Add workflow for generating base and uq runs from a single template c…

…onfig (#603)

* Add support for `-p` flag in `duqduq status`
* Add cli option `--output` to setup to set output directory
* Rename `--base` to `--no-sampling` in `duqduq create`
* Better output names for status and setup

src/duqtools/cli.py

@@ -273,7 +273,7 @@ def cli_setup(**kwargs):
 @click.option('--force',
               is_flag=True,
               help='Overwrite existing run directories and IDS data.')
-@click.option('--base',
+@click.option('--no-sampling',
               is_flag=True,
               help='Create base run (ignores `dimensions`/`sampler`).')
 @common_options(*all_options)

src/duqtools/create.py

@@ -228,7 +228,7 @@ def create_run(self, model: Run, *, force: bool = False):
 def create(*,
            force,
            config,
-           base: bool,
+           no_sampling: bool = False,
            absolute_dirpath: bool = False,
            **kwargs):
     """Create input for jetto and IDS data structures.
@@ -239,15 +239,15 @@ def create(*,
         Override protection if data and directories already exist.
     config : Path
         Config file location
-    base : bool
+    no_sampling : bool
         If true, create base run by ignoring `sampler`/`dimensions`.
 
     **kwargs
         Unused.
     """
     create_mgr = CreateManager()
 
-    ops_dict = create_mgr.generate_ops_dict(base_only=base)
+    ops_dict = create_mgr.generate_ops_dict(base_only=no_sampling)
 
     runs = create_mgr.make_run_models(
         ops_dict=ops_dict,

src/duqtools/large_scale_validation/cli.py

@@ -48,6 +48,7 @@ def cli(**kwargs):
 @click.option('--force',
               is_flag=True,
               help='Overwrite existing run config directories')
+@click.option('-o', '--output', type=str, help='Output subdirectory')
 @common_options(*logging_options, yes_option, dry_run_option)
 def cli_setup(**kwargs):
     """Set up large scale validation."""
@@ -75,7 +76,7 @@ def cli_setup(**kwargs):
     help=
     'Only create data for configs where `template_data` matches a handle in this data.csv.'
 )
-@click.option('--base',
+@click.option('--no-sampling',
               is_flag=True,
               help='Create base runs (ignores `dimensions`/`sampler`).')
 @common_options(*logging_options, yes_option, dry_run_option)
@@ -139,6 +140,12 @@ def cli_submit(**kwargs):
 @cli.command('status')
 @click.option('--detailed', is_flag=True, help='Detailed info on progress')
 @click.option('--progress', is_flag=True, help='Fancy progress bar')
+@click.option(
+    '-p',
+    '--pattern',
+    type=str,
+    help=
+    'Show status only for runs in subdirectories matching this glob pattern.')
 @common_options(*logging_options)
 def cli_status(**kwargs):
     """Check status large scale validation runs."""

src/duqtools/large_scale_validation/create.py

@@ -5,12 +5,12 @@
 from ..utils import read_imas_handles_from_file, work_directory
 
 
-def create(*, base: bool, input_file: str, pattern: str, **kwargs):
+def create(*, no_sampling: bool, input_file: str, pattern: str, **kwargs):
     """Create runs for large scale validation.
 
     Parameters
     ----------
-    base : bool
+    no_sampling : bool
         If true, create base runs by ignoring `sampler`/`dimensions`.
     input_file : str
         Only create for configs where template_data matches a handle in the data.csv
@@ -39,5 +39,5 @@ def create(*, base: bool, input_file: str, pattern: str, **kwargs):
         with work_directory(config_dir):
             duqtools_create(config=config_file,
                             absolute_dirpath=True,
-                            base=base,
+                            no_sampling=no_sampling,
                             **kwargs)

src/duqtools/large_scale_validation/setup.py

@@ -2,13 +2,16 @@
 from ..utils import read_imas_handles_from_file
 
 
-def setup(*, template_file, input_file, force, **kwargs):
+def setup(*, template_file, input_file, force: bool, output: str, **kwargs):
     """Setup large scale validation runs for template."""
     if not input_file:
         raise OSError('Input file not defined.')
 
     handles = read_imas_handles_from_file(input_file)
 
-    substitute_templates(handles=handles,
-                         template_file=template_file,
-                         force=force)
+    substitute_templates(
+        handles=handles,
+        template_file=template_file,
+        force=force,
+        output=output,
+    )

src/duqtools/large_scale_validation/status.py

@@ -7,7 +7,7 @@
 from ..status import Status, StatusError
 
 
-def status(*, progress: bool, detailed: bool, **kwargs):
+def status(*, progress: bool, detailed: bool, pattern: str, **kwargs):
     """Show status of nested runs.
 
     Parameters
@@ -16,11 +16,15 @@ def status(*, progress: bool, detailed: bool, **kwargs):
         Show progress bar.
     detailed : bool
         Show detailed progress for every job.
+    pattern : str
+        Show status only for subdirectories matching this glob pattern
     """
+    if pattern is None:
+        pattern = '**'
 
     cwd = Path.cwd()
 
-    config_files = cwd.glob('**/duqtools.yaml')
+    config_files = cwd.glob(f'{pattern}/duqtools.yaml')
 
     all_jobs: list[Job] = []
 
@@ -39,11 +43,11 @@ def status(*, progress: bool, detailed: bool, **kwargs):
         jobs = [Job(run.dirname) for run in Locations(config_dir).runs]
         all_jobs.extend(jobs)
 
-        name = config_file.parent.name
+        dirname = config_file.parent.relative_to(cwd)
         tag = cfg.tag
         status = ''.join(job.status_symbol for job in jobs)
 
-        click.echo(f'{name} ({tag}): {status}')
+        click.echo(f'{dirname} ({tag}): {status}')
 
     click.echo()
 

src/duqtools/large_scale_validation/submit.py

@@ -51,8 +51,8 @@ def submit(*, array, force, max_jobs, schedule, max_array_size: int,
 
     jobs: list[Job] = []
 
-    for dir in dirs:
-        config_file = dir / 'duqtools.yaml'
+    for drc in dirs:
+        config_file = drc / 'duqtools.yaml'
         cfg.parse_file(config_file)
 
         if handles and (cfg.create.template_data not in handles):

src/duqtools/models/_run.py

@@ -35,6 +35,10 @@ def to_imas_handle(self) -> ImasHandle:
     def from_path(cls, path: Path):
         return cls(shortname=path, dirname=path.resolve())
 
+    @property
+    def is_base(self):
+        return self.shortname == 'base'
+
 
 class Runs(BaseModel):
     __root__: list[Run] = []

src/duqtools/setup.py

@@ -4,7 +4,7 @@
 from collections import defaultdict
 from pathlib import Path
 from types import SimpleNamespace
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Optional
 
 import yaml
 from jinja2 import Environment, FileSystemLoader
@@ -150,8 +150,14 @@ def __getattr__(self, key: str):
         return value
 
 
-def substitute_templates(*, handles: dict[str, ImasHandle], template_file: str,
-                         force: bool):
+def substitute_templates(
+    *,
+    handles: dict[str, ImasHandle],
+    template_file: str,
+    force: bool,
+    base: bool = False,
+    output: Optional[str] = None,
+):
     """Handle template substitution.
 
     Parameters
@@ -162,6 +168,8 @@ def substitute_templates(*, handles: dict[str, ImasHandle], template_file: str,
         Path to template file.
     force : bool
         Overwrite files if set to true.
+    output : str
+        Output subdirectory.
     """
     cwd = Path.cwd()
 
@@ -173,7 +181,7 @@ def substitute_templates(*, handles: dict[str, ImasHandle], template_file: str,
         add_system_attrs = no_op  # default to no-op
 
     for name, handle in handles.items():
-        run = SimpleNamespace(name=name)
+        run = SimpleNamespace(name=name, output=output)
 
         add_system_attrs(run=run, handle=handle)
 
@@ -183,11 +191,15 @@ def substitute_templates(*, handles: dict[str, ImasHandle], template_file: str,
 
         Config.parse_raw(cfg)  # make sure config is valid
 
-        out_drc = cwd / name
+        if output:
+            out_drc = cwd / output / name
+        else:
+            out_drc = cwd / name
 
         if out_drc.exists() and not force:
-            op_queue.add_no_op(description='Directory exists',
-                               extra_description=name)
+            op_queue.add_no_op(
+                description='Directory exists',
+                extra_description=f'{name} ({out_drc.relative_to(cwd)})')
             op_queue.warning(description='Warning',
                              extra_description='Some targets already exist, '
                              'use --force to override')
@@ -200,7 +212,7 @@ def substitute_templates(*, handles: dict[str, ImasHandle], template_file: str,
                     'force': force
                 },
                 description='Setup run',
-                extra_description=name,
+                extra_description=f'{name} ({out_drc.relative_to(cwd)})',
             )