thyra 3.0.2__tar.gz → 3.0.3__tar.gz

{thyra-3.0.2 → thyra-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: thyra
-Version: 3.0.2
+Version: 3.0.3
 Summary: A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics
 License: MIT
 License-File: LICENSE

{thyra-3.0.2 → thyra-3.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "thyra"
-version = "3.0.2"
+version = "3.0.3"
 description = "A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics"
 authors = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]
 maintainers = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]

{thyra-3.0.2 → thyra-3.0.3}/thyra/__init__.py

@@ -36,7 +36,7 @@ warnings.filterwarnings(
     category=FutureWarning,
 )
 
-__version__ = "3.0.2"
+__version__ = "3.0.3"
 
 # Import key components - avoid wildcard imports
 try:

{thyra-3.0.2 → thyra-3.0.3}/thyra/__main__.py

@@ -350,7 +350,22 @@ def _handle_post_conversion(success: bool, output: Path) -> bool:
 
 
 class GroupedCommand(click.Command):
-    """Command that groups options into sections in --help output."""
+    """Command that groups options into sections in --help output.
+
+    Every visible option must appear in exactly one ``GROUPS`` entry.
+    Anything missing still shows up -- ``format_help`` sweeps the remainder
+    into a trailing ``Options:`` section rather than dropping it -- but that
+    section is a defect signal, not a home. It is where
+    ``--resample-gap-tolerance`` and ``--spectrum-type`` sat for two
+    releases, next to ``--version`` and ``--help``, while docs/cli.md told
+    readers the help was organised by category.
+
+    ``tests/unit/test_cli_help_grouping.py`` fails if the trailing section is
+    ever non-empty again, so adding an option without classifying it here is
+    caught before release rather than by a reader.
+
+    Section order is mirrored by docs/cli.md; keep the two in step.
+    """
 
     GROUPS = {
         "Conversion": [
@@ -371,8 +386,10 @@ class GroupedCommand(click.Command):
             "--resample-max-mz",
             "--resample-width-at-mz",
             "--resample-reference-mz",
+            "--resample-gap-tolerance",
         ],
         "Performance": ["--streaming", "--sparse-format"],
+        "imzML-specific": ["--spectrum-type"],
         "Bruker-specific": [
             "--use-recalibrated",
             "--no-recalibrated",
@@ -380,6 +397,7 @@ class GroupedCommand(click.Command):
             "--intensity-threshold",
         ],
         "Other": ["--dataset-id", "--handle-3d"],
+        "General": ["--version", "--help"],
     }
 
     def format_help(self, ctx: click.Context, formatter: click.HelpFormatter) -> None: