looper 1.6.0a1__py3-none-any.whl → 1.6.0a3__py3-none-any.whl

looper/_version.py

@@ -1 +1 @@
-__version__ = "1.6.0a1"
+__version__ = "1.6.0a3"

looper/cli_looper.py

@@ -495,6 +495,12 @@ def build_parser():
             help="Number of attributes to display",
             type=int,
         )
+        parser.add_argument(
+            "--commands",
+            action="version",
+            version="{}".format(" ".join(subparsers.choices.keys())),
+        )
+
         result.append(parser)
     return result
 

looper/project.py

@@ -111,9 +111,7 @@ class Project(peppyProject):
         compute settings.
     """
 
-    def __init__(
-        self, cfg=None, amendments=None, divcfg_path=None, runp=False, **kwargs
-    ):
+    def __init__(self, cfg=None, amendments=None, divcfg_path=None, **kwargs):
         super(Project, self).__init__(cfg=cfg, amendments=amendments)
         prj_dict = kwargs.get("project_dict")
         pep_config = kwargs.get("pep_config", None)
@@ -122,7 +120,7 @@ class Project(peppyProject):
 
         # init project from pephub pep_config:
         if prj_dict is not None and cfg is None:
-            self.from_dict(prj_dict)
+            self._from_dict(prj_dict)
             self["_config_file"] = os.getcwd()  # for finding pipeline interface
             self["pep_config"] = pep_config
 
@@ -916,7 +914,7 @@ def make_set(items):
     try:
         # Check if user input single integer value for inclusion/exclusion criteria
         if len(items) == 1:
-            items = list(map(int, items))  # list(int(items[0]))
+            items = list(map(str, items))  # list(int(items[0]))
     except:
         if isinstance(items, str):
             items = [items]

{looper-1.6.0a1.dist-info → looper-1.6.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: looper
-Version: 1.6.0a1
+Version: 1.6.0a3
 Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
 Home-page: https://github.com/pepkit/looper
 Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
@@ -23,7 +23,7 @@ Requires-Dist: logmuse >=0.2.0
 Requires-Dist: pandas >=2.0.2
 Requires-Dist: pephubclient >=0.1.2
 Requires-Dist: peppy >=0.40.0.a4
-Requires-Dist: pipestat >=v0.6.0a9
+Requires-Dist: pipestat >=0.6.0a9
 Requires-Dist: pyyaml >=3.12
 Requires-Dist: rich >=9.10.0
 Requires-Dist: ubiquerg >=0.5.2

{looper-1.6.0a1.dist-info → looper-1.6.0a3.dist-info}/RECORD

@@ -1,8 +1,8 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=8CX2ae8mUQNI_Z8pdBT4i5UFqROFX1awyFnuYCKuYXg,238
-looper/_version.py,sha256=UG64J_OfEJF5nBy02cxP-9wbnmfesoV9F5GvRWXpSfM,24
+looper/_version.py,sha256=XJ3CHO0NspbDhCNVnNqwEtFi_KpbeDM87P9-mGN9EXs,24
 looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
-looper/cli_looper.py,sha256=0SYyPAPg8MEGOnp_vjn0Mxohe7Annr56hwDBX_DqM5U,25769
+looper/cli_looper.py,sha256=unoNK8gtOg5r5T4vVhonoykegc7LzxCaxPPJfETon-g,25935
 looper/conductor.py,sha256=BmMATwtkHoPSsffYopCQ1WxK83O3UjOTFRrakgD6DzA,30231
 looper/const.py,sha256=bPj4lTuj2l6gwHROWqj16iHfJFo9ghZAz8THNREWW4U,8558
 looper/divvy.py,sha256=qa1ebbQTfNupAyDfhfEJ6mbZ_V3zk-D_E-Tck7miJ38,15688
@@ -12,7 +12,7 @@ looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
 looper/pipeline_interface.py,sha256=y46tB1_73d1FX8N1w4-GGvRBJ7rqhenuUYVtUfIhK5s,14974
 looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
 looper/processed_project.py,sha256=jZxoMYafvr-OHFxylc5ivGty1VwXBZhl0kgoFkY-174,9837
-looper/project.py,sha256=Ldsa__wLNnDpKFfN0cOCWQnL-pTuVrPbbHJPHFt9fcU,36196
+looper/project.py,sha256=nkNP7ftVs82Tnk2Yn6FUp60_D6bjE9sSvySE0SHqsmg,36171
 looper/utils.py,sha256=i7srIXPEnQjtNaoP0ziRpdYfB7HNY5_3rW5LoKIM15I,27257
 looper/default_config/divvy_config.yaml,sha256=wK5kLDGBV2wwoyqg2rl3X8SXjds4x0mwBUjUzF1Ln7g,1705
 looper/default_config/divvy_templates/localhost_bulker_template.sub,sha256=yn5VB9Brt7Hck9LT17hD2o8Kn-76gYJQk_A-8C1Gr4k,164
@@ -55,9 +55,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
 looper/schemas/pipeline_interface_schema_generic.yaml,sha256=D16Rkpj03H9WnvA_N18iNU-hH_HwOuyESJ8Hk5hZSXc,1518
 looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
 looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
-looper-1.6.0a1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-1.6.0a1.dist-info/METADATA,sha256=apZ1c5_AxHNy1MxlLtOxGrXRZzG3tYlvWFzZQKMw3kU,1741
-looper-1.6.0a1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-looper-1.6.0a1.dist-info/entry_points.txt,sha256=AEL1eb0gPLYvAEUewM35Ng4scXGZIWJK4Mxdj3Hm8Fw,83
-looper-1.6.0a1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-1.6.0a1.dist-info/RECORD,,
+looper-1.6.0a3.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-1.6.0a3.dist-info/METADATA,sha256=lA597TjPwGmRcOQI1iaK-G5uYld4h5XXbX6zDQkYY5o,1740
+looper-1.6.0a3.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+looper-1.6.0a3.dist-info/entry_points.txt,sha256=AEL1eb0gPLYvAEUewM35Ng4scXGZIWJK4Mxdj3Hm8Fw,83
+looper-1.6.0a3.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-1.6.0a3.dist-info/RECORD,,