Test that CLIs emit no warnings

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
   - id: check-shebang-scripts-are-executable
   # - id: check-symlinks
   # - id: check-toml
-  # - id: check-xml
+  - id: check-xml
   - id: check-yaml
   - id: debug-statements
   - id: destroyed-symlinks
@@ -27,6 +27,7 @@ repos:
   - id: fix-byte-order-marker
   - id: forbid-new-submodules
   - id: mixed-line-ending
+  - id: no-commit-to-branch
   - id: trailing-whitespace
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0

histomicstk/cli/BackgroundIntensity/BackgroundIntensity.xml

@@ -65,7 +65,7 @@
       <label>Output intensity in SDA space</label>
       <description>Output intensity in SDA space (*.anot)</description>
       <channel>output</channel>
-      <index>2</index>
+      <index>1</index>
     </file>
   </parameters>
   <parameters advanced="true">

histomicstk/cli/SeparateStainsXuSnmf/SeparateStainsXuSnmf.xml

@@ -139,8 +139,4 @@
       <default>256</default>
     </integer>
   </parameters>
-  <parameters>
-    <label>IO</label>
-    <description>Input/output parameters.</description>
-  </parameters>
 </executable>

tests/test_cli_xml.py

@@ -0,0 +1,19 @@
+import os
+from pathlib import Path
+
+import pytest
+
+cliDir = Path(__file__).parent / '..' / 'histomicstk' / 'cli'
+xmlList = {
+    cli: cliDir / cli / f'{cli}.xml' for cli in os.listdir(cliDir)
+    if (cliDir / cli).is_dir() and (cliDir / cli / f'{cli}.xml').is_file()
+}
+
+
+@pytest.mark.parametrize('cli', xmlList.keys())
+def testXMLParsing(cli, caplog):
+    import slicer_cli_web
+
+    slicer_cli_web.CLIArgumentParser(xmlList[cli])
+    for record in caplog.records:
+        assert record.levelname not in {'WARNING', 'ERROR'}