Merge pull request #5 from neuroinformatics-unit/small-cleanups

Author: IgorTatarnikov

index.qmd

@@ -60,10 +60,12 @@ format:
 ## Schedule {.smaller}
 ::: {.incremental}
 * Recap and Q&A
-* Using third party libraries from pip and conda
 * Functions and methods
 * Classes and objects
 * Errors and exceptions
+* Integrated Development Environments (IDEs)
+* Virtual environments
+* Modules and packages
 * Organising your code
 * Documenting your code
 :::
@@ -82,6 +84,39 @@ format:
 Please ask any **questions at any time**!
 :::
 
+# Installation
+
+## Install miniforge {.smaller}
+
+[Click here to go to the download page](https://conda-forge.org/download/)
+
+
+Add Miniforge to PATH when prompted during installation.
+
+![](img/miniforge_window_add_to_path.png){width="25%" fig-align="center"}
+
+Try the below in either your terminal (Mac/Linux) or Miniconda Prompt (Windows):
+```bash
+conda --version
+```
+
+::: {.callout-caution collapse="true"}
+## Windows troubleshooting
+- Did you had a previous version of Anaconda installed? You might need to uninstall it first.
+- `conda not found`? Run `conda init` in your terminal.
+:::
+
+## Install an IDE {.smaller}
+
+::: {.fragment .fade-in}
+* [Visual Studio Code](https://code.visualstudio.com/download) - customisable, extensible, open source
+* [PyCharm](https://www.jetbrains.com/pycharm/download/) - opinionated defaults, not fully free (free for educational use)
+:::
+
+## Install a text editor (macOS) {.smaller}
+* [Sublime Text](https://www.sublimetext.com/) - lightweight text editor
+* Windows can use the built-in Notepad or [Notepad++](https://notepad-plus-plus.org/downloads/)
+
 # Why learn Python?
 
 ## Why learn Python? {.smaller}

slides/basics.qmd

@@ -51,7 +51,7 @@ print(y)
 ```
 
 ## Data types
-::: {.fragment .incremental .smaller}
+::: {.incremental style="font-size: 80%;"}
 * Different kinds of data are stored in different ways in memory
 * You can use the `type()` function to find out what type of data a variable contains
 :::
@@ -159,6 +159,7 @@ print(1 + 2.1)
 ::: {.fragment .fade-in}
 * What about an **int** and a **str**?
 <br/>
+
 ```{python}
 #| echo: true
 #| output-location: fragment
@@ -298,11 +299,21 @@ my_tuple = (1, 2.0, 'cat', 'dog')
 
 print(type(my_tuple))
 print(my_tuple[2])
-
-my_tuple[2] = 'rabbit'
 ```
 ::::
 :::
+
+<br/>
+
+:::: {.fragment .fade-in}
+```{python}
+#| echo: true
+#| output-location: fragment
+#| error: true
+my_tuple[2] = 'new_element'
+print(my_tuple)
+```
+::::
 :::::
 
 ## Unpacking {.smaller}
@@ -479,6 +490,10 @@ for i in range(5):
 * You can loop over any iterable
 * Use `_` if you don't need the loop variable
 * `enumerate()` gives you the index and the value
+* `range()` generates a sequence of numbers
+    + `range(n)` from 0 to n-1
+    + `range(a, b)` from a to b-1
+    + `range(a, b, step)` from a to b-1 with jumps of step
 :::
 ::: {.column width="45%"}
 :::: {.fragment .fade-in}

slides/classes_and_objects.qmd

@@ -44,14 +44,19 @@ file_obj.close()
 ```{python}
 #| echo: true
 #| output-location: fragment
-#| code-line-numbers: "|1|2,3|5|6|"
+#| code-line-numbers: "|1|2,3|5,6|8,9|10|11|"
 
 class Animal():
     def __init__(self, species):
         self.species = species
 
+    def greet(self):
+        print(f"Hello, I am a {self.species}.")
+
 pingu = Animal("penguin")
+print(type(pingu))
 print(pingu.species)
+pingu.greet()
 ```
 :::::
 :::
@@ -73,13 +78,16 @@ pingu.make_noise() # Output: noot
 ```{python}
 #| echo: true
 #| output-location: fragment
-#| code-line-numbers: "|2|2,4|6,7|"
+#| code-line-numbers: "|2|2,4|9,10|"
 
 class Animal():
     def __init__(self, species, noise):
         self.species = species
         self.noise = noise
 
+    def greet(self):
+        print(f"{self.noise}, I am a {self.species}.")
+
     def make_noise(self):
         print(self.noise)
 

slides/errors_and_exceptions.qmd

@@ -94,10 +94,12 @@ a_list[5]
 ::::
 
 ## Tracebacks {.smaller}
+::: {.incremental}
 * Help you find the source of the error
 * Read from the bottom up
 * Look for the last line that is *your* code
 * [Debugging manifesto](https://wizardzines.com/images/debugging-manifesto.pdf) :bug:
+:::
 
 ## Tracebacks {.smaller}
 ```{python}
@@ -115,6 +117,22 @@ def call_func(x):
 z = call_func(10)
 ```
 
+## Tracebacks {.smaller}
+```{python}
+#| echo: true
+#| output-location: fragment
+#| error: true
+
+def none_function():
+    return None
+
+def get_file_name():
+    return none_function()
+
+file_name = none_function()
+open_file = open(file_name)
+```
+
 ## Handling exceptions {.smaller}
 * What if you know an error might happen?
 

slides/first_script.qmd

@@ -6,11 +6,6 @@
 * `Scripts` (.py)
 :::
 
-::: {.fragment .fade-in}
-Demo time! 🧑🏻‍💻👩🏻‍💻
-:::
-
-
 
 ## Writing your first Python script
 
@@ -19,5 +14,5 @@ Demo time! 🧑🏻‍💻👩🏻‍💻
 :::
 
 ::: {.fragment .fade-in}
-![](/img/your_first_script.png){width=70%}
+![](/img/your_first_script.png){width=70% fig-align="center"}
 :::

slides/functions.qmd

@@ -53,7 +53,7 @@ print(y)
 * Functions allow you to:
     + Reuse code
     + Break problems into smaller pieces
-    + Scope defined by indentation
+* Scope defined by indentation
 * Defined using the `def` keyword
 * Can take inputs (arguments) and return outputs
 :::
@@ -101,6 +101,7 @@ def is_valid_password(password):
 ```{python}
 #| echo: true
 #| output-location: fragment
+#| code-line-numbers: "|1|2,3|4,5|"
 def is_valid_password(password):
     if len(password) >= 8:
         return True
@@ -215,7 +216,7 @@ def longer_string(str1, str2=""):
 ```{python}
 #| echo: true
 #| output-location: fragment
-#| code-line-numbers: "|1|2,4|"
+#| code-line-numbers: "|1|2,3|4,5|7|"
 
 def longer_string(str1, str2=""):
     if len(str1) > len(str2):
@@ -225,8 +226,8 @@ def longer_string(str1, str2=""):
 
     print(long_str)
 
-print(longer_string("apple", "banana"))
-print(longer_string("apple"))
+longer_string("apple", "banana")
+longer_string("apple")
 ```
 
 ## Using `*` and `**` {.smaller}
@@ -241,26 +242,42 @@ print(longer_string("apple"))
 ```{python}
 #| echo: true
 #| output-location: fragment
+#| code-line-numbers: "|1|2,3|5,6|8,9|11,12|"
 def my_func(*args, **kwargs):
-    print(f"Unpacking list: {args}")
-    print(f"Unpacking dictionary: {kwargs}")
+    print(f"Unpacking positional arguments: {args}")
+    print(f"Unpacking keyword arguments: {kwargs}")
 
 my_list = [1, 2, 3, 4, 5]
 my_dict = {'a': 1, 'b': 2, 'c': 3}
 
-print("Unpacking list:")
 my_func(*my_list)
 
-print("Unpacking dictionary:")
 my_func(**my_dict)
 ```
 :::
 
+## Using `*` and `**` {.smaller}
+
+::: {.fragment .fade-in}
+```{python}
+#| echo: true
+#| output-location: fragment
+def my_func(*args, **kwargs):
+    print(f"Unpacking positional arguments: {args}")
+    print(f"Unpacking keyword arguments: {kwargs}")
+
+my_func(1, 'a', 3.14)
+my_func(name="John", age=30)
+my_func(1, 2, 3, name="Jane", city="New York")
+```
+:::
+
 ## How are `*args` and `**kwargs` useful? {.smaller}
 :::: {.columns}
 ::: {.column width="55%"}
 ::: {.incremental .smaller}
-* `*args` and `**kwargs` are useful when you don't know how many arguments will be passed to the function
+* `*args` and `**kwargs` are useful when you don't know which arguments will be passed to the function
+* Or when you wrap another function and want to pass all arguments to the wrapped function
 :::
 
 :::

slides/interactive_python.qmd

@@ -15,6 +15,6 @@ Demo time! 🧑🏻‍💻👩🏻‍💻
 :::
 
 ::: {.fragment .fade-in}
-![](/img/interactive_python.png){width=80%}
+![](/img/interactive_python.png){width=70% fig-align="center"}
 :::
 

slides/loading_and_saving.qmd

@@ -60,7 +60,7 @@ print(contents)
 :::::
 
 ## Demo
-* Write a script that saves the below data to a comma-separated file
+* Let's write a script that saves the below data to a comma-separated file
 
 ```{python}
 #| echo: true
@@ -71,16 +71,17 @@ samples = [(0, 12, 53), (1, 7, 23), (2, 15, 30)]
 ## Demo
 ```{python}
 #| echo: true
+#| code-line-numbers: "|4|5,6|8|9,10|8,11|"
 column_labels = "sample_id,speed,distance"
 samples = [(0, 12, 53), (1, 7, 23), (2, 15, 30)]
 
-with open("out.csv", "w") as file:
-    file.write(column_labels)
-    file.write("\n")
+with open("out.csv", "w") as data_file:
+    data_file.write(column_labels)
+    data_file.write("\n")
 
     for sample in samples:
         for value in sample:
-            file.write(str(value) + ",")
-        file.write("\n")
+            data_file.write(str(value) + ",")
+        data_file.write("\n")
 ```
 

slides/virtual_environments.qmd

@@ -1,5 +1,5 @@
 ## Scientific Python ecosystem {.smaller}
-![Diagram showing the scientific Python ecosystem.](/img/python-ecosystem.png)
+![](/img/python-ecosystem.png){alt="Scientific Python ecosystem"}
 
 ::: footer
 [Aaron Meurer, ‘Python Array API Standard’, SciPy 2023](https://www.youtube.com/watch?v=16rB-fosAWw)
@@ -17,7 +17,7 @@
 
 ## Virtual environments {.smaller}
 
-![[Comic from xkcd](https://xkcd.com/1987/)](https://imgs.xkcd.com/comics/python_environment.png){width="20%"}
+![[](https://xkcd.com/1987/)](https://imgs.xkcd.com/comics/python_environment.png){width="20%" alt="xkcd comic about Python environments"}
 
 ## Virtual environments {.smaller}
 
@@ -59,17 +59,6 @@
     -   Future you (HPC, etc...)
 :::
 
-## Install miniforge
-
-[Click here to go to the download page](https://conda-forge.org/download/)
-
-::: {.callout-caution collapse="true"}
-## Windows troubleshooting
-- Did you had a previous version of Anaconda installed? You might need to uninstall it first.
-- ![Remember to add Miniforge to your PATH! The installer will say is not required, but it is!](img/miniforge_window_add_to_path.png){width="25%"}
-- `conda not found`? Run `conda init` in your terminal.
-:::
-
 ## Environment management
 
 In your terminal (use Anaconda Prompt on Windows):