From 93e8d31848658cc45b8c76199bc63ea4c78d4465 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Wed, 19 Jun 2024 11:34:47 -0400
Subject: [PATCH] use deep_update for sample modifiers, bump ubiquerg version
 req

---
 looper/project.py                 | 10 ++++++----
 requirements/requirements-all.txt |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/looper/project.py b/looper/project.py
index e070233e..f8a4c7d6 100644
--- a/looper/project.py
+++ b/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)
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index bd28baa8..b7fd60ad 100644
--- a/requirements/requirements-all.txt
+++ b/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
\ No newline at end of file