Merge pull request #200 from PixelgenTechnologies/feature/exe-2075-fa…

…il-if-hard-and-dynamic-limit-both-set

Feature/exe 2075 fail if hard and dynamic size limits are both set

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 -   Support multiple targets in `plot_colocalization_diff_volcano` and `plot_colocalization_diff_heatmap`.
 -   If demultiplexing has a success rate lower than 50% the command will exit with a status of 1. This prevents further pipeline stages to be run on
     what is probably bad data.
+-   Clarify that `--min-size` and `--max-size` in the `annotate` stage should not be used at the same time as `--dynamic-filter`.
 
 ### Added
 

src/pixelator/cli/annotate.py

@@ -45,26 +45,25 @@
     required=False,
     type=click.INT,
     show_default=False,
-    help="The minimum size (edges) a component must have (default is disabled)",
+    help="The minimum size (edges) a component must have (default is disabled). Note that this cannot be set at the same time as --dynamic-filter.",
 )
 @click.option(
     "--max-size",
     default=None,
     required=False,
     type=click.INT,
     show_default=False,
-    help="The maximum size (edges) a component must have (default is disabled)",
+    help="The maximum size (edges) a component must have (default is disabled). Note that this cannot be set at the same time as --dynamic-filter.",
 )
 @click.option(
     "--dynamic-filter",
     required=False,
     default=None,
     type=click.Choice(["both", "min", "max"]),
     help=(
-        "Enable the estimation of dynamic size filters using a log-rank approach\n"
-        "\t both: estimate both min and max size"
-        "\t min: estimate min size (--min-size)"
-        "\t max: estimate max size (--max-size)"
+        "Enable the dynamic component size filters. The following modes are available: "
+        "both/max/min. both: estimates both min and max size, min: estimates min size, max: estimates max size. "
+        "Note that this cannot be set at the same time as --min-size or --max-size."
     ),
 )
 @click.option(
@@ -110,11 +109,17 @@ def annotate(
 
     # sanity check on thresholds and input parameters
     if min_size is not None and min_size < 0:
-        click.ClickException("--min-size cannot be less than 0")
+        raise click.ClickException("--min-size cannot be less than 0")
     if max_size is not None and max_size < 0:
-        click.ClickException("--max-size cannot be less than 0")
+        raise click.ClickException("--max-size cannot be less than 0")
     if max_size is not None and min_size is not None and max_size < min_size:
-        click.ClickException("--max-size cannot be less than --min-size")
+        raise click.ClickException("--max-size cannot be less than --min-size")
+
+    if min_size is not None or max_size is not None:
+        if dynamic_filter is not None:
+            raise click.ClickException(
+                "Cannot set --dynamic-filter and --min-size or --max-size at the same time"
+            )
 
     # warn if both --dynamic-filter and hard-coded sizes are input
     if min_size is not None and dynamic_filter in ["min", "both"]: