[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -15,13 +15,13 @@ repos:
       - id: check-json
   # spell check
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
       - id: codespell
         args: [-I, .github/WORDLIST]
   # Python formatting
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.16.8
     hooks:
       - id: ruff-check
         args: [--fix]

src/galaxysynth/galaxy_xml_synthesizer.py

@@ -3,17 +3,17 @@
 Galaxy XML Synthesizer - Generates Galaxy tool XML from blueprint JSON files.
 """
 
-import json
-import xml.etree.ElementTree as ET
-from xml.dom import minidom
-from pathlib import Path
-from typing import Dict, List, Any, Optional
 import argparse
+import json
 import os
 import re
-import sys
 import subprocess
+import sys
+import xml.etree.ElementTree as ET
 from collections import OrderedDict
+from pathlib import Path
+from typing import Any
+from xml.dom import minidom
 
 from .util import get_version, match_semver
 
@@ -35,7 +35,7 @@ class GalaxyXMLSynthesizer:
 
     def __init__(
         self,
-        blueprint: Dict[str, Any],
+        blueprint: dict[str, Any],
         docker_image: str = "nciccbr/mosuite:latest",
         citation_doi: str = "10.5281/zenodo.16371580",
         repo_name: str = "CCBR/MOSuite-Galaxy",
@@ -112,7 +112,7 @@ def _clean_text(self, text: str) -> str:
         text = text.replace("\\n", " ")
         return text.strip()
 
-    def _extract_docker_tag(self, docker_image: str) -> Optional[str]:
+    def _extract_docker_tag(self, docker_image: str) -> str | None:
         """Grab the tag portion from the docker image string."""
         if not docker_image:
             return None
@@ -125,10 +125,10 @@ def _extract_docker_tag(self, docker_image: str) -> Optional[str]:
         # No explicit tag present; assume latest
         return "latest"
 
-    def _get_git_short_sha(self) -> Optional[str]:
+    def _get_git_short_sha(self) -> str | None:
         """Return short git SHA using repo root, cwd, then GITHUB_SHA fallback."""
 
-        def normalize_short_sha(value: Optional[str]) -> Optional[str]:
+        def normalize_short_sha(value: str | None) -> str | None:
             if not value:
                 return None
             candidate = value.strip()
@@ -166,7 +166,7 @@ def _add_sanitizer(
         self,
         param: ET.Element,
         param_key: str,
-        custom_config: Optional[Dict[str, Any]] = None,
+        custom_config: dict[str, Any] | None = None,
     ):
         """
         Add sanitizer configuration to a parameter.
@@ -275,7 +275,7 @@ def _add_command(self, tool: ET.Element, tool_id: str):
         command.set("detect_errors", "exit_code")
         command.text = f"<![CDATA[{full_command}]]>"
 
-    def _group_parameters(self) -> Dict[Optional[str], List[Dict]]:
+    def _group_parameters(self) -> dict[str | None, list[dict]]:
         """Group parameters by their paramGroup field."""
         groups = OrderedDict()
 
@@ -421,7 +421,7 @@ def _add_inputs(self, tool: ET.Element):
                 elif item_type == "column":
                     self._add_column(section, item)
 
-    def _add_dataset_param(self, parent: ET.Element, dataset: Dict[str, Any]):
+    def _add_dataset_param(self, parent: ET.Element, dataset: dict[str, Any]):
         """Add dataset parameter."""
         param = ET.SubElement(parent, "param")
         param.set("name", dataset["key"])
@@ -441,7 +441,7 @@ def _add_dataset_param(self, parent: ET.Element, dataset: Dict[str, Any]):
         if dataset.get("description"):
             param.set("help", dataset["description"])
 
-    def _add_parameter(self, parent: ET.Element, param_def: Dict[str, Any]):
+    def _add_parameter(self, parent: ET.Element, param_def: dict[str, Any]):
         """Add parameter based on type with proper datatype handling and sanitizer support."""
         param_type = param_def.get("paramType", "STRING")
         param_key = param_def.get("key")
@@ -599,7 +599,7 @@ def _add_parameter(self, parent: ET.Element, param_def: Dict[str, Any]):
             # Check if this STRING parameter needs special sanitizer
             self._add_sanitizer(param, param_key, sanitizer_config)
 
-    def _add_column(self, parent: ET.Element, column: Dict[str, Any]):
+    def _add_column(self, parent: ET.Element, column: dict[str, Any]):
         """Add column parameter - using repeat for multi-value columns with sanitizer support."""
         param_key = column.get("key")
         display_name = column.get("displayName", param_key)

src/galaxysynth/util.py

@@ -2,8 +2,8 @@
 Utility functions for the package
 """
 
-import re
 import pathlib
+import re
 
 
 def repo_base(*paths):

templates/3_galaxy-tools/batch_correction.xml

@@ -111,7 +111,7 @@ Perform batch correction using sva::ComBat()
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/clean_raw_counts.xml

@@ -108,7 +108,7 @@ corrected. If your sample names are corrected here, be sure to make equivalent c
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/create_multi-omic_dataset_from_files.xml

@@ -61,7 +61,7 @@ Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/differential_analysis.xml

@@ -105,7 +105,7 @@ Differential expression analysis
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/filter_differential_features.xml

@@ -158,7 +158,7 @@ estimates and for sub-setting of contrasts and groups included in the output gen
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/filter_low_counts.xml

@@ -198,7 +198,7 @@ another based on unsupervised clustering.
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/normalization.xml

@@ -177,7 +177,7 @@ Normalize counts
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/pca_2d.xml

@@ -172,7 +172,7 @@ Perform and plot a 2D Principal Components Analysis
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/pca_3d.xml

@@ -151,7 +151,7 @@ Runs `MOSuite::plot_pca_3d()` - https://ccbr.github.io/MOSuite/reference/plot_pc
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/plot_expression_heatmap.xml

@@ -244,7 +244,7 @@ this heatmap if you explore the advanced options.
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/plot_volcano_-_enhanced.xml

@@ -127,7 +127,7 @@ list(list("https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.h
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/plot_volcano_-_summary.xml

@@ -4777,7 +4777,7 @@ useful to the Venn diagram template downstream.
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/venn_diagram.xml

@@ -874,7 +874,7 @@ specified intersections.
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

templates/3_galaxy-tools/write_multiomicdataset_properties.xml

@@ -56,7 +56,7 @@ Properties that are data frames are saved as CSV files, while all other objects
 **Version info**
 
 - Docker: nciccbr/mosuite:v0.3.0
-- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/fa69b26)
+- GitHub: [CCBR/MOSuite-Galaxy 0.1.0-alpha](https://github.com/CCBR/MOSuite-Galaxy/tree/b40e00d)
 
 ]]></help>
     <citations>

tests/test_cli.py

@@ -1,7 +1,7 @@
 # tests/test_cli.py
+import shutil
 import subprocess
 import sys
-import shutil
 
 from galaxysynth.util import get_version
 

tests/test_format_values.py

@@ -14,22 +14,23 @@
 """
 
 import json
-import pytest
 import sys
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from unittest.mock import patch
 
+import pytest
+
 # Import the format_values module
 sys.path.insert(0, str(Path(__file__).parent.parent / "templates" / "3_galaxy-tools"))
 from format_values import (
-    normalize_boolean,
     extract_list_from_repeat,
-    parse_delimited_text,
-    inject_output_configuration,
-    process_galaxy_params,
     flatten_json,
+    inject_output_configuration,
     main,
+    normalize_boolean,
+    parse_delimited_text,
+    process_galaxy_params,
 )
 
 

tests/test_galaxy_xml_synthesizer.py

@@ -12,17 +12,18 @@
 - Edge cases
 """
 
-import pytest
 import json
 import xml.etree.ElementTree as ET
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from unittest.mock import patch
 
+import pytest
+
 from galaxysynth.galaxy_xml_synthesizer import (
     GalaxyXMLSynthesizer,
-    process_blueprint,
     batch_process,
+    process_blueprint,
 )
 
 
@@ -572,8 +573,8 @@ def test_generate_help_release_links_to_version_tag(self):
         class _MatchNoPrerelease:
             def group(self, name):
                 if name == "prerelease":
-                    return None
-                return None
+                    return
+                return
 
         synth = GalaxyXMLSynthesizer(
             {
@@ -647,8 +648,8 @@ def test_generate_help_without_git_sha_uses_plain_text(self):
         class _MatchNoPrerelease:
             def group(self, name):
                 if name == "prerelease":
-                    return None
-                return None
+                    return
+                return
 
         synth = GalaxyXMLSynthesizer(
             {

tests/test_needs_regeneration.py

@@ -9,12 +9,13 @@
 - Edge cases and error handling
 """
 
-import pytest
 import json
+import time
 import xml.etree.ElementTree as ET
 from pathlib import Path
 from tempfile import TemporaryDirectory
-import time
+
+import pytest
 
 from galaxysynth.galaxy_xml_synthesizer import (
     needs_regeneration,