Support refgenconf 0.13.0

lib/galaxy/tools/data/__init__.py

@@ -116,7 +116,7 @@ class RefgenieToolDataTable(TabularToolDataTable):
 
     def parse_file_fields(self, filename, errors=None, here="__HERE__"):
         try:
-            rgc = refgenconf.RefGenConf(filename, writable=False, skip_read_lock=True)
+            rgc = refgenconf.RefGenConf.from_yaml_file(filename)
         except refgenconf.exceptions.RefgenconfError as e:
             log.error('Unable to load refgenie config file "%s": %s', filename, e)
             if errors is not None:

packages/app/setup.cfg

@@ -72,7 +72,7 @@ install_requires =
     python-slugify
     PyJWT
     PyYAML
-    refgenconf>=0.12.0
+    refgenconf>=0.13.0
     regex
     requests
     SQLAlchemy>=2.0.37,<2.1,!=2.0.41

pyproject.toml

@@ -88,7 +88,7 @@ dependencies = [
     "python-multipart",  # required to support form parsing in FastAPI/Starlette
     "python-slugify",
     "PyYAML",
-    "refgenconf>=0.12.0",
+    "refgenconf>=0.13.0",  # https://github.com/refgenie/refgenconf/pull/149
     "regex",
     "requests",
     "rocrate",