rowan-python 3.1.6__tar.gz → 3.1.7__tar.gz

{rowan_python-3.1.6 → rowan_python-3.1.7}/.claude-plugin/marketplace.json

@@ -9,7 +9,7 @@
     {
       "name": "computational-chemistry-and-biology",
       "source": "./skills/computational-chemistry-and-biology",
-      "description": "Run computational chemistry and structural biology calculations on the Rowan platform via the rowan Python package",
+      "description": "Run computational chemistry and structural biology calculations through Rowan MCP tools or rowan-python",
       "skills": ["./"],
       "strict": false
     }

{rowan_python-3.1.6 → rowan_python-3.1.7}/.codex-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "computational-chemistry-and-biology",
-  "version": "0.0.1",
-  "description": "Run computational chemistry and structural biology calculations on the Rowan platform via the rowan-python package",
+  "version": "0.0.2",
+  "description": "Run computational chemistry and structural biology calculations through Rowan MCP tools or rowan-python",
   "skills": "./skills/",
   "author": {
     "name": "Rowan",
@@ -20,7 +20,7 @@
   "interface": {
     "displayName": "Rowan Computational Chemistry",
     "shortDescription": "Run computational chemistry and structural biology workflows with Rowan.",
-    "longDescription": "Use Rowan to choose and run molecular and protein workflows, including quantum chemistry, docking, molecular dynamics, protein structure prediction, and cheminformatics. The bundled skill provides workflow selection guidance, safe defaults, result retrieval patterns, and links to detailed workflow references.",
+    "longDescription": "Use Rowan to choose and run molecular and protein workflows, including quantum chemistry, docking, molecular dynamics, protein structure prediction, and cheminformatics. The bundled skill provides shared scientific and workflow guidance for Rowan MCP tools and rowan-python, including safe defaults, result retrieval patterns, and detailed references.",
     "developerName": "Rowan",
     "category": "Science",
     "capabilities": [

{rowan_python-3.1.6 → rowan_python-3.1.7}/.github/workflows/test.yml

@@ -31,3 +31,4 @@ jobs:
       - run: pixi run fmt
       - run: pixi run lint
       - run: pixi run types
+      - run: pixi run test

{rowan_python-3.1.6 → rowan_python-3.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.6
+Version: 3.1.7
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -30,9 +30,27 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 ## Agent skill
 
-Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
+Ships with a [computational chemistry and biology skill](skills/computational-chemistry-and-biology/)
+that helps coding agents choose and run Rowan workflows through either Rowan MCP tools or the
+Rowan Python SDK.
 
-Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+### Claude Code
+
+```bash
+claude plugin marketplace add https://github.com/rowansci/rowan-python.git
+claude plugin install computational-chemistry-and-biology@rowan
+```
+
+### Codex
+
+```bash
+codex plugin marketplace add rowansci/rowan-python --ref master
+codex plugin add computational-chemistry-and-biology@rowan
+```
+
+Start a new Claude Code or Codex session after installation. For manual installation, download the
+[latest skill ZIP](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip)
+and extract it into your agent's skills directory.
 
 ## Running examples
 

{rowan_python-3.1.6 → rowan_python-3.1.7}/README.md

@@ -14,9 +14,27 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 ## Agent skill
 
-Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
+Ships with a [computational chemistry and biology skill](skills/computational-chemistry-and-biology/)
+that helps coding agents choose and run Rowan workflows through either Rowan MCP tools or the
+Rowan Python SDK.
 
-Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+### Claude Code
+
+```bash
+claude plugin marketplace add https://github.com/rowansci/rowan-python.git
+claude plugin install computational-chemistry-and-biology@rowan
+```
+
+### Codex
+
+```bash
+codex plugin marketplace add rowansci/rowan-python --ref master
+codex plugin add computational-chemistry-and-biology@rowan
+```
+
+Start a new Claude Code or Codex session after installation. For manual installation, download the
+[latest skill ZIP](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip)
+and extract it into your agent's skills directory.
 
 ## Running examples
 

{rowan_python-3.1.6 → rowan_python-3.1.7}/pixi.lock

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+      - pypi: https://files.pythonhosted.org/packages/6b/2c/222ba12a545189017120f8eddfc1a0bd4616b47d5d4a8d99421edb2fe4c6/coverage-7.15.2-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/77/f5/21d2de20e8b8b0408f0681956ca2c69f1320a3848ac50e6e7f39c6159675/babel-2.18.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/79/7b/2c79738432f5c924bef5071f933bcc9efd0473bac3b4aa584a6f7c1c8df8/mypy_extensions-1.1.0-py3-none-any.whl
@@ -286,6 +285,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/9e/c3/059298687310d527a58bb01f3b1965787ee3b40dce76752eda8b44e9a2c5/pexpect-4.9.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a0/c4/c2971a3ba4c6103a3d10c4b0f24f461ddc027f0f09763220cf35ca1401b3/nest_asyncio-1.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a0/f4/c67b0b3f1b9245e8d266f0f112c500d50e5b4e83cb6f3b71b6528104182a/requests-2.34.2-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/a6/d7/f6824ea5fc0ac2bcded7fb2626aa7a851a7f487645d5ae7b10f585f935a7/stjames-0.0.230-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/ad/1f/8970b150a4b4365623ae00fc88603491f763c627311ae8031e3111356d6e/pydantic_core-2.46.4-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/b5/64/7660f8a4a8e53c924d0fa05dc3a55c9cee10bbd82b11c5afb27d44b096ce/markupsafe-3.0.3-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
@@ -854,13 +854,6 @@ packages:
   requires_dist:
   - click>=5.0 ; extra == 'cli'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/13/d2/ee14d715889f216baf47301d9f469e08fff6995552aaf67e897b282865f6/coverage-7.15.1-cp314-cp314-macosx_11_0_arm64.whl
-  name: coverage
-  version: 7.15.1
-  sha256: 985657ebd707941de90d488d1cbb5efac20bdf81f7b91eba771624ccda4d36f4
-  requires_dist:
-  - tomli ; python_full_version <= '3.11' and extra == 'toml'
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/15/14/2ba1d61452d7c2a7fe12741e8d374e52b183476b07aa7f9e2a0d02b0720a/mypy-2.3.0-cp314-cp314-macosx_11_0_arm64.whl
   name: mypy
   version: 2.3.0
@@ -1023,17 +1016,6 @@ packages:
   requires_dist:
   - numpy
   - pillow
-- pypi: https://files.pythonhosted.org/packages/30/b1/1a42ac1eada0a193ecdaa17ce92efa6354bfdcf315c42aaafa69f237ae59/stjames-0.0.228-py3-none-any.whl
-  name: stjames
-  version: 0.0.228
-  sha256: 52f444feabe0dbe4fa3fe23a18a4e5cf0da2b45dd4ee32a023a431eaf176a464
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/3d/50/51c76d74014d04fb95b6506d286808984b78a2f7a41039094e6b2194ac48/librt-0.13.0-cp314-cp314-macosx_11_0_arm64.whl
   name: librt
   version: 0.13.0
@@ -1260,6 +1242,20 @@ packages:
   - markupsafe>=2.0
   - babel>=2.7 ; extra == 'i18n'
   requires_python: '>=3.7'
+- pypi: https://files.pythonhosted.org/packages/6b/2c/222ba12a545189017120f8eddfc1a0bd4616b47d5d4a8d99421edb2fe4c6/coverage-7.15.2-cp314-cp314-macosx_11_0_arm64.whl
+  name: coverage
+  version: 7.15.2
+  sha256: 075560438765b7a2ef43bf7aa7758661b53d889df47f062a31bda6c1ade553a2
+  requires_dist:
+  - tomli ; python_full_version <= '3.11' and extra == 'toml'
+  requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/6c/58/821b533b8db9e44cf1d8a97bd525149ced40dde1d0093da02cb78e715244/coverage-7.15.2-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+  name: coverage
+  version: 7.15.2
+  sha256: b9a6367e4aff723e8ee8190836836124284e8fcd4265e307c844010cfa074f3f
+  requires_dist:
+  - tomli ; python_full_version <= '3.11' and extra == 'toml'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/77/f5/21d2de20e8b8b0408f0681956ca2c69f1320a3848ac50e6e7f39c6159675/babel-2.18.0-py3-none-any.whl
   name: babel
   version: 2.18.0
@@ -1558,6 +1554,17 @@ packages:
   - pysocks>=1.5.6,!=1.5.7 ; extra == 'socks'
   - chardet>=3.0.2,<8 ; extra == 'use-chardet-on-py3'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/a6/d7/f6824ea5fc0ac2bcded7fb2626aa7a851a7f487645d5ae7b10f585f935a7/stjames-0.0.230-py3-none-any.whl
+  name: stjames
+  version: 0.0.230
+  sha256: 003fdbfc703542d6a34fcaca2e6f1575cc8bd0db2a56646bd63ed82e0fd05522
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/ad/1f/8970b150a4b4365623ae00fc88603491f763c627311ae8031e3111356d6e/pydantic_core-2.46.4-cp314-cp314-macosx_11_0_arm64.whl
   name: pydantic-core
   version: 2.46.4
@@ -1821,13 +1828,6 @@ packages:
   version: '26.2'
   sha256: 5fc45236b9446107ff2415ce77c807cee2862cb6fac22b8a73826d0693b0980e
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/e1/53/0d3dd963631259d794c898735d5436e68d6a8d40749c419a07ff7c171469/coverage-7.15.1-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
-  name: coverage
-  version: 7.15.1
-  sha256: bde0fe24083d0b7b3dbafa7a09f0796410af1afa2523f28f5f208d8340a4aaca
-  requires_dist:
-  - tomli ; python_full_version <= '3.11' and extra == 'toml'
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/e4/d3/5268aeabf2ad82658c4e2ff3a060648d0f02f3926cb53247c0e4d0dab49e/griffelib-2.1.0-py3-none-any.whl
   name: griffelib
   version: 2.1.0

{rowan_python-3.1.6 → rowan_python-3.1.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.6"
+version = "3.1.7"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.1.6 → rowan_python-3.1.7}/rowan/protein.py

@@ -400,22 +400,20 @@ def upload_protein(
     if isinstance(project_uuid, Project):
         project_uuid = project_uuid.uuid
     with api_client() as client:
-        # Step 1: Read the file and post it to the conversion endpoint.
         conversion_payload = {"name": name, "text": file_path.read_text()}
         conversion_response = client.post("/convert/pdb_file_to_protein", json=conversion_payload)
+        conversion_response.raise_for_status()
 
-        # Extract the JSON data from the conversion response.
         protein_data = conversion_response.json()
 
-        # Step 2: Use the converted data to create the final protein object.
         creation_payload = {
             "name": name,
             "protein_data": protein_data,
             "project_uuid": project_uuid,
         }
         final_response = client.post("/protein", json=creation_payload)
+        final_response.raise_for_status()
 
-        # Deserialize the final JSON response into a Protein object and return it.
         return Protein(**final_response.json())
 
 

rowan_python-3.1.7/rowan/test_utils.py

@@ -0,0 +1,54 @@
+"""Tests for Rowan request utilities."""
+
+import asyncio
+
+from pytest import MonkeyPatch, raises
+
+import rowan
+from rowan.utils import api_credentials, get_api_key, get_project_uuid
+
+
+def test_api_credentials_override_global_configuration(monkeypatch: MonkeyPatch) -> None:
+    """Prefer context-local credentials without changing global configuration."""
+    monkeypatch.setattr(rowan, "api_key", "global-key")
+    monkeypatch.setattr(rowan, "project_uuid", "global-project")
+    monkeypatch.setenv("ROWAN_API_KEY", "environment-key")
+
+    with api_credentials("context-key", project_uuid="context-project"):
+        assert get_api_key() == "context-key"
+        assert get_project_uuid() == "context-project"
+
+    assert get_api_key() == "global-key"
+    assert get_project_uuid() == "global-project"
+
+
+def test_api_credentials_restore_nested_context() -> None:
+    """Restore outer credentials after a nested context exits."""
+    with api_credentials("outer-key", project_uuid="outer-project"):
+        with api_credentials("inner-key"):
+            assert get_api_key() == "inner-key"
+            assert get_project_uuid() is None
+
+        assert get_api_key() == "outer-key"
+        assert get_project_uuid() == "outer-project"
+
+
+def test_api_credentials_isolate_async_tasks() -> None:
+    """Keep credentials isolated across concurrent asynchronous tasks."""
+
+    async def read_after_yield(api_key: str) -> str:
+        with api_credentials(api_key):
+            await asyncio.sleep(0)
+            return get_api_key()
+
+    async def run_workers() -> list[str]:
+        return list(await asyncio.gather(read_after_yield("first"), read_after_yield("second")))
+
+    assert asyncio.run(run_workers()) == ["first", "second"]
+
+
+def test_api_credentials_reject_empty_key() -> None:
+    """Reject empty context-local API keys."""
+    with raises(ValueError, match="cannot be empty"):
+        with api_credentials(""):
+            pass

{rowan_python-3.1.6 → rowan_python-3.1.7}/rowan/utils.py

@@ -1,5 +1,7 @@
 import os
 from contextlib import contextmanager
+from contextvars import ContextVar
+from dataclasses import dataclass
 from typing import Generator
 
 import httpx
@@ -10,6 +12,40 @@ import rowan
 from .constants import API_URL
 
 
+@dataclass(frozen=True, slots=True)
+class _APIContext:
+    """Store credentials isolated to the current execution context."""
+
+    api_key: str
+    project_uuid: str | None
+
+
+_api_context: ContextVar[_APIContext | None] = ContextVar("rowan_api_context", default=None)
+
+
+@contextmanager
+def api_credentials(api_key: str, project_uuid: str | None = None) -> Generator[None, None, None]:
+    """Temporarily use Rowan credentials in the current execution context.
+
+    Context-local credentials take precedence over module-level and environment configuration.
+    Nested contexts restore the previous credentials when they exit, and concurrent threads or
+    asynchronous tasks remain isolated from one another.
+
+    :param api_key: Rowan API key
+    :param project_uuid: active project UUID, if any
+    :yields: control while the credentials are active
+    :raises ValueError: API key is empty
+    """
+    if not api_key:
+        raise ValueError("API key cannot be empty.")
+
+    token = _api_context.set(_APIContext(api_key=api_key, project_uuid=project_uuid))
+    try:
+        yield
+    finally:
+        _api_context.reset(token)
+
+
 def get_api_key() -> str:
     """
     Get the API key from the environment variable ROWAN_API_KEY or the module-level attribute
@@ -19,6 +55,8 @@ def get_api_key() -> str:
 
     :returns: API key.
     """
+    if (context := _api_context.get()) is not None:
+        return context.api_key
     if hasattr(rowan, "api_key") and rowan.api_key:
         return rowan.api_key
     elif (api_key := os.environ.get("ROWAN_API_KEY")) is not None:
@@ -36,6 +74,8 @@ def get_project_uuid() -> str | None:
 
     :returns: Project UUID string, or None if not set.
     """
+    if (context := _api_context.get()) is not None:
+        return context.project_uuid
     if hasattr(rowan, "project_uuid") and rowan.project_uuid:
         return rowan.project_uuid
     return None

{rowan_python-3.1.6 → rowan_python-3.1.7}/skills/computational-chemistry-and-biology/SKILL.md

@@ -1,76 +1,22 @@
 ---
 name: computational-chemistry-and-biology
-description: Run computational chemistry and structural biology calculations on the Rowan platform via the `rowan` Python package. Use when the user wants to run Rowan workflows, or mentions Rowan, computational chemistry, structural biology, or molecular or protein simulation.
+description: Run computational chemistry and structural biology calculations on the Rowan platform through Rowan MCP tools or the `rowan` Python package. Use when the user wants to run Rowan workflows, or mentions Rowan, computational chemistry, structural biology, or molecular or protein simulation.
 ---
 
 # Computational Chemistry and Biology with Rowan
 
-Run simulations on the [Rowan](https://rowansci.com) platform via the `rowan` Python package. Every workflow follows the same flow: build an input, submit a workflow, then retrieve the result.
+Run simulations on the [Rowan](https://rowansci.com) platform through Rowan MCP tools or the `rowan` Python package. This skill provides shared scientific strategy and workflow guidance for both interfaces.
 
-**Package is for syntax, skill is for strategy.** For exact arguments, defaults, and valid values, introspect the installed package with `python3 -c "import rowan; help(rowan.submit_pka_workflow)"` (any name works). This skill tells you which workflow to use and recommends settings. If a value here is rejected, trust the package.
+**Interfaces are for syntax; skill is for strategy.** Use this skill and its workflow references to choose scientifically appropriate methods and settings. Trust `discover_workflow` or the installed package when an exact parameter differs from a reference.
 
-## Setup
+## Choose an interface
 
-Do this before calling the Rowan API. Use the resulting env's python for every later step.
+Both interfaces are first-class. Use the shared scientific guidance and workflow references below with either one.
 
-**1. Install `rowan`** (PyPI: `rowan-python`). Skip if `python3 -c "import rowan"` already succeeds. Otherwise add it through the project's env manager so it survives syncs. A bare `pip install` into a managed env gets wiped:
+- **MCP-connected chat:** when Rowan tools are available, read [MCP execution](reference/mcp_execution.md) before calling them. Do not install Python or request an API key; authentication belongs to the MCP connection. Use `discover_workflow` as the exact parameter contract.
+- **Python code, scripts, or notebooks:** when the user requests Python or no Rowan MCP tools are available, read [Python SDK](reference/python_sdk.md) before writing or running code. Trust the installed package when its exact API differs from an example.
 
-- **uv** (`uv.lock`): `uv add rowan-python`, then run with `uv run python`
-- **pixi** (`pixi.toml`): `pixi add --pypi rowan-python`, then `pixi run python`
-- **poetry** (`poetry.lock`): `poetry add rowan-python`, then `poetry run python`
-- **plain venv or system**: `python3 -m pip install rowan-python`
-
-**2. Set the key and verify.** Put `ROWAN_API_KEY=your-key-here` in a project `.env` (gitignored, and create a key at https://labs.rowansci.com/account), then run the preflight. It finds the nearest `.env`, validates the key against the API, and prints remaining credits (workflows cost credits). Run it from your project root, where `.env` lives, and point it at this skill's base dir rather than `cd`-ing into the skill:
-
-`python3 "<skill_dir>/scripts/check_env.py"`
-
-It exits with actionable guidance on each failure: a **missing** key (add it via `echo 'ROWAN_API_KEY=...' >> .env`), a **rejected** key (a 401, meaning invalid or expired, so regenerate it and stop to tell the user), or an **unreachable** API. Since shell state doesn't persist between commands, load `.env` in the same command as every later call, like `[ -f .env ] && set -a && source .env && set +a; <python ...>`, or set `rowan.api_key = os.environ["ROWAN_API_KEY"]` in Python.
-
-## Run & retrieve
-
-Every workflow is submitted and retrieved the same way, regardless of type. `submit_*_workflow(...)` returns a `Workflow` immediately, and results are fetched separately.
-
-```python
-import rowan
-
-folder = rowan.get_folder("my-project")          # path created if it doesn't exist
-wf = rowan.submit_<workflow>_workflow(            # see its reference file (Workflows below) for scientific args
-    ...,                                          # workflow-specific arguments
-    folder=folder,
-    name="my run",
-)
-result = wf.result()                              # blocks until done, returns a typed result
-```
-
-**Universal submit arguments.** On top of its scientific arguments, every `submit_*_workflow` accepts these, and they are not repeated in the per-workflow files:
-
-- `folder=` (or `folder_uuid=`) sets where the run lands. `rowan.get_folder("a/b/c")` returns the folder, creating the path if missing. For a specific project or benchmark, make a dedicated folder (e.g. `get_folder("project-name")`, with subpaths like `"project-name/docking"` for sub-experiments) and route all its runs there, so results stay grouped and easy to retrieve later. To browse or navigate an existing folder tree, or switch projects, see [reference/folders_and_projects.md](reference/folders_and_projects.md).
-- `name=` sets the label shown in the Rowan UI.
-- `max_credits=` caps the credits (≈ minutes of compute) a run may use — its runtime limit. Hitting it, or running out of credits, stops the run **permanently** (methods like DFT can't resume), so set it high enough to finish.
-- `webhook_url=` makes Rowan POST the result there on completion. See [reference/webhooks.md](reference/webhooks.md) if you're setting up webhooks.
-- `is_draft=True` stages the run without starting it, for estimation (below).
-
-**Three ways to retrieve results:**
-
-- **Block (default):** `result = wf.result()` waits (polling every 5 s) and returns a typed result. It raises `rowan.WorkflowError` if the run **failed** or was **stopped**, so catch it to report failures.
-- **Partial or progress:** `wf.result(wait=False)` returns whatever is ready now. `for r in wf.stream_result():` yields partial results each poll, then the final one.
-- **Fire-and-forget:** keep `wf.uuid`, let the session end, and reconnect later with `rowan.retrieve_workflow(uuid).result()`. `rowan.list_workflows()` lists recent runs. The UUID from `labs.rowansci.com/calculation/<uuid>` is a workflow UUID — use `retrieve_workflow`, not `retrieve_calculation`.
-
-**Inline calls vs. scripts.** Quick questions or retrieving a single result are fine inline with submit-and-wait (`.result()`). For long-running or multi-step work like experiments or benchmarks, put the calls in a script for reproducibility, and prefer a fire-and-forget run plus `retrieve_workflow(uuid)` later or a `webhook_url=` callback rather than blocking the session.
-
-**Estimate cost and runtime before committing.** Submit as a draft (nothing runs), inspect, then commit or discard:
-
-```python
-draft = rowan.submit_<workflow>_workflow(..., folder=folder, is_draft=True)
-print(draft.dispatch_info())   # DispatchInfo(to_be_dispatched, compute_hardware, estimated_runtime_minutes)
-draft.submit_draft()           # commit to running it  (or draft.delete() to discard)
-```
-
-**Status and control** (non-blocking): `wf.done()` and `wf.get_status()` check state without waiting, `wf.stop()` cancels a running workflow, and `wf.delete()` removes it and its data.
-
-**Resubmit and re-run.** Re-run from a settings dict with the generic `rowan.submit_workflow(workflow_type, workflow_data, initial_molecule=..., folder=folder)`. Pass a prior run's `result.data` unchanged for an identical re-run (insulated from later default or preset changes), edit the dict to change settings, or change `workflow_type` (with matching `workflow_data`) to submit as a different workflow.
-
-**Resubmit with a perturbed geometry.** `mol.perturb()` adds small Gaussian noise to break symmetry or escape a stuck optimization. `mol.displace_along_mode(mode, displacement)` shifts atoms along a vibrational normal mode — for a transition state, pick the imaginary mode (negative frequency) to slide toward reactant or product; requires `frequencies=True` in a prior calculation. See `examples/resubmit_with_perturbations.py`.
+For project or folder management, also read [folders and projects](reference/folders_and_projects.md). For callbacks, read [webhooks](reference/webhooks.md).
 
 ## Molecule inputs
 
@@ -88,9 +34,9 @@ After loading a protein with `rowan.create_protein_from_pdb_id` or `rowan.upload
 
 ## Workflows
 
-Pick the workflow matching the task by reading the descriptions, then open its reference file (linked at the end of each entry) for recommended settings and an example. Universal submit arguments (`folder`, `name`, `max_credits`, and so on) live in **Run & retrieve** above and aren't repeated per workflow.
+Pick the workflow matching the task by reading the descriptions, then open its reference file (linked at the end of each entry) for recommended settings and an example. Python's universal submit arguments live in [Python SDK](reference/python_sdk.md) and aren't repeated per workflow; MCP parameters come from `discover_workflow`.
 
-Not every key can run every workflow — `rowan.whoami().enabled_workflows` lists the types yours can submit (a few, e.g. FEP, are gated by plan).
+Not every account can run every workflow. MCP users must consult the `mcp_supported_workflows` field returned by `account_status`; Python users must consult `rowan.whoami().enabled_workflows` (a few workflows, such as FEP, are gated by plan).
 
 - **ADMET**: predict ADME-Tox properties (absorption, distribution, metabolism, excretion, toxicity) with an ML model, for fast early developability, PK, and tox triage. See [reference/admet.md](reference/admet.md).
 - **Analogue docking**: pose analogues of an already-bound reference ligand into consistent, analogous poses, to align and prepare a congeneric series, for example ahead of an RBFE screen. See [reference/analogue_docking.md](reference/analogue_docking.md).

rowan_python-3.1.7/skills/computational-chemistry-and-biology/reference/mcp_execution.md

@@ -0,0 +1,15 @@
+# MCP execution
+
+Use this path when Rowan MCP tools are available. Authentication is already attached to the MCP connection.
+
+1. Call `account_status` before reading workflow references. Use `mcp_supported_workflows` to limit selection and report available user and organization credits.
+2. Apply the scientific workflow guidance already selected by the entry skill. Retain its parameter rationale, interpretation guidance, caveats, and useful Python examples, but use `discover_workflow` for the exact MCP parameter contract.
+3. Call `discover_workflow` with the enabled workflow slug. Treat the returned parameter specification as authoritative; never guess an exact field name, type, default, or enum.
+4. Build a JSON `parameters` object from the user's inputs and the discovered specification. Ask only for scientifically meaningful missing values. For an attached PDB, SDF, MOL, MOL2, XYZ, EXTXYZ, or CIF file, call `import_structure` and use its `workflow_input` or returned molecule data in the discovered parameter. Inline import is for small text files; do not place a large file into model context.
+5. Call `create_workflow_draft`. This validates the inputs and creates a non-running draft. Inspect its `dispatch_estimate`, `max_credits`, and `available_credits`. If the user has not granted standing authorization that covers this workflow, its parameters, and its per-run and cumulative credit cost, review the draft with them and request approval.
+6. After specific draft approval, or when the draft remains within the user's standing authorization, call `submit_workflow_draft` with its `workflow_uuid`. Stop and request approval if its scope or cost exceeds that authorization. Preserve the UUID so the workflow can be recovered in another session.
+7. Call `workflow_status` without waiting, or set `wait_seconds` to at most 60 for bounded polling. Do not repeatedly occupy a turn waiting for a long workflow. Failed or stopped workflows include a bounded `log_tail`; report the actionable failure without dumping internal logs.
+8. Call `get_workflow_result` with no fields first. Inspect `available_fields` and `result_preview`, then request at most five desired fields per call. For nested arrays or objects, use `result_path`, `offset`, and `limit` rather than requesting the complete value.
+9. Use `get_structure_file` for PDB, XYZ, SDF, MOL, or MOL2 output from a protein or calculation reference. Use `get_workflow_file` for MSA and trajectory archives. These return deferred resources so file content is loaded only when the user or host needs it.
+
+Pass JSON-native parameters through MCP and use `import_structure` for supported structure files. If discovery requires another Rowan object and does not describe a supported JSON representation or reference, explain that limitation rather than inventing an encoding. A workflow reference remains useful when its executable example is Python: translate its scientific choices through the discovered MCP contract.