dh-cli 0.5.0__tar.gz → 0.5.2__tar.gz

{dh_cli-0.5.0 → dh_cli-0.5.2}/.gitignore

@@ -2,7 +2,6 @@
 
 # Pixi (managed by pixi.toml)
 .pixi/
-pixi.lock
 
 # Folders for heavy things
 /data/**

{dh_cli-0.5.0 → dh_cli-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dh-cli
-Version: 0.5.0
+Version: 0.5.2
 Summary: Dayhoff Labs developer CLI
 Author-email: Dayhoff Labs <dev@dayhofflabs.com>
 License: # PolyForm Noncommercial License 1.0.0

{dh_cli-0.5.0 → dh_cli-0.5.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "dh-cli"
-version = "0.5.0"
+version = "0.5.2"
 description = "Dayhoff Labs developer CLI"
 requires-python = ">=3.11"
 readme = "README.md"

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/aws_batch.py

@@ -6,15 +6,15 @@ import time
 from dataclasses import dataclass
 from typing import Any
 
+import boto3
+from botocore.exceptions import ClientError
+
 from dh_cli.batch.manifest import (
     BATCH_JOBS_BASE,
     JobStatus,
     load_manifest,
 )
 
-import boto3
-from botocore.exceptions import ClientError
-
 logger = logging.getLogger(__name__)
 
 
@@ -107,9 +107,7 @@ class BatchClient:
         """
         try:
             if image_override:
-                job_definition = self._register_image_override(
-                    job_definition, image_override
-                )
+                job_definition = self._register_image_override(job_definition, image_override)
 
             submit_args: dict[str, Any] = {
                 "jobName": job_name,
@@ -133,9 +131,7 @@ class BatchClient:
             if command:
                 container_overrides["command"] = command
             if environment:
-                container_overrides["environment"] = [
-                    {"name": k, "value": v} for k, v in environment.items()
-                ]
+                container_overrides["environment"] = [{"name": k, "value": v} for k, v in environment.items()]
             if resource_requirements:
                 container_overrides["resourceRequirements"] = resource_requirements
             if container_overrides:
@@ -162,9 +158,7 @@ class BatchClient:
         except ClientError as e:
             raise BatchError(f"Failed to submit job: {e}")
 
-    def _register_image_override(
-        self, base_definition: str, image: str
-    ) -> str:
+    def _register_image_override(self, base_definition: str, image: str) -> str:
         """Register a new revision of a job definition with a custom image.
 
         AWS Batch containerOverrides doesn't support an image field, so we
@@ -173,14 +167,10 @@ class BatchClient:
 
         Returns the ARN of the new revision.
         """
-        resp = self.batch.describe_job_definitions(
-            jobDefinitionName=base_definition, status="ACTIVE"
-        )
+        resp = self.batch.describe_job_definitions(jobDefinitionName=base_definition, status="ACTIVE")
         definitions = resp.get("jobDefinitions", [])
         if not definitions:
-            raise BatchError(
-                f"Job definition not found: {base_definition}"
-            )
+            raise BatchError(f"Job definition not found: {base_definition}")
 
         latest = sorted(definitions, key=lambda d: d["revision"])[-1]
         container_props = latest["containerProperties"].copy()
@@ -488,9 +478,7 @@ class BatchClient:
                 timestamp = event.get("timestamp", 0)
                 message = event.get("message", "")
                 # Format timestamp
-                dt = time.strftime(
-                    "%Y-%m-%d %H:%M:%S", time.localtime(timestamp / 1000)
-                )
+                dt = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(timestamp / 1000))
                 messages.append(f"[{dt}] {message}")
 
         except ClientError as e:
@@ -498,9 +486,7 @@ class BatchClient:
 
         return messages
 
-    def wait_for_job(
-        self, job_id: str, poll_interval: int = 30, timeout: int = 86400
-    ) -> str:
+    def wait_for_job(self, job_id: str, poll_interval: int = 30, timeout: int = 86400) -> str:
         """Wait for a job to complete.
 
         Args:
@@ -530,14 +516,10 @@ class BatchClient:
             time.sleep(poll_interval)
 
 
-AWS_BATCH_UUID_PATTERN = re.compile(
-    r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"
-)
+AWS_BATCH_UUID_PATTERN = re.compile(r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$")
 
 
-def resolve_dependency(
-    job_id_or_aws_id: str, base_path: str = BATCH_JOBS_BASE
-) -> str | None:
+def resolve_dependency(job_id_or_aws_id: str, base_path: str = BATCH_JOBS_BASE) -> str | None:
     """Accept either a Dayhoff job ID (e.g. dma-embed-20260309-abc123)
     or a raw AWS Batch job ID (UUID).
 

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/boltz.py

@@ -1,7 +1,6 @@
 """Boltz structure prediction pipeline command."""
 
 import math
-import os
 import shutil
 from pathlib import Path
 
@@ -17,10 +16,9 @@ from ..manifest import (
     JobStatus,
     OutputConfig,
     create_job_directory,
-    get_job_dir,
+    save_local_stub,
     save_manifest,
     save_manifest_s3,
-    save_local_stub,
 )
 from ..s3_transport import s3_job_prefix, upload_directory
 
@@ -48,9 +46,7 @@ def _is_primordial_path(path: Path) -> bool:
     type=int,
     help="Number of parallel workers [default: ~1 per 5 files]",
 )
-@click.option(
-    "--queue", default=DEFAULT_QUEUE, help=f"Batch queue [default: {DEFAULT_QUEUE}]"
-)
+@click.option("--queue", default=DEFAULT_QUEUE, help=f"Batch queue [default: {DEFAULT_QUEUE}]")
 @click.option(
     "--msa-dir",
     type=click.Path(exists=True),
@@ -62,9 +58,7 @@ def _is_primordial_path(path: Path) -> bool:
     is_flag=True,
     help="Run single complex locally instead of Batch",
 )
-@click.option(
-    "--shell", "run_shell", is_flag=True, help="Drop into container shell for debugging"
-)
+@click.option("--shell", "run_shell", is_flag=True, help="Drop into container shell for debugging")
 @click.option(
     "--full-output",
     is_flag=True,
@@ -176,9 +170,7 @@ def _submit_batch_job(
     # Determine storage mode
     use_s3 = not _is_primordial_path(input_path)
     if use_s3 and num_files > S3_MAX_FILES:
-        click.echo(
-            f"Error: {num_files} files exceeds S3 transport limit ({S3_MAX_FILES})."
-        )
+        click.echo(f"Error: {num_files} files exceeds S3 transport limit ({S3_MAX_FILES}).")
         click.echo("Use Primordial for large jobs: copy configs to /primordial/ first.")
         raise SystemExit(1)
 
@@ -254,7 +246,7 @@ def _submit_batch_job(
             except OSError:
                 click.echo("Copying MSA directory (this may take a while)...")
                 shutil.copytree(msa_src, msa_dest)
-                click.echo(f"Copied MSA directory")
+                click.echo("Copied MSA directory")
 
     # Create manifest
     manifest = JobManifest(
@@ -342,9 +334,7 @@ def _submit_batch_job(
         click.echo()
         click.echo("After completion:")
         finalize_output = "./structures/" if use_s3 else "/primordial/structures/"
-        click.echo(
-            f"  Finalize:      dh batch finalize {job_id} --output {finalize_output}"
-        )
+        click.echo(f"  Finalize:      dh batch finalize {job_id} --output {finalize_output}")
 
     except BatchError as e:
         manifest.status = JobStatus.FAILED
@@ -374,9 +364,7 @@ def _run_local_mode(input_path: Path):
         click.echo(click.style("Error: No YAML files found", fg="red"), err=True)
         raise SystemExit(1)
 
-    click.echo(
-        f"Found {len(yaml_files)} YAML files, will process: {yaml_files[0].name}"
-    )
+    click.echo(f"Found {len(yaml_files)} YAML files, will process: {yaml_files[0].name}")
 
     # Create a temporary job directory structure
     temp_job_dir = input_path / ".local_boltz_job"
@@ -425,17 +413,13 @@ def _run_local_mode(input_path: Path):
         result = subprocess.run(cmd)
         if result.returncode != 0:
             click.echo(
-                click.style(
-                    f"Container exited with code {result.returncode}", fg="red"
-                ),
+                click.style(f"Container exited with code {result.returncode}", fg="red"),
                 err=True,
             )
             raise SystemExit(result.returncode)
 
         # Check for output
-        output_dirs = (
-            list(temp_output_dir.iterdir()) if temp_output_dir.exists() else []
-        )
+        output_dirs = list(temp_output_dir.iterdir()) if temp_output_dir.exists() else []
         if output_dirs:
             click.echo()
             click.echo(click.style("✓ Prediction complete!", fg="green"))
@@ -447,9 +431,7 @@ def _run_local_mode(input_path: Path):
 
     except FileNotFoundError:
         click.echo(
-            click.style(
-                "Error: Docker not found. Is Docker installed and running?", fg="red"
-            ),
+            click.style("Error: Docker not found. Is Docker installed and running?", fg="red"),
             err=True,
         )
         raise SystemExit(1)
@@ -460,7 +442,7 @@ def _run_shell_mode(input_path: Path):
     import subprocess
 
     click.echo("Dropping into container shell...")
-    click.echo(f"Input will be available at: /input/")
+    click.echo("Input will be available at: /input/")
     click.echo()
 
     cmd = [
@@ -494,9 +476,7 @@ def _run_shell_mode(input_path: Path):
         subprocess.run(cmd)
     except FileNotFoundError:
         click.echo(
-            click.style(
-                "Error: Docker not found. Is Docker installed and running?", fg="red"
-            ),
+            click.style("Error: Docker not found. Is Docker installed and running?", fg="red"),
             err=True,
         )
         raise SystemExit(1)

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/cancel.py

@@ -58,9 +58,7 @@ def cancel(job_id, force, base_path):
         JobStatus.FINALIZED,
         JobStatus.CANCELLED,
     ):
-        click.echo(
-            f"Job {job_id} is already {manifest.status.value}, cannot cancel.", err=True
-        )
+        click.echo(f"Job {job_id} is already {manifest.status.value}, cannot cancel.", err=True)
         raise SystemExit(1)
 
     # Get Batch job ID
@@ -79,14 +77,10 @@ def cancel(job_id, force, base_path):
 
         if force:
             click.echo(f"Terminating job {batch_job_id}...")
-            client.terminate_job(
-                batch_job_id, reason="Terminated by user via dh batch cancel --force"
-            )
+            client.terminate_job(batch_job_id, reason="Terminated by user via dh batch cancel --force")
         else:
             click.echo(f"Cancelling job {batch_job_id}...")
-            client.cancel_job(
-                batch_job_id, reason="Cancelled by user via dh batch cancel"
-            )
+            client.cancel_job(batch_job_id, reason="Cancelled by user via dh batch cancel")
 
         # Update manifest
         manifest.status = JobStatus.CANCELLED
@@ -100,13 +94,9 @@ def cancel(job_id, force, base_path):
             if retry_info.batch_job_id:
                 try:
                     if force:
-                        client.terminate_job(
-                            retry_info.batch_job_id, reason="Parent job cancelled"
-                        )
+                        client.terminate_job(retry_info.batch_job_id, reason="Parent job cancelled")
                     else:
-                        client.cancel_job(
-                            retry_info.batch_job_id, reason="Parent job cancelled"
-                        )
+                        client.cancel_job(retry_info.batch_job_id, reason="Parent job cancelled")
                     click.echo(f"  Also cancelled retry job: {retry_info.retry_id}")
                 except BatchError:
                     pass  # Retry job may already be complete
@@ -152,13 +142,9 @@ def _cancel_retry_job(manifest, retry_id: str, force: bool, base_path: str):
             )
 
         click.echo()
-        click.echo(
-            click.style(f"✓ Retry job {retry_id} cancelled successfully", fg="green")
-        )
+        click.echo(click.style(f"✓ Retry job {retry_id} cancelled successfully", fg="green"))
         click.echo(f"Parent job: {manifest.job_id}")
 
     except BatchError as e:
-        click.echo(
-            click.style(f"✗ Failed to cancel retry job: {e}", fg="red"), err=True
-        )
+        click.echo(click.style(f"✗ Failed to cancel retry job: {e}", fg="red"), err=True)
         raise SystemExit(1)

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/clean.py

@@ -10,9 +10,11 @@ from ..manifest import (
     BATCH_JOBS_BASE,
     JobStatus,
     delete_job_directory,
+)
+from ..manifest import (
     list_jobs as list_manifests,
 )
-from .status import format_time_ago, _aws_status_to_job_status
+from .status import format_time_ago
 
 LOCAL_STAGING_DIR = "/primordial/.tmp/local-train"
 
@@ -49,9 +51,7 @@ def _clean_local_staging(dry_run: bool) -> bool:
     default=7,
     help="Only clean jobs older than N days [default: 7]",
 )
-@click.option(
-    "--dry-run", is_flag=True, help="Show what would be cleaned without deleting"
-)
+@click.option("--dry-run", is_flag=True, help="Show what would be cleaned without deleting")
 @click.option("--force", is_flag=True, help="Delete without confirmation")
 @click.option("--base-path", default=BATCH_JOBS_BASE, help="Base path for job data")
 @click.option(
@@ -129,9 +129,7 @@ def clean(user, older_than, dry_run, force, base_path, local_only):
             live_statuses = client.get_job_statuses_batch(batch_job_ids)
         except BatchError as e:
             click.echo(f"Error: Could not fetch status from AWS Batch: {e}", err=True)
-            click.echo(
-                "Cannot safely clean jobs without knowing their status.", err=True
-            )
+            click.echo("Cannot safely clean jobs without knowing their status.", err=True)
             raise SystemExit(1)
 
     # Find jobs that are safe to clean (SUCCEEDED or FAILED)
@@ -156,11 +154,7 @@ def clean(user, older_than, dry_run, force, base_path, local_only):
     click.echo("-" * 65)
 
     for manifest, status in safe_to_clean:
-        click.echo(
-            f"{manifest.job_id:<35} "
-            f"{status:<12} "
-            f"{format_time_ago(manifest.created):<12}"
-        )
+        click.echo(f"{manifest.job_id:<35} {status:<12} {format_time_ago(manifest.created):<12}")
 
     click.echo()
     click.echo(f"Found {len(safe_to_clean)} completed jobs to clean.")

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/embed_t5.py

@@ -1,6 +1,5 @@
 """T5 embedding pipeline command."""
 
-import os
 import shutil
 import subprocess
 from pathlib import Path
@@ -17,10 +16,9 @@ from ..manifest import (
     JobStatus,
     OutputConfig,
     create_job_directory,
-    get_job_dir,
+    save_local_stub,
     save_manifest,
     save_manifest_s3,
-    save_local_stub,
 )
 from ..s3_transport import s3_job_prefix, upload_directory
 
@@ -45,9 +43,7 @@ def _is_primordial_path(path: Path) -> bool:
     type=int,
     help=f"Number of parallel workers [default: {DEFAULT_WORKERS}]",
 )
-@click.option(
-    "--queue", default=DEFAULT_QUEUE, help=f"Batch queue [default: {DEFAULT_QUEUE}]"
-)
+@click.option("--queue", default=DEFAULT_QUEUE, help=f"Batch queue [default: {DEFAULT_QUEUE}]")
 @click.option(
     "--seqs-per-chunk",
     default=DEFAULT_SEQS_PER_CHUNK,
@@ -60,9 +56,7 @@ def _is_primordial_path(path: Path) -> bool:
     is_flag=True,
     help="Run single chunk locally instead of Batch",
 )
-@click.option(
-    "--shell", "run_shell", is_flag=True, help="Drop into container shell for debugging"
-)
+@click.option("--shell", "run_shell", is_flag=True, help="Drop into container shell for debugging")
 @click.option("--dry-run", is_flag=True, help="Show plan without submitting")
 @click.option("--base-path", default=BATCH_JOBS_BASE, help="Base path for job data")
 @click.option("--after", "after", multiple=True, help="Job ID(s) to wait for before starting")
@@ -153,9 +147,7 @@ def _submit_batch_job(
     click.echo(f"Found {num_sequences:,} sequences")
 
     if num_sequences == 0:
-        click.echo(
-            click.style("Error: No sequences found in input file", fg="red"), err=True
-        )
+        click.echo(click.style("Error: No sequences found in input file", fg="red"), err=True)
         raise SystemExit(1)
 
     # Determine storage mode
@@ -300,9 +292,7 @@ def _submit_batch_job(
         click.echo()
         click.echo("After completion:")
         finalize_output = "./embeddings.h5" if use_s3 else "/primordial/embeddings.h5"
-        click.echo(
-            f"  Finalize:      dh batch finalize {job_id} --output {finalize_output}"
-        )
+        click.echo(f"  Finalize:      dh batch finalize {job_id} --output {finalize_output}")
 
     except BatchError as e:
         manifest.status = JobStatus.FAILED
@@ -370,9 +360,7 @@ def _run_local_mode(input_path: Path):
         result = subprocess.run(cmd)
         if result.returncode != 0:
             click.echo(
-                click.style(
-                    f"Container exited with code {result.returncode}", fg="red"
-                ),
+                click.style(f"Container exited with code {result.returncode}", fg="red"),
                 err=True,
             )
             raise SystemExit(result.returncode)
@@ -394,9 +382,7 @@ def _run_local_mode(input_path: Path):
 
     except FileNotFoundError:
         click.echo(
-            click.style(
-                "Error: Docker not found. Is Docker installed and running?", fg="red"
-            ),
+            click.style("Error: Docker not found. Is Docker installed and running?", fg="red"),
             err=True,
         )
         raise SystemExit(1)
@@ -437,9 +423,7 @@ def _run_shell_mode(input_path: Path):
         subprocess.run(cmd)
     except FileNotFoundError:
         click.echo(
-            click.style(
-                "Error: Docker not found. Is Docker installed and running?", fg="red"
-            ),
+            click.style("Error: Docker not found. Is Docker installed and running?", fg="red"),
             err=True,
         )
         raise SystemExit(1)

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/finalize.py

@@ -42,9 +42,7 @@ from ..manifest import (
     help="Skip deduplication step (use if input has no duplicates)",
 )
 @click.option("--base-path", default=BATCH_JOBS_BASE, help="Base path for job data")
-def finalize(
-    job_id, output, force, keep_intermediates, full_output, skip_dedup, base_path
-):
+def finalize(job_id, output, force, keep_intermediates, full_output, skip_dedup, base_path):
     """Combine results and clean up job intermediates.
 
     For embedding jobs, combines H5 files into a single output file.
@@ -90,7 +88,7 @@ def finalize(
         click.echo(f"Output is a directory, writing to: {output_path}")
 
     if is_s3:
-        from ..s3_transport import download_directory, delete_prefix
+        from ..s3_transport import delete_prefix, download_directory
 
         # Download outputs from S3 to a temp directory
         s3_temp_dir = Path(tempfile.mkdtemp())
@@ -113,9 +111,7 @@ def finalize(
                 shutil.rmtree(s3_temp_dir, ignore_errors=True)
             raise SystemExit(1)
         click.echo()
-        click.echo(
-            click.style("Warning: Finalizing with incomplete chunks", fg="yellow")
-        )
+        click.echo(click.style("Warning: Finalizing with incomplete chunks", fg="yellow"))
 
     # Update status
     manifest.status = JobStatus.FINALIZING
@@ -130,11 +126,7 @@ def finalize(
         _finalize_embeddings(output_dir, output_path, skip_dedup=skip_dedup)
     elif manifest.pipeline == "boltz":
         # Check if S3 essential mode was used — output is already filtered
-        s3_essential = (
-            is_s3
-            and manifest.output
-            and getattr(manifest.output, "output_mode", "full") == "essential"
-        )
+        s3_essential = is_s3 and manifest.output and getattr(manifest.output, "output_mode", "full") == "essential"
         if full_output and s3_essential:
             click.echo(
                 click.style(
@@ -183,9 +175,7 @@ def finalize(
             click.echo(f"Job directory preserved: {job_dir}")
 
 
-def _check_completion(
-    job_id: str, base_path: str, output_dir: Path | None = None
-) -> list[int]:
+def _check_completion(job_id: str, base_path: str, output_dir: Path | None = None) -> list[int]:
     """Check which chunks are incomplete (no .done marker).
 
     Handles both original chunks (chunk_000.fasta) and resliced chunks
@@ -236,15 +226,9 @@ def _check_completion(
             # Find which retry covered this index and check if complete
             is_covered = False
             for retry in manifest.retries:
-                if (
-                    retry.reslice_prefix
-                    and retry.reslice_count
-                    and idx in retry.indices
-                ):
+                if retry.reslice_prefix and retry.reslice_count and idx in retry.indices:
                     # Check if all resliced chunks for this retry completed
-                    done_count = len(
-                        list(output_dir.glob(f"embed_{retry.reslice_prefix}_*.done"))
-                    )
+                    done_count = len(list(output_dir.glob(f"embed_{retry.reslice_prefix}_*.done")))
                     if done_count >= retry.reslice_count:
                         is_covered = True
                         break
@@ -316,17 +300,13 @@ def _finalize_embeddings(output_dir: Path, output_path: Path, skip_dedup: bool =
 
         if skip_dedup:
             click.echo("Optimizing chunks...")
-            optimize_protein_embedding_chunks(
-                str(combined_path), str(output_path)
-            )
+            optimize_protein_embedding_chunks(str(combined_path), str(output_path))
         else:
             deduped_path = Path(tmpdir) / "deduped.h5"
             click.echo("Deduplicating...")
             deduplicate_h5_file(str(combined_path), str(deduped_path))
             click.echo("Optimizing chunks...")
-            optimize_protein_embedding_chunks(
-                str(deduped_path), str(output_path)
-            )
+            optimize_protein_embedding_chunks(str(deduped_path), str(output_path))
 
     click.echo(click.style("✓ H5 files combined successfully", fg="green"))
 
@@ -341,11 +321,7 @@ def _finalize_boltz(output_dir: Path, output_path: Path, full_output: bool = Fal
                     extract only essential files (CIF structures and confidence JSON).
     """
     # Find all output directories (one per complex)
-    complex_dirs = [
-        d
-        for d in output_dir.iterdir()
-        if d.is_dir() and d.name.startswith("boltz_results_")
-    ]
+    complex_dirs = [d for d in output_dir.iterdir() if d.is_dir() and d.name.startswith("boltz_results_")]
 
     if not complex_dirs:
         click.echo("No output directories found.", err=True)
@@ -393,9 +369,7 @@ def _finalize_boltz(output_dir: Path, output_path: Path, full_output: bool = Fal
 
     click.echo()
     if skipped_count > 0:
-        click.echo(
-            f"Copied {copied_count} predictions, skipped {skipped_count} existing"
-        )
+        click.echo(f"Copied {copied_count} predictions, skipped {skipped_count} existing")
     else:
         click.echo(
             click.style(
@@ -421,9 +395,7 @@ def _extract_essential_boltz_files(source_dir: Path, dest_dir: Path, complex_nam
 
     predictions_dir = source_dir / "predictions"
     if not predictions_dir.exists():
-        click.echo(
-            f"    Warning: No predictions directory found for {complex_name}", err=True
-        )
+        click.echo(f"    Warning: No predictions directory found for {complex_name}", err=True)
         return
 
     # Find all subdirectories in predictions/ (usually just one named after the complex)
@@ -495,10 +467,30 @@ def _finalize_protmpnn(output_dir: Path, output_path: Path):
                     for pdb_file in config_pdbs.glob("*.pdb"):
                         shutil.copy2(pdb_file, pdbs_dest / pdb_file.name)
 
+    scores_dest = output_path / "scores"
+    has_scores = False
+    for config_dir in output_dir.iterdir():
+        if config_dir.is_dir():
+            config_scores = config_dir / "scores"
+            if config_scores.exists():
+                if not has_scores:
+                    scores_dest.mkdir(exist_ok=True)
+                    has_scores = True
+                for score_file in config_scores.iterdir():
+                    if score_file.is_file():
+                        shutil.copy2(score_file, scores_dest / score_file.name)
+            config_stats = config_dir / "stats"
+            if config_stats.exists():
+                if not has_scores:
+                    scores_dest.mkdir(exist_ok=True)
+                    has_scores = True
+                for pt_file in config_stats.glob("*.pt"):
+                    shutil.copy2(pt_file, scores_dest / pt_file.name)
+
+    if has_scores:
+        click.echo(f"Scores:  {scores_dest}/")
+
     top_conf = merged.iloc[0]["overall_confidence"] if num_variants > 0 else "N/A"
 
-    click.echo(
-        f"{num_variants} variants from {num_configs} config(s), "
-        f"top confidence: {top_conf}"
-    )
+    click.echo(f"{num_variants} variants from {num_configs} config(s), top confidence: {top_conf}")
     click.echo(click.style(f"Results: {output_path / 'results.csv'}", fg="green"))

{dh_cli-0.5.0 → dh_cli-0.5.2}/src/dh_cli/batch/commands/list_jobs.py

@@ -3,8 +3,9 @@
 import click
 
 from ..aws_batch import BatchClient, BatchError
-from ..manifest import BATCH_JOBS_BASE, JobStatus, list_jobs as list_manifests
-from .status import format_status, format_time_ago, _aws_status_to_job_status
+from ..manifest import BATCH_JOBS_BASE, JobStatus
+from ..manifest import list_jobs as list_manifests
+from .status import _aws_status_to_job_status, format_status, format_time_ago
 
 
 @click.command("list")
@@ -16,9 +17,7 @@ from .status import format_status, format_time_ago, _aws_status_to_job_status
     help="Filter by status",
 )
 @click.option("--pipeline", help="Filter by pipeline type")
-@click.option(
-    "--limit", default=20, type=int, help="Maximum number of jobs to show [default: 20]"
-)
+@click.option("--limit", default=20, type=int, help="Maximum number of jobs to show [default: 20]")
 @click.option("--base-path", default=BATCH_JOBS_BASE, help="Base path for job data")
 def list_jobs(user, status_filter, pipeline, limit, base_path):
     """List recent batch jobs.
@@ -98,9 +97,7 @@ def list_jobs(user, status_filter, pipeline, limit, base_path):
 
     # Print header
     click.echo()
-    click.echo(
-        f"{'JOB ID':<35} {'STATUS':<12} {'PIPELINE':<12} {'USER':<10} {'CREATED':<12}"
-    )
+    click.echo(f"{'JOB ID':<35} {'STATUS':<12} {'PIPELINE':<12} {'USER':<10} {'CREATED':<12}")
     click.echo("-" * 85)
 
     for manifest, live_status in display_data: