amina-cli 0.2.8__tar.gz → 0.3.0__tar.gz

{amina_cli-0.2.8 → amina_cli-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amina-cli
-Version: 0.2.8
+Version: 0.3.0
 Summary: CLI for AminoAnalytica protein engineering platform
 Project-URL: Homepage, https://aminoanalytica.com
 Project-URL: Documentation, https://docs.aminoanalytica.com

{amina_cli-0.2.8 → amina_cli-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "amina-cli"
-version = "0.2.8"
+version = "0.3.0"
 description = "CLI for AminoAnalytica protein engineering platform"
 readme = "README.md"
 license = {text = "Apache-2.0"}

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/__init__.py

@@ -9,4 +9,4 @@ Quick start:
     amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH"
 """
 
-__version__ = "0.2.8"
+__version__ = "0.3.0"

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/jobs_cmd.py

@@ -468,12 +468,20 @@ def download(
 
     # Download results
     result = status_result.get("result", {})
+
+    # Persist the structured response payload so it matches the on-disk layout
+    # produced by `amina run <tool> -o <dir>` (response.json alongside artifacts).
+    output.mkdir(parents=True, exist_ok=True)
+    response_path = output / "response.json"
+    response_path.write_text(json.dumps(result, indent=2, default=str))
+
     try:
         downloaded = download_results(result, output)
         if downloaded:
             console.print(f"[green]\u2713[/green] Downloaded {len(downloaded)} file(s) to {output}/")
             for path in downloaded:
                 console.print(f"  - {path.name}")
+            console.print(f"  - {response_path.name}")
             # Also display tool response data alongside files
             if result.get("data"):
                 from amina_cli.commands.tools import get_tool
@@ -482,6 +490,7 @@ def download(
                 tool_metadata = get_tool(job_info.get("tool_name", ""))
                 render_tool_output(result, tool_metadata)
         else:
+            console.print(f"[green]\u2713[/green] Saved response to {response_path}")
             # Show tool response data even when there are no files
             if result.get("data"):
                 from amina_cli.commands.tools import get_tool
@@ -496,6 +505,7 @@ def download(
         signed_urls = result.get("signed_urls", {})
         if signed_urls:
             console.print(f"[yellow]Warning:[/yellow] Could not download automatically: {e}")
+            console.print(f"[dim]Response saved to {response_path}[/dim]")
             console.print("\n[bold]Files available at:[/bold]")
             for file_type, url in signed_urls.items():
                 if url:

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/__init__.py

@@ -6,6 +6,7 @@ Each tool file exports METADATA dict and register() function.
 """
 
 import importlib
+import json
 from pathlib import Path
 from typing import Iterator, Optional
 import typer
@@ -91,7 +92,7 @@ def run_tool_with_progress(
     Args:
         tool_name: Name of the tool to run
         params: Tool-specific parameters
-        output_dir: Directory to save output files (required unless background=True)
+        output_dir: Directory to save output files (required)
         timeout: Request timeout in seconds (default: 10 hours)
         background: If True, submit job and return immediately without waiting
     """
@@ -106,6 +107,10 @@ def run_tool_with_progress(
     from amina_cli.registry import ToolNotFoundError
     from amina_cli.storage import download_results, StorageError
 
+    if output_dir is None:
+        console.print("[red]Error:[/red] --output / -o is required")
+        raise typer.Exit(1)
+
     # Handle background submission
     if background:
         try:
@@ -125,6 +130,11 @@ def run_tool_with_progress(
             # Save to local job history
             save_job(result)
 
+            # Persist the structured submission payload for downstream agents/scripts
+            output_dir.mkdir(parents=True, exist_ok=True)
+            submission_path = output_dir / "submission.json"
+            submission_path.write_text(json.dumps(result, indent=2, default=str))
+
             # Handle queued vs submitted status
             if result.get("status") == "queued":
                 queue_position = result.get("queue_position", 0)
@@ -136,6 +146,7 @@ def run_tool_with_progress(
                 console.print(f"\n[green]\u2713[/green] Job submitted: [bold]{result['job_id']}[/bold]")
                 console.print(f"  Tool: {display_name}")
                 console.print(f"  Call ID: {result.get('call_id', 'N/A')}")
+            console.print(f"[dim]Submission saved to {submission_path}[/dim]")
             console.print(f"\n[dim]Check status:[/dim]  amina jobs status {result['job_id'][:8]}")
             console.print(f"[dim]Wait for completion:[/dim]  amina jobs wait {result['job_id'][:8]}")
             console.print(f"[dim]Download results:[/dim]  amina jobs download {result['job_id'][:8]} -o <output_dir>")
@@ -277,7 +288,13 @@ def run_tool_with_progress(
                 else:
                     console.print(f"\n[yellow]Warning:[/yellow] Download failed: {e}")
 
-        _display_result(result, downloaded, output_dir, params, tool_info)
+            # Persist the structured response payload (success or failure) so agents
+            # and scripts can read metrics/warnings/cost without re-parsing stdout.
+            output_dir.mkdir(parents=True, exist_ok=True)
+            response_path = output_dir / "response.json"
+            response_path.write_text(json.dumps(result, indent=2, default=str))
+
+        _display_result(result, downloaded, output_dir, params, tool_info, response_path)
 
     except AuthenticationError as e:
         console.print(
@@ -405,6 +422,7 @@ def _display_result(
     output_dir: Path,
     input_params: dict | None = None,
     metadata: dict | None = None,
+    response_path: Path | None = None,
 ):
     """Display tool execution result using the generic renderer."""
     status = result.get("status", "unknown")
@@ -414,13 +432,16 @@ def _display_result(
         exec_time = result.get("execution_time_seconds", 0)
         time_str = f" ({exec_time:.1f}s)" if exec_time else ""
 
+        console.print(f"\n[green]\u2713[/green] Completed{time_str}")
         if downloaded:
-            console.print(f"\n[green]\u2713[/green] Completed{time_str}")
             console.print(f"[green]\u2713[/green] Downloaded {len(downloaded)} file(s) to {output_dir}/")
             for path in downloaded:
                 console.print(f"  - {path.name}")
-        else:
-            console.print(f"\n[green]\u2713[/green] Completed{time_str}")
+            if response_path is not None:
+                console.print(f"  - {response_path.name}")
+        elif response_path is not None:
+            console.print(f"[green]\u2713[/green] Saved to {output_dir}/")
+            console.print(f"  - {response_path.name}")
 
         # Show cost charged (from gateway)
         cost_usd = result.get("cost_usd") or result.get("credits_charged", 0)
@@ -493,3 +514,5 @@ def _display_result(
                 border_style="red",
             )
         )
+        if response_path is not None:
+            console.print(f"[dim]Response saved to {response_path}[/dim]")

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/hydrophobicity.py

@@ -31,7 +31,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -68,8 +68,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools hydrophobicity"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read PDB file content

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/mmseqs2_cluster.py

@@ -48,7 +48,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         job_name: Optional[str] = typer.Option(
             None,
@@ -65,8 +65,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools mmseqs2-cluster"""
         # Validate output
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate at least one FASTA file

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/residue_accessibility.py

@@ -31,7 +31,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         residues: Optional[str] = typer.Option(
             None,
@@ -65,8 +65,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools residue-accessibility"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate residue format if provided

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/rmsd.py

@@ -71,7 +71,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -88,8 +88,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools rmsd-analysis"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read file contents

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/sasa.py

@@ -31,7 +31,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -53,8 +53,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools sasa"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read PDB file content

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/simple_rmsd.py

@@ -48,7 +48,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -65,8 +65,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools simple-rmsd"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read file contents

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/surface_charge.py

@@ -31,7 +31,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -104,8 +104,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools surface-charge"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate forcefield

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/analysis/usalign.py

@@ -63,7 +63,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -80,8 +80,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools usalign"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate mode

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/design/esm_if1.py

@@ -72,7 +72,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -89,8 +89,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools esm-if1"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate mode

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/design/protein_mc.py

@@ -55,7 +55,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -71,9 +71,9 @@ def register(app: typer.Typer):
         ),
     ):
         """For full documentation including parameters, metrics, and usage: amina tools protein-mc"""
-        # Validate output is provided unless --background
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        # Validate output is provided
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate input

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/design/proteinmpnn.py

@@ -70,7 +70,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -87,8 +87,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools proteinmpnn"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read PDB file content

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/design/rfdiffusion.py

@@ -42,7 +42,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -274,9 +274,9 @@ def register(app: typer.Typer):
                     console.print(f"[red]Invalid JSON in --advanced-config: {e}[/red]")
                     raise typer.Exit(1)
 
-        # Validate output is provided unless --background
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        # Validate output is provided
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Run the tool

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/boltz2.py

@@ -8,6 +8,7 @@ import typer
 from pathlib import Path
 from typing import List, Optional, Set, Tuple
 from rich.console import Console
+from amina_cli.commands.tools.doccard import load_doccard
 
 
 def parse_sequence_with_chain_id(value: str, used_chains: Set[str]) -> Tuple[Optional[str], str, bool]:
@@ -56,8 +57,6 @@ def parse_sequence_with_chain_id(value: str, used_chains: Set[str]) -> Tuple[Opt
 
 # METADATA loaded from doccard YAML — the single source of truth for tool documentation.
 # Parameter definitions are canonical in docs/boltz2.yaml — keep in sync with Typer options below.
-from amina_cli.commands.tools.doccard import load_doccard
-
 METADATA = load_doccard("folding", "boltz2")
 
 console = Console()

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/docs/openfold3.yaml

@@ -238,15 +238,12 @@ output_metrics:
   ipsae:
     display_name: ipSAE
     description: |
-      **ipSAE** (Interface Predicted Symmetrized Alignment Error) scores
-      protein-protein interfaces using the Dunbrack Lab algorithm. Unlike
-      ipTM, it uses only interchain residue pairs with low PAE (< 10 A
-      cutoff), normalizing by the number of confident interface residues
-      rather than total sequence length. This makes it insensitive to
-      disordered regions and non-interacting domains. Returns a dictionary
-      with six variants: d0res_max/min, d0chn_max/min, d0dom_max/min.
-      The primary metric for binder screening is **d0res_min** (worst
-      direction's best residue normalization).
+      **ipSAE** (Interaction prediction Score from Aligned Errors) scores
+      protein-protein interfaces using only interchain residue pairs with
+      low PAE, normalizing by the number of confident interface residues
+      rather than total sequence length. Unlike ipTM, it is insensitive
+      to disordered regions and non-interacting domains. Computed directly
+      from the PAE matrix output by the structure prediction model.
     range: [0, 1]
     interpretation: |
       - d0res_min > 0.5: Confident interface — strong predicted contacts

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/docs/protenix.yaml

@@ -304,9 +304,9 @@ output_metrics:
       non-protein entities (ligands, DNA, RNA, ions) are excluded.
     range: [0, 1]
     interpretation: |
-      - >0.5: Confident interface — strong predicted contacts
-      - 0.3-0.5: Moderate interface confidence
-      - <0.3: Weak or uncertain interface
+      - >0.7: Confident interface — strong predicted contacts
+      - 0.5-0.7: Moderate interface confidence
+      - <0.5: Weak or uncertain interface
 
   ipsae_per_chain_pair:
     display_name: ipSAE per Chain Pair

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/esmfold.py

@@ -37,7 +37,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         job_name: Optional[str] = typer.Option(
             None,
@@ -54,8 +54,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools esmfold"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate input

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/openfold3.py

@@ -9,6 +9,7 @@ import typer
 from pathlib import Path
 from typing import List, Optional, Set, Tuple
 from rich.console import Console
+from amina_cli.commands.tools.doccard import load_doccard
 
 
 def parse_sequence_with_chain_id(value: str, used_chains: Set[str]) -> Tuple[Optional[str], str]:
@@ -48,8 +49,6 @@ def parse_sequence_with_chain_id(value: str, used_chains: Set[str]) -> Tuple[Opt
 
 # METADATA loaded from doccard YAML — the single source of truth for tool documentation.
 # Parameter definitions are canonical in docs/openfold3.yaml — keep in sync with Typer options below.
-from amina_cli.commands.tools.doccard import load_doccard
-
 METADATA = load_doccard("folding", "openfold3")
 
 console = Console()
@@ -177,7 +176,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         job_name: Optional[str] = typer.Option(
             None,
@@ -194,8 +193,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools openfold3"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate quality preset

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/folding/protenix.py

@@ -5,6 +5,7 @@ import typer
 from pathlib import Path
 from typing import List, Optional, Set, Tuple, Union
 from rich.console import Console
+from amina_cli.commands.tools.doccard import load_doccard
 
 
 def parse_sequence_with_chain_id(value: str, used_chains: Set[str]) -> Tuple[Optional[str], str]:
@@ -54,8 +55,6 @@ def _auto_chain_id(used_chains: Set[str]) -> str:
 
 # METADATA loaded from doccard YAML — the single source of truth for tool documentation.
 # Parameter definitions are canonical in docs/protenix.yaml — keep in sync with Typer options below.
-from amina_cli.commands.tools.doccard import load_doccard
-
 METADATA = load_doccard("folding", "protenix")
 
 console = Console()
@@ -222,7 +221,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         job_name: Optional[str] = typer.Option(
             None,
@@ -285,8 +284,8 @@ def register(app: typer.Typer):
         ions = ions or []
 
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Count entities from flags

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/interactions/autodock_vina.py

@@ -104,7 +104,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -121,8 +121,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools autodock-vina"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate ligand input (exactly one of --ligand or --smiles)

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/interactions/diffdock.py

@@ -70,7 +70,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -87,8 +87,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools diffdock"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Validate protein input (exactly one required)

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/interactions/dockq.py

@@ -51,7 +51,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -68,8 +68,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools dockq"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read file contents

{amina_cli-0.2.8 → amina_cli-0.3.0}/src/amina_cli/commands/tools/interactions/emngly.py

@@ -39,7 +39,7 @@ def register(app: typer.Typer):
             None,
             "--output",
             "-o",
-            help="Output directory for results (required unless --background)",
+            help="Output directory for results (required)",
         ),
         background: bool = typer.Option(
             False,
@@ -56,8 +56,8 @@ def register(app: typer.Typer):
     ):
         """For full documentation including parameters, metrics, and usage: amina tools emngly"""
         # Validate required options
-        if output is None and not background:
-            console.print("[red]Error:[/red] --output / -o is required (unless using --background)")
+        if output is None:
+            console.print("[red]Error:[/red] --output / -o is required")
             raise typer.Exit(1)
 
         # Read PDB file content