NEW: Documentation on RachisWarning (#161)

Co-authored-by: Colin Wood <woodcolin38@gmail.com>

Author: Macabe222

book/_toc.yml

@@ -45,6 +45,7 @@ parts:
             - file: plugins/how-to-guides/usage-examples
             - file: plugins/how-to-guides/format-validation-levels
             - file: plugins/how-to-guides/handle-exceptions-in-parallel-pipelines
+            - file: plugins/how-to-guides/raise-visible-warning
         - file: plugins/explanations/intro
           sections:
             - file: plugins/explanations/actions

book/plugins/how-to-guides/create-register-transformer.md

@@ -4,7 +4,7 @@
 Transformers are often short Python functions that convert one file format or data type to another file format or data type.
 These functions are never directly called by users or developers, so by convention they don't get informative function names (as the annotations of the input and output provide complete detail on what they do).
 
-Here's are two example `transformer` that are [defined and registered in `q2-types`](https://github.com/qiime2/q2-types/blob/e25f9355958755343977e037bbe39110cfb56a63/q2_types/distance_matrix/_transformer.py#L16):
+Here are two example `transformer` that are [defined and registered in `q2-types`](https://github.com/qiime2/q2-types/blob/e25f9355958755343977e037bbe39110cfb56a63/q2_types/distance_matrix/_transformer.py#L16):
 
 ```python
 import skbio

book/plugins/how-to-guides/raise-visible-warning.md

@@ -0,0 +1,33 @@
+(howto-raise-visible-warning)=
+
+# Use the RachisWarning Class: An Always-Visible Warning
+
+Warnings issued by the Python `warning` library are suppressed by defualt when using the command line interface (CLI).
+In order to make sure the warnings issued by your plugin are visible in the CLI you must use the `RachisWarning` class.
+This class can be imported from the QIIME2 framework, specifically from `qiime2.core.exceptions`.
+Below is an [excerpt](https://github.com/qiime2/q2-feature-table/blob/b6a312e612338db0f69c97641372e7f0005b43f5/q2_feature_table/_merge.py#L90C12-L93C14) from the `q2-feature-table` plugin that may issue such a warning.
+
+```python
+from qiime2.core.excpetions import RachisWarnings
+
+def merge_taxa(data: pd.DataFrame) -> pd.DataFrame:
+    if len(data) > 1:
+        depths = []
+        for taxonomy in data:
+            max = 0
+            for _, row in taxonomy.iterrows():
+                depth = row['Taxon'].count(';')
+                if depth > max:
+                    max = depth
+
+            depths.append(max)
+
+        if len(set(depths)) != 1:
+            warnings.warn(
+                "You are merging taxonomies with different depths.",
+                RachisWarning
+            )
+```
+
+This action issues a `RachisWarning` when the taxonomies have different depths.
+Since the `RachisWarning` class is an empty subclass of `UserWarning` from the Python `warnings` [library](https://docs.python.org/3/library/warnings.html), the only difference in behavior is command line visibility.