Normalize docs API and option links

Author: tobiasraabe

docs/source/how_to_guides/bp_complex_task_repetitions.md

@@ -37,8 +37,8 @@ to iterate over instances of this object in a single loop. Here and for the lack
 better name, we will call the object an experiment.
 
 Lastly, we will also use the
-[pytask.DataCatalog](../api/core_classes_and_exceptions.md#pytask.DataCatalog) to not be
-bothered with defining paths.
+[`pytask.DataCatalog`](../api/core_classes_and_exceptions.md#pytask.DataCatalog) to not
+be bothered with defining paths.
 
 !!! note
 
@@ -68,7 +68,7 @@ we use them.
 As you see, we lost a level of indentation and we moved all the generations of names and
 paths to the dimensions and multi-dimensional objects.
 
-Using a [pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) allows us to
+Using a [`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) allows us to
 hash the model and reexecute the task if we define other model settings.
 
 ## Adding another level

docs/source/how_to_guides/extending_pytask.md

@@ -19,8 +19,8 @@ More general information about pluggy can be found in its
 There are two ways to add new
 [hook implementations](../glossary.md#hook-implementation).
 
-1. Using the `pytask build --hook-module` commandline option or the `hook_module`
-    configuration value.
+1. Using the [`pytask build --hook-module`](../commands/build.md#options) commandline
+    option or the `hook_module` configuration value.
 1. Packaging your [plugin](../glossary.md#plugin) as a Python package to publish and
     share it.
 

docs/source/how_to_guides/hashing_inputs_of_tasks.md

@@ -2,28 +2,28 @@
 
 Any input to a task function is parsed by pytask's nodes. For example,
 [`pathlib.Path`][]s are parsed by
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode)s. The
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode) handles among other things
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode)s. The
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode) handles among other things
 how changes in the underlying file are detected.
 
 If an input is not parsed by any more specific node type, the general
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) is used.
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) is used.
 
 In the following example, the argument `text` will be parsed as a
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode).
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode).
 
 ```py
 --8<-- "docs_src/how_to_guides/hashing_inputs_of_tasks_example_1_py310.py"
 ```
 
 By default, pytask does not detect changes in
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) and if the value would
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) and if the value would
 change (without changing the task module), pytask would not rerun the task.
 
 We can also hash the value of
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode)s so that pytask knows
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode)s so that pytask knows
 when the input changed. For that, we need to use the
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) explicitly and set
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) explicitly and set
 `hash = True`.
 
 ```py
@@ -54,7 +54,7 @@ information). pytask will hash them using the `hashlib` module to create a stabl
 
 `list` and `dict` are not hashable by default. Luckily, there are libraries who provide
 this functionality like `deepdiff`. We can use them to pass a function to the
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) that generates a stable
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) that generates a stable
 hash.
 
 First, install `deepdiff`.

docs/source/how_to_guides/interfaces_for_dependencies_products.md

@@ -39,11 +39,11 @@ You can pass a value to a task as a default argument.
 It is possible to include the value in the type annotation.
 
 It is especially helpful if you pass a
-[pytask.PNode](../api/nodes_and_tasks.md#pytask.PNode) to the task. If you passed a node
-as the default argument, type checkers like mypy would expect the node to enter the
+[`pytask.PNode`](../api/nodes_and_tasks.md#pytask.PNode) to the task. If you passed a
+node as the default argument, type checkers like mypy would expect the node to enter the
 task, but the value injected into the task depends on the nodes
-[pytask.PNode.load](../api/nodes_and_tasks.md#pytask.PNode.load) method. For a
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode)
+[`pytask.PNode.load`](../api/nodes_and_tasks.md#pytask.PNode.load) method. For a
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode)
 
 ```py
 --8<-- "docs_src/how_to_guides/interfaces/dependencies_annotation.py"
@@ -72,7 +72,7 @@ applies to dependencies and products alike.
 ### `Product` annotation
 
 The syntax is the same as [default argument](#default-argument), but the
-[pytask.Product](../api/utilities_and_typing.md#pytask.Product) annotation turns the
+[`pytask.Product`](../api/utilities_and_typing.md#pytask.Product) annotation turns the
 argument into a task product.
 
 ```py
@@ -82,7 +82,7 @@ argument into a task product.
 ### `Product` annotation with value
 
 The syntax is the same as [annotation](#annotation), but the
-[pytask.Product](../api/utilities_and_typing.md#pytask.Product) annotation turns the
+[`pytask.Product`](../api/utilities_and_typing.md#pytask.Product) annotation turns the
 argument into a task product.
 
 ```py

docs/source/how_to_guides/migrating_from_scripts_to_pytask.md

@@ -59,7 +59,7 @@ An `if __name__ == "__main__"` block must be deleted.
 To let pytask know the order in which to execute tasks and when to re-run them, you'll
 need to specify task dependencies and products. Add dependencies as arguments to the
 function with default values. Do the same for products, but also add the special
-[pytask.Product](../api/utilities_and_typing.md#pytask.Product) annotation with
+[`pytask.Product`](../api/utilities_and_typing.md#pytask.Product) annotation with
 `Annotated[Path, Product]`. For example:
 
 ```py

docs/source/how_to_guides/provisional_nodes_and_task_generators.md

@@ -28,13 +28,13 @@ as the task module because it is a relative path.
 ```
 
 Since the names of the files are not known when pytask is started, we need to use a
-[pytask.DirectoryNode](../api/nodes_and_tasks.md#pytask.DirectoryNode) to define the
+[`pytask.DirectoryNode`](../api/nodes_and_tasks.md#pytask.DirectoryNode) to define the
 task's product. With a
-[pytask.DirectoryNode](../api/nodes_and_tasks.md#pytask.DirectoryNode) we can specify
+[`pytask.DirectoryNode`](../api/nodes_and_tasks.md#pytask.DirectoryNode) we can specify
 where pytask can find the files. The files are described with a root path (default is
 the directory of the task module) and a glob pattern (default is `*`).
 
-When we use the [pytask.DirectoryNode](../api/nodes_and_tasks.md#pytask.DirectoryNode)
+When we use the [`pytask.DirectoryNode`](../api/nodes_and_tasks.md#pytask.DirectoryNode)
 as a product annotation, we get access to the `root_dir` as a
 [`pathlib.Path`][] object inside the function, which allows us to store
 the files.
@@ -64,11 +64,11 @@ downloaded.
 ```
 
 To reference the files that will be downloaded, we use
-[pytask.DirectoryNode](../api/nodes_and_tasks.md#pytask.DirectoryNode) as a dependency.
+[`pytask.DirectoryNode`](../api/nodes_and_tasks.md#pytask.DirectoryNode) as a dependency.
 Before the task is executed, the list of files in the folder defined by the root path
 and the pattern are automatically collected and passed to the task.
 
-If we use a [pytask.DirectoryNode](../api/nodes_and_tasks.md#pytask.DirectoryNode) with
+If we use a [`pytask.DirectoryNode`](../api/nodes_and_tasks.md#pytask.DirectoryNode) with
 the same `root_dir` and `pattern` in both tasks, pytask will automatically recognize
 that the second task depends on the first. If that is not true, you might need to make
 this dependency more explicit by using `@task(after=...)`, which is explained

docs/source/how_to_guides/the_data_catalog.md

@@ -1,20 +1,20 @@
 # The `DataCatalog` - Revisited
 
 This guide explains more details about the
-[pytask.DataCatalog](../api/core_classes_and_exceptions.md#pytask.DataCatalog) that were
-left out of the [tutorial](../tutorials/using_a_data_catalog.md). Please, read the
+[`pytask.DataCatalog`](../api/core_classes_and_exceptions.md#pytask.DataCatalog) that
+were left out of the [tutorial](../tutorials/using_a_data_catalog.md). Please, read the
 tutorial for a basic understanding.
 
 ## Changing the default node
 
 The data catalog uses the
-[pytask.PickleNode](../api/nodes_and_tasks.md#pytask.PickleNode) by default to serialize
-any kind of Python object. You can use any other node that follows the
-[pytask.PNode](../api/nodes_and_tasks.md#pytask.PNode) protocol and register it when
+[`pytask.PickleNode`](../api/nodes_and_tasks.md#pytask.PickleNode) by default to
+serialize any kind of Python object. You can use any other node that follows the
+[`pytask.PNode`](../api/nodes_and_tasks.md#pytask.PNode) protocol and register it when
 creating the data catalog.
 
-For example, use the [pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) as
-the default.
+For example, use the [`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode)
+as the default.
 
 ```python
 from pytask import PythonNode
@@ -27,7 +27,7 @@ data_catalog = DataCatalog(default_node=PythonNode)
 Or, learn to write your node by reading [writing custom nodes](writing_custom_nodes.md).
 
 Here, is an example for a
-[pytask.PickleNode](../api/nodes_and_tasks.md#pytask.PickleNode) that uses cloudpickle
+[`pytask.PickleNode`](../api/nodes_and_tasks.md#pytask.PickleNode) that uses cloudpickle
 instead of the normal `pickle` module.
 
 ```py

docs/source/how_to_guides/using_task_returns.md

@@ -22,7 +22,7 @@ where the return of the function, a string, should be stored.
 ```
 
 It works because internally the path is converted to a
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode) that is able to store
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode) that is able to store
 objects of type `str` and `bytes`.
 
 !!! note

docs/source/how_to_guides/writing_custom_nodes.md

@@ -2,9 +2,9 @@
 
 In the previous tutorials and how-to guides, you learned that dependencies and products
 can be represented as plain Python objects with
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode) or as paths where every
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode) or as paths where every
 [`pathlib.Path`][] is converted to a
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode).
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode).
 
 In this how-to guide, you will learn about the general concept of nodes and how to write
 your own to improve your workflows.
@@ -21,7 +21,7 @@ paths to point to inputs and outputs and call [`pandas.read_pickle`][] and
 ```
 
 To remove IO operations from the task and delegate them to pytask, we will replicate the
-[pytask.PickleNode](../api/nodes_and_tasks.md#pytask.PickleNode) that automatically
+[`pytask.PickleNode`](../api/nodes_and_tasks.md#pytask.PickleNode) that automatically
 loads and stores Python objects.
 
 And we pass the value to `df` via [`typing.Annotated`][] to preserve
@@ -49,15 +49,15 @@ A custom node needs to follow an interface so that pytask can perform several ac
 - Load and save values when tasks are executed.
 
 This interface is defined by protocols. A custom node must follow at least the protocol
-[pytask.PNode](../api/nodes_and_tasks.md#pytask.PNode) or, even better,
-[pytask.PPathNode](../api/nodes_and_tasks.md#pytask.PPathNode) if it is based on a path.
-The common node for paths, [pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode),
-follows the protocol [pytask.PPathNode](../api/nodes_and_tasks.md#pytask.PPathNode).
+[`pytask.PNode`](../api/nodes_and_tasks.md#pytask.PNode) or, even better,
+[`pytask.PPathNode`](../api/nodes_and_tasks.md#pytask.PPathNode) if it is based on a path.
+The common node for paths, [`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode),
+follows the protocol [`pytask.PPathNode`](../api/nodes_and_tasks.md#pytask.PPathNode).
 
 ## `PickleNode`
 
-Since our [pytask.PickleNode](../api/nodes_and_tasks.md#pytask.PickleNode) will only
-vary slightly from [pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode), we use
+Since our [`pytask.PickleNode`](../api/nodes_and_tasks.md#pytask.PickleNode) will only
+vary slightly from [`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode), we use
 it as a template, and with some minor modifications, we arrive at the following class.
 
 ```py
@@ -67,7 +67,7 @@ it as a template, and with some minor modifications, we arrive at the following
 Here are some explanations.
 
 - The node does not need to inherit from the protocol
-    [pytask.PPathNode](../api/nodes_and_tasks.md#pytask.PPathNode), but you can do it to
+    [`pytask.PPathNode`](../api/nodes_and_tasks.md#pytask.PPathNode), but you can do it to
     be more explicit.
 
 - The node has two attributes
@@ -88,7 +88,7 @@ Here are some explanations.
     For custom nodes, make sure the lockfile id stays stable and unique within a task.
 
 - The classmethod
-    [pytask.PickleNode.from_path](../api/nodes_and_tasks.md#pytask.PickleNode.from_path)
+    [`pytask.PickleNode.from_path`](../api/nodes_and_tasks.md#pytask.PickleNode.from_path)
     is a convenient method to instantiate the class.
 
 - The method
@@ -101,7 +101,7 @@ Here are some explanations.
     [`pytask.PickleNode.load`](../api/nodes_and_tasks.md#pytask.PickleNode.load) when it
     collects the values of function arguments to run the function. The argument
     `is_product` signals that the node is loaded as a product with a
-    [pytask.Product](../api/utilities_and_typing.md#pytask.Product) annotation or via
+    [`pytask.Product`](../api/utilities_and_typing.md#pytask.Product) annotation or via
     `produces`.
 
     When the node is loaded as a dependency, we want to inject the value of the pickle
@@ -127,8 +127,8 @@ Nodes are an important in concept pytask. They allow to pytask to build a
 IO operations from the task function into the nodes.
 
 pytask only implements two node types,
-[pytask.PathNode](../api/nodes_and_tasks.md#pytask.PathNode) and
-[pytask.PythonNode](../api/nodes_and_tasks.md#pytask.PythonNode), but many more are
+[`pytask.PathNode`](../api/nodes_and_tasks.md#pytask.PathNode) and
+[`pytask.PythonNode`](../api/nodes_and_tasks.md#pytask.PythonNode), but many more are
 possible. In the future, there should probably be a [plugin](../glossary.md#plugin) that
 implements nodes for many other data sources like AWS S3 or databases. See
 [Kedro datasets](https://docs.kedro.org/en/stable/kedro_datasets.html) for one example.

docs/source/reference_guides/configuration.md

@@ -113,7 +113,8 @@ information.
 pytask can ignore files and directories and exclude some tasks or reduce the duration of
 the collection.
 
-To ignore some file/folder via the command line, use the `--ignore` flag multiple times.
+To ignore some file/folder via the command line, use the
+[`--ignore`](../commands/build.md#options) flag multiple times.
 
 ```console
 $ pytask --ignore some_file.py --ignore some_directory/*
@@ -201,8 +202,9 @@ that provide additional features such as syntax highlighting and tab completion:
 pdbcls = "pdbp:Pdb"
 ```
 
-The custom debugger will be used when you invoke the `--pdb` flag for post-mortem
-debugging or when using `breakpoint()` in your task code.
+The custom debugger will be used when you invoke the
+[`--pdb`](../commands/build.md#options) flag for post-mortem debugging or when using
+`breakpoint()` in your task code.
 
 ### `show_errors_immediately`