19 | 20 | # Contents 21 | ## Guides folder 22 | ### How to choose a language (for chemists and the chemistry-adjacent) 23 | [https://github.com/supersciencegrl/codingForChemists/blob/main/guides/choosing_a_language.md](guides/choosing_a_language.md) 24 |
How to choose a language, for whichever use case(s) you are interested in, for example: 25 | - General purpose programming languages 26 | - Data collection, cleaning, processing, and visualization 27 | - Machine learning and artificial intellignece 28 | - Systems programming & scripting 29 | - Instruments & devices 30 | - Numerical computation 31 | - Web programming 32 | - GUI applications 33 | ### How to install Python and create environments 34 | [https://github.com/supersciencegrl/codingForChemists/blob/main/guides/python_environment_setup.md](guides/python_environment_setup.md) 35 | - Why Python environments? 36 | - Option 1: Installing Anaconda or Miniconda 37 | - Option 2: Installing Python from python.org 38 | - Other options 39 | -------------------------------------------------------------------------------- /guides/choosing_a_language.md: -------------------------------------------------------------------------------- 1 | # How to Choose a Programming Language 2 | ## For Chemists and the Chemistry-Adjacent 3 | 4 | ### Table of Contents 5 | 6 | - [How to Choose a Programming Language](#how-to-choose-a-programming-language) 7 | - [For Chemists and the Chemistry-Adjacent](#for-chemists-and-the-chemistry-adjacent) 8 | - [Table of Contents](#table-of-contents) 9 | - [Introduction](#introduction) 10 | - [General Purpose Programming Languages](#general-purpose-programming-languages) 11 | - [Data Collection, Cleaning, Processing, and Visualization](#data-collection-cleaning-processing-and-visualization) 12 | - [Machine Learning and Artificial Intelligence](#machine-learning-and-artificial-intelligence) 13 | - [Systems Programming and Scripting](#systems-programming-and-scripting) 14 | - [Instruments and Devices](#instruments-and-devices) 15 | - [Numerical Computation](#numerical-computation) 16 | - [Web Programming](#web-programming) 17 | - [GUI Applications](#gui-applications) 18 | - [Distributing Applications](#distributing-applications) 19 | - [Desktop Applictions](#desktop-applictions) 20 | - [Mobile Applications](#mobile-applications) 21 | - [Conclusion](#conclusion) 22 | 23 | 24 | ### Introduction 25 | 26 | If you are interested in programming, 27 | but don't know where to start, 28 | answering the question "What programming language should I learn?" 29 | is the first obstacle to overcome. 30 | 31 | This is an (opinionated, non-authoritative) guide 32 | to help people answer that question for themselves. 33 | The author will try to make their personal opinions 34 | and lack of knowledge clear as warranted. 35 | Corrections and additions to this guide are welcome! 36 | 37 | This guide will mention the most commonly-encountered languages 38 | that are either particularly useful to chemists, 39 | or are particularly well suited for people just starting to learn programming. 40 | 41 | Whatever language you choose, 42 | once you dive into it you will also learn tools, skills and habits 43 | that are not language-specific. 44 | If you spend some time learning one language, and decide to try another, 45 | you will have the pieces in place to pick up the next language 46 | and start working with it. 47 | 48 | This guide is structured around the likely answers to that question: 49 | 50 | **

Why are you interested in programming?

** 51 | 52 | ### General Purpose Programming Languages 53 | 54 | Most of this guide will be for people that already have some idea 55 | of what they want to do with their new coding superpowers. 56 | However, maybe you just think coding sounds generally useful, 57 | interesting, or fun. 58 | If that is the case, 59 | the author's *opinionated* answer is: 60 | 61 | **

[Python.](https://www.python.org/)

** 62 | 63 | Python has been described as being "the second-best language for everything". 64 | In particular, it's a top-tier language for data processing and visualization, 65 | machine learning (ML), and artificial intelligence (AI). 66 | There is a huge ecosystem of scientific and numeric packages for Python as well. 67 | 68 | Plus, (in the author's opinion), Python is easy to pick up 69 | and start doing useful things with. 70 | The language is *expressive*, almost reading like "pseudo-code" at times. 71 | For example, let's say you wanted to tell the computer: 72 | 73 | ```text 74 | "for each name in my list of guests: Amy, Bob, Cathy and Doug, 75 | print "Hi, (name of guest!)" 76 | ``` 77 | 78 | This is what it would look like in Python: 79 | 80 | ```python 81 | for name in ['Amy', 'Bob', 'Cathy', 'Doug']: 82 | print(f'Hi, {name}!') 83 | ``` 84 | 85 | In contrast, this is what it would look like written in c: 86 | 87 | ```c 88 | #include 89 | #include 90 | int main(void) { 91 | char guests[4][10] = {"Amy", "Bob", "Cathy", "Doug"}; 92 | for (int i = 0; i < 4; i++) { 93 | printf("Hello, %s!\n", guests[i]); 94 | } 95 | return EXIT_SUCCESS; 96 | } 97 | ``` 98 | >#### When might "Python" not be the best answer? 99 | > 100 | >The following situations can be problematic with Python, to varying degrees. 101 | > 102 | >- Running on multiple CPUs ("multithreading"): 103 | this is possible, but Python has the notorious 104 | [Global Interpreter Lock (GIL)](https://www.python.org/) 105 | that makes this cumbersome. 106 | >- speed-critical applications: Python is a slow language. 107 | However, it can interface with faster languages. 108 | For example, the widely-used `numpy` libary for numerical computation 109 | uses Fortran libraries "under the hood", 110 | and its possible to write Python code 111 | where the faster language is performing most of the work. 112 | However, if you are designing a computer 113 | to perform stock market micro-transactions so fast 114 | that your speed is limited by how long the wire is 115 | between your computer and the stock exchange across the street, 116 | you don't want to be using Python. 117 | >- creating cross-platform desktop applications 118 | that you can distribute to non-programmer friends. 119 | This is doable, especially for small applications, 120 | but can get tricky as your application gets more complicated. 121 | Third-party tools are required 122 | to bundle your python code as a one-file application. 123 | >- writing applications for mobile devices. VERY DIFFICULT. 124 | Possible (e.g. with [kivy](https://kivy.org) or [BeeWare](https://beeware.org), but Here Be Dragons. 125 | 126 | An honorable mention goes to 127 | [the Julia programming language](https://julialang.org). 128 | The author does not have Julia experience, 129 | and the Julia community is much smaller than the Python community. 130 | However, it is a multi-purpose language 131 | that seems particularly well-suited for scientific computing, 132 | data science and visualization, machine learning and numerical computation. 133 | It is also much faster than Python, if computation speed is a concern. 134 | 135 | A final consideration is JavaScript (plus HTML and css), which is useful in many of the contexts listed later in this guide. 136 | 137 | ### Data Collection, Cleaning, Processing, and Visualization 138 | 139 | Python and [R](https://www.tidyverse.org/) are excellent choices. 140 | 141 | An advantage of R is that there is a 142 | "[tidyverse](https://www.tidyverse.org/)" of widely-adopted packages, 143 | where there is a clear favorite way to do something, 144 | such as make a plot or a web application. A disadvantage is that is focused on working with data, so e.g. you wouldn't write a desktop application in R. 145 | 146 | Python has the advantage of being useful in many contexts beyond data science. However, you may find yourself spoiled for choice when selecting tools, e.g. what library to use for plotting graphs. 147 | 148 | Other considerations: 149 | 150 | - Julia 151 | - [SQL (structured query language)](https://en.wikipedia.org/wiki/SQL): 152 | If you find yourself needing to work with databases, adding some SQL knowledge on top of your preferred programming language will be useful. 153 | - See also 154 | [this article on Codecademy](https://www.codecademy.com/resources/blog/data-science-languages/) 155 | describing these and other options. 156 | 157 | ### Machine Learning and Artificial Intelligence 158 | 159 | You will find more ML/AI resources that use Python than any other language. There is a lot to learn in this field, so the author's suggestion is start learning using Python to get up to speed before considering another language. 160 | 161 | ### Systems Programming and Scripting 162 | 163 | If your interest is working with the nuts and bolts of a computer system 164 | (working with files and directories, scheduling automated tasks, etc.), 165 | Python is a great place to start. 166 | There is a popular 167 | [book written about automating tasks with Python](https://automatetheboringstuff.com). 168 | It's a good resource for both learning Python and finding ideas for projects. 169 | 170 | Whatever programming language you choose, 171 | you will need to learn how to use the command line interface 172 | ('CLI'; 'terminal'). 173 | On Unix-like systems (macOS; linux) this means learning bash 174 | or a closely-related variant 175 | (Macs recently switched from bash to zsh, but they are mostly the same). 176 | Windows comes with PowerShell, but you can install a bash CLI as well. 177 | 178 | Basic commands such as navigating a directory, creating files and folders, 179 | and running your programs can be learned in minutes. 180 | If you dig deeper, the command line can be extremely powerful. 181 | As a motivational example, here is a one-line command that will: 182 | - recursively search through a tree of nested NMR data folders; 183 | - find the temperature each experiment was run at; and 184 | - save a .csv that lists all NMR jobs and temperatures: 185 | 186 | ```bash 187 | $ grep -r "##\$TE=" --include="*acqus" . | cut -c 3- | sort | sed -e 's/:##\$TE= /,/' > T_pH7.csv 188 | ``` 189 | 190 | That may look incomprehensible, 191 | but it's composed from several individual bash commands 192 | that you would learn in any basic bash guide. 193 | With very little bash experience, 194 | the author could accomplish in one terminal command 195 | a task that would require many lines of Python or equivalent code. 196 | 197 | Both Python and Bash are widely used for writing executable "scripts" 198 | to automate common tasks. 199 | 200 | There is a large family of "curly-brace" languages 201 | that are all good "professional programmer" choices for system programming: 202 | c++, Go, Java, Rust, etc. 203 | The author's advice is to avoid languages that are so "low-level" 204 | that you have to constantly consider fussy things, such as: 205 | - where and how variables are stored in memory and accessed; 206 | - how to manage memory allocation; 207 | - determining "which one of these nine types of integers is best 208 | to represent my number?". 209 | 210 | However, if you really want to learn programming 211 | from the viewpoint of a computer scientist or a software engineer, 212 | a language such as c/c++ will make you learn 213 | what goes on "under the hood" of your computer. 214 | 215 | ### Instruments and Devices 216 | 217 | If you want to get started with devices, microcontrollers, 218 | and Internet of Things (IoT) projects, Python is a good choice. 219 | It's the default choice if you are working on a Raspberry Pi. 220 | Many controllers can be programmed with Python 221 | or a subset of Python (e.g. [CircuitPython](https://circuitpython.org)). 222 | 223 | [Arduino microcontrollers](https://www.arduino.cc) use a variant of c++ for their programs, but Python is also supported (via [MicroPython](https://docs.arduino.cc/learn/programming/arduino-and-python)). 224 | 225 | It's not possible to generalize across scientific instrumentation, 226 | but you may find low-level languages like c being used. 227 | 228 | ### Numerical Computation 229 | 230 | Even though Python is a slow language, 231 | it can make use of libraries that run faster code 232 | (e.g. FORTRAN, c) "under the hood". 233 | An example of this is 234 | [the `numpy` library](https://numpy.org) for numerical computation. 235 | With optimization, Python can often be fast enough for your needs. 236 | 237 | There are libraries that can help speed up your Python code, 238 | e.g. by [implementing "just-in-time" compiling](https://numba.pydata.org) 239 | or [GPU acceleration](https://cupy.dev). 240 | There is also a version of Python, 241 | [PyPy](https://www.pypy.org), that runs faster than standard Python. 242 | 243 | If your code needs to run faster than Python is capable of, here are some alternatives to consider: 244 | 245 | - Julia 246 | - MATLAB is widely used by scientists and engineers, 247 | but it's proprietary. 248 | If your workplace has bought a license for it, 249 | and you do a lot of numerical work (e.g. linear algebra), 250 | it can be very useful. 251 | - You could consider the "curly-brace" languages such as c/c++, 252 | but the learning curve will be steeper. 253 | If others in your field use one of these languages, 254 | it may be worth it. 255 | 256 | ### Web Programming 257 | 258 | If your primary interest in things Web-related 259 | (creating web pages, webservers, online databases etc.), 260 | JavaScript (JS) is ubiquitous in Web programming. 261 | It is also a great choice for a first language to learn. 262 | It can be used for both "front-end" web development 263 | (writing JS/HTML/CSS code for display in a web browser), 264 | and in "back-end" development (setting up a web server). 265 | Most beginners will be interested in the front-end work of creating a website, and let a web hosting service take care of the back end. 266 | 267 | Python is also a good choice, especially for back-end work[^1]. 268 | Popular web frameworks include Flask, Django, and FastAPI. 269 | For example, 270 | if you have data in a database 271 | that you want to make available over the internet, 272 | you can use one of these frameworks 273 | to create a web API (Application Programming Interface) 274 | that will let people around the world access and use your data. 275 | 276 | [^1]: A promising new development is PyScript, 277 | first announced at PyCon US 2022. 278 | PyScript is a Python interpreter plus some of the most popular libraries, 279 | bundled together and compiled into Web Assembly language (WASM). 280 | There are other languages also finding their way into the browser via WASM, 281 | such as Rust. 282 | 283 | If you are not programming in a language that is native to mobile devices 284 | (e.g Swift for iOS or Java for Android), 285 | another way to get your program onto users' phones 286 | is to create a web application. 287 | Then, any device with a web browser would have access to your app. 288 | 289 | ### GUI Applications 290 | 291 | If you want to create an application with a graphical user interface (GUI), 292 | many languages will allow you to do this, including Python. 293 | If your *primary* interest in programming 294 | is that you want to create a desktop or mobile application, read on. 295 | 296 | #### Distributing Applications 297 | 298 | Some desktop programs come bundled in a single file. 299 | For example, 300 | you might download the file and drag it to your Applications folder, 301 | and then double-click it to run. 302 | Other programs run an installer 303 | to set up the required files on your user's system. 304 | If you are not a professional programmer, 305 | the one-file app is probably easier, 306 | and certainly safer for your intended user. 307 | However, some languages make bundling your program 308 | as a one-file desktop application easier than others. 309 | 310 | If you want to create a mobile application, 311 | you first have to consider if you want to target iOS, android, or both. 312 | Then, you have to consider the limitations of developing on that platform. 313 | For example, on iOS you will need to create a developer account. 314 | If you want other people to use your application on their iPhone, 315 | you'll need to pay Apple money and get a digital signature for verification. 316 | 317 | #### Desktop Applictions 318 | 319 | If you want to create an application 320 | that has the native look and feel of your favorite operating system 321 | (macOS or Windows), 322 | your main choices are Swift on macOS and C# ("C-sharp") on Windows. 323 | The author doesn't have much experience with these languages. 324 | However, C# and Microsoft's .NET platform make cross-platform 325 | and mobile apps possible as well, 326 | whereas Swift's primary focus is macOS applications[^2]. 327 | 328 | [^2]: The author has a bias against heavy investment in a language 329 | that can depends on a parent company for its existence. 330 | For example, Apple could decide that they're dropping Swift 331 | as the preferred language for their platforms. 332 | Java's corporate sponsor, Oracle, 333 | has engaged in shady practices in the past, including 334 | [update installer that would try to install unwanted applications ('bloatware' or 'crapware) on its users' systems](https://www.zdnet.com/article/a-close-look-at-how-oracle-installs-deceptive-software-with-java-updates/). 335 | Visual Basic 6 (VB6) was very popular, 336 | allowing scientists, business people and hobbyists to create 337 | their own Windows applications. 338 | Microsoft's shift to the .NET platform 339 | effectively orphaned any development of VB6 programs. 340 | Using one of these languages can still be the right choice for you, 341 | but go in with eyes open. 342 | 343 | If you are also interested in web programming as well, 344 | [Electron apps written with JavaScript](https://www.electronjs.org) 345 | are a great solution. 346 | The author wrote this guide using Microsoft's VS Code, 347 | which is an Electron app. 348 | Other examples of Electron apps that you may be familiar with include: 349 | Discord, Dropbox, Slack, GitHub Desktop, and Microsoft Teams. 350 | 351 | Simple desktop applications in Python are not too difficult, 352 | but as the complexity goes up you may run into difficulties. 353 | You will need to choose a GUI framework and learn how to use it, 354 | and then you will need to use a tool to create the one-file application bundle. 355 | These applications basically copy an entire Python environment into the bundle, 356 | so a Python app tends to take up much more memory on a hard drive 357 | than a similar program written in a compiled language. 358 | 359 | In the less-beginner-friendly category, Java and c++ are commonly used to write cross-platform applications. 360 | 361 | #### Mobile Applications 362 | 363 | The author doesn't recommend first-time programmers learning a language focused on mobile development. That said: 364 | 365 | - For iOS, Swift is the language of choice. 366 | 367 | - For android: 368 | - Java is the historical choice 369 | - Kotlin has become very popular for android development 370 | - other c++-like languages are also supported 371 | 372 | ### Conclusion 373 | 374 | The journey of a thousand miles starts with a single step. 375 | This guide hopefully helps you take a step in the right direction. 376 | Even if you decide that a programming language is not for you, 377 | hopefully your interest in programming is now kindled, 378 | and the guide can help you retrace your steps and set out again. 😄 379 | -------------------------------------------------------------------------------- /guides/python_environment_setup.md: -------------------------------------------------------------------------------- 1 | # Creating a Python Environment 2 | 3 | ## Contents 4 | 5 | - [Creating a Python Environment](#creating-a-python-environment) 6 | - [Contents](#contents) 7 | - [Introduction](#introduction) 8 | - [Why Python Environments?](#why-python-environments) 9 | - [Option 1: Installing Anaconda or Miniconda](#option-1-installing-anaconda-or-miniconda) 10 | - [Creating and Using a `conda` Environment](#creating-and-using-a-conda-environment) 11 | - [Installing Packages Into Your `conda` Environment](#installing-packages-into-your-conda-environment) 12 | - [Option 2: Installing Python from python.org](#option-2-installing-python-from-pythonorg) 13 | - [Creating and Using a `venv` Virtual Environment](#creating-and-using-a-venv-virtual-environment) 14 | - [Installing Packages Into Your `venv` Environment](#installing-packages-into-your-venv-environment) 15 | - [Other Options](#other-options) 16 | 17 | ## Introduction 18 | 19 | The goal is to enable you to create a python "environment" 20 | for each of your projects, 21 | tailored to its requirements. 22 | 23 | This guide will be opinionated. 24 | If you want to use another method than one described here, 25 | my advice would be to use that one method consistently. 26 | If you start using multiple methods, 27 | you run the risk of becoming XKCD \#1987: 28 | 29 | ![XKCD #1987](https://imgs.xkcd.com/comics/python_environment.png) 30 | 31 | This guide is focused on macOS and Windows installations. 32 | Linux can be trickier. 33 | One warning for Linux users: 34 | If you want to create virtual environments using `venv`, 35 | as described in this guide, 36 | some Linux distributions don't include `venv` with python, 37 | and you'll have to install it separately. 38 | 39 | ## Why Python Environments? 40 | 41 | You may think, 42 | "my computer already has Python on it. Why can't I just use that?" 43 | The problem is that this "system Python" is used by your operating system, 44 | and if you try to customize it by installing Python packages 45 | something might break. 46 | It's Python's extensibility 47 | that makes it so powerful and so widely useful, 48 | so it is highly likely that you will want 49 | to install additional libraries at some point. 50 | 51 | For example, if you want to do data analysis and visualization, 52 | you are very early on going to be installing libraries 53 | such as `pandas` and `matplotlib`. 54 | If you are following a tutorial, 55 | and at some point it the instructions say something like: 56 | 57 | ```bash 58 | pip install pandas 59 | ``` 60 | 61 | or 62 | 63 | ```bash 64 | conda install pandas 65 | ``` 66 | 67 | you will want to make sure you are installing these 68 | into a Python environment of your own, separate from system Python. 69 | 70 | At this point, if you started searching online 71 | how to go about downloading Python 72 | and creating environments, 73 | you'd probably find many, conflicting, recommendations on how to do this. 74 | I will recommend two methods in this guide: 75 | 76 | 1. Installing Anaconda (or miniconda), 77 | and managing virtual environments with `conda`. 78 | This is probably the best solution for people, 79 | particularly those with scientific interests, to get started. 80 | If you're interested in programming for data analysis and visualization, 81 | you can also obtain R this way. 82 | An Anaconda installation also makes it easy to start using Jupyter Notebooks, 83 | which are a great way to start learning Python interactively. 84 | 2. Installing Python directly from python.org, 85 | and creating virtual environments with `venv`. 86 | This is a minimalist approach. 87 | 88 | ## Option 1: Installing Anaconda or Miniconda 89 | 90 | A full Anaconda installs a lot of stuff on your computer 91 | that you may not need. 92 | However, if you're just starting out in programming, 93 | this is the easiest option. 94 | If hard drive space is a concern, you can install miniconda instead. 95 | [This guide](https://docs.anaconda.com/free/anaconda/getting-started/distro-or-miniconda/) 96 | on the Anaconda web site summarizes how to choose between the two. 97 | 98 | [Caltech's Be/Bi103 course](https://bebi103a.github.io/lessons/00/index.html) 99 | (Introduction to Data Analysis in the Biological Sciences) 100 | has great guides for setting up a python environment via Anaconda. 101 | The key steps are summarized below. 102 | 103 | 1. Download the 104 | [Anaconda](https://www.anaconda.com/download/) 105 | or [miniconda](https://docs.conda.io/en/latest/miniconda.html) 106 | installer and run it. 107 | 108 | - choose "Install for Me Only" if you are given that option 109 | - you may be prompted to install a (free) JetBrains IDE 110 | such as PyCharm or DataSpell. 111 | Unless you know you want to use it, skip this— 112 | you can always install it later if you want. 113 | 2. Open a command-line interface (CLI). 114 | - On macOS or Linux, 115 | where a bash-like command line is standard, 116 | a command prompt ending in "`$`" 117 | precedes the cursor where you start typing. 118 | Its exact text will be specific to your computer 119 | and where you opened the CLI from. 120 | However, your prompt should include "`(base)`", 121 | which indicates which conda environment you're currently using 122 | (here, the default "base" environment). 123 | For the terminal commands below, 124 | "`(environmentname)$`" represents the command prompt 125 | (and is not part of the commands you are entering in the CLI). 126 | - Windows users should use the "Anaconda Prompt" as the CLI. 127 | This is similar to Windows' "command prompt" CLI, 128 | but with redirections ("PATH") to conda libraries 129 | automatically set up for you. 130 | You can enter "anaconda prompt" into the Windows search bar 131 | to find this application. 132 | 3. Update your base conda installation and environment. 133 | It is a good idea to run the following commands 134 | not only after the initial installation, 135 | but every few weeks-to-months[^1]. 136 | 137 | [^1]: When the author returned to his office computer 138 | after COVID remote working ended, 139 | its `conda` was so far out of date 140 | that `conda update conda` would no longer work. 141 | The `conda` updater needed a newer version of python, which could not be updated using the old `conda` version—Catch 22. 142 | A complete uninstall and reinstall of Anaconda was required. 143 | 144 | ```bash 145 | (base)$ conda update conda 146 | ``` 147 | Follow the prompts to update conda itself, and then: 148 | ```bash 149 | (base)$ conda update --all 150 | ``` 151 | and follow the prompts to update all the installed libraries. 152 | 153 | ### Creating and Using a `conda` Environment 154 | 155 | Although you can work from the base conda environment, 156 | for your own projects you will want to create an isolated environment. 157 | You'll be able to install only what you need for that project, 158 | and you can specify the versions of all the libraries to avoid conflicts. 159 | It is very easy to create environments with conda, 160 | and switch between environments as needed. 161 | 162 | A detailed guide can be found on the 163 | [Anaconda website](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). 164 | To get started, here are the most useful commands: 165 | 166 | - `conda create` is used to create a new environment. 167 | For example, 168 | if you were taking the Be/Bi 103 course 169 | and wanted to create an environment for it, 170 | you could do the following: 171 | ```bash 172 | (base)$ conda create --name bebi103 173 | ``` 174 | However, that course requires that Python 3.9 is used, 175 | to make sure that all their code runs as originally written. 176 | Most likely, when you downloaded conda, 177 | you chose the most recent python for the base conda environment. 178 | If you know you need a specific python version, 179 | include it when you create the environment: 180 | ```bash 181 | (base)$ conda create --name bebi103 python=3.9 182 | ``` 183 | You can also add specific packages that you want via this command, but it's not necessary. Installing packages is covered in the next section. 184 | - `conda env list` will list all your environments, e.g.: 185 | ```bash 186 | (base)$ conda env list 187 | # conda environments: 188 | # 189 | base * /Users/myname/opt/anaconda3 190 | bebi103 /Users/myname/opt/anaconda3/envs/bebi103 191 | ``` 192 | The asterisk indicates the current active environment, which is still `base`. 193 | Note the location of your new environment inside the `/envs` folder. 194 | Every conda environment you create will be in a subfolder of `/envs`. 195 | - `conda activate` is used to switch to another environment, e.g.: 196 | ```bash 197 | (base)$ conda activate bebi103 198 | (bebi103)$ 199 | ``` 200 | - `conda list` will list all the packages installed in the active environment. 201 | 202 | - To deactivate the environment and return to using your base conda python: 203 | ```bash 204 | (bebi103)$ deactivate 205 | (base) 206 | ``` 207 | - If you are already in your base conda environment, and you `deactivate`, 208 | you may exit conda completely. 209 | You'll no longer see an environment name in parentheses, 210 | and you'll be using whatever the non-conda default python is. 211 | If you didn't intend to do this, 212 | you can use `conda activate base` to go back. 213 | 214 | 215 | ### Installing Packages Into Your `conda` Environment 216 | 217 | An important difference when using conda environments is that, 218 | as much as possible, 219 | packages should **not** be installed using a `pip install`-like command, 220 | which is normally how Python packages are installed. 221 | For the packages you want to install, 222 | search online for installation instructions 223 | and see if there is a conda option. 224 | 225 | If there is, 226 | often `conda install {packagename}` works, 227 | but sometimes a specific "channel" must be listed 228 | for conda to find the package. 229 | For example, to install `pandas`, 230 | [follow the online instructions](https://anaconda.org/anaconda/pandas) 231 | to install it from the "anaconda" channel: 232 | ```bash 233 | (bebi103)$ conda install -c anaconda pandas 234 | ``` 235 | 236 | Some packages do not have a conda installer. 237 | To "pip install" packages into your environment: 238 | 239 | 1. Make sure `pip` is installed in your current environment 240 | (and not just the base environment), e.g. 241 | ```bash 242 | (current_environment)$ conda install -n bebi103 pip 243 | ``` 244 | This will install `pip` specifically to the bebi103 environment, 245 | regardless of whatever `current_environment` may be active. 246 | 2. To install a python package into your current environment: 247 | ``` 248 | python -m pip install name_of_package 249 | ``` 250 | **Note the use of `python -m`.** 251 | If you just `pip install` a package, 252 | [it may not get installed where you intended](https://snarky.ca/why-you-should-use-python-m-pip/). 253 | 254 | You can always find out which python interpreter you're currently using 255 | by entering `which python`(macOS/linux) or `where python`(Windows) 256 | in the command line. 257 | Then, `python -m pip install` will install packages to that environment. 258 | 259 | ## Option 2: Installing Python from python.org 260 | 261 | [This guide](https://pythontest.com/python/installing-python-3-11/) from Brian Okken covers the basic installation: 262 | 1. Go to [python.org](https://www.python.org/). 263 | 2. Hover over "Downloads". If you want the most recent release of Python, 264 | a button for its download will appear in the popup window. 265 | If you want to install a different Python version, 266 | or additional Python versions, 267 | you can click on "view the full list of downloads", 268 | and download a specific version from their list. 269 | 3. Run the installer. 270 | - **Windows users**: Check out Okken's guide. 271 | Specifically, don't click too quickly through the installer dialog. 272 | When you reach “Advanced Features”, 273 | check the box for “Add Python to environment variables”. 274 | 275 | ### Creating and Using a `venv` Virtual Environment 276 | A new user searching online can find many, conflicting ways 277 | to create a virtual environment. 278 | The current standard method is to 279 | [use the `venv` command](https://docs.python.org/3/library/venv.html). 280 | Ignore any guides that use the `virtualenv` command instead— 281 | these are out of date. 282 | 283 | Whereas conda environments can be used across projects, 284 | it is most common to include venv environments 285 | either in the top level of your project folder, 286 | or one folder above it. 287 | The former seems to be more common. 288 | So, if your project's code is contained in the directory `my_awesome_project`: 289 | 290 | 1. Open a terminal with `my_awesome_project` as the current working directory. 291 | For example, on macOS/linux using a bash terminal 292 | you can switch to that directory using `cd`, 293 | then double-check that you are in the right place using `pwd`: 294 | ```bash 295 | $ cd ~/my/path/to/my_awesome_project 296 | $ pwd 297 | /Users/myname/my/path/to/my_awesome_project 298 | ``` 299 | 2. From the command line, enter: 300 | ```bash 301 | python -m venv .venv 302 | ``` 303 | This creates a folder named .venv within my_awesome_project 304 | that contains your virtual environment. 305 | This would use your default python version. 306 | If you want to use another installed python version for a project, 307 | you can specify it like: 308 | ```bash 309 | python3.9 -m venv .venv 310 | ``` 311 | > Naming the environment `.venv` or `.env` is a common convention, 312 | > but you can use whatever name you want. 313 | > Note that file names that begin with "." 314 | > are often hidden from you by default. 315 | > It's a way of denoting files 316 | > that you usually don't want to modify directly, 317 | > e.g. critical system files are often named this way 318 | > to protect them from accidental corruption by users. 319 | > To see hidden folders using your OS's file browser, 320 | > see [this guide](https://www.sonarworks.com/support/sonarworks/360003040160-Troubleshooting/360003204140-Troubleshooting/5005750481554-How-to-show-hidden-files-Mac-and-Windows-). 321 | > To include hidden files when using `ls` from a bash command line, 322 | > use `ls -a`. 323 | 324 | 3. Activate the virtual environment: 325 | assuming a virtual environment folder named `.venv` 326 | (as in the previous step): 327 | macOS: 328 | ```bash 329 | $ source .venv/bin/activate 330 | ``` 331 | 332 | Windows cmd.exe command line: 333 | ```cmd 334 | $ .venv\Scripts\activate.bat 335 | ``` 336 | 337 | Windows Powershell: 338 | ```powershell 339 | $ .venv\Scripts\Activate.ps1 340 | ``` 341 | 342 | Note: if PowerShell gives an error message saying running scripts is disabled, 343 | enter the following command in PowerShell[^2]: 344 | 345 | [^2]: See [the python venv documentation]() for details. 346 | 347 | ```powershell 348 | $ Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser 349 | ``` 350 | To deactivate the environment and return to using your system python: 351 | ```bash 352 | deactivate 353 | ``` 354 | 355 | ### Installing Packages Into Your `venv` Environment 356 | 357 | To "pip install" packages into your environment: 358 | 359 | 1. Activate the environment as described in the previous section. 360 | 2. Check that you are using the python inside your virtual environment, 361 | using `which python`(macOS) or `where python`(Windows). 362 | 3. To install a python package into your current environment: 363 | ``` 364 | python -m pip install name_of_package 365 | ``` 366 | **Note the use of `python -m`.** 367 | If you just `pip install` a package, 368 | [it may not get installed where you intended](https://snarky.ca/why-you-should-use-python-m-pip/). 369 | 370 | ## Other Options 371 | 372 | - On macOS, homebrew can be used to install Python. 373 | However, the author thinks that combining homebrew python installation 374 | with other methods such as (Ana)conda can lead to XKCD #1987. 375 | - Power users, especially those writing python packages, 376 | can look at pyenv or asdf. 377 | The author strongly recommends 378 | [*Publishing Python Packages*](https://www.manning.com/books/publishing-python-packages) 379 | by Dane Hillard to see an example 380 | of a publishing toolset that includes asdf. 381 | -------------------------------------------------------------------------------- /snippets/GCal_recurrence.md: -------------------------------------------------------------------------------- 1 | # GCal event recurrence 2 | ### This is an example method for quickly adding recurrence to existing Google Calendar url invitations, created for Dr Jennifer Polk! 3 | 4 | **Original url** 5 | 6 | https://calendar.google.com/calendar/event?action=TEMPLATE&tmeid=MzBtNzNpZWhoYWxzM3B2OWttMGVnanZkZW9fMjAyMzA2MTdUMjAwMDAwWiBqZW5uaWZlci5wb2xrQG0&tmsrc=jennifer.polk%40gmail.com&scp=ALL 7 | 8 | **New url** 9 | 10 | https://calendar.google.com/calendar/event?action=TEMPLATE&tmeid=MzBtNzNpZWhoYWxzM3B2OWttMGVnanZkZW9fMjAyMzA2MTdUMjAwMDAwWiBqZW5uaWZlci5wb2xrQG0&tmsrc=jennifer.polk%40gmail.com&scp=ALL&recur=RRULE:FREQ=DAILY;UNTIL=20230620 11 | 12 | **What has been added?** 13 | 14 | The url remains as before, except a 'recur' parameter has been added to the end. This looks as such 15 | `&recur=RRULE:FREQ=DAILY;UNTIL=20230620`. The RRULE parameter follows strict guidelines, which can be found [here](https://datatracker.ietf.org/doc/html/rfc5545#section-3.8.5.3). 16 | 17 | Some of the most simple cases contain `FREQ=DAILY`, `FREQ=WEEKLY`, `FREQ=MONTHLY`. 18 | Any more complex repeat can also be made, for example "every other month on the second Friday of the month" - see the above link for details which include the `INTERVAL`, `BYDAY`, and `BYMONTHDAY` parameters. 19 | The `UNTIL` parameter takes a date in YYYYMMDD format, at minimum. A specific time and timezone can be added in **T**HHMMSS**Z** format (eg: "T000000Z", where "Z" indicates the UTC timezone, but it seems this superfluous detail is not required by Google Calendar. 20 | --------------------------------------------------------------------------------