looper 2.0.0a2__py3-none-any.whl → 2.0.1__py3-none-any.whl

looper/_version.py

@@ -1,2 +1,2 @@
-__version__ = "2.0.0a2"
+__version__ = "2.0.1"
 # 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="2.0.0a2",
+        version="2.0.1",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)

looper/command_models/__init__.py

@@ -1,6 +1,6 @@
 """
 This package holds `pydantic` models that describe commands and their arguments.
 
-These can be used either by an HTTP API or with the `pydantic-argparse` 
+These can be used either by an HTTP API or with the `pydantic-argparse`
 library to build a CLI.
 """

looper/command_models/arguments.py

@@ -184,6 +184,12 @@ class ArgumentEnum(enum.Enum):
         default=(str, None),
         description="Output directory",
     )
+    REPORT_OUTPUT_DIR = Argument(
+        name="report_dir",
+        alias="-r",
+        default=(str, None),
+        description="Set location for looper report and looper table outputs",
+    )
 
     GENERIC = Argument(
         name="generic",

looper/command_models/commands.py

@@ -124,7 +124,9 @@ RunProjectParser = Command(
 TableParser = Command(
     "table",
     MESSAGE_BY_SUBCOMMAND["table"],
-    [],
+    [
+        ArgumentEnum.REPORT_OUTPUT_DIR.value,
+    ],
 )
 
 
@@ -134,6 +136,7 @@ ReportParser = Command(
     MESSAGE_BY_SUBCOMMAND["report"],
     [
         ArgumentEnum.PORTABLE.value,
+        ArgumentEnum.REPORT_OUTPUT_DIR.value,
     ],
 )
 

looper/conductor.py

@@ -1,4 +1,4 @@
-""" Pipeline job submission orchestration """
+"""Pipeline job submission orchestration"""
 
 import importlib
 import logging
@@ -18,7 +18,7 @@ from eido import read_schema, get_input_files_size
 from eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY
 from jinja2.exceptions import UndefinedError
 
-from peppy.const import CONFIG_KEY, SAMPLE_NAME_ATTR, SAMPLE_YAML_EXT
+from peppy.const import CONFIG_KEY, SAMPLE_YAML_EXT
 from peppy.exceptions import RemoteYAMLError
 from pipestat import PipestatError
 from ubiquerg import expandpath
@@ -77,7 +77,7 @@ def _get_yaml_path(namespaces, template_key, default_name_appendix="", filename=
         # default YAML location
         f = (
             filename
-            or f"{namespaces['sample'][SAMPLE_NAME_ATTR]}"
+            or f"{namespaces['sample'][namespaces['sample']['_project'].sample_table_index]}"
             f"{default_name_appendix}"
             f"{SAMPLE_YAML_EXT[0]}"
         )

looper/const.py

@@ -1,4 +1,4 @@
-""" Shared project constants """
+"""Shared project constants"""
 
 import os
 from enum import Enum

looper/divvy.py

@@ -1,4 +1,4 @@
-""" Computing configuration representation """
+"""Computing configuration representation"""
 
 import logging
 import os
@@ -111,9 +111,12 @@ class ComputingConfiguration(YAMLConfigManager):
 
         :return str: path to folder with default submission templates
         """
-        return os.path.join(
-            os.path.dirname(__file__), "default_config", "divvy_templates"
-        )
+        if self.filepath:
+            return os.path.join(os.path.dirname(self.filepath), "divvy_templates")
+        else:
+            return os.path.join(
+                os.path.dirname(__file__), "default_config", "divvy_templates"
+            )
 
     def activate_package(self, package_name):
         """
@@ -155,11 +158,18 @@ class ComputingConfiguration(YAMLConfigManager):
             # but now, it makes more sense to do it here so we can piggyback on
             # the default update() method and not even have to do that.
             if not os.path.isabs(self.compute["submission_template"]):
+
                 try:
-                    self.compute["submission_template"] = os.path.join(
-                        os.path.dirname(self.default_config_file),
-                        self.compute["submission_template"],
-                    )
+                    if self.filepath:
+                        self.compute["submission_template"] = os.path.join(
+                            os.path.dirname(self.filepath),
+                            self.compute["submission_template"],
+                        )
+                    else:
+                        self.compute["submission_template"] = os.path.join(
+                            os.path.dirname(self.default_config_file),
+                            self.compute["submission_template"],
+                        )
                 except AttributeError as e:
                     # Environment and environment compute should at least have been
                     # set as null-valued attributes, so execution here is an error.

looper/exceptions.py

@@ -1,4 +1,4 @@
-""" Exceptions for specific looper issues. """
+"""Exceptions for specific looper issues."""
 
 from abc import ABCMeta
 from collections.abc import Iterable
@@ -15,6 +15,7 @@ _all__ = [
     "PipelineInterfaceConfigError",
     "PipelineInterfaceRequirementsError",
     "MisconfigurationException",
+    "LooperReportError",
 ]
 
 
@@ -109,3 +110,10 @@ class PipelineInterfaceRequirementsError(LooperError):
             )
         )
         self.error_specs = typename_by_requirement
+
+
+class LooperReportError(LooperError):
+    """Looper reporting errors"""
+
+    def __init__(self, reason):
+        super(LooperReportError, self).__init__(reason)

looper/looper.py

@@ -46,6 +46,7 @@ from .utils import (
     sample_folder,
 )
 from pipestat.reports import get_file_for_table
+from pipestat.exceptions import PipestatSummarizeError
 
 _PKGNAME = "looper"
 _LOGGER = logging.getLogger(_PKGNAME)
@@ -94,11 +95,19 @@ class Checker(Executor):
 
             for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
-                    psms[piface.psm.pipeline_name] = piface.psm
-                    s = piface.psm.get_status() or "unknown"
+                    if piface.psm.pipeline_name not in psms:
+                        psms[piface.psm.pipeline_name] = piface.psm
+            for pl_name, psm in psms.items():
+                all_project_level_records = psm.select_records()
+                for record in all_project_level_records["records"]:
+                    s = piface.psm.get_status(
+                        record_identifier=record["record_identifier"]
+                    )
                     status.setdefault(piface.psm.pipeline_name, {})
-                    status[piface.psm.pipeline_name][self.prj.name] = s
-                    _LOGGER.debug(f"{self.prj.name} ({piface.psm.pipeline_name}): {s}")
+                    status[piface.psm.pipeline_name][record["record_identifier"]] = s
+                    _LOGGER.debug(
+                        f"{self.prj.name} ({record['record_identifier']}): {s}"
+                    )
 
         else:
             for sample in self.prj.samples:
@@ -559,15 +568,26 @@ class Reporter(Executor):
 
         portable = args.portable
 
+        report_dir = getattr(args, "report_dir", None)
+
         psms = {}
 
         if project_level:
 
             for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
-                    psms[piface.psm.pipeline_name] = piface.psm
-                    report_directory = piface.psm.summarize(
-                        looper_samples=self.prj.samples, portable=portable
+                    if piface.psm.pipeline_name not in psms:
+                        psms[piface.psm.pipeline_name] = piface.psm
+            for pl_name, psm in psms.items():
+                try:
+                    report_directory = psm.summarize(
+                        looper_samples=self.prj.samples,
+                        portable=portable,
+                        output_dir=report_dir,
+                    )
+                except PipestatSummarizeError as e:
+                    raise LooperReportError(
+                        f"Looper report error due to the following exception: {e}"
                     )
                 print(f"Report directory: {report_directory}")
                 self.debug["report_directory"] = report_directory
@@ -575,12 +595,21 @@ class Reporter(Executor):
         else:
             for piface in self.prj.pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.SAMPLE.value:
-                    psms[piface.psm.pipeline_name] = piface.psm
-                    report_directory = piface.psm.summarize(
-                        looper_samples=self.prj.samples, portable=portable
+                    if piface.psm.pipeline_name not in psms:
+                        psms[piface.psm.pipeline_name] = piface.psm
+            for pl_name, psm in psms.items():
+                try:
+                    report_directory = psm.summarize(
+                        looper_samples=self.prj.samples,
+                        portable=portable,
+                        output_dir=report_dir,
+                    )
+                except PipestatSummarizeError as e:
+                    raise LooperReportError(
+                        f"Looper report error due to the following exception: {e}"
                     )
-                    print(f"Report directory: {report_directory}")
-                    self.debug["report_directory"] = report_directory
+                print(f"Report directory: {report_directory}")
+                self.debug["report_directory"] = report_directory
             return self.debug
 
 
@@ -618,18 +647,23 @@ class Tabulator(Executor):
     def __call__(self, args):
         # p = self.prj
         project_level = getattr(args, "project", None)
+        report_dir = getattr(args, "report_dir", None)
         results = []
         psms = {}
         if project_level:
             for piface in self.prj.project_pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.PROJECT.value:
-                    psms[piface.psm.pipeline_name] = piface.psm
-                    results = piface.psm.table()
+                    if piface.psm.pipeline_name not in psms:
+                        psms[piface.psm.pipeline_name] = piface.psm
+            for pl_name, psm in psms.items():
+                results = psm.table(output_dir=report_dir)
         else:
             for piface in self.prj.pipeline_interfaces:
                 if piface.psm.pipeline_type == PipelineLevel.SAMPLE.value:
-                    psms[piface.psm.pipeline_name] = piface.psm
-                    results = piface.psm.table()
+                    if piface.psm.pipeline_name not in psms:
+                        psms[piface.psm.pipeline_name] = piface.psm
+            for pl_name, psm in psms.items():
+                results = psm.table(output_dir=report_dir)
         # Results contains paths to stats and object summaries.
         return results
 

looper/parser_types.py

@@ -1,4 +1,4 @@
-""" Definitions of the parser argument types """
+"""Definitions of the parser argument types"""
 
 from yacman import YAMLConfigManager
 

looper/pipeline_interface.py

@@ -1,4 +1,4 @@
-""" Model the connection between a pipeline and a project or executor. """
+"""Model the connection between a pipeline and a project or executor."""
 
 import os
 from collections.abc import Mapping

looper/project.py

@@ -1,4 +1,4 @@
-""" Looper version of NGS project model. """
+"""Looper version of NGS project model."""
 
 import itertools
 import os

looper/utils.py

@@ -1,4 +1,4 @@
-""" Helpers without an obvious logical home. """
+"""Helpers without an obvious logical home."""
 
 import argparse
 from collections import defaultdict
@@ -1112,7 +1112,6 @@ def inspect_looper_config_file(looper_config_dict) -> None:
 
 
 def expand_nested_var_templates(var_templates_dict, namespaces):
-
     "Takes all var_templates as a dict and recursively expands any paths."
 
     result = {}
@@ -1127,7 +1126,6 @@ def expand_nested_var_templates(var_templates_dict, namespaces):
 
 
 def render_nested_var_templates(var_templates_dict, namespaces):
-
     "Takes all var_templates as a dict and recursively renders the jinja templates."
 
     result = {}

{looper-2.0.0a2.dist-info → looper-2.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: looper
-Version: 2.0.0a2
+Version: 2.0.1
 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
@@ -16,19 +16,28 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: colorama>=0.3.9
-Requires-Dist: eido>=0.2.3
+Requires-Dist: eido>=0.2.4
 Requires-Dist: jinja2
 Requires-Dist: logmuse>=0.2.0
 Requires-Dist: pandas>=2.0.2
 Requires-Dist: pephubclient>=0.4.0
-Requires-Dist: pipestat>=0.10.2
+Requires-Dist: pipestat>=0.12.0a1
 Requires-Dist: peppy>=0.40.6
 Requires-Dist: pyyaml>=3.12
 Requires-Dist: rich>=9.10.0
-Requires-Dist: ubiquerg>=0.8.1a1
+Requires-Dist: ubiquerg>=0.8.1
 Requires-Dist: yacman==0.9.3
 Requires-Dist: pydantic-argparse>=0.9.0
 Requires-Dist: psutil
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 # <img src="docs/img/looper_logo.svg" alt="looper logo" height="70">
 

{looper-2.0.0a2.dist-info → looper-2.0.1.dist-info}/RECORD

@@ -1,24 +1,24 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=OOCmI-dPUvInnJHkHNMf54cblNJ3Yl9ELOwZcfOXmD8,240
-looper/_version.py,sha256=mX3fglKqsJRTjP938X3Xm2eAJT9fve28fdydFnJFimc,121
+looper/_version.py,sha256=DW9L8zOJPcNY9ZbgS_iQmVE_rIc1YpAHFt8cZRRXFZU,119
 looper/cli_divvy.py,sha256=_VGbOFLkXtKdkZA6omlzgXbXkuUM5aLQ50aTTtbTrVI,5975
-looper/cli_pydantic.py,sha256=uysPJfTrfG7-k7u6oDpaLG-3hD6U8YVrDiOW54ySniI,14425
-looper/conductor.py,sha256=lzY6Gzsb8oX-KLzLkRa0XrYWSxLeiy6jRmmD15WNAkw,35116
-looper/const.py,sha256=OscEELQsyLKlSrmwuXfyLRwpAUJUEpGD2UxBeLJDXgw,8703
-looper/divvy.py,sha256=eiYhcp8ZgQ0uzlk0c5yJp0QaiVrQYfSeEtmQBJiScOM,15417
-looper/exceptions.py,sha256=AxYCTLxKb_fJFgU9VBnPYaRX2lGhmMEYaCbJOi-27Wk,3384
-looper/looper.py,sha256=ZWTulMz6NobnYFUjev513TJwXqknrb4_gZrV-a_fT9g,30041
-looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
-looper/pipeline_interface.py,sha256=mN4-XICyZzuVLTOq3b0ijppYe6ib_Ljlyf6KxZCJh2A,14537
+looper/cli_pydantic.py,sha256=KS26gh_vF9fxjVpuBbI1K4sgokT1PWme4klwwcphLWQ,14423
+looper/conductor.py,sha256=EvVSZ9czG8-cRDLl2aXHZPeQ02J4xM0T_Y6mYO_2jTQ,35131
+looper/const.py,sha256=eClmwc0c1r7zjQKrqBPa_OUOnoCqNNe0e64xElvLQHA,8701
+looper/divvy.py,sha256=KQSIxgeiFJf73c7xpAV8CoxUIuXjcfMphNWKSZXmuP0,15858
+looper/exceptions.py,sha256=-VEExHqjAtOSacBx45DA_9c-2i4EqxqGRLttTKxXXgg,3570
+looper/looper.py,sha256=zNszsV50ZkC5ioaLHgMg9H3hSTEHAAV-jBpLra3OIKw,31624
+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=SFHdi58eRBWtye5lUFhwzBcG7ejrMurmDzmkrC3XAic,34339
-looper/utils.py,sha256=-4QlScIB7eewIbmEJdAv2d0ZE0qr_q9acm2XUOiMEek,39769
+looper/project.py,sha256=uoh8zGP4pdo630pcxLW5hdB5a2cP-YK8-CFd6F26Yus,34337
+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
-looper/command_models/__init__.py,sha256=6QWC2TewowEL7dATli5YpMmFWuXaLEPktofJCXkYUBI,187
-looper/command_models/arguments.py,sha256=wGGc5tleHC31F0etbiYaumHwP5xlJsSXapJ10lhltHg,8830
-looper/command_models/commands.py,sha256=RMTiHg0txBGDb_fHfhTWujP3VnnB6ROCHqByiwgMS4c,9716
+looper/command_models/__init__.py,sha256=suzlc6tiNFQlv9b--aZdE9uyklTcKQ_z4YGyLfO0Ru0,186
+looper/command_models/arguments.py,sha256=I9IUdDcklfctA9gdYvxyy29WawSCYPO5FwozgisCO94,9025
+looper/command_models/commands.py,sha256=nBD8uOxpjby2G0n-PuMKvRBM6m5tra_Mz_nlZALwmRE,9813
 looper/default_config/divvy_config.yaml,sha256=wK5kLDGBV2wwoyqg2rl3X8SXjds4x0mwBUjUzF1Ln7g,1705
 looper/default_config/divvy_templates/localhost_bulker_template.sub,sha256=yn5VB9Brt7Hck9LT17hD2o8Kn-76gYJQk_A-8C1Gr4k,164
 looper/default_config/divvy_templates/localhost_docker_template.sub,sha256=XRr7AlR7-TP1L3hyBMfka_RgWRL9vzOlS5Kd1xSNwT0,183
@@ -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-2.0.0a2.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-2.0.0a2.dist-info/METADATA,sha256=s4IlCgd597EhgR8H0LIB-3Qz02absf63sudpuFG1rKM,1760
-looper-2.0.0a2.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-looper-2.0.0a2.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
-looper-2.0.0a2.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-2.0.0a2.dist-info/RECORD,,
+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-2.0.0a2.dist-info → looper-2.0.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any