fix pep_config not populating during runp

pepkit · Nov 30, 2023 · bd1bd85 · bd1bd85
1 parent c9521e8
commit bd1bd85
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Showing 3 changed files with 7 additions and 0 deletions.
diff --git a/looper/const.py b/looper/const.py
@@ -219,6 +219,7 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
 SAMPLE_PL_ARG = "sample_pipeline_interfaces"
 PROJECT_PL_ARG = "project_pipeline_interfaces"
 
+
 DEFAULT_CFG_PATH = os.path.join(os.getcwd(), LOOPER_DOTFILE_NAME)
 CLI_PROJ_ATTRS = [
     OUTDIR_KEY,
@@ -232,6 +233,7 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
     SAMPLE_PL_ARG,
     PIPESTAT_KEY,
     DEFAULT_PIPESTAT_CONFIG_ATTR,
+    PEP_CONFIG_KEY,
 ]
 
 # resource package TSV-related consts

diff --git a/looper/project.py b/looper/project.py
@@ -107,6 +107,8 @@ def __init__(
         super(Project, self).__init__(cfg=cfg, amendments=amendments)
         prj_dict = kwargs.get("project_dict")
         pep_config = kwargs.get("pep_config", None)
+        if pep_config:
+            self["pep_config"] = pep_config
 
         # init project from pephub pep_config:
         if prj_dict is not None and cfg is None:

diff --git a/looper/utils.py b/looper/utils.py
@@ -473,7 +473,10 @@ def read_looper_config_file(looper_config_path: str) -> dict:
         dp_data = yaml.safe_load(dotfile)
 
     if PEP_CONFIG_KEY in dp_data:
+        # Looper expects the config path to live at looper.config_file
+        # However, user may wish to access the pep at looper.pep_config
         return_dict[PEP_CONFIG_FILE_KEY] = dp_data[PEP_CONFIG_KEY]
+        return_dict[PEP_CONFIG_KEY] = dp_data[PEP_CONFIG_KEY]
 
     # TODO: delete it in looper 2.0
     elif DOTFILE_CFG_PTH_KEY in dp_data: