make stable links

fabridamicelli · fabridamicelli · commit eff9d5b97c3b · 2025-11-07T18:03:11.000+01:00
diff --git a/.gitignore b/.gitignore
@@ -160,3 +160,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+_book/
diff --git a/book/01_1_getting_started.ipynb b/book/01_1_getting_started.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Getting Started\n",
     "toc: true\n",
+    "output-file: getting_started.html\n",
     "---"
    ]
   },
diff --git a/book/01_2_executing_code.ipynb b/book/01_2_executing_code.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Executing Code\n",
     "toc: true\n",
+    "output-file: executing.html\n",
     "---"
    ]
   },
diff --git a/book/02_types_data_structures.ipynb b/book/02_types_data_structures.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Syntax Basics\n",
     "toc: true\n",
+    "output-file: basics.html\n",
     "---"
    ]
   },
diff --git a/book/03_1_flow_control.ipynb b/book/03_1_flow_control.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Flow Control\n",
     "toc: true\n",
+    "output-file: flow_control.html\n",
     "---"
    ]
   },
diff --git a/book/03_2_error_handling.ipynb b/book/03_2_error_handling.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Error Handling \n",
     "toc: true\n",
+    "output-file: error_handling.html\n",
     "---"
    ]
   },
diff --git a/book/041_scope.ipynb b/book/041_scope.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Scope\n",
     "toc: true\n",
+    "output-file: scope.html\n",
     "---"
    ]
   },
@@ -46,7 +47,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/04_functions.ipynb b/book/04_functions.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Functions\n",
     "toc: true\n",
+    "output-file: functions.html\n",
     "---"
    ]
   },
diff --git a/book/051_oop.ipynb b/book/051_oop.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Object Oriented Programming\n",
     "toc: true\n",
+    "output-file: oop.html\n",
     "---"
    ]
   },
@@ -580,7 +581,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/05_comprehensions.ipynb b/book/05_comprehensions.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Comprehensions \n",
     "toc: true\n",
+    "output-file: comprehensions.html\n",
     "---"
    ]
   },
diff --git a/book/062_read_and_write.ipynb b/book/062_read_and_write.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Read/Write Files\n",
     "toc: true\n",
+    "output-file: read_write.html\n",
     "---"
    ]
   },
diff --git a/book/063_common_data_formats.ipynb b/book/063_common_data_formats.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Common Data Formats\n",
     "toc: true\n",
+    "output-file: common_data_formats.html\n",
     "---"
    ]
   },
diff --git a/book/06_imports.ipynb b/book/06_imports.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Importing Code\n",
     "toc: true\n",
+    "output-file: imports.html\n",
     "---"
    ]
   },
diff --git a/book/07_generators.ipynb b/book/07_generators.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Generators\n",
     "toc: true\n",
+    "output-file: generators.html\n",
     "---"
    ]
   },
@@ -215,7 +216,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/081_pandas.ipynb b/book/081_pandas.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Pandas\n",
     "toc: true\n",
+    "output-file: pandas.html\n",
     "---"
    ]
   },
diff --git a/book/08_numpy.ipynb b/book/08_numpy.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Numpy\n",
     "toc: true\n",
+    "output-file: numpy.html\n",
     "---"
    ]
   },
@@ -332,7 +333,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/09_plotting.ipynb b/book/09_plotting.ipynb
diff --git a/book/10_testing.ipynb b/book/10_testing.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Testing\n",
     "toc: true\n",
+    "output-file: testing.html\n",
     "---"
    ]
   },
@@ -17,13 +18,15 @@
    "metadata": {},
    "source": [
     "## Why bother writing tests?\n",
-    "**Correctness:** This is our goal number one when writing code, since incorrect code is arguably useless.\n",
-    "By incorrect we do not mean proper business logic nor being statistically sound.\n",
-    "We mean something much simpler: The code does what we think it is doing.  \n",
-    "One way to build some confidence about the correctness of code is to write tests.\n",
-    "We are going to deal here with so-called [unit tests](https://en.wikipedia.org/wiki/Unit_testing).\n",
-    "As the name suggests, these tests target pieces, blocks (units) of code that we can test isolated.\n",
-    "For example, here's a simple function that computes the square of a number and a little test:"
+    "**Correctness**  \n",
+    "Incorrect code is arguably useless.\n",
+    "By incorrect we do not mean proper business logic nor being statistically sound.  \n",
+    "We mean something much simpler: The code does _what we think it is doing_.  \n",
+    "\n",
+    "One way to build some confidence about the correctness of our code is to write tests.\n",
+    "Here we'll be looking at so-called [unit tests](https://en.wikipedia.org/wiki/Unit_testing).  \n",
+    "These tests target atomic pieces (units) of code that we can test isolated.\n",
+    "For example, here's a simple function that computes the square of a number and a unit test:"
    ]
   },
   {
@@ -40,27 +43,20 @@
     "    assert square(-1) == 1\n",
     "    assert square(1) == 1\n",
     "    assert square(2) == 4\n",
-    "    assert square(5) == 25\n",
-    "\n",
-    "test_square()"
+    "    assert square(5) == 25"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "57a0c9de-0ba4-437c-8154-b150c939226e",
    "metadata": {},
    "source": [
-    "**Refactoring:** Having tests in place can be also useful when we want to modify working code, since they will give us at least some degree of confidence that we are not breaking the functionality when we refactor the code, for example, while optimizing running time."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "d23504f5-2423-4284-b42a-c9d69bd1aa09",
-   "metadata": {},
-   "source": [
-    "As we saw above we can write the assertions about our code in a function that we then call.\n",
-    "Calling each test manually is a bit cumbersome and error prone.\n",
-    "We will use instead a testing framework that will do this automatically for us (plus, it's going to provide us with a whole bunch of handy functionalities out of the box)."
+    "**Refactoring**  \n",
+    "When we want to modify working code, since tests can give us some degree of confidence that we are not breaking the functionality, for example, while optimizing running time.\n",
+    "\n",
+    "\n",
+    "**Documentation**  \n",
+    "Tests can serve as a way to communicate other people (our ourselves) the expected behaviour of our code."
    ]
   },
   {
@@ -74,7 +70,8 @@
     "Those are of course questions that depend on the context and the system we are testing.  \n",
     "We will focus on two aspects that are important in the context of working with data: Verifying assumptions about the data (content, shape, etc.) and checking that transformations in a data processing pipeline are doing the right thing.\n",
     "Further examples of aspects to be tested include: Verifying responses from an API, check that a machine learning model can deal with a given input, etc.\n",
-    "Testing software is in itself a whole field, there are even [dedicated testing conferences](https://testingconferences.org/)!"
+    "\n",
+    "Testing software is in itself a whole field in itself, there are even [dedicated testing conferences](https://testingconferences.org/)!"
    ]
   },
   {
@@ -87,6 +84,16 @@
     ":::"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "93ceacdb-7a73-454b-96f4-b89cf7deadaa",
+   "metadata": {},
+   "source": [
+    "As we saw above we can write the assertions about our code in a function that we then call.\n",
+    "Calling each test manually is a bit cumbersome and error prone.\n",
+    "We will use instead a testing framework that will do this automatically for us (plus, it's going to provide us with a whole bunch of handy functionalities out of the box)."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "a5cb2472-ab0b-4cb6-a00f-eaa9e962c25d",
@@ -264,7 +271,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/111_debugging.ipynb b/book/111_debugging.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Debugging\n",
     "toc: true\n",
+    "output-file: debugging.html\n",
     "---"
    ]
   },
@@ -260,11 +261,7 @@
    "source": [
     "Now, your collaborator has written this script to extract the mean value of the \"SAR\" entry from across all subjects bold data.\n",
     "\n",
-    "6) Put this script into the folder (create if it does not yet exist) `pycourse/scripts/sar_mean.py` and make the necessary modifications to make it run as a script.\n",
-    "\n",
-    "7) Run it using `uv run scripts/sar_mean.py` and see it fail. Set a breakpoint inside the `get_subjects_sar_mean` function. Run it again and try to find the bug inside the debugger.\n",
-    "\n",
-    "8) Add some error handling to make sure the script runs."
+    "6) Put this script into the folder (create if it does not yet exist) `pycourse/scripts/sar_mean.py` and make the necessary modifications to make it run as a script."
    ]
   },
   {
@@ -294,16 +291,28 @@
     "# that prints the sar-mean when run"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "5484d18e-a0c7-4f89-aa9c-bf40729203ac",
+   "metadata": {},
+   "source": [
+    "7) Run it using `uv run scripts/sar_mean.py` and see it fail. Set a breakpoint inside the `get_subjects_sar_mean` function. Run it again and try to find the bug inside the debugger.\n",
+    "\n",
+    "8) Add some error handling to make sure the script runs."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "1e080ee5-eea8-4f16-bb1d-a992e4eed409",
    "metadata": {},
    "source": [
-    "To recap, so far our project should have these files:\n",
+    "To recap, so far our project should look more or less like this:\n",
+    "\n",
+    "![](./images/files.png){width=150}\n",
     "\n",
-    "![](./images/files.png)\n",
+    "And if we expand the folders:\n",
     "\n",
-    "![](./images/tree-2.png)"
+    "![](./images/tree-2.png){width=150}"
    ]
   },
   {
diff --git a/book/11_cli.ipynb b/book/11_cli.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Command Line Interfaces (CLI)\n",
     "toc: true\n",
+    "output-file: cli.html\n",
     "---"
    ]
   },
@@ -38,7 +39,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/13_tools.ipynb b/book/13_tools.ipynb
@@ -8,6 +8,8 @@
     "---\n",
     "title: Useful Tools and Patterns\n",
     "toc: true\n",
+    "\n",
+    "output-file: tools_patterns.html\n",
     "---"
    ]
   },
@@ -87,7 +89,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/999_glossary.ipynb b/book/999_glossary.ipynb
@@ -8,6 +8,7 @@
     "---\n",
     "title: Glossary \n",
     "toc: true\n",
+    "output-file: glossary.html\n",
     "---"
    ]
   },
@@ -123,7 +124,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,
diff --git a/book/_quarto.yml b/book/_quarto.yml
@@ -49,7 +49,7 @@ book:
     - 08_numpy.ipynb
     - 081_pandas.ipynb
     - 09_plotting.ipynb
-    - 10_tests.ipynb
+    - 10_testing.ipynb
     - lab_explore_data_exercises.ipynb
     - 11_cli.ipynb
     - 13_tools.ipynb

Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Getting Started\n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: getting_started.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Executing Code\n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: executing.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Syntax Basics\n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: basics.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Flow Control\n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: flow_control.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Error Handling \n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: error_handling.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Functions\n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: functions.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"---\n",`
`9`	`9`	`"title: Comprehensions \n",`
`10`	`10`	`"toc: true\n",`
	`11`	`+ "output-file: comprehensions.html\n",`
`11`	`12`	`"---"`
`12`	`13`	`]`
`13`	`14`	`},`