fix accessing looper.pep_config #424, add building out looper namespa…

…ce based on config file #423
pepkit · Oct 23, 2023 · 99d2a8f · 99d2a8f
1 parent d99ad5f
commit 99d2a8f
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/looper/cli_looper.py b/looper/cli_looper.py
@@ -643,6 +643,7 @@ def main(test_args=None):
                 project_dict=PEPHubClient()._load_raw_pep(
                     registry_path=args.config_file
                 ),
+                pep_config=args.config_file,
                 **{
                     attr: getattr(args, attr) for attr in CLI_PROJ_ATTRS if attr in args
                 },

diff --git a/looper/conductor.py b/looper/conductor.py
@@ -470,7 +470,9 @@ def _build_looper_namespace(self, pool, size):
         :return yacman.YAMLConfigManager: looper/submission related settings
         """
         settings = YAMLConfigManager()
-        settings["pep_config"] = self.prj.config_file
+        settings["config_file"] = self.prj.config_file
+        settings["pep_config"] = self.prj.pep_config
+
         settings[RESULTS_SUBDIR_KEY] = self.prj.results_folder
         settings[SUBMISSION_SUBDIR_KEY] = self.prj.submission_folder
         settings[OUTDIR_KEY] = self.prj.output_dir

diff --git a/looper/project.py b/looper/project.py
@@ -106,11 +106,13 @@ def __init__(
     ):
         super(Project, self).__init__(cfg=cfg, amendments=amendments)
         prj_dict = kwargs.get("project_dict")
+        pep_config = kwargs.get("pep_config", None)
 
-        # init project from pephub:
+        # init project from pephub pep_config:
         if prj_dict is not None and cfg is None:
             self.from_dict(prj_dict)
-            self["_config_file"] = os.getcwd()
+            self["_config_file"] = os.getcwd()  # for finding pipeline interface
+            self["pep_config"] = pep_config
 
         self[EXTRA_KEY] = {}
 

diff --git a/looper/utils.py b/looper/utils.py
@@ -473,9 +473,6 @@ 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_KEY] = dp_data[PEP_CONFIG_KEY]
         return_dict[PEP_CONFIG_FILE_KEY] = dp_data[PEP_CONFIG_KEY]
 
     # TODO: delete it in looper 2.0