Merge pull request #316 from EIT-ALIVE/update_docs

Update documentation

docs/api/mixins.md

@@ -0,0 +1,12 @@
+# Mixins
+
+::: eitprocessing.datahandling.mixins.equality.Equivalence
+::: eitprocessing.datahandling.mixins.slicing.SelectByIndex
+::: eitprocessing.datahandling.mixins.slicing.SelectByTime
+    options:
+      members:
+        - select_by_time
+        - t
+
+::: eitprocessing.datahandling.mixins.slicing.TimeIndexer
+

eitprocessing/categories.py

@@ -27,16 +27,24 @@ class Category(Node):
     subsub(...)category, `category.has_subcategory("<name>")` can be used. The keyword `in` can be used as a shorthand.
 
     Example:
+    ```
     >>> "tea" in category  # is the same as:
+    True
     >>> category.has_subcategory("tea")
+    True
+    ```
 
-    To select a subcategory, category["<name>"] can be used. You can select multiple categories at once. This will
+    To select a subcategory, `category["<name>"]` can be used. You can select multiple categories at once. This will
     create a new tree with a temporary root, containing only the selected categories.
 
     Example:
+    ```
     >>> foobar = categories["foo", "bar"]
-    >>> print(foobar)  # Category('/temporary root')
-    >>> print(foobar.children)  # (Category('/temporary root/foo'), Category('/temporary root/bar'))
+    >>> print(foobar)
+    Category('/temporary root')
+    >>> print(foobar.children)
+    (Category('/temporary root/foo'), Category('/temporary root/bar'))
+    ```
 
     Categories can be hand-crafted, created from a dictionary or a YAML string. See [`anytree.DictionaryImporter`
     documentation](https://anytree.readthedocs.io/en/latest/importer/dictimporter.html) for more info on the dictionary
@@ -61,10 +69,15 @@ class Category(Node):
     algorithms.
 
     Example:
+    ```
     >>> categories = get_default_categories()
-    >>> print(categories)  # Category('/category')
-    >>> print("pressure" in categories)  # True
-    >>> categories["pressure"]  # Category('/category/physical measurements/pressure')
+    >>> print(categories)
+    Category('/category')
+    >>> print("pressure" in categories)
+    True
+    >>> categories["pressure"]
+    Category('/category/physical measurement/pressure')
+    ```
     """
 
     readonly = True

eitprocessing/config/categories-compact.yaml

@@ -1,5 +1,5 @@
 root:
-- physical measurements:
+- physical measurement:
   - gas content:
     - partial pressure:
       - partial pressure of carbon dioxide

eitprocessing/datahandling/loading/__init__.py

@@ -47,8 +47,12 @@ def load_eit_data(
 
     Example:
     ```
-    sequence = load_data(["path/to/file1", "path/to/file2"], vendor="sentec", label="initial_measurement")
-    pixel_impedance = sequence.eit_data["raw"].pixel_impedance
+    >>> sequence = load_eit_data(
+    ...     ["path/to/file1", "path/to/file2"],
+    ...     vendor="sentec",
+    ...     label="initial_measurement"
+    ... )
+    >>> pixel_impedance = sequence.eit_data["raw"].pixel_impedance
     ```
     """
     from eitprocessing.datahandling.loading import draeger, sentec, timpel  # not in top level to avoid circular import

eitprocessing/datahandling/sequence.py

@@ -145,7 +145,7 @@ def select_by_time(
     ) -> Self:
         """Return a sliced version of the Sequence.
 
-        See SelectByTime.select_by_time().
+        See `SelectByTime.select_by_time()`.
         """
         if not label:
             label = f"copy_of_<{self.label}>"

eitprocessing/features/breath_detection.py

@@ -24,11 +24,18 @@ class BreathDetection:
     implemented as the minimum time between peaks and between valleys.
 
     Examples:
+    ```
     >>> bd = BreathDetection(minimum_duration=0.5)
-    >>> breaths = bd.find_breaths(sequency=seq, continuousdata_label="global_impedance_(raw)")
+    >>> breaths = bd.find_breaths(
+    ...     sequency=seq,
+    ...     continuousdata_label="global_impedance_(raw)"
+    ... )
+    ```
 
+    ```
     >>> global_impedance = seq.continuous_data["global_impedance_(raw)"]
     >>> breaths = bd.find_breaths(continuous_data=global_impedance)
+    ```
 
     Args:
         minimum_duration: minimum expected duration of breaths, defaults to 2/3 of a second

eitprocessing/features/pixel_breath.py

@@ -21,11 +21,13 @@ class PixelBreath:
     of inspiration and expiration. These points are then used to find the start/end of pixel
     inspiration/expiration in pixel impedance data.
 
-    Examples:
+    Example:
+    ```
     >>> pi = PixelBreath()
     >>> eit_data = sequence.eit_data['raw']
     >>> continuous_data = sequence.continuous_data['global_impedance_(raw)']
     >>> pixel_breaths = pi.find_pixel_breaths(eit_data, continuous_data, sequence)
+    ```
 
     Args:
     breath_detection_kwargs (dict): A dictionary of keyword arguments for breath detection.

eitprocessing/parameters/eeli.py

@@ -26,8 +26,10 @@ def compute_parameter(self, continuous_data: ContinuousData) -> np.ndarray:
         """Compute the EELI for each breath in the impedance data.
 
         Example:
+        ```
         >>> global_impedance = sequence.continuous_data["global_impedance_(raw)"]
-        >>> eeli_values = EELI().compute_parameter(global_impedance)
+        >>> eeli_data = EELI().compute_parameter(global_impedance)
+        ```
 
         Args:
             continuous_data: a ContinuousData object containing impedance data.

mkdocs.yml

@@ -55,6 +55,7 @@ nav:
   - api/features.md
   - api/parameters.md
   - api/categories.md
+  - api/mixins.md
 - About:
   - Contributing: contributing_doc.md
   - Code of Conduct: code_of_conduct_doc.md
@@ -82,6 +83,7 @@ markdown_extensions:
 - pymdownx.highlight:
     anchor_linenums: true
     pygments_lang_class: true
+    default_lang: "py"
 - pymdownx.extra
 - pymdownx.tabbed:
     alternate_style: true