dyno-phi 0.2.0__tar.gz → 0.2.3__tar.gz

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/.claude/skills/phi/SKILL.md

@@ -63,8 +63,6 @@ phi research \
   --dataset-id <ID>
 
 # Stream results live
-phi research --question "..." --stream
-
 # Append notes to a local file and cloud storage
 phi research --question "..." --notes-file ./research.md --dataset-id <ID>
 

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/CHANGELOG.md

@@ -7,6 +7,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.3] - 2026-03-17
+
+### Added
+- `phi research` now accepts `--dataset_id` (underscore) as an alias for `--dataset-id` — consistent with all other commands
+- `phi notes` command implemented: fetches and displays accumulated research notes for a dataset
+
+### Changed
+- `phi design` (`rfdiffusion3`) and `phi boltzgen` no longer appear in `phi --help` or usage line — they remain accessible internally via `DYNO_ENABLE_DESIGN=1`
+
+### Fixed
+- Missing imports (`_request`, `PhiApiError`, `Panel`, `Markdown`, `_C_BLUE`, `_C_SAND`, `json`) in `phi notes` command
+- mypy `Cannot assign to a method` error replaced with a proper `_FilteredSubParsersAction` subclass
+
+## [0.2.2] - 2026-03-17
+
+### Added
+- `phi tutorial` — downloads example PD-L1 binder structures from the API and prints a step-by-step scoring walkthrough
+
+### Fixed
+- GCS internal paths (`gs://...`) no longer shown in status output, research notes, or `phi fetch` results
+- `phi design` / `phi boltzgen` feature-flagged behind `DYNO_ENABLE_DESIGN=1` env var
+- macOS SSL certificate error when downloading tutorial files via signed URLs
+
 ## [0.2.0] - 2026-03-17
 
 ### Added

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/CLI-REFERENCE.md

@@ -5,7 +5,7 @@ Submit and monitor computational biology jobs, manage datasets, run structure
 prediction and inverse-folding pipelines, and download results — all from your
 terminal.
 
-**Version:** 0.2.0 · **Package:** `dyno-phi` · **Requires:** Python ≥ 3.9
+**Version:** 0.2.2 · **Package:** `dyno-phi` · **Requires:** Python ≥ 3.9
 
 ---
 
@@ -679,7 +679,6 @@ phi research --question QUESTION [options]
 | `--dataset-id ID` | — | Associate notes with a dataset and sync to cloud storage |
 | `--notes-file FILE` | `./research.md` | Local append-only notes file |
 | `--no-save` | — | Skip saving the report to the local notes file |
-| `--stream` | — | Stream results live via SSE (skips job tracking) |
 
 **Examples:**
 ```bash

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dyno-phi
-Version: 0.2.0
+Version: 0.2.3
 Summary: Phi CLI and biomodals for the dyno protein design platform
 Project-URL: Homepage, https://dynotx.com
 Project-URL: Repository, https://github.com/dynotx/phi-cli
@@ -97,43 +97,34 @@ phi login
 
 ## Quick start
 
-### Single-sequence / single-structure jobs
+### Try the tutorial
 
-```bash
-# Structure prediction (ESMFold)
-phi folding --fasta sequences.fasta
-
-# Complex structure prediction (AlphaFold2 multimer)
-phi complex_folding --fasta binder_target.fasta
+The fastest way to get started — downloads five example PD-L1 binder structures
+and walks you through the full pipeline:
 
-# Sequence design via inverse folding (ProteinMPNN)
-phi inverse_folding --pdb design.pdb --num-sequences 20
+```bash
+phi tutorial
 ```
 
-### Batch scoring workflow
+This fetches the example files, prints step-by-step instructions, and leaves
+you ready to run `phi filter`.
+
+### Scoring your own structures
 
 ```bash
-# 1. Upload a directory of PDB/CIF files
+# 1. Upload PDB/CIF files
 phi upload ./designs/
 
-# Output:
-#   dataset_id  d7c3a1b2-...
-#   Dashboard:  https://design.dynotx.com/dashboard/datasets/d7c3a1b2-...
-#   Run a job against this dataset:
-#     phi folding          --dataset-id d7c3a1b2-...
-#     phi complex_folding  --dataset-id d7c3a1b2-...
-#     phi inverse_folding  --dataset-id d7c3a1b2-...
-#     phi filter           --dataset-id d7c3a1b2-... --preset default --wait
-
-# 2. Run the full filter pipeline (inverse folding → folding → complex folding → score)
-phi filter --dataset-id d7c3a1b2-... --preset default --wait
+# 2. Run the full filter pipeline
+phi filter --preset default --wait
 
-# 3. Download results (structures, scores CSV, raw score JSONs)
+# 3. View scores and download results
+phi scores
 phi download --out ./results/
 ```
 
-After each command, `phi` prints the active dataset and job IDs and a link to
-the dashboard:
+After each command, `phi` prints the active dataset and a link to the
+dashboard:
 
 ```
 Active: dataset [d7c3a1b2-...] · job [cb4553f5-...]
@@ -146,6 +137,7 @@ Dashboard: https://design.dynotx.com/dashboard/datasets/d7c3a1b2-...
 
 | Command | Alias | Description |
 |---|---|---|
+| `phi tutorial` | — | Download example structures and print a step-by-step walkthrough |
 | `phi login` | — | Verify API key and print identity |
 | `phi upload` | — | Upload PDB/CIF files or a directory |
 | `phi fetch` | — | Download a structure from RCSB PDB or AlphaFold DB, crop, and optionally upload |

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/README.md

@@ -56,43 +56,34 @@ phi login
 
 ## Quick start
 
-### Single-sequence / single-structure jobs
+### Try the tutorial
 
-```bash
-# Structure prediction (ESMFold)
-phi folding --fasta sequences.fasta
-
-# Complex structure prediction (AlphaFold2 multimer)
-phi complex_folding --fasta binder_target.fasta
+The fastest way to get started — downloads five example PD-L1 binder structures
+and walks you through the full pipeline:
 
-# Sequence design via inverse folding (ProteinMPNN)
-phi inverse_folding --pdb design.pdb --num-sequences 20
+```bash
+phi tutorial
 ```
 
-### Batch scoring workflow
+This fetches the example files, prints step-by-step instructions, and leaves
+you ready to run `phi filter`.
+
+### Scoring your own structures
 
 ```bash
-# 1. Upload a directory of PDB/CIF files
+# 1. Upload PDB/CIF files
 phi upload ./designs/
 
-# Output:
-#   dataset_id  d7c3a1b2-...
-#   Dashboard:  https://design.dynotx.com/dashboard/datasets/d7c3a1b2-...
-#   Run a job against this dataset:
-#     phi folding          --dataset-id d7c3a1b2-...
-#     phi complex_folding  --dataset-id d7c3a1b2-...
-#     phi inverse_folding  --dataset-id d7c3a1b2-...
-#     phi filter           --dataset-id d7c3a1b2-... --preset default --wait
-
-# 2. Run the full filter pipeline (inverse folding → folding → complex folding → score)
-phi filter --dataset-id d7c3a1b2-... --preset default --wait
+# 2. Run the full filter pipeline
+phi filter --preset default --wait
 
-# 3. Download results (structures, scores CSV, raw score JSONs)
+# 3. View scores and download results
+phi scores
 phi download --out ./results/
 ```
 
-After each command, `phi` prints the active dataset and job IDs and a link to
-the dashboard:
+After each command, `phi` prints the active dataset and a link to the
+dashboard:
 
 ```
 Active: dataset [d7c3a1b2-...] · job [cb4553f5-...]
@@ -105,6 +96,7 @@ Dashboard: https://design.dynotx.com/dashboard/datasets/d7c3a1b2-...
 
 | Command | Alias | Description |
 |---|---|---|
+| `phi tutorial` | — | Download example structures and print a step-by-step walkthrough |
 | `phi login` | — | Verify API key and print identity |
 | `phi upload` | — | Upload PDB/CIF files or a directory |
 | `phi fetch` | — | Download a structure from RCSB PDB or AlphaFold DB, crop, and optionally upload |

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/phi-plugin/skills/phi/SKILL.md

@@ -63,8 +63,6 @@ phi research \
   --dataset-id <ID>
 
 # Stream results live
-phi research --question "..." --stream
-
 # Append notes to a local file and cloud storage
 phi research --question "..." --notes-file ./research.md --dataset-id <ID>
 

dyno_phi-0.2.3/src/phi/_version.py

@@ -0,0 +1 @@
+__version__ = "0.2.3"

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/cli.py

@@ -16,6 +16,7 @@ from phi.commands.models import (
 )
 from phi.commands.research import cmd_notes, cmd_research
 from phi.commands.structure import cmd_fetch
+from phi.commands.tutorial import cmd_tutorial
 from phi.config import _load_state
 from phi.display import _C_BLUE, _die, console
 from phi.parser import build_parser
@@ -23,6 +24,7 @@ from phi.types import PhiApiError
 
 COMMANDS = {
     "login": cmd_login,
+    "tutorial": cmd_tutorial,
     "upload": cmd_upload,
     "ingest-session": cmd_ingest_session,
     "datasets": cmd_datasets,

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/commands/models.py

@@ -1,4 +1,7 @@
+from __future__ import annotations
+
 import argparse
+import os
 from pathlib import Path
 
 from phi.api import _require_key, _submit
@@ -6,6 +9,13 @@ from phi.display import _die, _print_status, _print_submission, console
 from phi.download import _download_job, _read_fasta
 from phi.polling import _poll
 
+_DESIGN_ENABLED = os.environ.get("DYNO_ENABLE_DESIGN", "").lower() in ("1", "true", "yes")
+
+
+def _require_design_flag() -> None:
+    if not _DESIGN_ENABLED:
+        _die("This command is not yet available.")
+
 
 def _run_model_job(job_type: str, params: dict, args: argparse.Namespace) -> None:
     from phi.config import POLL_INTERVAL as _INTERVAL
@@ -92,6 +102,7 @@ def cmd_boltz(args: argparse.Namespace) -> None:
 
 
 def cmd_rfdiffusion3(args: argparse.Namespace) -> None:
+    _require_design_flag()
     params: dict = {
         "num_designs": args.num_designs,
         "inference_steps": args.steps,
@@ -129,6 +140,7 @@ def cmd_rfdiffusion3(args: argparse.Namespace) -> None:
 
 
 def cmd_boltzgen(args: argparse.Namespace) -> None:
+    _require_design_flag()
     params: dict = {
         "protocol": args.protocol,
         "num_designs": args.num_designs,

dyno_phi-0.2.3/src/phi/commands/research.py

@@ -0,0 +1,90 @@
+from __future__ import annotations
+
+import argparse
+import json
+import os
+from pathlib import Path
+
+from rich.markdown import Markdown
+from rich.panel import Panel
+
+from phi.api import _request
+from phi.display import _C_BLUE, _C_ROSE, _C_SAND, _die, console
+from phi.research import _stream_research
+from phi.types import PhiApiError
+
+_ERROR_REPORT_PREFIXES = ("# Research Failed", "# Error", "Error: Command failed")
+
+
+def _is_error_report(report: str) -> bool:
+    stripped = report.strip()
+    return any(stripped.startswith(prefix) for prefix in _ERROR_REPORT_PREFIXES)
+
+
+def cmd_research(args: argparse.Namespace) -> None:
+    notes_file: Path | None = None if args.no_save else Path(args.notes_file)
+    dataset_id: str | None = args.dataset_id
+
+    stream_url = os.environ.get("DYNO_RESEARCH_STREAM_URL") or args.url
+
+    context: str | None = None
+    if args.context_file:
+        try:
+            prior = Path(args.context_file).read_text(encoding="utf-8")
+            existing = args.context or ""
+            context = (prior + "\n\n" + existing).strip() if existing else prior
+        except Exception as exc:
+            console.print(f"[{_C_ROSE}]Warning: could not read context file:[/] {exc}")
+    elif args.context:
+        context = args.context
+
+    _stream_research(
+        question=args.question,
+        base_url=stream_url,
+        notes_file=notes_file,
+        dataset_id=dataset_id,
+        context=context,
+    )
+
+
+def cmd_notes(args: argparse.Namespace) -> None:
+    dataset_id: str = args.dataset_id
+
+    try:
+        data = _request("GET", f"/datasets/{dataset_id}/research-notes")
+    except PhiApiError as exc:
+        _die(str(exc))
+
+    if not data.get("exists"):
+        console.print(f"[{_C_ROSE}]No research notes found[/] for dataset {dataset_id}")
+        return
+
+    content: str = data.get("content") or ""
+    data.get("gcs_url")
+    data.get("gcs_uri")
+
+    if args.out:
+        out = Path(args.out)
+        if out.suffix.lower() == ".md":
+            dest = out
+        else:
+            out.mkdir(parents=True, exist_ok=True)
+            dest = out / "research.md"
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        dest.write_text(content, encoding="utf-8")
+        console.print(f"[{_C_SAND}]Notes saved[/] → {dest}")
+        return
+
+    if args.json:
+        print(json.dumps(data, indent=2))
+        return
+
+    console.print()
+    console.print(
+        Panel(
+            Markdown(content),
+            title=f"[{_C_BLUE}]Research Notes[/] — {dataset_id[:8]}…",
+            border_style=_C_BLUE,
+            padding=(1, 2),
+        )
+    )

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/commands/structure.py

@@ -153,14 +153,12 @@ def _fetch_and_upload(
         ("Source  ", source_url),
         ("File    ", str(out_path)),
         ("Dataset ", dataset_id),
-        ("GCS URI ", gcs_uri),
     ]:
         console.print(f"  [bold]{label}[/bold] {value}")
     console.print()
     console.print("  [dim]Next steps:[/dim]")
-    console.print(
-        f"  [dim]  phi design --target-pdb-gcs {gcs_uri} --hotspots <A45,A67> --num-designs 50[/dim]"
-    )
+    console.print(f"  [dim]  phi upload {out_path}[/dim]")
+    console.print("  [dim]  phi filter --preset default --wait[/dim]")
     console.rule()
 
 

dyno_phi-0.2.3/src/phi/commands/tutorial.py

@@ -0,0 +1,88 @@
+from __future__ import annotations
+
+import argparse
+import urllib.request
+from pathlib import Path
+
+from phi.api import _request
+from phi.config import _save_state, _ssl_context
+from phi.display import _C_BLUE, _C_SAND, _die, console
+
+
+def cmd_tutorial(args: argparse.Namespace) -> None:
+    out = Path(args.out)
+
+    # ── 1. Fetch manifest (standard Clerk JWT auth, same as all endpoints) ───
+    console.print("[dim]Fetching tutorial dataset …[/]")
+    try:
+        manifest = _request("GET", "/tutorial")
+    except Exception as exc:
+        _die(
+            f"Could not reach the tutorial endpoint: {exc}\n"
+            "  Check your connection and API key, then try again."
+        )
+
+    files: list[dict] = manifest.get("files", [])
+    dataset_id: str | None = manifest.get("dataset_id")
+    message: str | None = manifest.get("message")
+
+    if not files:
+        _die("No tutorial files returned by the API.")
+
+    # ── 2. Download each file (plain HTTP — signed URLs are self-authenticating)
+    out.mkdir(parents=True, exist_ok=True)
+    console.print(f"  Downloading {len(files)} file(s) to [{_C_BLUE}]{out}/[/] …\n")
+
+    for entry in files:
+        filename: str = entry["filename"]
+        url: str = entry["url"]
+        dest = out / filename
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        try:
+            req = urllib.request.Request(url)
+            with urllib.request.urlopen(req, context=_ssl_context()) as resp:
+                dest.write_bytes(resp.read())
+            console.print(f"  [bold {_C_SAND}]✓[/]  {filename}")
+        except Exception as exc:
+            _die(f"Failed to download {filename}: {exc}")
+
+    # ── 3. Cache dataset_id so phi filter needs zero extra flags ─────────────
+    if dataset_id:
+        _save_state({"dataset_id": dataset_id})
+        console.print(
+            f"\n[dim]dataset_id [{_C_BLUE}]{dataset_id}[/] cached — "
+            f"run [bold]phi filter[/] to start scoring.[/]"
+        )
+
+    # ── 4. Print step-by-step guide ──────────────────────────────────────────
+    if message:
+        console.print(f"\n[dim]{message}[/]")
+
+    if dataset_id:
+        upload_step = "[dim]  (skipped — dataset already ready)[/]"
+    else:
+        upload_step = f"  [{_C_SAND}]phi upload {out}/[/]"
+
+    console.print(f"""
+[bold]── Tutorial: PD-L1 binder scoring pipeline ──────────────────[/]
+
+You have {len(files)} example binder structures in [{_C_BLUE}]{out}/[/].
+
+[bold]Step 1 — Upload[/]
+{upload_step}
+
+[bold]Step 2 — Run the filter pipeline[/]
+  [{_C_SAND}]phi filter --preset default --wait[/]
+
+  Runs:  ProteinMPNN → ESMFold → AlphaFold2 → score
+  Typical runtime: 10–30 min for {len(files)} structures.
+
+[bold]Step 3 — View scores[/]
+  [{_C_SAND}]phi scores[/]
+
+[bold]Step 4 — Download results[/]
+  [{_C_SAND}]phi download --out ./results[/]
+
+[bold]Dashboard[/]
+  [{_C_BLUE}]https://design.dynotx.com/dashboard[/]
+""")

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/display.py

@@ -272,7 +272,8 @@ def _print_status(s: dict) -> None:
         table.add_column("filename", style=_C_BLUE, no_wrap=True)
         table.add_column("type", style="dim")
         for f in files[:10]:
-            fname = f.get("filename") or f.get("gcs_url", "?")
+            raw = f.get("filename") or f.get("gcs_url", "?")
+            fname = raw.split("/")[-1] if raw.startswith("gs://") else raw
             ftype = f.get("artifact_type", "")
             table.add_row(fname, ftype)
         if len(files) > 10:

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/parser.py

@@ -1,18 +1,21 @@
+from __future__ import annotations
+
 import argparse
 
 from phi._version import __version__
 from phi.config import _FILTER_PRESETS, POLL_INTERVAL
 
 _CLI_EPILOG = """\
+Quick start:
+  phi tutorial               # download example structures + print step-by-step guide
+  phi filter --preset default --wait
+  phi scores
+  phi download --out ./results
+
 Fetch and prepare target structures:
   phi fetch --pdb 4ZQK --chain A --residues 56-290 --out target.pdb
   phi fetch --uniprot Q9NZQ7 --trim-low-confidence 70 --upload
 
-Design (backbone generation):
-  phi design      --target-pdb target.pdb --hotspots A45,A67 --num-designs 50
-  phi design      --length 80 --num-designs 20
-  phi boltzgen    --yaml design.yaml --protocol protein-anything --num-designs 10
-
 Validation (fold + score):
   phi esmfold     --fasta sequences.fasta
   phi alphafold   --fasta complex.fasta
@@ -20,10 +23,10 @@ Validation (fold + score):
   phi esm2        --fasta sequences.fasta
   phi boltz       --fasta complex.fasta
 
-Batch filter pipeline (100-50,000 designs):
-  phi upload --dir ./designs/ --file-type pdb
-  phi filter --dataset-id <id> --preset default --wait
-  phi download   --out ./results
+Batch filter pipeline:
+  phi upload ./designs/
+  phi filter --preset default --wait
+  phi download --out ./results
 
 Dataset management:
   phi datasets               # list your datasets
@@ -43,6 +46,8 @@ def _add_fasta_args(p: argparse.ArgumentParser) -> None:
     g.add_argument("--fasta-str", metavar="FASTA", help="FASTA content as a string (for scripting)")
     g.add_argument(
         "--dataset-id",
+        "--dataset_id",
+        dest="dataset_id",
         metavar="DATASET_ID",
         help="Pre-ingested dataset ID (for batch runs of 100–50,000 files)",
     )
@@ -54,6 +59,8 @@ def _add_pdb_args(p: argparse.ArgumentParser) -> None:
     g.add_argument("--pdb-gcs", metavar="URI", help="Cloud storage URI to PDB (gs://…)")
     g.add_argument(
         "--dataset-id",
+        "--dataset_id",
+        dest="dataset_id",
         metavar="DATASET_ID",
         help="Pre-ingested dataset ID (for batch runs of 100–50,000 files)",
     )
@@ -232,6 +239,13 @@ def _add_boltzgen_args(p: argparse.ArgumentParser) -> None:
     )
 
 
+class _FilteredSubParsersAction(argparse._SubParsersAction):
+    """Subparser action that omits choices with help=SUPPRESS from help output."""
+
+    def _get_subactions(self) -> list[argparse.Action]:
+        return [a for a in self._choices_actions if a.help is not argparse.SUPPRESS]
+
+
 def build_parser() -> argparse.ArgumentParser:
     root = argparse.ArgumentParser(
         prog="phi",
@@ -251,8 +265,20 @@ def build_parser() -> argparse.ArgumentParser:
         metavar="S",
         help=f"Seconds between status-poll requests (default: {POLL_INTERVAL})",
     )
+    root.register("action", "parsers", _FilteredSubParsersAction)
     sub = root.add_subparsers(dest="command", required=True)
 
+    p = sub.add_parser(
+        "tutorial",
+        help="Download example structures and print a step-by-step scoring walkthrough",
+    )
+    p.add_argument(
+        "--out",
+        metavar="DIR",
+        default="examples",
+        help="Directory to download example files into (default: ./examples)",
+    )
+
     p = sub.add_parser("login", help="Verify API key and print connection + identity details")
     p.add_argument("--json", action="store_true")
 
@@ -415,14 +441,14 @@ def build_parser() -> argparse.ArgumentParser:
     p = sub.add_parser(
         "rfdiffusion3",
         aliases=["design"],
-        help="All-atom backbone generation: binder design, de novo, motif scaffolding (2–5 min/design)",
+        help=argparse.SUPPRESS,
     )
     _add_rfdiffusion3_args(p)
     _add_job_args(p)
 
     p = sub.add_parser(
         "boltzgen",
-        help="All-atom generative design from a YAML spec — proteins, peptides, small molecules (10–20 min)",
+        help=argparse.SUPPRESS,
     )
     _add_boltzgen_args(p)
     _add_job_args(p)
@@ -469,7 +495,9 @@ def build_parser() -> argparse.ArgumentParser:
     )
     p.add_argument(
         "--dataset-id",
+        "--dataset_id",
         metavar="ID",
+        dest="dataset_id",
         help="Associate notes with a dataset and sync to cloud storage",
     )
     p.add_argument(
@@ -482,17 +510,12 @@ def build_parser() -> argparse.ArgumentParser:
         "--no-save", action="store_true", help="Skip saving the report to the local notes file"
     )
     p.add_argument(
-        "--stream",
-        action="store_true",
-        help="Stream results live from Modal SSE endpoint (skips job tracking)",
-    )
-    p.add_argument(
-        "--stream-url",
+        "--url",
         metavar="URL",
         default="https://dynotx--research-agent-streaming-fastapi-app.modal.run",
-        help="Override the SSE base URL",
+        help="Override the SSE streaming base URL",
     )
-    _add_job_args(p)
+    p.add_argument("--out", metavar="DIR", help="Save report and citations to DIR")
 
     p = sub.add_parser("notes", help="View accumulated research notes for a dataset")
     p.add_argument(
@@ -547,6 +570,8 @@ def build_parser() -> argparse.ArgumentParser:
     )
     p.add_argument(
         "--dataset-id",
+        "--dataset_id",
+        dest="dataset_id",
         default=None,
         metavar="ID",
         help="Dataset of PDB/CIF designs (default: cached from last upload or `phi use`)",
@@ -640,4 +665,8 @@ def build_parser() -> argparse.ArgumentParser:
     p.add_argument("--out", metavar="FILE", help="Save scores CSV to file")
     p.add_argument("--json", action="store_true", help="Output raw JSON")
 
+    # Hide internal/unreleased commands from the usage line.
+    _hidden_cmds = {"rfdiffusion3", "design", "boltzgen"}
+    sub.metavar = "{" + ",".join(c for c in sub.choices if c not in _hidden_cmds) + "}"
+
     return root

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/src/phi/research.py

@@ -150,13 +150,14 @@ def _stream_research(
     max_turns: int = 15,
     notes_file: Path | None = None,
     dataset_id: str | None = None,
+    context: str | None = None,
 ) -> None:
-    url = f"{base_url.rstrip('/')}/research/stream?" + urllib.parse.urlencode(
-        {"question": question, "max_turns": max_turns}
-    )
+    params: dict = {"question": question, "max_turns": max_turns}
+    if context:
+        params["context"] = context
+    url = f"{base_url.rstrip('/')}/research/stream?" + urllib.parse.urlencode(params)
 
-    console.print(f"\n[{_C_BLUE}]Connecting to research stream…[/]")
-    console.print(f"[dim]{url}[/]\n")
+    console.print(f"\n[{_C_BLUE}]Connecting to research stream…[/]\n")
 
     state = _ResearchStreamState()
     req = urllib.request.Request(url, headers={"Accept": "text/event-stream"})

{dyno_phi-0.2.0 → dyno_phi-0.2.3}/tests/test_research.py

@@ -3,6 +3,7 @@ from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
 
+from phi.commands.research import _is_error_report
 from phi.research import (
     _build_research_section,
     _dispatch_sse_event,
@@ -85,6 +86,31 @@ def test_build_research_section_includes_citations() -> None:
     assert "Sources (2)" in section
 
 
+def test_is_error_report_detects_research_failed() -> None:
+    report = "# Research Failed\n\nError: Command failed with exit code 1"
+    assert _is_error_report(report) is True
+
+
+def test_is_error_report_detects_error_header() -> None:
+    assert _is_error_report("# Error\n\nSomething went wrong") is True
+
+
+def test_is_error_report_detects_bare_error_prefix() -> None:
+    assert _is_error_report("Error: Command failed with exit code 1") is True
+
+
+def test_is_error_report_passes_valid_report() -> None:
+    assert _is_error_report("# AAV Biology\n\nAAVs are...") is False
+
+
+def test_is_error_report_passes_empty() -> None:
+    assert _is_error_report("") is False
+
+
+def test_is_error_report_handles_leading_whitespace() -> None:
+    assert _is_error_report("  # Research Failed\n\nError") is True  # strip() normalises whitespace
+
+
 def test_build_research_section_handles_invalid_citations() -> None:
     section = _build_research_section("query", "report", "not-valid-json")
     assert "query" in section

dyno_phi-0.2.0/src/phi/_version.py

@@ -1 +0,0 @@
-__version__ = "0.2.0"

dyno_phi-0.2.0/src/phi/commands/research.py

@@ -1,145 +0,0 @@
-from __future__ import annotations
-
-import argparse
-import json
-from pathlib import Path
-
-from rich.markdown import Markdown
-from rich.panel import Panel
-
-import phi.config as config
-from phi.api import _request, _submit
-from phi.display import _C_BLUE, _C_ROSE, _C_SAND, _die, _print_status, _print_submission, console
-from phi.download import _download_job
-from phi.polling import _poll
-from phi.research import _append_research_notes, _stream_research
-from phi.types import PhiApiError
-
-
-def cmd_research(args: argparse.Namespace) -> None:
-    notes_file: Path | None = None if args.no_save else Path(args.notes_file)
-    dataset_id: str | None = args.dataset_id
-
-    if args.stream:
-        _stream_research(
-            question=args.question,
-            base_url=args.stream_url,
-            notes_file=notes_file,
-            dataset_id=dataset_id,
-        )
-        return
-
-    params: dict = {
-        "question": args.question,
-        "databases": [d.strip() for d in args.databases.split(",") if d.strip()],
-        "max_papers": args.max_papers,
-        "include_structures": args.structures,
-    }
-    if args.target:
-        params["target"] = args.target
-
-    if args.context_file:
-        try:
-            prior = Path(args.context_file).read_text(encoding="utf-8")
-            existing = args.context or ""
-            params["context"] = (prior + "\n\n" + existing).strip() if existing else prior
-        except Exception as exc:
-            console.print(f"[{_C_ROSE}]Warning: could not read context file:[/] {exc}")
-    elif args.context:
-        params["context"] = args.context
-
-    result = _submit("research", params, run_id=args.run_id)
-    _print_submission(result)
-    if args.wait:
-        console.print(f"\n[dim]Polling every {config.POLL_INTERVAL}s …[/]")
-        final = _poll(result["job_id"])
-        _print_status(final)
-
-        report = (final.get("outputs") or {}).get("report_md")
-        citations_raw = (final.get("outputs") or {}).get("citations")
-
-        if report:
-            if notes_file is not None:
-                _append_research_notes(
-                    notes_file=notes_file,
-                    question=args.question,
-                    report=report,
-                    citations_raw=citations_raw,
-                    dataset_id=dataset_id,
-                )
-
-            if args.out:
-                out = Path(args.out)
-                out.mkdir(parents=True, exist_ok=True)
-                (out / "research_report.md").write_text(report)
-                console.print(f"\n[{_C_SAND}]Report written[/] → {out}/research_report.md")
-                if citations_raw:
-                    try:
-                        citations = json.loads(citations_raw)
-                        (out / "citations.json").write_text(json.dumps(citations, indent=2))
-                        console.print(f"[{_C_SAND}]Citations written[/] → {out}/citations.json")
-                    except Exception:
-                        pass
-            else:
-                console.print("\n" + "─" * 60)
-                console.print(report)
-                if citations_raw:
-                    try:
-                        citations = json.loads(citations_raw)
-                        console.print(f"\n[{_C_BLUE}]Sources ({len(citations)})[/]")
-                        for i, src in enumerate(citations[:10], 1):
-                            title = src.get("title") or src.get("pmid") or str(src)
-                            console.print(f"  [{_C_BLUE}]{i}.[/] {title}")
-                        if len(citations) > 10:
-                            console.print(f"  [dim]… and {len(citations) - 10} more[/]")
-                    except Exception:
-                        pass
-        elif args.out and final.get("status") == "completed":
-            _download_job(final, args.out)
-
-
-def cmd_notes(args: argparse.Namespace) -> None:
-    dataset_id: str = args.dataset_id
-
-    try:
-        data = _request("GET", f"/datasets/{dataset_id}/research-notes")
-    except PhiApiError as exc:
-        _die(str(exc))
-
-    if not data.get("exists"):
-        console.print(f"[{_C_ROSE}]No research notes found[/] for dataset {dataset_id}")
-        return
-
-    content: str = data.get("content") or ""
-    gcs_url: str | None = data.get("gcs_url")
-    gcs_uri: str | None = data.get("gcs_uri")
-
-    if args.out:
-        out = Path(args.out)
-        if out.suffix.lower() == ".md":
-            dest = out
-        else:
-            out.mkdir(parents=True, exist_ok=True)
-            dest = out / "research.md"
-        dest.parent.mkdir(parents=True, exist_ok=True)
-        dest.write_text(content, encoding="utf-8")
-        console.print(f"[{_C_SAND}]Notes saved[/] → {dest}")
-        if gcs_url:
-            console.print(f"[dim]Download URL:[/] {gcs_url}")
-        return
-
-    if args.json:
-        print(json.dumps(data, indent=2))
-        return
-
-    console.print()
-    console.print(
-        Panel(
-            Markdown(content),
-            title=f"[{_C_BLUE}]Research Notes[/] — {dataset_id[:8]}…",
-            border_style=_C_BLUE,
-            padding=(1, 2),
-        )
-    )
-    if gcs_uri:
-        console.print(f"[dim]Storage URI:[/] {gcs_uri}")