looper 2.0.0a1__py3-none-any.whl → 2.0.0a3__py3-none-any.whl

looper/_version.py

@@ -1,2 +1,2 @@
-__version__ = "2.0.0a1"
+__version__ = "2.0.0a3"
 # You must change the version in parser = pydantic_argparse.ArgumentParser in cli_pydantic.py!!!

looper/cli_divvy.py

@@ -53,10 +53,10 @@ def build_argparser():
 
     for sp in [sps["list"], sps["write"], sps["submit"], sps["inspect"]]:
         sp.add_argument(
-            "config", nargs="?", default=None, help="Divvy configuration file."
+            "--config", nargs="?", default=None, help="Divvy configuration file."
         )
 
-    sps["init"].add_argument("config", default=None, help="Divvy configuration file.")
+    sps["init"].add_argument("--config", default=None, help="Divvy configuration file.")
 
     for sp in [sps["inspect"]]:
         sp.add_argument(
@@ -124,9 +124,11 @@ def main():
         sys.exit(0)
 
     _LOGGER.debug("Divvy config: {}".format(args.config))
+
     divcfg = select_divvy_config(args.config)
+
     _LOGGER.info("Using divvy config: {}".format(divcfg))
-    dcc = ComputingConfiguration(filepath=divcfg)
+    dcc = ComputingConfiguration.from_yaml_file(filepath=divcfg)
 
     if args.command == "list":
         # Output header via logger and content via print so the user can
@@ -142,11 +144,13 @@ def main():
         for pkg_name, pkg in dcc.compute_packages.items():
             if pkg_name == args.package:
                 found = True
-                with open(pkg.submission_template, "r") as f:
+                with open(pkg["submission_template"], "r") as f:
                     print(f.read())
-                _LOGGER.info("Submission command is: " + pkg.submission_command + "\n")
+                _LOGGER.info(
+                    "Submission command is: " + pkg["submission_command"] + "\n"
+                )
                 if pkg_name == "docker":
-                    print("Docker args are: " + pkg.docker_args)
+                    print("Docker args are: " + pkg["docker_args"])
 
         if not found:
             _LOGGER.info("Package not found. Use 'divvy list' to see list of packages.")

looper/cli_pydantic.py

@@ -26,8 +26,6 @@ from eido import inspect_project
 from pephubclient import PEPHubClient
 from pydantic_argparse.argparse.parser import ArgumentParser
 
-from divvy import select_divvy_config
-
 from . import __version__
 
 from .command_models.arguments import ArgumentEnum
@@ -128,15 +126,8 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         console = Console()
         console.clear()
         console.rule(f"\n[magenta]Looper initialization[/magenta]")
-        console.print(
-            "[bold]Would you like to follow a guided tutorial?[/bold]  [green]Y[/green] / [red]n[/red]..."
-        )
-
-        selection = None
-        while selection not in ["y", "n"]:
-            selection = console.input("\nSelection: ").lower().strip()
-
-        if selection == "n":
+        selection = subcommand_args.generic
+        if selection is True:
             console.clear()
             return int(
                 not initiate_looper_config(
@@ -172,11 +163,14 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
             else:
                 setattr(subcommand_args, looper_config_key, looper_config_item)
 
-    except OSError:
-        parser.print_help(sys.stderr)
-        _LOGGER.warning(
-            f"Looper config file does not exist. Use looper init to create one at {looper_cfg_path}."
-        )
+    except OSError as e:
+        if subcommand_args.config:
+            _LOGGER.warning(
+                f"\nLooper config file does not exist at given path {subcommand_args.config}. Use looper init to create one at {looper_cfg_path}."
+            )
+        else:
+            _LOGGER.warning(e)
+
         sys.exit(1)
 
     subcommand_args = enrich_args_via_cfg(
@@ -225,7 +219,7 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
                 amendments=subcommand_args.amend,
                 divcfg_path=divcfg,
                 runp=subcommand_name == "runp",
-                project_dict=PEPHubClient()._load_raw_pep(
+                project_dict=PEPHubClient().load_raw_pep(
                     registry_path=subcommand_args.pep_config
                 ),
                 **{
@@ -340,13 +334,13 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
                 _LOGGER.warning("No looper configuration was supplied.")
 
 
-def main(test_args=None) -> None:
+def main(test_args=None) -> dict:
     parser = pydantic_argparse.ArgumentParser(
         model=TopLevelParser,
         prog="looper",
         description="Looper: A job submitter for Portable Encapsulated Projects",
         add_help=True,
-        version="2.0.0a1",
+        version="2.0.0a3",
     )
 
     parser = add_short_arguments(parser, ArgumentEnum)
@@ -359,6 +353,10 @@ def main(test_args=None) -> None:
     return run_looper(args, parser, test_args=test_args)
 
 
+def main_cli() -> None:
+    main()
+
+
 def _proc_resources_spec(args):
     """
     Process CLI-sources compute setting specification. There are two sources
@@ -385,20 +383,29 @@ def _proc_resources_spec(args):
         settings_data = {}
     if not spec:
         return settings_data
-    pairs = [(kv, kv.split("=")) for kv in spec]
-    bads = []
-    for orig, pair in pairs:
-        try:
-            k, v = pair
-        except ValueError:
-            bads.append(orig)
-        else:
-            settings_data[k] = v
-    if bads:
-        raise ValueError(
-            "Could not correctly parse itemized compute specification. "
-            "Correct format: " + EXAMPLE_COMPUTE_SPEC_FMT
-        )
+    if isinstance(
+        spec, str
+    ):  # compute: "partition=standard time='01-00:00:00' cores='32' mem='32000'"
+        spec = spec.split(sep=" ")
+    if isinstance(spec, list):
+        pairs = [(kv, kv.split("=")) for kv in spec]
+        bads = []
+        for orig, pair in pairs:
+            try:
+                k, v = pair
+            except ValueError:
+                bads.append(orig)
+            else:
+                settings_data[k] = v
+        if bads:
+            raise ValueError(
+                "Could not correctly parse itemized compute specification. "
+                "Correct format: " + EXAMPLE_COMPUTE_SPEC_FMT
+            )
+    elif isinstance(spec, dict):
+        for key, value in spec.items():
+            settings_data[key] = value
+
     return settings_data
 
 

looper/command_models/arguments.py

@@ -184,6 +184,20 @@ 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",
+        alias="-g",
+        default=(bool, False),
+        description="Use generic looper config?",
+    )
+
     SAMPLE_PIPELINE_INTERFACES = Argument(
         name="sample_pipeline_interfaces",
         alias="-S",
@@ -228,6 +242,7 @@ class ArgumentEnum(enum.Enum):
     )
     PACKAGE = Argument(
         name="package",
+        alias="-p",
         default=(str, None),
         description="Name of computing resource package to use",
     )

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,
     ],
 )
 
@@ -187,6 +190,7 @@ InitParser = Command(
         ArgumentEnum.PEP_CONFIG.value,
         ArgumentEnum.SAMPLE_PIPELINE_INTERFACES.value,
         ArgumentEnum.PROJECT_PIPELINE_INTERFACES.value,
+        ArgumentEnum.GENERIC.value,
     ],
 )
 

looper/conductor.py

@@ -661,6 +661,7 @@ class SubmissionConductor(object):
                 "record_identifier": psm.record_identifier,
                 "config_file": psm.config_path,
                 "output_schema": psm.cfg["_schema_path"],
+                "pephub_path": psm.cfg["pephub_path"],
             }
             filtered_namespace = {k: v for k, v in full_namespace.items() if v}
             return YAMLConfigManager(filtered_namespace)

looper/divvy.py

@@ -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.
@@ -200,6 +210,11 @@ class ComputingConfiguration(YAMLConfigManager):
         """
         return self.compute
 
+    @property
+    def compute_packages(self):
+
+        return self["compute_packages"]
+
     def list_compute_packages(self):
         """
         Returns a list of available compute packages.
@@ -396,11 +411,13 @@ def divvy_init(config_path, template_config_path):
         _LOGGER.error("You must specify a template config file path.")
         return
 
+    if not os.path.isabs(config_path):
+        config_path = os.path.abspath(config_path)
+
     if config_path and not os.path.exists(config_path):
-        # dcc.write(config_path)
         # Init should *also* write the templates.
         dest_folder = os.path.dirname(config_path)
-        copytree(os.path.dirname(template_config_path), dest_folder)
+        copytree(os.path.dirname(template_config_path), dest_folder, dirs_exist_ok=True)
         template_subfolder = os.path.join(dest_folder, "divvy_templates")
         _LOGGER.info("Wrote divvy templates to folder: {}".format(template_subfolder))
         new_template = os.path.join(

looper/exceptions.py

@@ -15,6 +15,7 @@ _all__ = [
     "PipelineInterfaceConfigError",
     "PipelineInterfaceRequirementsError",
     "MisconfigurationException",
+    "LooperReportError",
 ]
 
 
@@ -31,7 +32,7 @@ class SampleFailedException(LooperError):
 
 
 class MisconfigurationException(LooperError):
-    """Duplication of pipeline identifier precludes unique pipeline ref."""
+    """Looper not properly configured"""
 
     def __init__(self, key):
         super(MisconfigurationException, self).__init__(key)
@@ -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/utils.py

@@ -17,6 +17,7 @@ from ubiquerg import convert_value, expandpath, parse_registry_path, deep_update
 from pephubclient.constants import RegistryPath
 from pydantic import ValidationError
 from yacman import load_yaml
+from yaml.parser import ParserError
 
 from .const import *
 from .command_models.commands import SUPPORTED_COMMANDS
@@ -263,31 +264,29 @@ def enrich_args_via_cfg(
     cli_modifiers=None,
 ):
     """
-    Read in a looper dotfile and set arguments.
+    Read in a looper dotfile, pep config and set arguments.
 
-    Priority order: CLI > dotfile/config > parser default
+    Priority order: CLI > dotfile/config > pep_config > parser default
 
     :param subcommand name: the name of the command used
     :param argparse.Namespace parser_args: parsed args by the original parser
-    :param argparse.Namespace aux_parser: parsed args by the a parser
+    :param argparse.Namespace aux_parser: parsed args by the argument parser
         with defaults suppressed
+    :param dict test_args: dict of args used for pytesting
+    :param dict cli_modifiers: dict of args existing if user supplied cli args in looper config file
     :return argparse.Namespace: selected argument values
     """
+
+    # Did the user provide arguments in the PEP config?
     cfg_args_all = (
         _get_subcommand_args(subcommand_name, parser_args)
         if os.path.exists(parser_args.pep_config)
         else dict()
     )
-
-    # If user provided project-level modifiers in the looper config, they are prioritized
-    if cfg_args_all:
-        for key, value in cfg_args_all.items():
-            if getattr(parser_args, key, None):
-                new_value = getattr(parser_args, key)
-                cfg_args_all[key] = new_value
-    else:
+    if not cfg_args_all:
         cfg_args_all = {}
 
+    # Did the user provide arguments/modifiers in the looper config file?
     looper_config_cli_modifiers = None
     if cli_modifiers:
         if str(subcommand_name) in cli_modifiers:
@@ -312,6 +311,13 @@ def enrich_args_via_cfg(
     else:
         cli_args, _ = aux_parser.parse_known_args()
 
+    # If any CLI args were provided, make sure they take priority
+    if cli_args:
+        r = getattr(cli_args, subcommand_name)
+        for k, v in cfg_args_all.items():
+            if k in r:
+                cfg_args_all[k] = getattr(r, k)
+
     def set_single_arg(argname, default_source_namespace, result_namespace):
         if argname not in POSITIONAL or not hasattr(result, argname):
             if argname in cli_args:
@@ -324,6 +330,8 @@ def enrich_args_via_cfg(
             elif cfg_args_all is not None and argname in cfg_args_all:
                 if isinstance(cfg_args_all[argname], list):
                     r = [convert_value(i) for i in cfg_args_all[argname]]
+                elif isinstance(cfg_args_all[argname], dict):
+                    r = cfg_args_all[argname]
                 else:
                     r = convert_value(cfg_args_all[argname])
             else:
@@ -432,9 +440,8 @@ def init_generic_pipeline(pipelinepath: Optional[str] = None):
     generic_pipeline_dict = {
         "pipeline_name": "default_pipeline_name",
         "output_schema": "output_schema.yaml",
-        "var_templates": {"pipeline": "{looper.piface_dir}/count_lines.sh"},
         "sample_interface": {
-            "command_template": "{pipeline.var_templates.pipeline} {sample.file} "
+            "command_template": "{looper.piface_dir}/count_lines.sh {sample.file} "
             "--output-parent {looper.sample_output_folder}"
         },
     }
@@ -627,8 +634,6 @@ def looper_config_tutorial():
     console.print("Use [yellow]`looper run`[/yellow] afterwards to run the pipeline.")
     console.print("Press [yellow]^C[/yellow] at any time to quit.\n")
 
-    console.input("> ... ")
-
     DEFAULTS = {  # What you get if you just press enter
         "pep_config": "databio/example",
         "output_dir": "results",
@@ -636,73 +641,58 @@ def looper_config_tutorial():
         "project_name": os.path.basename(os.getcwd()),
     }
 
-    creating = True
+    cfg["project_name"] = (
+        console.input(f"Project name: [yellow]({DEFAULTS['project_name']})[/yellow] >")
+        or DEFAULTS["project_name"]
+    )
 
-    while creating:
-        cfg["project_name"] = (
-            console.input(
-                f"Project name: [yellow]({DEFAULTS['project_name']})[/yellow] >"
-            )
-            or DEFAULTS["project_name"]
+    cfg["pep_config"] = (
+        console.input(
+            f"Registry path or file path to PEP: [yellow]({DEFAULTS['pep_config']})[/yellow] >"
         )
+        or DEFAULTS["pep_config"]
+    )
 
-        cfg["pep_config"] = (
-            console.input(
-                f"Registry path or file path to PEP: [yellow]({DEFAULTS['pep_config']})[/yellow] >"
-            )
-            or DEFAULTS["pep_config"]
+    if not os.path.exists(cfg["pep_config"]) and not is_pephub_registry_path(
+        cfg["pep_config"]
+    ):
+        console.print(
+            f"Warning: PEP file does not exist at [yellow]'{cfg['pep_config']}[/yellow]'"
         )
 
-        if not os.path.exists(cfg["pep_config"]):
-            console.print(
-                f"Warning: PEP file does not exist at [yellow]'{cfg['pep_config']}[/yellow]'"
-            )
+    cfg["output_dir"] = (
+        console.input(
+            f"Path to output directory: [yellow]({DEFAULTS['output_dir']})[/yellow] >"
+        )
+        or DEFAULTS["output_dir"]
+    )
 
-        cfg["output_dir"] = (
+    add_more_pifaces = True
+    piface_paths = []
+    while add_more_pifaces:
+        piface_path = (
             console.input(
-                f"Path to output directory: [yellow]({DEFAULTS['output_dir']})[/yellow] >"
+                "Add each path to a pipeline interface: [yellow](pipeline_interface.yaml)[/yellow] >"
             )
-            or DEFAULTS["output_dir"]
+            or None
         )
+        if piface_path is None:
+            if piface_paths == []:
+                piface_paths.append(DEFAULTS["piface_path"])
+            add_more_pifaces = False
+        else:
+            piface_paths.append(piface_path)
 
-        add_more_pifaces = True
-        piface_paths = []
-        while add_more_pifaces:
-            piface_path = (
-                console.input(
-                    "Add each path to a pipeline interface: [yellow](pipeline_interface.yaml)[/yellow] >"
-                )
-                or None
-            )
-            if piface_path is None:
-                if piface_paths == []:
-                    piface_paths.append(DEFAULTS["piface_path"])
-                add_more_pifaces = False
-            else:
-                piface_paths.append(piface_path)
-
-        console.print("\n")
-
-        console.print(
-            f"""\
-    [yellow]pep_config:[/yellow] {cfg['pep_config']}
-    [yellow]output_dir:[/yellow] {cfg['output_dir']}
-    [yellow]pipeline_interfaces:[/yellow]
-      - {piface_paths}
-    """
-        )
+    console.print("\n")
 
-        console.print(
-            "[bold]Does this look good?[/bold]  [bold green]Y[/bold green]/[red]n[/red]..."
-        )
-        selection = None
-        while selection not in ["y", "n"]:
-            selection = console.input("\nSelection: ").lower().strip()
-        if selection == "n":
-            console.print("Starting over...")
-            pass
-        if selection == "y":
-            creating = False
+    console.print(
+        f"""\
+[yellow]pep_config:[/yellow] {cfg['pep_config']}
+[yellow]output_dir:[/yellow] {cfg['output_dir']}
+[yellow]pipeline_interfaces:[/yellow]
+  - {piface_paths}
+"""
+    )
 
     for piface_path in piface_paths:
         if not os.path.exists(piface_path):
@@ -727,7 +717,7 @@ def looper_config_tutorial():
     looper_config_dict = {}
     looper_config_dict["pep_config"] = cfg["pep_config"]
     looper_config_dict["output_dir"] = cfg["output_dir"]
-    looper_config_dict["pipeline_interfaces"] = [piface_paths]
+    looper_config_dict["pipeline_interfaces"] = piface_paths
 
     with open(looper_cfg_path, "w") as fp:
         yaml.dump(looper_config_dict, fp)
@@ -747,7 +737,15 @@ def determine_pipeline_type(piface_path: str, looper_config_path: str):
 
     if piface_path is None:
         return None, None
-    piface_path = expandpath(piface_path)
+    try:
+        piface_path = expandpath(piface_path)
+    except TypeError as e:
+        _LOGGER.warning(
+            f"Pipeline interface not found at given path: {piface_path}. Type Error: "
+            + str(e)
+        )
+        return None, None
+
     if not os.path.isabs(piface_path):
         piface_path = os.path.realpath(
             os.path.join(os.path.dirname(looper_config_path), piface_path)
@@ -755,6 +753,7 @@ def determine_pipeline_type(piface_path: str, looper_config_path: str):
     try:
         piface_dict = load_yaml(piface_path)
     except FileNotFoundError:
+        _LOGGER.warning(f"Pipeline interface not found at given path: {piface_path}")
         return None, None
 
     pipeline_types = []
@@ -783,12 +782,18 @@ def read_looper_config_file(looper_config_path: str) -> dict:
     :raise MisconfigurationException: incorrect configuration.
     """
     return_dict = {}
-    with open(looper_config_path, "r") as dotfile:
-        dp_data = yaml.safe_load(dotfile)
+
+    try:
+        with open(looper_config_path, "r") as dotfile:
+            dp_data = yaml.safe_load(dotfile)
+    except ParserError as e:
+        _LOGGER.warning(
+            "Could not load looper config file due to the following exception"
+        )
+        raise ParserError(context=str(e))
 
     if PEP_CONFIG_KEY in dp_data:
         return_dict[PEP_CONFIG_KEY] = dp_data[PEP_CONFIG_KEY]
-
     else:
         raise MisconfigurationException(
             f"Looper dotfile ({looper_config_path}) is missing '{PEP_CONFIG_KEY}' key"
@@ -846,6 +851,7 @@ def read_looper_config_file(looper_config_path: str) -> dict:
     for k, v in return_dict.items():
         if k == SAMPLE_PL_ARG or k == PROJECT_PL_ARG:
             # Pipeline interfaces are resolved at a later point. Do it there only to maintain consistency. #474
+
             pass
         if isinstance(v, str):
             v = expandpath(v)

{looper-2.0.0a1.dist-info → looper-2.0.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: looper
-Version: 2.0.0a1
+Version: 2.0.0a3
 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
@@ -15,20 +15,19 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: colorama >=0.3.9
-Requires-Dist: divvy >=0.5.0
-Requires-Dist: eido >=0.2.1
+Requires-Dist: colorama>=0.3.9
+Requires-Dist: eido>=0.2.3
 Requires-Dist: jinja2
-Requires-Dist: logmuse >=0.2.0
-Requires-Dist: pandas >=2.0.2
-Requires-Dist: pephubclient >=0.4.0
-Requires-Dist: pipestat >=0.9.2
-Requires-Dist: peppy >=0.40.2
-Requires-Dist: pyyaml >=3.12
-Requires-Dist: rich >=9.10.0
-Requires-Dist: ubiquerg >=0.8.1a1
-Requires-Dist: yacman ==0.9.3
-Requires-Dist: pydantic-argparse >=0.9.0
+Requires-Dist: logmuse>=0.2.0
+Requires-Dist: pandas>=2.0.2
+Requires-Dist: pephubclient>=0.4.0
+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: yacman==0.9.3
+Requires-Dist: pydantic-argparse>=0.9.0
 Requires-Dist: psutil
 
 # <img src="docs/img/looper_logo.svg" alt="looper logo" height="70">

{looper-2.0.0a1.dist-info → looper-2.0.0a3.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=wJ2KiFRb6QXaKu1tfxwKmo9CE2xP4f3BkEUYoIJeUkQ,121
-looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
-looper/cli_pydantic.py,sha256=saAD0dwizLi_VajVKElQmYRqtn0Yyl_r712znxZMxRQ,14209
-looper/conductor.py,sha256=oNfqANA2tIhQTAQFxd-rQ4ccPA60D933EGo3rfbJGFo,35061
+looper/_version.py,sha256=MwJwmoXPcF0oLwdO3af_PLuTBNXWHfGxew5Q7p37mTQ,121
+looper/cli_divvy.py,sha256=_VGbOFLkXtKdkZA6omlzgXbXkuUM5aLQ50aTTtbTrVI,5975
+looper/cli_pydantic.py,sha256=BA-jq6lyFnGoNNLCKAFrfqMQ7qRR3qxYK62PfMEoKA4,14425
+looper/conductor.py,sha256=lzY6Gzsb8oX-KLzLkRa0XrYWSxLeiy6jRmmD15WNAkw,35116
 looper/const.py,sha256=OscEELQsyLKlSrmwuXfyLRwpAUJUEpGD2UxBeLJDXgw,8703
-looper/divvy.py,sha256=5x8hV1lT5tEQdAUtVjn0rNwYnJroNij0RyDn-wHf4QE,15251
-looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
-looper/looper.py,sha256=ZWTulMz6NobnYFUjev513TJwXqknrb4_gZrV-a_fT9g,30041
+looper/divvy.py,sha256=yokD0--xN0kaxPuPRZrRPgKinl0Sqt0cvkmNMvwe94A,15860
+looper/exceptions.py,sha256=weSXsPadikAHVJvUUOT1uE56C_nKqgC3iBOvDebPDVE,3572
+looper/looper.py,sha256=zNszsV50ZkC5ioaLHgMg9H3hSTEHAAV-jBpLra3OIKw,31624
 looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
 looper/pipeline_interface.py,sha256=mN4-XICyZzuVLTOq3b0ijppYe6ib_Ljlyf6KxZCJh2A,14537
 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=VXKaEYXW0XEQNy__hNBv42i-sz5qB7QiwpXzhXs_3Wk,39556
+looper/utils.py,sha256=-4QlScIB7eewIbmEJdAv2d0ZE0qr_q9acm2XUOiMEek,39769
 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=sRrJWCSQmnjGLnOo-Wl6_PnvTZz8VIWII79svI3BqFk,8653
-looper/command_models/commands.py,sha256=EvKyjNdUBspXnOUMprxIY0C4VPka2PBj8CJgtd5Ya9w,9680
+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-2.0.0a1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-2.0.0a1.dist-info/METADATA,sha256=OZPEqy9PPCjzJ110u-HazaRkaUIiuesCZMC3jpfl2vQ,1800
-looper-2.0.0a1.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-looper-2.0.0a1.dist-info/entry_points.txt,sha256=ejZpghZG3OoTK69u9rTW-yLyI6SC63bBTUb-Vw26HG4,87
-looper-2.0.0a1.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-2.0.0a1.dist-info/RECORD,,
+looper-2.0.0a3.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-2.0.0a3.dist-info/METADATA,sha256=tP0InSt3Xn7098v19ZDWawfATd2Ez2zoMsecZKv6SCM,1762
+looper-2.0.0a3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+looper-2.0.0a3.dist-info/entry_points.txt,sha256=iHltI2_Jdved27vccmWhvmcHWUZ7Mf6CfDV6QkY1Lc8,91
+looper-2.0.0a3.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-2.0.0a3.dist-info/RECORD,,

{looper-2.0.0a1.dist-info → looper-2.0.0a3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{looper-2.0.0a1.dist-info → looper-2.0.0a3.dist-info}/entry_points.txt

@@ -1,3 +1,3 @@
 [console_scripts]
 divvy = looper.__main__:divvy_main
-looper = looper.cli_pydantic:main
+looper = looper.cli_pydantic:main_cli