use deep_update for sample modifiers, bump ubiquerg version req

looper/project.py

@@ -20,7 +20,7 @@
 from peppy import Project as peppyProject
 from peppy.utils import make_abs_via_cfg
 from pipestat import PipestatError, PipestatManager
-from ubiquerg import expandpath, is_command_callable
+from ubiquerg import expandpath, is_command_callable, deep_update
 from yacman import YAMLConfigManager
 from .conductor import write_pipestat_config
 
@@ -138,10 +138,12 @@ def __init__(self, cfg=None, amendments=None, divcfg_path=None, **kwargs):
         # add sample pipeline interface to the project
         if kwargs.get(SAMPLE_MODS_KEY) and self._modifier_exists():
             _LOGGER.warning(
-                "Sample modifiers were provided in Looper config. Overwriting those in  PEP."
+                "Sample modifiers were provided in Looper Config and in PEP Project Config. Merging..."
+            )
+            deep_update(self.config["sample_modifiers"], kwargs.get(SAMPLE_MODS_KEY))
+            _LOGGER.debug(
+                msg=f"Merged sample modifiers: {self.config['sample_modifiers']}"
             )
-            self.config.setdefault("sample_modifiers", {})
-            self.config["sample_modifiers"] = kwargs.get(SAMPLE_MODS_KEY)
         elif kwargs.get(SAMPLE_MODS_KEY):
             self.config.setdefault("sample_modifiers", {})
             self.config["sample_modifiers"] = kwargs.get(SAMPLE_MODS_KEY)

requirements/requirements-all.txt

@@ -9,7 +9,7 @@ pipestat>=0.9.2
 peppy>=0.40.2
 pyyaml>=3.12
 rich>=9.10.0
-ubiquerg>=0.5.2
+ubiquerg>=0.8.1
 yacman==0.9.3
 pydantic2-argparse>=0.9.2
 psutil