Dev rename args 455

looper/cli_pydantic.py

@@ -54,9 +54,11 @@
     read_yaml_file,
     inspect_looper_config_file,
     is_PEP_file_type,
+    looper_config_tutorial,
 )
 
 from typing import List, Tuple
+from rich.console import Console
 
 
 def opt_attr_pair(name: str) -> Tuple[str, str]:
@@ -122,52 +124,60 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         sys.exit(1)
 
     if subcommand_name == "init":
-        return int(
-            not initiate_looper_config(
-                dotfile_path(),
-                subcommand_args.pep_config,
-                subcommand_args.output_dir,
-                subcommand_args.sample_pipeline_interfaces,
-                subcommand_args.project_pipeline_interfaces,
-                subcommand_args.force_yes,
-            )
+
+        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":
+            console.clear()
+            return int(
+                not initiate_looper_config(
+                    dotfile_path(),
+                    subcommand_args.pep_config,
+                    subcommand_args.output_dir,
+                    subcommand_args.sample_pipeline_interfaces,
+                    subcommand_args.project_pipeline_interfaces,
+                    subcommand_args.force_yes,
+                )
+            )
+        else:
+            console.clear()
+            return int(looper_config_tutorial())
+
     if subcommand_name == "init_piface":
         sys.exit(int(not init_generic_pipeline()))
 
     _LOGGER.info("Looper version: {}\nCommand: {}".format(__version__, subcommand_name))
 
-    if subcommand_args.config_file is None:
-        looper_cfg_path = os.path.relpath(dotfile_path(), start=os.curdir)
-        try:
-            if subcommand_args.looper_config:
-                looper_config_dict = read_looper_config_file(
-                    subcommand_args.looper_config
-                )
+    looper_cfg_path = os.path.relpath(dotfile_path(), start=os.curdir)
+    try:
+        if subcommand_args.config:
+            looper_config_dict = read_looper_config_file(subcommand_args.config)
+        else:
+            looper_config_dict = read_looper_dotfile()
+            _LOGGER.info(f"Using looper config ({looper_cfg_path}).")
+
+        cli_modifiers_dict = None
+        for looper_config_key, looper_config_item in looper_config_dict.items():
+            if looper_config_key == CLI_KEY:
+                cli_modifiers_dict = looper_config_item
             else:
-                looper_config_dict = read_looper_dotfile()
-                _LOGGER.info(f"Using looper config ({looper_cfg_path}).")
-
-            cli_modifiers_dict = None
-            for looper_config_key, looper_config_item in looper_config_dict.items():
-                if looper_config_key == CLI_KEY:
-                    cli_modifiers_dict = looper_config_item
-                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}."
-            )
-            sys.exit(1)
-    else:
+                setattr(subcommand_args, looper_config_key, looper_config_item)
+
+    except OSError:
+        parser.print_help(sys.stderr)
         _LOGGER.warning(
-            "This PEP configures looper through the project config. This approach is deprecated and will "
-            "be removed in future versions. Please use a looper config file. For more information see "
-            "looper.databio.org/en/latest/looper-config"
+            f"Looper config file does not exist. Use looper init to create one at {looper_cfg_path}."
         )
+        sys.exit(1)
 
     subcommand_args = enrich_args_via_cfg(
         subcommand_name,
@@ -191,12 +201,12 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         subcommand_args.ignore_flags = True
 
     # Initialize project
-    if is_PEP_file_type(subcommand_args.config_file) and os.path.exists(
-        subcommand_args.config_file
+    if is_PEP_file_type(subcommand_args.pep_config) and os.path.exists(
+        subcommand_args.pep_config
     ):
         try:
             p = Project(
-                cfg=subcommand_args.config_file,
+                cfg=subcommand_args.pep_config,
                 amendments=subcommand_args.amend,
                 divcfg_path=divcfg,
                 runp=subcommand_name == "runp",
@@ -209,14 +219,14 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         except yaml.parser.ParserError as e:
             _LOGGER.error(f"Project config parse failed -- {e}")
             sys.exit(1)
-    elif is_pephub_registry_path(subcommand_args.config_file):
+    elif is_pephub_registry_path(subcommand_args.pep_config):
         if vars(subcommand_args)[SAMPLE_PL_ARG]:
             p = Project(
                 amendments=subcommand_args.amend,
                 divcfg_path=divcfg,
                 runp=subcommand_name == "runp",
                 project_dict=PEPHubClient()._load_raw_pep(
-                    registry_path=subcommand_args.config_file
+                    registry_path=subcommand_args.pep_config
                 ),
                 **{
                     attr: getattr(subcommand_args, attr)
@@ -252,7 +262,7 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         # Check at the beginning if user wants to use pipestat and pipestat is configurable
         is_pipestat_configured = (
             prj._check_if_pipestat_configured(pipeline_type=PipelineLevel.PROJECT.value)
-            if getattr(subcommand_args, "project", None)
+            if getattr(subcommand_args, "project", None) or subcommand_name == "runp"
             else prj._check_if_pipestat_configured()
         )
 

looper/command_models/arguments.py

@@ -162,13 +162,9 @@ class ArgumentEnum(enum.Enum):
         default=(int, None),
         description="Skip samples by numerical index",
     )
-    CONFIG_FILE = Argument(
-        name="config_file",
-        default=(str, None),
-        description="Project configuration file",
-    )
-    LOOPER_CONFIG = Argument(
-        name="looper_config",
+    CONFIG = Argument(
+        name="config",
+        alias="-c",
         default=(str, None),
         description="Looper configuration file (YAML)",
     )
@@ -237,7 +233,6 @@ class ArgumentEnum(enum.Enum):
     )
     COMPUTE = Argument(
         name="compute",
-        alias="-c",
         default=(List, []),
         description="List of key-value pairs (k1=v1)",
     )

looper/command_models/commands.py

@@ -53,8 +53,7 @@ def create_model(self) -> Type[pydantic.BaseModel]:
     ArgumentEnum.SKIP.value,
     ArgumentEnum.PEP_CONFIG.value,
     ArgumentEnum.OUTPUT_DIR.value,
-    ArgumentEnum.CONFIG_FILE.value,
-    ArgumentEnum.LOOPER_CONFIG.value,
+    ArgumentEnum.CONFIG.value,
     ArgumentEnum.SAMPLE_PIPELINE_INTERFACES.value,
     ArgumentEnum.PROJECT_PIPELINE_INTERFACES.value,
     ArgumentEnum.PIPESTAT.value,

looper/conductor.py

@@ -198,6 +198,9 @@ def __init__(
 
         self.collate = collate
         self.section_key = PROJECT_PL_KEY if self.collate else SAMPLE_PL_KEY
+        self.pipeline_interface_type = (
+            "project_interface" if self.collate else "sample_interface"
+        )
         self.pl_iface = pipeline_interface
         self.pl_name = self.pl_iface.pipeline_name
         self.prj = prj
@@ -681,7 +684,11 @@ def write_script(self, pool, size):
             pipeline=self.pl_iface,
             compute=self.prj.dcc.compute,
         )
-        templ = self.pl_iface["command_template"]
+
+        if self.pipeline_interface_type is None:
+            templ = self.pl_iface["command_template"]
+        else:
+            templ = self.pl_iface[self.pipeline_interface_type]["command_template"]
         if not self.override_extra:
             extras_template = (
                 EXTRA_PROJECT_CMD_TEMPLATE

looper/pipeline_interface.py

@@ -56,15 +56,6 @@ def __init__(self, config, pipeline_type=None):
             )
         self.update(config)
         self._validate(schema_src=PIFACE_SCHEMA_SRC)
-        if "path" in self:
-            warn(
-                message="'path' specification as a top-level pipeline "
-                "interface key is deprecated and will be removed with "
-                "the next release. Please use 'paths' section "
-                "from now on.",
-                category=DeprecationWarning,
-            )
-            self._expand_paths(["path"])
         self._expand_paths(["compute", "dynamic_variables_script_path"])
 
     @property

looper/project.py

@@ -413,10 +413,12 @@ def _get_pipestat_configuration(self, pipeline_type=PipelineLevel.SAMPLE.value):
                 pipestat_config_path = self._check_for_existing_pipestat_config(piface)
 
                 if not pipestat_config_path:
-                    self._create_pipestat_config(piface)
+                    self._create_pipestat_config(piface, pipeline_type)
                 else:
                     piface.psm = PipestatManager(
-                        config_file=pipestat_config_path, multi_pipelines=True
+                        config_file=pipestat_config_path,
+                        multi_pipelines=True,
+                        pipeline_type="sample",
                     )
 
         elif pipeline_type == PipelineLevel.PROJECT.value:
@@ -426,10 +428,12 @@ def _get_pipestat_configuration(self, pipeline_type=PipelineLevel.SAMPLE.value):
                 )
 
                 if not pipestat_config_path:
-                    self._create_pipestat_config(prj_piface)
+                    self._create_pipestat_config(prj_piface, pipeline_type)
                 else:
                     prj_piface.psm = PipestatManager(
-                        config_file=pipestat_config_path, multi_pipelines=True
+                        config_file=pipestat_config_path,
+                        multi_pipelines=True,
+                        pipeline_type="project",
                     )
         else:
             _LOGGER.error(
@@ -469,7 +473,7 @@ def _check_for_existing_pipestat_config(self, piface):
         else:
             return None
 
-    def _create_pipestat_config(self, piface):
+    def _create_pipestat_config(self, piface, pipeline_type):
         """
         Each piface needs its own config file and associated psm
         """
@@ -512,8 +516,6 @@ def _create_pipestat_config(self, piface):
             pipestat_config_dict.update({"pipeline_name": piface.data["pipeline_name"]})
         else:
             pipeline_name = None
-        if "pipeline_type" in piface.data:
-            pipestat_config_dict.update({"pipeline_type": piface.data["pipeline_type"]})
 
         # Warn user if there is a mismatch in pipeline_names from sources!!!
         if pipeline_name != output_schema_pipeline_name:

looper/schemas/pipeline_interface_schema_generic.yaml

@@ -9,12 +9,20 @@ properties:
     type: string
     enum: ["project", "sample"]
     description: "type of the pipeline, either 'project' or 'sample'"
-  command_template:
-    type: string
-    description: "Jinja2-like template to construct the command to run"
-  path:
-    type: string
-    description: "path to the pipeline program. Relative to pipeline interface file or absolute."
+  sample_interface:
+    type: object
+    description: "Section that defines compute environment settings"
+    properties:
+      command_template:
+        type: string
+        description: "Jinja2-like template to construct the command to run"
+  project_interface:
+    type: object
+    description: "Section that defines compute environment settings"
+    properties:
+      command_template:
+        type: string
+        description: "Jinja2-like template to construct the command to run"
   compute:
     type: object
     description: "Section that defines compute environment settings"