40 |
41 | These lecture notes and exercises are licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.
42 | 43 | © Copyright 2018-2024. 44 |
38 |
39 |
40 |
41 | These lecture notes and exercises are licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.
42 |
43 | © Copyright 2018-2024.
44 |
![](\"https://www.python.org/static/community_logos/python-logo.png\"){kind=logo}
This chapter contains some instructions about how to install Python on your personal computer.\n",
15 | "\n",
16 | "There are many ways to install Python on your computer (and while most of them work, some of them are less practical than others for scientific applications). Unless you know what you are doing (i.e.: you have been doing this before), please follow these instructions exactly.\n",
17 | "\n",
18 | "\n",
19 | "```{admonition} Important! What to do if you **already** have python installed on your laptop \n",
20 | ":class: warning, dropdown\n",
21 | " \n",
22 | "**If you already have anaconda / conda / miniconda installed**:\n",
23 | "\n",
24 | "You can keep your installation if it works for you. If you want to start from scratch, uninstall anaconda and start again as explained below. \n",
25 | "\n",
26 | "---\n",
27 | "\n",
28 | "**If you don't know what I'm talking about:** \n",
29 | "\n",
30 | "Then you should probably follow the instructions below.\n",
31 | "```"
32 | ]
33 | },
34 | {
35 | "cell_type": "markdown",
36 | "metadata": {},
37 | "source": [
38 | "```{admonition} Important! For Windows 7 users\n",
39 | ":class: warning, dropdown\n",
40 | "\n",
41 | "Windows 7 is [not supported since January 2020](https://en.wikipedia.org/wiki/Windows_7). It seems that you can't install `mambaforge` on Windows 7. Regardless of python, I strongly recommend to update to a version with security updates. \n",
42 | "```"
43 | ]
44 | },
45 | {
46 | "cell_type": "markdown",
47 | "metadata": {},
48 | "source": [
49 | "## Install Miniconda "
50 | ]
51 | },
52 | {
53 | "cell_type": "markdown",
54 | "metadata": {},
55 | "source": [
56 | "### On Windows \n",
57 | "\n",
58 | "Go to the miniforge download website: https://github.com/conda-forge/miniforge#mambaforge\n",
59 | "\n",
60 | "Download the installers for **Mambaforge** and your operating system (Windows, Mac OS or Linux).\n",
61 | "Unless you have an uncommon architecture (unlikely), you should choose the `x86_64` files.\n",
62 | "\n",
63 | "![](\"../img/download_options.png\")
![](\"../img/install_options.png\")
\n",
72 | "\n",
73 | "### On Mac OS and Linux \n",
74 | "\n",
75 | "For these platforms, no need to download the files yourself. Open a terminal and do:\n",
76 | "\n",
77 | "```none\n",
78 | "curl -L -O \"https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\"\n",
79 | "bash Mambaforge-$(uname)-$(uname -m).sh\n",
80 | "```\n",
81 | "\n",
82 | "or, if this doesn't work:\n",
83 | "\n",
84 | "```none\n",
85 | "wget \"https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\"\n",
86 | "bash Mambaforge-$(uname)-$(uname -m).sh\n",
87 | "```\n",
88 | "\n",
89 | "The first command downloads the tool, and the second installs it. Follow the prompts on the installer screens.\n",
90 | "\n",
91 | "If you are unsure about any setting, accept the defaults **except for the last question asking you if you wish to run `conda init`: here, answer \"yes\".**\n",
92 | "\n",
93 | "To make the changes take effect, close and then re-open your terminal window.\n",
94 | "\n",
95 | "### Testing your installation\n",
96 | "\n",
97 | "\n",
98 | "To see if everything worked well, open a terminal (Mac and Linux). On Windows, open the `miniforge prompt` (from the Start menu, search for and open \"miniforge prompt\"):\n",
99 | "\n",
100 | "![](\"../img/miniforge.png\")
![](\"../img/cmd.png\")
![](\"../img/term.png\")
![](\"https://www.spyder-ide.org/spyder_website_banner.png\")
"
258 | ]
259 | },
260 | {
261 | "cell_type": "markdown",
262 | "metadata": {},
263 | "source": [
264 | "[Spyder](https://www.spyder-ide.org) is an open-source integrated development environment ([IDE](https://www.spyder-ide.org/)) for scientific pythom, and it is the best for beginners. To open spyder, simply open your conda environment and type:\n",
265 | "\n",
266 | "```\n",
267 | "spyder\n",
268 | "```\n",
269 | "\n",
270 | "This should open a window like the above. \n",
271 | "\n",
272 | "I think that you will learn spyder fast enough while coding, but if you want some tips to get started, the [official documentation](https://docs.spyder-ide.org/current/videos/first-steps-with-spyder.html) is a good place to go first! "
273 | ]
274 | },
275 | {
276 | "cell_type": "markdown",
277 | "metadata": {},
278 | "source": [
279 | "## Learning checklist"
280 | ]
281 | },
282 | {
283 | "cell_type": "markdown",
284 | "metadata": {},
285 | "source": [
286 | "\n",
287 | " \n",
288 | " "
289 | ]
290 | }
291 | ],
292 | "metadata": {
293 | "hide_input": false,
294 | "kernelspec": {
295 | "display_name": "Python 3 (ipykernel)",
296 | "language": "python",
297 | "name": "python3"
298 | },
299 | "language_info": {
300 | "codemirror_mode": {
301 | "name": "ipython",
302 | "version": 3
303 | },
304 | "file_extension": ".py",
305 | "mimetype": "text/x-python",
306 | "name": "python",
307 | "nbconvert_exporter": "python",
308 | "pygments_lexer": "ipython3",
309 | "version": "3.10.6"
310 | },
311 | "latex_envs": {
312 | "LaTeX_envs_menu_present": true,
313 | "autoclose": false,
314 | "autocomplete": true,
315 | "bibliofile": "biblio.bib",
316 | "cite_by": "apalike",
317 | "current_citInitial": 1,
318 | "eqLabelWithNumbers": true,
319 | "eqNumInitial": 1,
320 | "hotkeys": {
321 | "equation": "Ctrl-E",
322 | "itemize": "Ctrl-I"
323 | },
324 | "labels_anchors": false,
325 | "latex_user_defs": false,
326 | "report_style_numbering": false,
327 | "user_envs_cfg": false
328 | },
329 | "nbTranslate": {
330 | "displayLangs": [
331 | "*"
332 | ],
333 | "hotkey": "alt-t",
334 | "langInMainMenu": true,
335 | "sourceLang": "en",
336 | "targetLang": "fr",
337 | "useGoogleTranslate": true
338 | },
339 | "toc": {
340 | "base_numbering": 3,
341 | "nav_menu": {},
342 | "number_sections": true,
343 | "sideBar": true,
344 | "skip_h1_title": false,
345 | "title_cell": "Table of Contents",
346 | "title_sidebar": "Contents",
347 | "toc_cell": true,
348 | "toc_position": {},
349 | "toc_section_display": "block",
350 | "toc_window_display": true
351 | }
352 | },
353 | "nbformat": 4,
354 | "nbformat_minor": 4
355 | }
356 |
--------------------------------------------------------------------------------
/book/week_02/Assignment-02.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #02"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "Today's exercises have to be done with help of the python **standard library** alone! **No external module can be used**.\n",
15 | "\n",
16 | ":::{tip}\n",
17 | "Can you remember what the \"standard library\" is? [Here](https://docs.python.org/3/library/) is a list of all the modules and built-ins it provides: so quite a lot!\n",
18 | ":::"
19 | ]
20 | },
21 | {
22 | "cell_type": "markdown",
23 | "metadata": {},
24 | "source": [
25 | "## #02-01: cryptography for Roman Emperors"
26 | ]
27 | },
28 | {
29 | "cell_type": "markdown",
30 | "metadata": {},
31 | "source": [
32 | "A very simple encryption technique is called the [Caesar cipher](http://en.wikipedia.org/wiki/Caesar_cipher). The basic idea is that each letter is replaced by a letter that is a certain number of letters away, so for example if the shift was 2, then A would become C, B would become D, and Z will become B.\n",
33 | "\n",
34 | "**A. Write a function that given a string and a shift, will produce the encrypted string for that shift**. The rules are:\n",
35 | "- you should accept lowercase and uppercase letters, and return letters of the same case\n",
36 | "- spaces or other punctuation characters should not be changed.\n",
37 | "\n",
38 | "There are several ways to reach this result. Just pick the one which makes more sense to you. Then, decrypt the following message, which was encrypted with a shift of 13:\n",
39 | " \n",
40 | " Pbatenghyngvbaf, lbh unir fhpprrqrq va qrpelcgvat gur fgevat.\n",
41 | " \n",
42 | "**B. Now write a decoding script** `caesar.py` which, when run in the command line, prints the decoded phrase after asking the user to enter a phrase and a shift with which it was encrypted. Test your script on the sentence above. \n",
43 | "\n",
44 | ":::{tip}\n",
45 | "Make use of python's [input()](https://docs.python.org/3/library/functions.html#input) function\n",
46 | ":::\n",
47 | "\n",
48 | "**C. Now try to decrypt this sentence, for which the shift is unknown**:\n",
49 | " \n",
50 | " Gwc uivioml bw nqvl bpm zqopb apqnb.\n",
51 | " \n",
52 | "One way to solve this problem involves human decision, but another way can be fully automated (and implies more work). Pick the one you want! You can also add the decryption option to your script if you want."
53 | ]
54 | },
55 | {
56 | "cell_type": "markdown",
57 | "metadata": {},
58 | "source": [
59 | "## #02-02: the substitution cipher"
60 | ]
61 | },
62 | {
63 | "cell_type": "markdown",
64 | "metadata": {},
65 | "source": [
66 | "Since we managed to crack the code above so easily, maybe we should use a better cryptographic algorithm from now on. \n",
67 | "\n",
68 | "The Caesar cipher is a special case of the more general [substitution cipher](https://en.wikipedia.org/wiki/Substitution_cipher). In this cipher, any new combined alphabet (or sequence of bits, characters, numbers...) can be used in place of the regular alphabet.\n",
69 | "\n",
70 | "To simplify things a bit, we will use python's `random` module and in particular it's [shuffle](https://docs.python.org/3/library/random.html#random.shuffle) function to do the job. To generate a random (but predictable) substitution table we can use the mechanism of \"seeds\", which can be seen as a secret key that you'll have to (privately) give to your forbidden lover for him/her to decipher your message. This works as following: "
71 | ]
72 | },
73 | {
74 | "cell_type": "code",
75 | "execution_count": null,
76 | "metadata": {},
77 | "outputs": [],
78 | "source": [
79 | "alphabet = 'abcdefghijklmnopqrstuvwxyz'\n",
80 | "seed = 42 # the secret key known by both parties \n",
81 | "\n",
82 | "import random\n",
83 | "random.seed(seed)\n",
84 | "\n",
85 | "new_alphabet = list(alphabet)\n",
86 | "random.shuffle(new_alphabet)\n",
87 | "print(new_alphabet)"
88 | ]
89 | },
90 | {
91 | "cell_type": "markdown",
92 | "metadata": {},
93 | "source": [
94 | "**A. Building upon the template from the previous exercise, create a script `substitute.py` which now asks:**\n",
95 | " 1. for a phrase to encrypt or decrypt\n",
96 | " 2. whether the script should Encrypt (E) or Decrypt (D) the phrase\n",
97 | " 3. which seed should be used (it should always be an integer, but can be any integer)"
98 | ]
99 | },
100 | {
101 | "cell_type": "markdown",
102 | "metadata": {},
103 | "source": [
104 | "**B. Since your cipher still preserves the location of punctuation (space, points, exclamation marks, etc.), it is easier to crack. Can you think of a very simple way to substitute these characters as well for better encoding?** (minimal change in code)"
105 | ]
106 | },
107 | {
108 | "cell_type": "code",
109 | "execution_count": null,
110 | "metadata": {},
111 | "outputs": [],
112 | "source": []
113 | }
114 | ],
115 | "metadata": {
116 | "hide_input": false,
117 | "kernelspec": {
118 | "display_name": "Python 3 (ipykernel)",
119 | "language": "python",
120 | "name": "python3"
121 | },
122 | "language_info": {
123 | "codemirror_mode": {
124 | "name": "ipython",
125 | "version": 3
126 | },
127 | "file_extension": ".py",
128 | "mimetype": "text/x-python",
129 | "name": "python",
130 | "nbconvert_exporter": "python",
131 | "pygments_lexer": "ipython3",
132 | "version": "3.10.6"
133 | },
134 | "latex_envs": {
135 | "LaTeX_envs_menu_present": true,
136 | "autoclose": false,
137 | "autocomplete": true,
138 | "bibliofile": "biblio.bib",
139 | "cite_by": "apalike",
140 | "current_citInitial": 1,
141 | "eqLabelWithNumbers": true,
142 | "eqNumInitial": 1,
143 | "hotkeys": {
144 | "equation": "Ctrl-E",
145 | "itemize": "Ctrl-I"
146 | },
147 | "labels_anchors": false,
148 | "latex_user_defs": false,
149 | "report_style_numbering": false,
150 | "user_envs_cfg": false
151 | },
152 | "nbTranslate": {
153 | "displayLangs": [
154 | "*"
155 | ],
156 | "hotkey": "alt-t",
157 | "langInMainMenu": true,
158 | "sourceLang": "en",
159 | "targetLang": "fr",
160 | "useGoogleTranslate": true
161 | },
162 | "toc": {
163 | "base_numbering": 1,
164 | "nav_menu": {},
165 | "number_sections": false,
166 | "sideBar": true,
167 | "skip_h1_title": false,
168 | "title_cell": "Table of Contents",
169 | "title_sidebar": "Contents",
170 | "toc_cell": false,
171 | "toc_position": {},
172 | "toc_section_display": "block",
173 | "toc_window_display": false
174 | }
175 | },
176 | "nbformat": 4,
177 | "nbformat_minor": 4
178 | }
179 |
--------------------------------------------------------------------------------
/book/week_02/my_python_script.py:
--------------------------------------------------------------------------------
1 | a = 3
2 | b = 6
3 | c = a * b
4 | print('The product of {} and {} is {}'.format(a, b, c))
5 |
--------------------------------------------------------------------------------
/book/week_03/02-Strings-Paths.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# String formatting and file paths"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "A scientific data analysis workflow almost invariably implies downloading, manipulating and opening files. Often, it also implies writing new files (for example with post-processed data). Fortunately, python comes with many handy tools to format strings."
15 | ]
16 | },
17 | {
18 | "cell_type": "markdown",
19 | "metadata": {},
20 | "source": [
21 | "## String Formatting"
22 | ]
23 | },
24 | {
25 | "cell_type": "markdown",
26 | "metadata": {},
27 | "source": [
28 | "\"String formatting\" refers to formatting the content of variables (strings, numbers, paths, etc.) into strings, for example to display them on screen or to write them to a text file. Unfortunately, there are more than one way to format strings in python (actually there are at least 4!). This short section will guide you to the ones you should preferably use."
29 | ]
30 | },
31 | {
32 | "cell_type": "markdown",
33 | "metadata": {},
34 | "source": [
35 | "### The modern way: formatted string (\"f-string\") literals"
36 | ]
37 | },
38 | {
39 | "cell_type": "markdown",
40 | "metadata": {},
41 | "source": [
42 | "Consider the following example:"
43 | ]
44 | },
45 | {
46 | "cell_type": "code",
47 | "execution_count": null,
48 | "metadata": {},
49 | "outputs": [],
50 | "source": [
51 | "name = 'Assane'\n",
52 | "print(f'Hello {name}!')"
53 | ]
54 | },
55 | {
56 | "cell_type": "markdown",
57 | "metadata": {},
58 | "source": [
59 | "The important bits here is the **`f` prefix** to the string literal which indicates to the interpreter that the string might contain **curly braces**, which contain variable names that will be replaced with their values.\n",
60 | "\n",
61 | "Not only strings can be formatted into a string. Numbers can too:"
62 | ]
63 | },
64 | {
65 | "cell_type": "code",
66 | "execution_count": null,
67 | "metadata": {},
68 | "outputs": [],
69 | "source": [
70 | "n = 3\n",
71 | "print(f'{name} has {n} cats.')"
72 | ]
73 | },
74 | {
75 | "cell_type": "code",
76 | "execution_count": null,
77 | "metadata": {},
78 | "outputs": [],
79 | "source": [
80 | "pi = 3.14 \n",
81 | "print(f'pi ≈ {pi}')"
82 | ]
83 | },
84 | {
85 | "cell_type": "markdown",
86 | "metadata": {},
87 | "source": [
88 | "f-strings are quite powerful. They can evaluate arbitrary expressions:"
89 | ]
90 | },
91 | {
92 | "cell_type": "code",
93 | "execution_count": null,
94 | "metadata": {},
95 | "outputs": [],
96 | "source": [
97 | "print(f'2 pi ≈ {2 * pi}')"
98 | ]
99 | },
100 | {
101 | "cell_type": "markdown",
102 | "metadata": {},
103 | "source": [
104 | "This feature is to be used with care, you probably don't want to have very complicated expressions within your f-strings!"
105 | ]
106 | },
107 | {
108 | "cell_type": "markdown",
109 | "metadata": {},
110 | "source": [
111 | "### Formatting numbers in strings"
112 | ]
113 | },
114 | {
115 | "cell_type": "markdown",
116 | "metadata": {},
117 | "source": [
118 | "Very often, you want your strings to be of predictable length and format. For example, you may want float numbers to be printed only with a chosen precision:"
119 | ]
120 | },
121 | {
122 | "cell_type": "code",
123 | "execution_count": null,
124 | "metadata": {},
125 | "outputs": [],
126 | "source": [
127 | "frac = 2 / 3\n",
128 | "print(f'Set free: {frac}')\n",
129 | "print(f'Formatted to 2 decimals: {frac:.2f}') # f is for \"float\"\n",
130 | "print(f'Formatted to an integer: {int(frac)}')\n",
131 | "print(f'Formatted to a rounded integer: {round(frac)}')\n",
132 | "print(f'Formatted to a rounded integer with leading spaces: {round(frac):4d}') # d is for \"int\"\n",
133 | "print(f'Formatted to a rounded integer with leading zeros: {round(frac):04d}')"
134 | ]
135 | },
136 | {
137 | "cell_type": "markdown",
138 | "metadata": {},
139 | "source": [
140 | "### Formatting dates in strings "
141 | ]
142 | },
143 | {
144 | "cell_type": "markdown",
145 | "metadata": {},
146 | "source": [
147 | "Also possible:"
148 | ]
149 | },
150 | {
151 | "cell_type": "code",
152 | "execution_count": null,
153 | "metadata": {},
154 | "outputs": [],
155 | "source": [
156 | "import datetime\n",
157 | "now = datetime.datetime.now()\n",
158 | "\n",
159 | "print(now)\n",
160 | "print(f'{now:%Y-%m-%d %H:%M}')"
161 | ]
162 | },
163 | {
164 | "cell_type": "markdown",
165 | "metadata": {},
166 | "source": [
167 | "### The old ways to format strings"
168 | ]
169 | },
170 | {
171 | "cell_type": "markdown",
172 | "metadata": {},
173 | "source": [
174 | "f-strings have been added to python in version 3.6 (end of 2016: that's only a few years back!). Before that, two other string formatting tools were available and are still used today. Therefore, you should learn them as well."
175 | ]
176 | },
177 | {
178 | "cell_type": "markdown",
179 | "metadata": {},
180 | "source": [
181 | "#### The \"not too old\" way: `.format()` (still useful!)"
182 | ]
183 | },
184 | {
185 | "cell_type": "markdown",
186 | "metadata": {},
187 | "source": [
188 | "This string formatting method was introduced with python 3 (so that's already a bit older). It works with appending a call to the `.format()` method to a string:"
189 | ]
190 | },
191 | {
192 | "cell_type": "code",
193 | "execution_count": null,
194 | "metadata": {},
195 | "outputs": [],
196 | "source": [
197 | "print('Hello, {}!'.format(name))"
198 | ]
199 | },
200 | {
201 | "cell_type": "markdown",
202 | "metadata": {},
203 | "source": [
204 | "No `f` prefix here (don't mix them up!). Otherwise, it works more or less the same:"
205 | ]
206 | },
207 | {
208 | "cell_type": "code",
209 | "execution_count": null,
210 | "metadata": {},
211 | "outputs": [],
212 | "source": [
213 | "print('{} has {} cats.'.format(name, n))\n",
214 | "print('{name_of_person} has {n_cats:02d} cats, right?'.format(n_cats=n, name_of_person=name))"
215 | ]
216 | },
217 | {
218 | "cell_type": "markdown",
219 | "metadata": {},
220 | "source": [
221 | "You see where this is going! This is pretty much the same syntax, but a bit more verbose. f-strings are generally more readable and should be preferred, but the `.format()` can be useful in very specific cases, as shown in the `greetings` example from the previous lesson which I adapt here: "
222 | ]
223 | },
224 | {
225 | "cell_type": "code",
226 | "execution_count": null,
227 | "metadata": {},
228 | "outputs": [],
229 | "source": [
230 | "template_string = 'Hey {name}! I think you should come over to {city} and visit {place}.'\n",
231 | "# some code ommitted here...\n",
232 | "print(template_string.format(name='Lesedi', city='Cape Town', place='Table Mountain'))"
233 | ]
234 | },
235 | {
236 | "cell_type": "markdown",
237 | "metadata": {},
238 | "source": [
239 | "The nice thing in the example above is that you can create a template string early in your script, that you can \"fill\" with values later in your program."
240 | ]
241 | },
242 | {
243 | "cell_type": "markdown",
244 | "metadata": {},
245 | "source": [
246 | "#### The very old way: the `%` operator"
247 | ]
248 | },
249 | {
250 | "cell_type": "markdown",
251 | "metadata": {},
252 | "source": [
253 | "This was the standard in python 2 but is still working today (and will continue to work in the future):"
254 | ]
255 | },
256 | {
257 | "cell_type": "code",
258 | "execution_count": null,
259 | "metadata": {},
260 | "outputs": [],
261 | "source": [
262 | "print('Hello %s!' % name)"
263 | ]
264 | },
265 | {
266 | "cell_type": "markdown",
267 | "metadata": {},
268 | "source": [
269 | "We don't like this way, but you may encounter it in some older code."
270 | ]
271 | },
272 | {
273 | "cell_type": "markdown",
274 | "metadata": {},
275 | "source": [
276 | "### Take home: string formatting "
277 | ]
278 | },
279 | {
280 | "cell_type": "markdown",
281 | "metadata": {},
282 | "source": [
283 | "- there is probably *no string format* you can think of that doesn't have a formatting solution (people are manipulating strings all the time)\n",
284 | "- use f-strings! They are great.\n",
285 | "- sometimes, use `.format()`. This is also great.\n",
286 | "- if you want more examples, read [this tutorial from the python docs](https://docs.python.org/3/tutorial/inputoutput.html)"
287 | ]
288 | },
289 | {
290 | "cell_type": "markdown",
291 | "metadata": {},
292 | "source": [
293 | "## Path handling in python"
294 | ]
295 | },
296 | {
297 | "cell_type": "markdown",
298 | "metadata": {},
299 | "source": [
300 | "Handling file paths is one of the not-so-fun parts of a scientist's job, I agree. But we just have to do it, there is no way around it.\n",
301 | "\n",
302 | "Please read this [short blog post](https://medium.com/@ageitgey/python-3-quick-tip-the-easy-way-to-deal-with-file-paths-on-windows-mac-and-linux-11a072b58d5f) which is a good entry-level tutorial to path handling."
303 | ]
304 | },
305 | {
306 | "cell_type": "markdown",
307 | "metadata": {},
308 | "source": [
309 | "### Take home: path handling"
310 | ]
311 | },
312 | {
313 | "cell_type": "markdown",
314 | "metadata": {},
315 | "source": [
316 | "- never use `+` and other string shenanigans to handle your file paths\n",
317 | "- [os.path](https://docs.python.org/3/library/os.path.html) and, in particular, `os.path.join` is a simple way to deal with paths as strings\n",
318 | "- [pathlib](https://docs.python.org/3/library/pathlib.html) is the new cool kid in the block. It works very well but might be a bit confusing at first."
319 | ]
320 | }
321 | ],
322 | "metadata": {
323 | "hide_input": false,
324 | "kernelspec": {
325 | "display_name": "Python 3 (ipykernel)",
326 | "language": "python",
327 | "name": "python3"
328 | },
329 | "language_info": {
330 | "codemirror_mode": {
331 | "name": "ipython",
332 | "version": 3
333 | },
334 | "file_extension": ".py",
335 | "mimetype": "text/x-python",
336 | "name": "python",
337 | "nbconvert_exporter": "python",
338 | "pygments_lexer": "ipython3",
339 | "version": "3.10.6"
340 | },
341 | "latex_envs": {
342 | "LaTeX_envs_menu_present": true,
343 | "autoclose": false,
344 | "autocomplete": true,
345 | "bibliofile": "biblio.bib",
346 | "cite_by": "apalike",
347 | "current_citInitial": 1,
348 | "eqLabelWithNumbers": true,
349 | "eqNumInitial": 1,
350 | "hotkeys": {
351 | "equation": "Ctrl-E",
352 | "itemize": "Ctrl-I"
353 | },
354 | "labels_anchors": false,
355 | "latex_user_defs": false,
356 | "report_style_numbering": false,
357 | "user_envs_cfg": false
358 | },
359 | "nbTranslate": {
360 | "displayLangs": [
361 | "*"
362 | ],
363 | "hotkey": "alt-t",
364 | "langInMainMenu": true,
365 | "sourceLang": "en",
366 | "targetLang": "fr",
367 | "useGoogleTranslate": true
368 | },
369 | "toc": {
370 | "base_numbering": "8",
371 | "nav_menu": {},
372 | "number_sections": true,
373 | "sideBar": true,
374 | "skip_h1_title": false,
375 | "title_cell": "Table of Contents",
376 | "title_sidebar": "Contents",
377 | "toc_cell": true,
378 | "toc_position": {
379 | "height": "calc(100% - 180px)",
380 | "left": "10px",
381 | "top": "150px",
382 | "width": "384px"
383 | },
384 | "toc_section_display": "block",
385 | "toc_window_display": true
386 | }
387 | },
388 | "nbformat": 4,
389 | "nbformat_minor": 4
390 | }
391 |
--------------------------------------------------------------------------------
/book/week_03/03-Tips-and-Tricks.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Tips and tricks"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "It is very early in the lecture, but you are now already well equipped to write more complex scripts and algorithms: you know (almost ;)) everything you need to know about the syntax, but you might be a little lost in all the possibilities that the python language is now offering to you. *Which tool should I use to do this and that? How was this function signature again?* are very common interrogations, and it is normal to feel a bit overwhelmed.\n",
15 | "\n",
16 | "This chapter will give you some brief tips to help you during your assignments."
17 | ]
18 | },
19 | {
20 | "cell_type": "markdown",
21 | "metadata": {},
22 | "source": [
23 | "## Batteries included "
24 | ]
25 | },
26 | {
27 | "cell_type": "markdown",
28 | "metadata": {},
29 | "source": [
30 | "You may have read this expression (\"batteries included\") during your research about the Python language. It is widely used to indicate that if you choose python, it's not only for its syntax: it's for all the tools that come with it. And there are PLENTY. Spend a minute or two to scroll through the list of tools available in the [standard library](https://docs.python.org/3/library/index.html). The **standard library** is available per default with any python installation. It is very robust and provides the core functionality of the language.\n",
31 | "\n",
32 | "As you will see, there is not much for us scientists in this list though (no plotting library for example). This is why **third party packages** were developed. And there are so many of them that one can easily be overwhelmed: for this week's assignment we will continue to use the standard library only, but starting next week we will use external packages as well."
33 | ]
34 | },
35 | {
36 | "cell_type": "markdown",
37 | "metadata": {},
38 | "source": [
39 | "## Getting help"
40 | ]
41 | },
42 | {
43 | "cell_type": "markdown",
44 | "metadata": {},
45 | "source": [
46 | "In order to become a good programmer, **nothing is more important than being able to find help**, either online or with your friends and colleagues."
47 | ]
48 | },
49 | {
50 | "cell_type": "markdown",
51 | "metadata": {},
52 | "source": [
53 | "### Online resources "
54 | ]
55 | },
56 | {
57 | "cell_type": "markdown",
58 | "metadata": {},
59 | "source": [
60 | "Fortunately, getting help has become quite easy nowadays. Here are some resources to get you started:\n",
61 | "- the [official python documentation](https://docs.python.org/3/) is definitely the best place to look for everything related to the standard library. It is also THE reference, and as such can sometimes be too detailed or complex. If this fails, then you'll have to refer to \n",
62 | "- **your favorite search engine**. Ask your question as precisely as possible! With some experience you'll learn to detect the sources you can trust, and learn to filter out outdated information (e.g. related to the old python 2 language). Very often your web search will lead you to\n",
63 | "- [Stackoverflow](https://stackoverflow.com/). In recent years, the Stack Exchange community of sites has emerged as a major resource for answering technical and other questions and is even the preferred forum for many open-source projects. Their system of rewards for well formulated questions and correct answers clearly makes finding the right solution easier than in many other forums."
64 | ]
65 | },
66 | {
67 | "cell_type": "markdown",
68 | "metadata": {},
69 | "source": [
70 | "Here is a general rule. When you encounter a problem, ask yourself the following question: **is it likely that someone else had this problem before me?** In a large majority of the cases, the answer will be \"yes\" (believe me on this one). The trick is to find the answer to your question: use as few words as possible, but put in all the keywords, that makes your question unambiguous. Here is the example outcome of two google searches:\n",
71 | "- [how to download a file python](https://www.google.at/search?q=how+to+download+a+file+python)\n",
72 | "- [how to download a file python3](https://www.google.at/search?q=how+to+download+a+file+python3)\n",
73 | "\n",
74 | "The latter is the one you want and will lead you to the right answer. With time, you are going to get used to using the search engine more efficiently, but if everything else fails, then you might have to ask a question yourself:"
75 | ]
76 | },
77 | {
78 | "cell_type": "markdown",
79 | "metadata": {},
80 | "source": [
81 | "### Ask questions the smart way"
82 | ]
83 | },
84 | {
85 | "cell_type": "markdown",
86 | "metadata": {},
87 | "source": [
88 | "If you want to ask a question on stackoverflow or somewhere else (e.g. by sending an email to your teacher), please spend some time reading [this resource](http://www.catb.org/esr/faqs/smart-questions.html). Believe me, this will help you to get better answers!"
89 | ]
90 | },
91 | {
92 | "cell_type": "markdown",
93 | "metadata": {},
94 | "source": [
95 | "### Getting help VS learning "
96 | ]
97 | },
98 | {
99 | "cell_type": "markdown",
100 | "metadata": {},
101 | "source": [
102 | "I'll be honest: without an internet connection, I am a very bad python programmer. I don't expect you to learn all the python commands by heart for the exam (yes, you will have an internet access during the exam). Similarly, I encourage you to use the internet to find help to solve the weekly exercises.\n",
103 | "\n",
104 | "However, there is a difference between \"getting help to find how to realize a specific task\" and \"asking for someone to do my homework for me\". The border line between the two might be subtle, but I'm sure you'll know when you cross it: at the moment you stopped using your brain and simply copy/pasted code from one site to your assignment script, you crossed it."
105 | ]
106 | },
107 | {
108 | "cell_type": "markdown",
109 | "metadata": {},
110 | "source": [
111 | "## Python IDEs\n",
112 | ""
113 | ]
114 | },
115 | {
116 | "cell_type": "markdown",
117 | "metadata": {},
118 | "source": [
119 | "While it is possible to write python programs using a basic text editor, the majority of you will find it useful to use an [integrated development environment](https://en.wikipedia.org/wiki/Integrated_development_environment) (short: IDE) instead. The advantages of IDEs is that they ship with tools that make your life easier when programming. \n",
120 | "\n",
121 | "Here is a non-exhaustive (and subjective) list of the tools a good IDE should have:\n",
122 | "- linter: automatic detection of syntax errors and style violations\n",
123 | "- [debugger](https://en.wikipedia.org/wiki/Debugger): helping you find where the errors in your program come from\n",
124 | "- [intelligent code completion](https://en.wikipedia.org/wiki/Intelligent_code_completion): automatic `TAB` completion, module recognition, etc.\n",
125 | "- project explorer and code exploration tools\n",
126 | "- for interactive languages: a command line and variable explorer\n",
127 | "- appealing colors and graphics\n",
128 | "- ...\n",
129 | "\n",
130 | "For more advanced uses, you will also look for version control tools and automated build and testing tools.\n",
131 | "\n",
132 | "There are many Python IDEs around, but here are some of the ones that come up most often as recommendations on forums or blogposts (they are all free):\n",
133 | "- [Spyder](https://www.spyder-ide.org): the IDE made by and for scientists. It resembles the Matlab IDE and has many nice features such as variable exploration and an integrated ipython console. It is very easy to install with conda, and is therefore available on linux at the university (``$ spyder &``). **It is my recommended IDE for this semester's course**.\n",
134 | "- [PyCharm](https://www.jetbrains.com/pycharm/): this is my current personal favorite. It is however quite heavyweight and can be confusing for beginners. The community version of PyCharm is free, and has enough functionality for most use cases.\n",
135 | "- [Visual Studio Code](https://code.visualstudio.com/) (from Microsoft) is one of the newest \"cool kids\" around. I have not tested it myself, but people seem to be very happy with it. It's very minimal, and you'll have to install plugins for it to become a true python IDE.\n",
136 | "- [vim](https://www.vim.org/) or [emacs](https://www.gnu.org/software/emacs/): for people allergic to the mouse. Not recommended for most of us, but the people who learned to use them are (allegedly) the fastest programmers ever."
137 | ]
138 | },
139 | {
140 | "cell_type": "markdown",
141 | "metadata": {},
142 | "source": [
143 | "## Debugging code"
144 | ]
145 | },
146 | {
147 | "cell_type": "markdown",
148 | "metadata": {},
149 | "source": [
150 | "**It is impossible to write bug free code in one go** (just accept it and get used to it). There will always be mistakes. Syntax errors and other obvious problems (e.g. `NameError`) will most often be picked up by your IDE's linter. The other \"easier ones\" (e.g. `TypeError`) are also likely to be corrected after a first couple of test runs of your code. But then, sometimes, the error is not obvious: the code runs, but doesn't produce the expected output. What to do in these cases? "
151 | ]
152 | },
153 | {
154 | "cell_type": "markdown",
155 | "metadata": {},
156 | "source": [
157 | "- use `print` statements (bad): with this method, you can inspect variables at run time by printing their values. It is a quick and dirty way to debug, and should not be used too often because error prone (indeed, by adding print statements you modify your code, might forget about them afterwards, and they are often not very useful). If you need more than 3 or 4 print statements to track the source of an issue, it's time for opening a debugger.\n",
158 | "- **use a debugger** (good): a [debugger](https://en.wikipedia.org/wiki/Debugger) will allow to interrupt a program's execution and *give you access to the program's state* at a predefined location (called a **break point**). It is extremely more useful than `print`, because it allows you to explore many variables at once. Spyder comes with a debugger [included](https://docs.spyder-ide.org/5/panes/debugging.html), and we will make a short demo in class.\n",
159 | "- go for a walk (very good): think about something else for a while and come back with a fresh, open mind\n",
160 | "- talk to your colleagues about your problem (very good): they might see the issue (or typo) from a different angle and detect the problem easily\n",
161 | "- if you have no one around to talk to, [talk to a duck](https://en.m.wikipedia.org/wiki/Rubber_duck_debugging) (very good)"
162 | ]
163 | }
164 | ],
165 | "metadata": {
166 | "hide_input": false,
167 | "kernelspec": {
168 | "display_name": "Python 3 (ipykernel)",
169 | "language": "python",
170 | "name": "python3"
171 | },
172 | "language_info": {
173 | "codemirror_mode": {
174 | "name": "ipython",
175 | "version": 3
176 | },
177 | "file_extension": ".py",
178 | "mimetype": "text/x-python",
179 | "name": "python",
180 | "nbconvert_exporter": "python",
181 | "pygments_lexer": "ipython3",
182 | "version": "3.10.6"
183 | },
184 | "latex_envs": {
185 | "LaTeX_envs_menu_present": true,
186 | "autoclose": false,
187 | "autocomplete": true,
188 | "bibliofile": "biblio.bib",
189 | "cite_by": "apalike",
190 | "current_citInitial": 1,
191 | "eqLabelWithNumbers": true,
192 | "eqNumInitial": 1,
193 | "hotkeys": {
194 | "equation": "Ctrl-E",
195 | "itemize": "Ctrl-I"
196 | },
197 | "labels_anchors": false,
198 | "latex_user_defs": false,
199 | "report_style_numbering": false,
200 | "user_envs_cfg": false
201 | },
202 | "nbTranslate": {
203 | "displayLangs": [
204 | "*"
205 | ],
206 | "hotkey": "alt-t",
207 | "langInMainMenu": true,
208 | "sourceLang": "en",
209 | "targetLang": "fr",
210 | "useGoogleTranslate": true
211 | },
212 | "toc": {
213 | "base_numbering": "8",
214 | "nav_menu": {},
215 | "number_sections": true,
216 | "sideBar": true,
217 | "skip_h1_title": false,
218 | "title_cell": "Table of Contents",
219 | "title_sidebar": "Contents",
220 | "toc_cell": true,
221 | "toc_position": {
222 | "height": "calc(100% - 180px)",
223 | "left": "10px",
224 | "top": "150px",
225 | "width": "384px"
226 | },
227 | "toc_section_display": "block",
228 | "toc_window_display": true
229 | }
230 | },
231 | "nbformat": 4,
232 | "nbformat_minor": 4
233 | }
234 |
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/book/week_03/04-Good-practices.ipynb:
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1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Good practices, programming style and conventions"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "Python is a very versatile programming language, and it has a very flexible syntax. Therefore, it is also very easy to write *ugly code* in python. This chapter reviews a number of guidelines and conventions widely accepted by the community. At this stage of the lecture we won't go in depth for each of these points, but try to keep them in mind while writing your assignments and also while checking my suggested solution to the assignments."
15 | ]
16 | },
17 | {
18 | "cell_type": "markdown",
19 | "metadata": {},
20 | "source": [
21 | "## Use PEP 8"
22 | ]
23 | },
24 | {
25 | "cell_type": "markdown",
26 | "metadata": {},
27 | "source": [
28 | "[PEP 8](https://www.python.org/dev/peps/pep-0008/) is a style guide for python code. It introduces new rules where the syntax leaves them open. As an example:"
29 | ]
30 | },
31 | {
32 | "cell_type": "code",
33 | "execution_count": null,
34 | "metadata": {},
35 | "outputs": [],
36 | "source": [
37 | "# Syntax OK but not PEP8 compliant \n",
38 | "x=2+1\n",
39 | "x= x * 2-1\n",
40 | "# Syntax OK *and* PEP8 compliant\n",
41 | "x = 2 + 1\n",
42 | "x = x * 2 - 1"
43 | ]
44 | },
45 | {
46 | "cell_type": "markdown",
47 | "metadata": {},
48 | "source": [
49 | "PEP8 gives *guidelines*, not strict rules. It is your choice to comply with them or not. As a matter of fact however, many open source projects have adopted PEP8 and require to use it if you want to contribute. If you want to use it too, a good choice is to turn on PEP8 checking in your favorite IDE (in Spyder: ``Tools -> Preferences -> Completion and linting -> Code style -> `` Tick ``Enable code style linting`` for PEP8 style analysis)."
50 | ]
51 | },
52 | {
53 | "cell_type": "markdown",
54 | "metadata": {},
55 | "source": [
56 | "## Give meaningful names to variables and functions"
57 | ]
58 | },
59 | {
60 | "cell_type": "markdown",
61 | "metadata": {},
62 | "source": [
63 | "The text space that code is taking is less important than your time. Give meaningful name to your variables and functions, even if it makes them quite long! For example, prefer:"
64 | ]
65 | },
66 | {
67 | "cell_type": "markdown",
68 | "metadata": {},
69 | "source": [
70 | "```python\n",
71 | "def fahrenheit_to_celsius(temp_fahrenheit):\n",
72 | "```"
73 | ]
74 | },
75 | {
76 | "cell_type": "markdown",
77 | "metadata": {},
78 | "source": [
79 | "to the shorter but less explicit:"
80 | ]
81 | },
82 | {
83 | "cell_type": "markdown",
84 | "metadata": {},
85 | "source": [
86 | "```python\n",
87 | "def f2c(tf):\n",
88 | "```"
89 | ]
90 | },
91 | {
92 | "cell_type": "markdown",
93 | "metadata": {},
94 | "source": [
95 | "The same rule applies for variables. Prefer `language` over `l` and `area` over `a`."
96 | ]
97 | },
98 | {
99 | "cell_type": "markdown",
100 | "metadata": {},
101 | "source": [
102 | "## Prefer writing many small functions instead of monolithic code blocks"
103 | ]
104 | },
105 | {
106 | "cell_type": "markdown",
107 | "metadata": {},
108 | "source": [
109 | "[Separation of concerns](https://en.wikipedia.org/wiki/Separation_of_concerns) is an important design principle for separating a computer program into distinct sections, such that each section addresses a separate concern. This increases the code readability and facilitates unit testing (as we will see).\n",
110 | "\n",
111 | "For example, a scientific script can often be organized in well defined steps:\n",
112 | "- data input (read a file)\n",
113 | "- data pre-processing (filtering missing data, discarding useless variables)\n",
114 | "- data processing (actual computation)\n",
115 | "- output (writing the processed data to a file for later use)\n",
116 | "- data visualization (producing a plot)\n",
117 | "\n",
118 | "Each of these steps and sub-steps should be separated in different functions, maybe even in different scripts. When discussing your assignment solutions, we will always discuss how your code is organized for readability and testing."
119 | ]
120 | },
121 | {
122 | "cell_type": "markdown",
123 | "metadata": {},
124 | "source": [
125 | "## Document your code "
126 | ]
127 | },
128 | {
129 | "cell_type": "markdown",
130 | "metadata": {},
131 | "source": [
132 | "Write comments in your code, and document the functions with docstrings. We will have a full lecture about it, but it's good to start early. Here again, there are [some conventions](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard) that I recommend to follow.\n",
133 | "\n",
134 | "Note that this is useful even if you don't plan to share your code. At the very last there is at least one person reading your code: yourself! And it's always a good idea to be nice to yourself! (see the related [Abstruse Goose comic](http://abstrusegoose.com/432))"
135 | ]
136 | },
137 | {
138 | "cell_type": "markdown",
139 | "metadata": {},
140 | "source": [
141 | "## The Zen of Python "
142 | ]
143 | },
144 | {
145 | "cell_type": "code",
146 | "execution_count": null,
147 | "metadata": {},
148 | "outputs": [],
149 | "source": [
150 | "import this"
151 | ]
152 | },
153 | {
154 | "cell_type": "code",
155 | "execution_count": null,
156 | "metadata": {},
157 | "outputs": [],
158 | "source": []
159 | }
160 | ],
161 | "metadata": {
162 | "hide_input": false,
163 | "kernelspec": {
164 | "display_name": "Python 3 (ipykernel)",
165 | "language": "python",
166 | "name": "python3"
167 | },
168 | "language_info": {
169 | "codemirror_mode": {
170 | "name": "ipython",
171 | "version": 3
172 | },
173 | "file_extension": ".py",
174 | "mimetype": "text/x-python",
175 | "name": "python",
176 | "nbconvert_exporter": "python",
177 | "pygments_lexer": "ipython3",
178 | "version": "3.10.6"
179 | },
180 | "latex_envs": {
181 | "LaTeX_envs_menu_present": true,
182 | "autoclose": false,
183 | "autocomplete": true,
184 | "bibliofile": "biblio.bib",
185 | "cite_by": "apalike",
186 | "current_citInitial": 1,
187 | "eqLabelWithNumbers": true,
188 | "eqNumInitial": 1,
189 | "hotkeys": {
190 | "equation": "Ctrl-E",
191 | "itemize": "Ctrl-I"
192 | },
193 | "labels_anchors": false,
194 | "latex_user_defs": false,
195 | "report_style_numbering": false,
196 | "user_envs_cfg": false
197 | },
198 | "nbTranslate": {
199 | "displayLangs": [
200 | "*"
201 | ],
202 | "hotkey": "alt-t",
203 | "langInMainMenu": true,
204 | "sourceLang": "en",
205 | "targetLang": "fr",
206 | "useGoogleTranslate": true
207 | },
208 | "toc": {
209 | "base_numbering": "9",
210 | "nav_menu": {},
211 | "number_sections": true,
212 | "sideBar": true,
213 | "skip_h1_title": false,
214 | "title_cell": "Table of Contents",
215 | "title_sidebar": "Contents",
216 | "toc_cell": true,
217 | "toc_position": {
218 | "height": "calc(100% - 180px)",
219 | "left": "10px",
220 | "top": "150px",
221 | "width": "384px"
222 | },
223 | "toc_section_display": "block",
224 | "toc_window_display": true
225 | }
226 | },
227 | "nbformat": 4,
228 | "nbformat_minor": 4
229 | }
230 |
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/book/week_03/Assignment-03.ipynb:
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1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #03"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "Today's exercises have to be done with help of the python standard library alone! No external module can be used (except for the `--plot` option where you can use the helper packages)."
15 | ]
16 | },
17 | {
18 | "cell_type": "markdown",
19 | "metadata": {},
20 | "source": [
21 | "## Exercise #03-01: automated data download"
22 | ]
23 | },
24 | {
25 | "cell_type": "markdown",
26 | "metadata": {
27 | "hidePrompt": true
28 | },
29 | "source": [
30 | "[SRTM](https://en.wikipedia.org/wiki/Shuttle_Radar_Topography_Mission) is a digital elevation model (DEM) at ~90 m resolution covering almost the entire globe (up to $\\pm$ 60° latitude). The data is organized in 5°x5° tiles. To see a map of the tiles have a look at [this download page](http://srtm.csi.cgiar.org/srtmdata/). This tool is nice to use if you know which tile you want, but not very useful if you want more than one tile at different places of the globe.\n",
31 | "\n",
32 | "Fortunately, the entire dataset is available on this server: `srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/`\n",
33 | "\n",
34 | "In order to protect from disruptive \"download all\" behavior, the files stored here cannot be listed (i.e. automated data scraping won't work). Fortunately for us, the file naming convention is very simple:\n",
35 | "- example file: [http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/srtm_39_04.zip](http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/srtm_39_04.zip)\n",
36 | "- the first two digits give the location of the tile in the longitudes (starting at 180° West)\n",
37 | "- the last two digits give the location of the tile in the latitudes (starting at 60° North and going southwards)\n",
38 | "\n",
39 | "Here are some examples of locations and their associated tile:\n",
40 | "- (-179, 59) -> 'srtm_01_01.zip'\n",
41 | "- (-179, 51) -> 'srtm_01_02.zip'\n",
42 | "- (-174, 54) -> 'srtm_02_02.zip'\n",
43 | "- (-180, 60) -> 'srtm_01_01.zip' (upper-left corner case)\n",
44 | "\n",
45 | "And so forth.\n",
46 | "\n",
47 | "**A. Write a script which, given a longitude and a latitude as arguments, downloads the corresponding file** in the current directory. The tool should print an error message when the given location is not valid and exit the script. \n",
48 | "\n",
49 | "*Hint A1: define \"valid\" locations first: some are easy to catch, some cannot be caught automatically. Do we really have to deal with those?*\n",
50 | "\n",
51 | "*Hint A2: unlike last week where we asked for user input, here I'm asking for a script with [command line arguments](https://docs.python.org/3/tutorial/stdlib.html?highlight=sys%20argv#command-line-arguments). The command `%run download_srtm.py 9 44` (in an ipython interpreter) should download the file at the location 9°E, 44°N.*\n",
52 | "\n",
53 | "*Hint A3: although I agree with the python documentation that `argparse` is more robust (and much better) than parsing `sys.argv` yourself, for the purpose of learning I would like you to use `sys.argv` today and handle the command line arguments yourselves.*\n",
54 | "\n",
55 | "**B.** Extend this script to be a bit more clever: **download the data file only if the file isn't already available in the current directory**. This is particularly useful because the server is not very fast. \n",
56 | "\n",
57 | "**C.** Extend this script to be even more clever: **given a range of longitudes and latitudes, it should download all the files covering this area**. For example, the range 9°E to 18°E and 44°N to 47°N would download 6 files. **In order to avoid manual mistakes, warn the user by announcing the number of files that the command is going to download, and ask for confirmation before going on** (by using the `input()` function).\n",
58 | "\n",
59 | "*Hint C1: the command should now be `%run download_srtm.py 9 44 18 47`.*\n",
60 | "\n",
61 | "**D.** Let's add even more functionality to our script:\n",
62 | "\n",
63 | "**D1.** **print a message to the user announcing if the file was downloaded or was already on disk**\n",
64 | "\n",
65 | "**D2.** **print the size of the file after download** - choose [an appropriate unit](https://wiki.ubuntu.com/UnitsPolicy) for the text\n",
66 | "\n",
67 | "**D3.** let's assume that the user actually wants to download the files in a specific folder instead of the current directory (i.e. a folder where she stores all her DEMs). Let's give this opportunity to her by adding two options to the script:\n",
68 | "- `--output-dir /path/to/a/dir` should **write the file (and check for its existence) in the directory given as argument**\n",
69 | "- if the target directory does not exist, print a message to the screen indicating that you can't continue and exit the script\n",
70 | "\n",
71 | "**D4.** (optional: see the warning about windows below) **if the user asks for a plot, write a plot to disk** (alongside the DEM file) with the file name `srtm_39_04.png` (if the tile 39, 4 was asked for). The user may ask for a plot by adding a `--plot` to the list of arguments. I.e. `%run download_srtm.py 9 44 18 47 --plot` would write 6 plots in the user-chosen default directory. \n",
72 | "\n",
73 | "Here is a template for your plotting function:\n",
74 | "\n",
75 | "```python\n",
76 | "import matplotlib.pyplot as plt\n",
77 | "import rioxarray as rioxr\n",
78 | "\n",
79 | "# This is some real magic: we open the file from within the zip\n",
80 | "f = 'zip://srtm_39_04.zip!srtm_39_04.tif'\n",
81 | "\n",
82 | "# Read the data and plot\n",
83 | "with rioxr.open_rasterio(f) as da:\n",
84 | " da.sel(band=1).plot.imshow(cmap='terrain', vmin=0)\n",
85 | " plt.ylabel('Lat (°)'); plt.xlabel('Lon (°)'); plt.title('srtm_39_04'); \n",
86 | "plt.savefig('srtm_39_04.png')\n",
87 | "plt.close()\n",
88 | "```\n",
89 | "\n",
90 | "No need to add more features to the plot than that: we haven't talked about these libraries yet! Just make sure that the filename is set to the correct value.\n",
91 | "\n",
92 | "```{tip}\n",
93 | "You'll need the matplotlib, xarray and rioxarray libraries installed for this to work. Remember how to install libraries?\n",
94 | "```"
95 | ]
96 | }
97 | ],
98 | "metadata": {
99 | "hide_input": false,
100 | "kernelspec": {
101 | "display_name": "Python 3 (ipykernel)",
102 | "language": "python",
103 | "name": "python3"
104 | },
105 | "language_info": {
106 | "codemirror_mode": {
107 | "name": "ipython",
108 | "version": 3
109 | },
110 | "file_extension": ".py",
111 | "mimetype": "text/x-python",
112 | "name": "python",
113 | "nbconvert_exporter": "python",
114 | "pygments_lexer": "ipython3",
115 | "version": "3.10.6"
116 | },
117 | "latex_envs": {
118 | "LaTeX_envs_menu_present": true,
119 | "autoclose": false,
120 | "autocomplete": true,
121 | "bibliofile": "biblio.bib",
122 | "cite_by": "apalike",
123 | "current_citInitial": 1,
124 | "eqLabelWithNumbers": true,
125 | "eqNumInitial": 1,
126 | "hotkeys": {
127 | "equation": "Ctrl-E",
128 | "itemize": "Ctrl-I"
129 | },
130 | "labels_anchors": false,
131 | "latex_user_defs": false,
132 | "report_style_numbering": false,
133 | "user_envs_cfg": false
134 | },
135 | "nbTranslate": {
136 | "displayLangs": [
137 | "*"
138 | ],
139 | "hotkey": "alt-t",
140 | "langInMainMenu": true,
141 | "sourceLang": "en",
142 | "targetLang": "fr",
143 | "useGoogleTranslate": true
144 | },
145 | "toc": {
146 | "base_numbering": 1,
147 | "nav_menu": {},
148 | "number_sections": false,
149 | "sideBar": true,
150 | "skip_h1_title": false,
151 | "title_cell": "Table of Contents",
152 | "title_sidebar": "Contents",
153 | "toc_cell": false,
154 | "toc_position": {},
155 | "toc_section_display": "block",
156 | "toc_window_display": false
157 | }
158 | },
159 | "nbformat": 4,
160 | "nbformat_minor": 4
161 | }
162 |
--------------------------------------------------------------------------------
/book/week_03/greetings.py:
--------------------------------------------------------------------------------
1 | """A module to say hi in several langages."""
2 |
3 | base = {
4 | 'en': 'Hi {}!',
5 | 'fr': 'Salut {}!',
6 | 'cn': '你好 {}!',
7 | }
8 |
9 |
10 | def say_hi(name, language='en'):
11 | """Say hi in the current language."""
12 | print(base[language].format(name))
13 |
14 |
15 | if __name__ == '__main__':
16 | # execute only if run as a script
17 | import sys
18 | nargs = len(sys.argv)
19 | if nargs == 3:
20 | say_hi(sys.argv[1], language=sys.argv[2])
21 | else:
22 | print('Syntax:')
23 | print('%run greetings.py name language')
24 | print('Languages available: {}'.format(list(base)))
25 |
--------------------------------------------------------------------------------
/book/week_04/Assignment-04.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #04"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "## Exercise #04-01: a glimpse in the C language"
15 | ]
16 | },
17 | {
18 | "cell_type": "markdown",
19 | "metadata": {},
20 | "source": [
21 | "This exercise can be done on a linux machine only! \n",
22 | "\n",
23 | "```{tip}\n",
24 | "You can use MyBinder's terminal if you don't have Linux!\n",
25 | "```\n",
26 | "\n",
27 | "Here is the C code sample from the lecture:\n",
28 | "\n",
29 | "```c\n",
30 | "#include ![](\"../img/18_temp_pic.png\")
"
255 | ]
256 | },
257 | {
258 | "cell_type": "markdown",
259 | "metadata": {},
260 | "source": [
261 | "## Exercise #05-05: ACINN meteorological data"
262 | ]
263 | },
264 | {
265 | "cell_type": "markdown",
266 | "metadata": {},
267 | "source": [
268 | "```{warning}\n",
269 | "Online access to ACINN data does not work anymore. For a similar excercise I recommend to have a look at GeoSphere Austria's API. I may update the resources here in the future.\n",
270 | "```\n",
271 | "\n",
272 | "The institute website provides raw data from several stations around Innsbruck using a live feed at the following addresses:\n",
273 | "- https://acinn-data.uibk.ac.at/innsbruck/3 for the three days data\n",
274 | "- https://acinn-data.uibk.ac.at/innsbruck/7 for the seven days data\n",
275 | "\n",
276 | "The datasets for the other stations are available, per analogy:\n",
277 | "- https://acinn-data.uibk.ac.at/ellboegen/3\n",
278 | "- https://acinn-data.uibk.ac.at/obergurgl/3\n",
279 | "- https://acinn-data.uibk.ac.at/sattelberg/3\n",
280 | "\n",
281 | "The data is shared by ACINN under a [Creative Commons Attribution-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-sa/4.0/).\n",
282 | "\n",
283 | "\n",
284 | " ![](\"https://i.creativecommons.org/l/by-sa/4.0/88x31.png\"/)
\n",
285 | ""
286 | ]
287 | },
288 | {
289 | "cell_type": "markdown",
290 | "metadata": {},
291 | "source": [
292 | "The data is provided in the [json](https://www.json.org/) format, often used for web applications. Fortunately, this is very easy to read in python:"
293 | ]
294 | },
295 | {
296 | "cell_type": "code",
297 | "execution_count": null,
298 | "metadata": {},
299 | "outputs": [],
300 | "source": [
301 | "from urllib.request import Request, urlopen\n",
302 | "import json\n",
303 | "\n",
304 | "url = 'https://acinn-data.uibk.ac.at/innsbruck/3'\n",
305 | "# Parse the given url\n",
306 | "req = urlopen(Request(url)).read()\n",
307 | "# Read the data\n",
308 | "data = json.loads(req.decode('utf-8'))"
309 | ]
310 | },
311 | {
312 | "cell_type": "markdown",
313 | "metadata": {},
314 | "source": [
315 | "Now I will help you to parse the timestamp of the data:"
316 | ]
317 | },
318 | {
319 | "cell_type": "code",
320 | "execution_count": null,
321 | "metadata": {},
322 | "outputs": [],
323 | "source": [
324 | "from datetime import datetime, timedelta\n",
325 | "data['time'] = [datetime(1970, 1, 1) + timedelta(milliseconds=ds) for ds in data['datumsec']]"
326 | ]
327 | },
328 | {
329 | "cell_type": "markdown",
330 | "metadata": {},
331 | "source": [
332 | "And make a first plot to get you started:"
333 | ]
334 | },
335 | {
336 | "cell_type": "code",
337 | "execution_count": null,
338 | "metadata": {},
339 | "outputs": [],
340 | "source": [
341 | "import matplotlib.pyplot as plt\n",
342 | "plt.plot(data['time'], data['dd'], '.');\n",
343 | "plt.ylabel('Wind direction (°)'); \n",
344 | "plt.title('Wind direction at Innsbruck');"
345 | ]
346 | },
347 | {
348 | "cell_type": "markdown",
349 | "metadata": {},
350 | "source": [
351 | "You will get much more time to get used to these data in the mid-semester projects. For today, I'm asking to **write a script that takes the station and number of days as input (either as command line arguments or user input, your choice) and prints the following information in the terminal:**\n",
352 | "\n",
353 | "\n",
354 | " At station XXX, over the last X days, the dominant wind direction was XX (xx% of the time). \n",
355 | " The second most dominant wind direction was XX (xx% of the time), the least dominant wind\n",
356 | " direction was XX (xx% of the time). The maximum wind speed was XX m/s (DATE and TIME), \n",
357 | " while the strongest wind speed averaged over an hour was XX m/s (DATE and TIME).\n",
358 | "\n",
359 | "\n",
360 | "With the wind directions being of 8 classes: N, NW, W, SW, S, SE, E, NE."
361 | ]
362 | }
363 | ],
364 | "metadata": {
365 | "hide_input": false,
366 | "kernelspec": {
367 | "display_name": "Python 3 (ipykernel)",
368 | "language": "python",
369 | "name": "python3"
370 | },
371 | "language_info": {
372 | "codemirror_mode": {
373 | "name": "ipython",
374 | "version": 3
375 | },
376 | "file_extension": ".py",
377 | "mimetype": "text/x-python",
378 | "name": "python",
379 | "nbconvert_exporter": "python",
380 | "pygments_lexer": "ipython3",
381 | "version": "3.12.4"
382 | },
383 | "latex_envs": {
384 | "LaTeX_envs_menu_present": true,
385 | "autoclose": false,
386 | "autocomplete": true,
387 | "bibliofile": "biblio.bib",
388 | "cite_by": "apalike",
389 | "current_citInitial": 1,
390 | "eqLabelWithNumbers": true,
391 | "eqNumInitial": 1,
392 | "hotkeys": {
393 | "equation": "Ctrl-E",
394 | "itemize": "Ctrl-I"
395 | },
396 | "labels_anchors": false,
397 | "latex_user_defs": false,
398 | "report_style_numbering": false,
399 | "user_envs_cfg": false
400 | },
401 | "nbTranslate": {
402 | "displayLangs": [
403 | "*"
404 | ],
405 | "hotkey": "alt-t",
406 | "langInMainMenu": true,
407 | "sourceLang": "en",
408 | "targetLang": "fr",
409 | "useGoogleTranslate": true
410 | },
411 | "toc": {
412 | "base_numbering": 1,
413 | "nav_menu": {},
414 | "number_sections": false,
415 | "sideBar": true,
416 | "skip_h1_title": false,
417 | "title_cell": "Table of Contents",
418 | "title_sidebar": "Contents",
419 | "toc_cell": false,
420 | "toc_position": {},
421 | "toc_section_display": "block",
422 | "toc_window_display": false
423 | }
424 | },
425 | "nbformat": 4,
426 | "nbformat_minor": 4
427 | }
428 |
--------------------------------------------------------------------------------
/book/week_06/Assignment-06.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #06: exceptions and testing"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "This week you have learned two important new concepts: unit testing and exceptions handling. In today's assignment we will revisit old code in order to properly test it and make it more robust."
15 | ]
16 | },
17 | {
18 | "cell_type": "markdown",
19 | "metadata": {},
20 | "source": [
21 | "## Exercise #06-01: refactor and test old code"
22 | ]
23 | },
24 | {
25 | "cell_type": "markdown",
26 | "metadata": {},
27 | "source": [
28 | "- **Write a test suite for the following past exercises: \"#02: cryptography\", \"#03: automated data download\", and \"#05-05: wind statistics\"** (one ``test_*.py`` file per module). The test suite must contain unit tests for each function you programmed. While doing so, you might find it very useful to refactor your code following the [good practices](../week_03/04-Good-practices): write small functions with a task clearly defined, which you can test for. If you can't test it, the function is possibly not written the right way: either too broad, or not useful enough.\n",
29 | "- **Apply the exception handling methods learned in the [Exceptions chapter](01-Exceptions.ipynb) to the download function(s) of exercise #03**. Add a test to your test suite to verify that exceptions are raised when an invalid tile is requested for download."
30 | ]
31 | }
32 | ],
33 | "metadata": {
34 | "hide_input": false,
35 | "kernelspec": {
36 | "display_name": "Python 3 (ipykernel)",
37 | "language": "python",
38 | "name": "python3"
39 | },
40 | "language_info": {
41 | "codemirror_mode": {
42 | "name": "ipython",
43 | "version": 3
44 | },
45 | "file_extension": ".py",
46 | "mimetype": "text/x-python",
47 | "name": "python",
48 | "nbconvert_exporter": "python",
49 | "pygments_lexer": "ipython3",
50 | "version": "3.8.5"
51 | },
52 | "latex_envs": {
53 | "LaTeX_envs_menu_present": true,
54 | "autoclose": false,
55 | "autocomplete": true,
56 | "bibliofile": "biblio.bib",
57 | "cite_by": "apalike",
58 | "current_citInitial": 1,
59 | "eqLabelWithNumbers": true,
60 | "eqNumInitial": 1,
61 | "hotkeys": {
62 | "equation": "Ctrl-E",
63 | "itemize": "Ctrl-I"
64 | },
65 | "labels_anchors": false,
66 | "latex_user_defs": false,
67 | "report_style_numbering": false,
68 | "user_envs_cfg": false
69 | },
70 | "nbTranslate": {
71 | "displayLangs": [
72 | "*"
73 | ],
74 | "hotkey": "alt-t",
75 | "langInMainMenu": true,
76 | "sourceLang": "en",
77 | "targetLang": "fr",
78 | "useGoogleTranslate": true
79 | },
80 | "toc": {
81 | "base_numbering": 1,
82 | "nav_menu": {},
83 | "number_sections": false,
84 | "sideBar": true,
85 | "skip_h1_title": false,
86 | "title_cell": "Table of Contents",
87 | "title_sidebar": "Contents",
88 | "toc_cell": false,
89 | "toc_position": {},
90 | "toc_section_display": "block",
91 | "toc_window_display": false
92 | }
93 | },
94 | "nbformat": 4,
95 | "nbformat_minor": 4
96 | }
97 |
--------------------------------------------------------------------------------
/book/week_07/02-ClimVis.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Term project: the ClimVis package"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "This is the main project of this semester, and will count for 30% of the final grade. The submission is going to happen in three stages:\n",
15 | "\n",
16 | "**Careful!!! New deadlines after the student vote on November 30.**\n",
17 | "\n",
18 | "- **First submission deadline: Monday 09.01.2023 at 00H00** (midnight on Sunday): one ``.zip`` file per group containing their version of the climvis package\n",
19 | "- Code review by me and ~30 min feedback round per group: (online) meeting between January 10th and 13th, to be scheduled individually\n",
20 | "- **Second submission deadline: Tuesday 31.01.2023 at 00H00** (midnight on Monday). Same project with reviews addressed (reviews are small requested changes to the existing project, not a big change) \n",
21 | "- **Bonus:** on Tuesday 31.01, I will ask all the groups to shortly \"showcase\" their project, i.e. run their app for the class and show what it can be used for. This is not graded, and is more for fun and exchange than anything else!\n",
22 | "\n",
23 | "Here is an *indicative* table I'll use for the grading:\n",
24 | "\n",
25 | "**Group grade (10 points):**\n",
26 | "- Documentation: 3 *(project documentation + narrative report + individual contributions' docstrings, i.e. no individual grade here)*\n",
27 | "- Integration tests: 1 *(tool / project level tests)*\n",
28 | "- pep8: 1 *(compliance to pep8)*\n",
29 | "- Coherence: 2 *(how do the individual contributions fit together, i.e. was there an effort of documentation at least)*\n",
30 | "- Traceability: 1 *(who did what, are the author(s) name(s) provided in the function's docstrings)*\n",
31 | "- Response to reviews: 2 *(reaction to the code reviews and updates: an inadequate or failure to respond to the review can lead to a refusal)*\n",
32 | "\n",
33 | "**Individual grade (10 points):**\n",
34 | "- Narrative self-report: 2 *(quality and honesty of the self-report)*\n",
35 | "- Complexity: 3 *(level and complexity of the implemented tools, i.e. amount of programming work)*\n",
36 | "- Originality: 3 *(did you do something more than following the list of suggestions)*\n",
37 | "- Unit tests: 2 *(individual, function tests)*\n",
38 | "\n",
39 | "```{important}\n",
40 | "I will try and test the code (using `pytest`) on my computer - any new data or library that is necessary should be documented in the code, or in the command line utility documentation!\n",
41 | "```"
42 | ]
43 | },
44 | {
45 | "cell_type": "markdown",
46 | "metadata": {},
47 | "source": [
48 | "## The climvis package"
49 | ]
50 | },
51 | {
52 | "cell_type": "markdown",
53 | "metadata": {},
54 | "source": [
55 | "I've written a small package called **climvis**. Its design is based on the [template package](https://github.com/fmaussion/scispack), but this time it really does something.\n",
56 | "\n",
57 | "**Download the zipped package from [here](https://github.com/fmaussion/climvis/archive/master.zip) and extract it. Read the README and the package requirements first. You will have to install the [motionless](https://github.com/ryancox/motionless) package (`mamba install motionless`) for it to work.**\n",
58 | "\n",
59 | "**Now install climvis in development mode. If you are working on your own computer run:**\n",
60 | "\n",
61 | " pip install -e .\n",
62 | " \n",
63 | "from the root directory. **If you are working on a computer on which you have no admin rights, run:**\n",
64 | "\n",
65 | " pip install --user -e .\n",
66 | " \n",
67 | "instead."
68 | ]
69 | },
70 | {
71 | "cell_type": "markdown",
72 | "metadata": {},
73 | "source": [
74 | "**Try the command line interface (``cruvis -h``) from a terminal. Now explore ``setup.py``: can you identify what makes the command available from the terminal? Where is the code executing the command ``cruvis``?**"
75 | ]
76 | },
77 | {
78 | "cell_type": "markdown",
79 | "metadata": {},
80 | "source": [
81 | "**Familiarize yourself with the tool. Can you understand what the role of each function is?**"
82 | ]
83 | },
84 | {
85 | "cell_type": "markdown",
86 | "metadata": {},
87 | "source": [
88 | "**Can you run the tests successfully? Probably not. Somewhere in ``cfg.py``, a hard coded path is pointing to a non-existing directory.**\n",
89 | "\n",
90 | "**If you are working on your own computer, change the path to a local folder of yours and download the necessary data:**\n",
91 | "- [temperature](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.03/cruts.1905011326.v4.03/tmp/cru_ts4.03.1901.2018.tmp.dat.nc.gz)\n",
92 | "- [precipitation](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.03/cruts.1905011326.v4.03/pre/cru_ts4.03.1901.2018.pre.dat.nc.gz)\n",
93 | "- [elevation](https://cluster.klima.uni-bremen.de/~fmaussion/teaching/scipro/cru_cl1_topography.nc)\n",
94 | "\n",
95 | "**Careful! The total decompressed output is about 6GB large.**"
96 | ]
97 | },
98 | {
99 | "cell_type": "markdown",
100 | "metadata": {},
101 | "source": [
102 | "Make sure you are able to run the command succesfully before going on. For example, ``cruvis -l 12 47`` should work fine and display a page in your browser."
103 | ]
104 | },
105 | {
106 | "cell_type": "markdown",
107 | "metadata": {},
108 | "source": [
109 | "## Guided exercise: make the tool more robust"
110 | ]
111 | },
112 | {
113 | "cell_type": "markdown",
114 | "metadata": {},
115 | "source": [
116 | "Here are a couple of smaller tasks to get you started:\n",
117 | "- The hard coded path in ``cfg.py`` is very ugly. At the same time, we really need the CRU data for the tool to run! Add a safety check in the code in order to make sure the files are available. If the CRU files are not available, print the following message and exit the program:\n",
118 | "\n",
119 | " ``The CRU files are not available on this system. For cruvis (part of the climvis package) to work properly, please create a file called \".climvis\" in your HOME directory, and indicate the path to the CRU directory in it.``\n",
120 | "\n",
121 | "- Add a small function in ``cfg.py`` which parses this new ``.climvis`` file and uses the given directory in place of the hard-coded one. Tip: you could make good use of [os.path.expanduser](https://docs.python.org/3/library/os.path.html#os.path.expanduser) for this function. Optional: you can even write a small command line program (e.g. `cruvis_setup`) which asks the user for the path of the CRU folder, checks if the data is available and if yes, write the file for the user.\n",
122 | "\n",
123 | "- Selecting a location over the oceans will raise a very uninformative python error message. Make the ``write_html`` function more robust: if the data contains NaNs, print a warning and exit the program."
124 | ]
125 | },
126 | {
127 | "cell_type": "markdown",
128 | "metadata": {},
129 | "source": [
130 | "## Project: make the tool better"
131 | ]
132 | },
133 | {
134 | "cell_type": "markdown",
135 | "metadata": {},
136 | "source": [
137 | "Now you should be ready to contribute to this great package! **Add at least N+1 simple functionalities** to it, where N is your group size. This functionality can be anything you want, as long as it makes you write some code. \n",
138 | "\n",
139 | "Here are some ideas of functionalities that you can adapt at wish.\n",
140 | "- you could add a plot of the 1901-2018 timeseries for this grid point, and make a robust trend analysis for the period.\n",
141 | "- you could add [other data from CRU](https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.03/) to the plot.\n",
142 | "- you could add a new command to the tool called ``uibkvis``, which instead plots the data from the UIBK weather stations. For example, you could plot the temperature for all stations, or even better: give choices to the user as to what they want to plot. You'll have to document its command line options of course. You can get inspiration from the wind statistics we did together, but with more variables.\n",
143 | "- you could use a python [windrose](https://github.com/python-windrose/windrose) package to plot a windrose from the uibk data, and add the plot to a webpage\n",
144 | "- you could add an option to ``cruvis``, which accepts a city name instead of the lon and lat of the point. You could use the file shipped with the package for this (`world_cities.csv`: careful - it is quite a badly maintained file - i.e. duplicates and missing cities - and you might want to find another one).\n",
145 | "- you could add a new command line tool to compare the climate at two locations in one webpage.\n",
146 | "- you could parse any other data you'd find interesting from the web and plot it! For example, [upper air soundings](http://weather.uwyo.edu/upperair/sounding.html)? \n",
147 | "- you could use an interactive plotting library like [Bokeh](https://bokeh.pydata.org) (possibly by making use of higher level tools like [holoviews](http://holoviews.org/)) to make reactive plots in your HTML page. For example to visualize the ACINN data interactively?\n",
148 | "- **any idea you find interesting**! You can discuss some ideas with me beforehand if you are unsure if your idea is not enough or too much. Examples from previous years include:\n",
149 | " - a \"fly safe\" info webpage, which scrapped data from the web specifically for flying\n",
150 | " - an interactive bokeh app to visualize CRU climate trends in various cities\n",
151 | " - an El Niño advisory page - warning people when El Niño is likely to occur\n",
152 | " - a bokeh tool to visualize radio soundings\n",
153 | " - and more..."
154 | ]
155 | },
156 | {
157 | "cell_type": "markdown",
158 | "metadata": {},
159 | "source": [
160 | "## Expectations "
161 | ]
162 | },
163 | {
164 | "cell_type": "markdown",
165 | "metadata": {},
166 | "source": [
167 | "**New in WS22/23: each group member and the entire group needs to write a short narrative self-report (a few lines per point) addressing the following point:**\n",
168 | "- what was your programming objective when you started? (in the case of a true group work: what task was assigned to you when you started?)\n",
169 | "- what changed during the implementation? I.e., what is the outcome of the project?\n",
170 | "- what was the biggest challenge you faced in the implementation?\n",
171 | "- group question: what was the biggest challenge when merging everyone's work into one package?\n",
172 | "\n",
173 | "**The narrative report should be written in the README in markdown format, and will count towards grading in the elements \"Documentation\" and \"Coherence\" for the group grade, and \"self-report\" in the individual grade.**\n",
174 | "\n",
175 | "Some tasks in the list above are significantly simpler than others. Some of you might pick a project which is too ambitious and then reduce their expectations with time. Others might pick one of the simpler task and be finished very quickly.\n",
176 | "\n",
177 | "If you struggle to know what is expected of you, please just be honest with yourselves and with me. I am reluctant to impose thresholds on the number of lines of code, because I find this measure silly (many lines of code is NOT a measure of quality). My goal is that you all get better at programming after the project then when you started, regardless of your starting level. \n",
178 | "\n",
179 | "The list of possible topics should help you to decide on what to code, but otherwise I can provide a vague rule of thumb: if you coded 10 lines of code (without comments), that's probably not enough (unless they are very clever lines of code). If you coded 1000 lines of code, that's probably too much.\n",
180 | "\n",
181 | "I don't mind if you take an easy task, as long as you write something on your own, and write good code. The difficulty of the task will decide on the base grade, and the quality of the code / tests will add points on top. If you pick an \"easy\" task, you may pick two or three tasks instead of just one. Try to split the tasks within the group to get a coherent product!\n",
182 | "\n",
183 | "You all have very different backgrounds and interest. Try to find a project you like, and convince me that you pushed your own programming limit a little bit and that you learned something in the process.\n",
184 | "\n",
185 | "Ah! And **don't forget to write tests.**"
186 | ]
187 | }
188 | ],
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/book/week_09/Assignment-07.ipynb:
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1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #07: Pydemic"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "[Pydemic](https://github.com/fmaussion/pydemic) is a simple [agent-based model](https://en.wikipedia.org/wiki/Agent-based_model) of a pandemic.\n",
15 | "\n",
16 | "Agents are perfect to teach the basics of object-oriented programming. Note that I wrote the program with this goal in mind, *not* for performance or accuracy. I also just wrote the program in a few hours, so there is room for improvement. You are welcome to help me out!\n",
17 | "\n",
18 | "Start by getting an overview of the model structure.\n",
19 | "\n",
20 | "**Sensitivity analyses**: starting from the default parameter values, vary one parameter at a time and study the consequences for the temporal trajectory of the pandemic. Of particular relevance are the following: (i) agent density (number of agents per pixel), (ii) initial number of infected agents (is it possible to start a pandemic with a single infected individual? What are the settings that favor this?), (iii) agent mobility, (iv) probability of infection, (v) time until recover.\n",
21 | "\n",
22 | "**Add at least one functionality to the model.** Ideas:\n",
23 | "- add a timer for immunity loss: agents loose their immunity after N days (this can be complexified by computing the probability of infection as a function of time since infection / vaccination).\n",
24 | "- add vaccination as a way to gain immunity\n",
25 | "- add a healthcare threshold: above a certain number of people in the hospital, the hospitalized patients are more likely to die.\n",
26 | "- add politics: when a certain contamination threshold is reached, impose a lockdown (reduce agent mobility).\n",
27 | "- etc.\n",
28 | "\n",
29 | "You don't have to add too many of these options (unless you have a lot of fun). Pydemic will keep us busy for the next couple of weeks, so take it easy!"
30 | ]
31 | }
32 | ],
33 | "metadata": {
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43 | "version": 3
44 | },
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46 | "mimetype": "text/x-python",
47 | "name": "python",
48 | "nbconvert_exporter": "python",
49 | "pygments_lexer": "ipython3",
50 | "version": "3.10.8"
51 | },
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/book/week_10/Assignment-08.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Assignment #08: Pydemic - second wave"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "[Pydemic](https://github.com/fmaussion/pydemic) is a simple [agent-based model](https://en.wikipedia.org/wiki/Agent-based_model) of a pandemic.\n",
15 | "\n",
16 | "We already used it for the previous assignment.\n",
17 | "\n",
18 | "This time, we want to illustrate how to use inheritance in OOP. Your task is to develop a child class of `NaiveAgent` called `PolicyAwareAgent`. These agents behave much like `NaiveAgents`, with one exception: they can go into quarantine. After a given incubation time (say 3 days) during which the agents are contagious but unaware that they are sick, the agents will go into quarantine and therefore are out of the domain and do not pose a risk to the other agents.\n",
19 | "\n",
20 | "*Other possible enhancements:*\n",
21 | "- *`PolicyAwareAgents` are aware of the number of contagious agents at a given time and decide to quarantine themselves when the infection rate is high*\n",
22 | "- *the simulation is a mix of `NaiveAgents` and `PolicyAwareAgents`*\n",
23 | "- *etc.*"
24 | ]
25 | }
26 | ],
27 | "metadata": {
28 | "hide_input": false,
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32 | "name": "python3"
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40 | "mimetype": "text/x-python",
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45 | },
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/book/week_10/ascii_art.py:
--------------------------------------------------------------------------------
1 | cat_trick = (' /\\\n \ \\\n '
2 | '\ \\\n / /\n / /\n '
3 | '_\ \_/\/\\\n / * \@@ =\n | |Y/\n '
4 | ' | |~\n \ /_\ /\n \\ //\n '
5 | ' |||\n _|||_\n ( / \ )')
6 |
--------------------------------------------------------------------------------
/book/welcome.ipynb:
--------------------------------------------------------------------------------
1 | {
2 | "cells": [
3 | {
4 | "cell_type": "markdown",
5 | "metadata": {},
6 | "source": [
7 | "# Welcome"
8 | ]
9 | },
10 | {
11 | "cell_type": "markdown",
12 | "metadata": {},
13 | "source": [
14 | "```{figure} img/logo_acinn_small.jpg\n",
15 | "---\n",
16 | "figclass: margin\n",
17 | "---\n",
18 | "```\n",
19 | "```{figure} img/logo_uob_small.jpg\n",
20 | "---\n",
21 | "figclass: margin\n",
22 | "---\n",
23 | "```\n",
24 | "\n",
25 | "Lecture notes of the master lecture [707716 - Scientific Programming](https://lfuonline.uibk.ac.at/public/lfuonline_lv.details?sem_id_in=22W&lvnr_id_in=707716&sprache_in=en), taught to 1st semester students following a [Master in Atmospheric Sciences](https://www.uibk.ac.at/acinn/studies/master-in-atmospheric-sciences.html.en) curriculum from the Department of Atmospheric and Cryospheric Sciences ([ACINN](https://www.uibk.ac.at/acinn)) at the University of Innsbruck.\n",
26 | "\n",
27 | "This lecture is tailored for a 15 weeks-long class, but these notes might also be of interest to other (geo-)scientists wanting to learn the fundamentals of scientific programming. **Welcome to you all!**"
28 | ]
29 | },
30 | {
31 | "cell_type": "markdown",
32 | "metadata": {},
33 | "source": [
34 | ""
35 | ]
36 | },
37 | {
38 | "cell_type": "markdown",
39 | "metadata": {},
40 | "source": [
41 | "```{note}\n",
42 | "👨🏫 I gave this class in Innsbruck for the last time in the Winter 2022/23, before moving to Bristol. This content will remain online for the foreseable future, and I hope it will be useful to you. Enjoy!\n",
43 | "\n",
44 | "If you find errors, broken links, etc. Please report it [on Github](https://github.com/fmaussion/scientific_programming).\n",
45 | "```"
46 | ]
47 | },
48 | {
49 | "cell_type": "markdown",
50 | "metadata": {},
51 | "source": [
52 | "## Authors"
53 | ]
54 | },
55 | {
56 | "cell_type": "markdown",
57 | "metadata": {},
58 | "source": [
59 | "- [Fabien Maussion](http://fabienmaussion.info/) wrote these notes (unless specified otherwise, e.g. for some tutorials)\n",
60 | "- [Matthias Göbel](https://www.uibk.ac.at/acinn/people/matthias-goebel.html.en) and [Lilian Schuster](https://www.uibk.ac.at/acinn/people/lilian-schuster.html.en) (student assistants in 2018 and 2019) reviewed and proof read them"
61 | ]
62 | }
63 | ],
64 | "metadata": {
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69 | "name": "python3"
70 | },
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73 | "name": "ipython",
74 | "version": 3
75 | },
76 | "file_extension": ".py",
77 | "mimetype": "text/x-python",
78 | "name": "python",
79 | "nbconvert_exporter": "python",
80 | "pygments_lexer": "ipython3",
81 | "version": "3.12.4"
82 | },
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95 | },
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128 |
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/build.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 |
3 | jupyter-book clean --html book
4 | jupyter-book build book
5 |
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"RGI60-06.00365", "RGI60-06.00366", "RGI60-06.00369", "RGI60-06.00365", "RGI60-06.00368", "RGI60-06.00365", "RGI60-06.00356", "RGI60-06.00365"], "RGIId_1": ["RGI60-06.00313", "RGI60-06.00313", "RGI60-06.00313", "RGI60-06.00313", "RGI60-06.00313", "RGI60-06.00314", "RGI60-06.00314", "RGI60-06.00314", "RGI60-06.00315", "RGI60-06.00315", "RGI60-06.00316", "RGI60-06.00316", "RGI60-06.00316", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00317", "RGI60-06.00318", "RGI60-06.00318", "RGI60-06.00319", "RGI60-06.00319", "RGI60-06.00319", "RGI60-06.00319", "RGI60-06.00319", "RGI60-06.00320", "RGI60-06.00320", "RGI60-06.00320", "RGI60-06.00320", "RGI60-06.00320", "RGI60-06.00321", "RGI60-06.00321", "RGI60-06.00321", "RGI60-06.00321", "RGI60-06.00321", "RGI60-06.00322", "RGI60-06.00322", "RGI60-06.00322", "RGI60-06.00322", "RGI60-06.00323", "RGI60-06.00323", 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"RGI60-06.00362", "RGI60-06.00362", "RGI60-06.00363", "RGI60-06.00364", "RGI60-06.00365", "RGI60-06.00365", "RGI60-06.00365", "RGI60-06.00366", "RGI60-06.00366", "RGI60-06.00367", "RGI60-06.00368", "RGI60-06.00368", "RGI60-06.00369", "RGI60-06.00369", "RGI60-06.00564", "RGI60-06.00565"]}
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/linkcheck.sh:
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1 | #!/bin/bash
2 |
3 | jupyter-book build book --builder linkcheck
4 |
5 |
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/push.sh:
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1 | #!/bin/bash
2 |
3 | ghp-import -n -p -f book/_build/html
4 | git push origin master
5 |
6 |
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