looper 2.0.1__py3-none-any.whl → 2.0.3__py3-none-any.whl

looper/_version.py

@@ -1,2 +1,2 @@
-__version__ = "2.0.1"
+__version__ = "2.0.3"
 # You must change the version in parser = pydantic_argparse.ArgumentParser in cli_pydantic.py!!!

looper/cli_pydantic.py

@@ -340,7 +340,7 @@ def main(test_args=None) -> dict:
         prog="looper",
         description="Looper: A job submitter for Portable Encapsulated Projects",
         add_help=True,
-        version="2.0.1",
+        version="2.0.3",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)

looper/conductor.py

@@ -662,6 +662,7 @@ class SubmissionConductor(object):
                 "config_file": psm.config_path,
                 "output_schema": psm.cfg["_schema_path"],
                 "pephub_path": psm.cfg["pephub_path"],
+                "flag_file_dir": psm.cfg["_config"].data.get("flag_file_dir"),
             }
             filtered_namespace = {k: v for k, v in full_namespace.items() if v}
             return YAMLConfigManager(filtered_namespace)

looper/project.py

@@ -553,6 +553,17 @@ class Project(peppyProject):
         except KeyError:
             flag_file_dir = None
 
+        try:
+            pephub_path = expandpath(pipestat_config_dict["pephub_path"])
+            if is_pephub_registry_path(pephub_path):
+                pipestat_config_dict.update({"pephub_path": pephub_path})
+            else:
+                _LOGGER.warning(
+                    msg=f"Warning: PEPhub path provided is NOT a PEPhub registry {pephub_path}"
+                )
+        except KeyError:
+            pephub_path = None
+
         # Pipestat_dict_ is now updated from all sources and can be written to a yaml.
         pipestat_config_path = os.path.join(
             output_dir,
@@ -889,11 +900,10 @@ def fetch_samples(
 
 
 def make_set(items):
-    try:
-        # Check if user input single integer value for inclusion/exclusion criteria
-        if len(items) == 1:
-            items = list(map(str, items))  # list(int(items[0]))
-    except:
-        if isinstance(items, str):
-            items = [items]
+    if isinstance(items, str):
+        items = [items]
+    elif len(items) == 1:
+        items = list(map(str, items))  # list(int(items[0]))
+    else:
+        pass
     return items

{looper-2.0.1.dist-info → looper-2.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: looper
-Version: 2.0.1
+Version: 2.0.3
 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
@@ -36,6 +36,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: summary
 

{looper-2.0.1.dist-info → looper-2.0.3.dist-info}/RECORD

@@ -1,9 +1,9 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
-looper/_version.py,sha256=DW9L8zOJPcNY9ZbgS_iQmVE_rIc1YpAHFt8cZRRXFZU,119
+looper/_version.py,sha256=Te42CMj8Eo19N4meF9piQ1i5pXJrVS5ew4-34m1pIRQ,119
 looper/cli_divvy.py,sha256=_VGbOFLkXtKdkZA6omlzgXbXkuUM5aLQ50aTTtbTrVI,5975
-looper/cli_pydantic.py,sha256=KS26gh_vF9fxjVpuBbI1K4sgokT1PWme4klwwcphLWQ,14423
-looper/conductor.py,sha256=EvVSZ9czG8-cRDLl2aXHZPeQ02J4xM0T_Y6mYO_2jTQ,35131
+looper/cli_pydantic.py,sha256=lyMG_B0f_9hLKy0nhpYiKn38zUAxAtw5WFMuf2xiHLQ,14423
+looper/conductor.py,sha256=aCbXhUrWq5q5wnaKWpBslQyRvFXADTvvoH1zvRjkudY,35210
 looper/const.py,sha256=eClmwc0c1r7zjQKrqBPa_OUOnoCqNNe0e64xElvLQHA,8701
 looper/divvy.py,sha256=KQSIxgeiFJf73c7xpAV8CoxUIuXjcfMphNWKSZXmuP0,15858
 looper/exceptions.py,sha256=-VEExHqjAtOSacBx45DA_9c-2i4EqxqGRLttTKxXXgg,3570
@@ -12,7 +12,7 @@ looper/parser_types.py,sha256=PgAdrtCGvXhXcX7UbW8E3oC414uv1mKV4sTnXVHtIzE,2325
 looper/pipeline_interface.py,sha256=NSAHx1ITmODy--Eh_b2oO4hP4mSHvs_7lkwuFLXbjsE,14535
 looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
 looper/processed_project.py,sha256=jZxoMYafvr-OHFxylc5ivGty1VwXBZhl0kgoFkY-174,9837
-looper/project.py,sha256=uoh8zGP4pdo630pcxLW5hdB5a2cP-YK8-CFd6F26Yus,34337
+looper/project.py,sha256=cV8MOyB7aLUiHRqecgnc058Z2Ov7ZqjhheZoiZ5yMRE,34677
 looper/utils.py,sha256=42YP5Qz41TDUW45ptDio_2w8f3iEi2judeBo9d5yJh0,39765
 looper/command_models/DEVELOPER.md,sha256=eRxnrO-vqNJjExzamXKEq5wr_-Zw6PQEwkS9RPinYrk,2775
 looper/command_models/README.md,sha256=3RGegeZlTZYnhcHXRu6bdI_81WZom2q7QYMV-KGYY7U,588
@@ -60,9 +60,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
 looper/schemas/pipeline_interface_schema_generic.yaml,sha256=3YfKFyRUIwxG41FEidR1dXe9IU6ye51LSUBfSpmMuss,1773
 looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
 looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
-looper-2.0.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-2.0.1.dist-info/METADATA,sha256=GPVKXrQreBCtmdWPvAiXb1Hci6InnMu3OgawD_IDcF0,1943
-looper-2.0.1.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-looper-2.0.1.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
-looper-2.0.1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-2.0.1.dist-info/RECORD,,
+looper-2.0.3.dist-info/licenses/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-2.0.3.dist-info/METADATA,sha256=21sNJtgpJtyVxV14yobD3ty65o-ZUpSyEg8hHUL_x3w,1965
+looper-2.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+looper-2.0.3.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
+looper-2.0.3.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-2.0.3.dist-info/RECORD,,

{looper-2.0.1.dist-info → looper-2.0.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.2)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any