rowan-python 3.1.16__tar.gz → 3.2.1__tar.gz

rowan_python-3.2.1/.editorconfig

@@ -0,0 +1,16 @@
+# http://editorconfig.org/#file-format-details
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

rowan_python-3.2.1/.envrc

@@ -0,0 +1,6 @@
+watch_file pyproject.toml
+watch_file uv.lock
+dotenv_if_exists .env
+
+uv sync --frozen
+source .venv/bin/activate

{rowan_python-3.1.16 → rowan_python-3.2.1}/.github/workflows/build-and-deploy-docs.yml

@@ -1,8 +1,8 @@
 name: Build & Deploy Rowan Python Docs
 
 on:
-  release:
-    types: [published]
+  push:
+    branches: [master]
   workflow_dispatch:
 
 permissions:
@@ -10,23 +10,26 @@ permissions:
 
 jobs:
   build-and-deploy-docs:
+    if: github.repository == 'rowansci/rowan-python' && github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7.0.1
         with:
           fetch-depth: 0
           ref: master
 
-      - name: Install Pixi
-        uses: prefix-dev/setup-pixi@v0.9.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.2.0
         with:
-          pixi-version: "latest"
-          activate-environment: true
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --locked --no-dev --group docs
 
       - name: Build MkDocs site
-        run: pixi run mkdocs-build
+        run: uv run --no-sync mkdocs build --clean
 
       - name: Install SSH Key
         uses: shimataro/ssh-key-action@v2
@@ -39,5 +42,8 @@ jobs:
 
       - name: Deploy with rsync
         run: |
-          rsync -avz --delete ./ \
-            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:${{ secrets.DOCS_TARGET_DIR }}
+          rsync -avz --delete site/ \
+            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:${{ secrets.DOCS_TARGET_DIR }}/site/
+
+      - name: Verify deployed docs
+        run: curl --fail --silent --show-error --location --retry 5 --retry-delay 5 --retry-all-errors https://docs.rowansci.com/api/python/v3/ -o /dev/null

{rowan_python-3.1.16 → rowan_python-3.2.1}/.github/workflows/publish-skill.yml

@@ -16,7 +16,7 @@ jobs:
     if: github.repository == 'rowansci/rowan-python'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7.0.1
       - name: Zip skill
         run: cd skills && zip -r ../computational-chemistry-and-biology-skill.zip computational-chemistry-and-biology
       - name: Publish/refresh release

rowan_python-3.2.1/.github/workflows/python-publish.yml

@@ -0,0 +1,54 @@
+name: Publish
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}
+  cancel-in-progress: false
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    # Enable after configuring the repository environment.
+    # environment:
+    #   name: pypi
+    # permissions:
+    #   id-token: write
+    #   contents: read
+    steps:
+      - name: Skip if running with act
+        if: ${{ env.ACT == 'true' }}
+        run: exit 1
+
+      - name: Checkout
+        uses: actions/checkout@v7.0.1
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.2.0
+
+      - name: Install Python
+        run: uv python install
+
+      - name: Build
+        run: uv build
+
+      - name: Smoke test (wheel)
+        run: >-
+          uv run --isolated --no-project --directory "$RUNNER_TEMP"
+          --with "$GITHUB_WORKSPACE"/dist/*.whl python -c "import rowan"
+
+      - name: Smoke test (source distribution)
+        run: >-
+          uv run --isolated --no-project --directory "$RUNNER_TEMP"
+          --with "$GITHUB_WORKSPACE"/dist/*.tar.gz python -c "import rowan"
+
+      - name: Publish
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        run: uv publish

rowan_python-3.2.1/.github/workflows/test.yml

@@ -0,0 +1,55 @@
+name: Test
+
+on:
+  pull_request: {}
+  push:
+    branches: master
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.14"]
+        os: [ubuntu-latest]
+
+    name: Python ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v7.0.1
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v10.2.0
+        with:
+          enable-cache: true
+
+      - name: Install Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --locked
+
+      - name: Check TOML/YAML/whitespace
+        run: |
+          uv run -- prek run --all-files --show-diff-on-failure --color=always \
+            check-toml \
+            check-yaml \
+            trailing-whitespace \
+            end-of-file-fixer
+
+      - run: uv run rumdl fmt --check --diff .
+      - run: uv run rumdl check .
+
+      - run: uv run ruff format --check --diff .
+      - run: uv run ruff check .
+
+      - run: uv run ty check
+
+      - run: uv run pytest --cov --cov-report=xml

rowan_python-3.2.1/.gitignore

@@ -0,0 +1,66 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Packaging
+build/
+dist/
+*.egg-info/
+
+# Testing and coverage
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+
+# uv
+.venv/
+
+# rumdl
+.rumdl_cache/
+
+# direnv
+.direnv/
+
+# Editors
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.env
+.env.*
+.app.json
+
+# Documentation and notebooks
+/site/
+.ipynb_checkpoints/
+
+# Legacy environments
+.pixi/
+
+# Scientific application output
+timer.dat
+psi*.clean
+*.CP
+*.CPC
+*.lprof
+pyscf.chk
+local/
+cyp/
+msa_directory/
+
+# Local notes and machine-specific agent settings
+notes.md
+/.claude/settings.local.json

rowan_python-3.2.1/.python-version

@@ -0,0 +1 @@
+3.14

rowan_python-3.2.1/.rumdl.toml

@@ -0,0 +1,21 @@
+[global]
+
+disable = [
+    "MD013",  # line length
+    "MD033",  # no inline HTML
+]
+
+exclude = [
+    ".git",
+    ".venv",
+    "node_modules",
+    "vendor",
+    "dist",
+    "build",
+]
+
+respect-gitignore = true
+
+[per-file-ignores]
+# Skill files start with frontmatter, not headings
+"**/skills/**/*.md" = ["MD041"]

{rowan_python-3.1.16 → rowan_python-3.2.1}/PKG-INFO

@@ -1,32 +1,39 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.1.16
+Version: 3.2.1
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
-Author-email: Corin Wagen <corin@rowansci.com>
+Author-email: Corin Wagen <corin@rowansci.com>, Eli Mann <eli@rowansci.com>
+License-Expression: MIT
 License-File: LICENSE
 Requires-Python: >=3.12
 Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.261
+Requires-Dist: stjames>=0.0.275
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
 
 [![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
-[![pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
-[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://docs.astral.sh/uv/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Downloads](https://img.shields.io/pypi/dm/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python/)
+[![License](https://img.shields.io/github/license/rowansci/rowan-python)](LICENSE)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/rowansci/rowan-python/test.yml?branch=master&logo=github-actions)](https://github.com/rowansci/rowan-python/actions)
+[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty)
+[![Markdown style: rumdl](https://img.shields.io/badge/md%20style-rumdl-000000.svg)](https://rumdl.dev)
 
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+The Rowan Python library is the Python SDK for running Rowan computational chemistry workflows
+programmatically. Use it from scripts and applications to submit calculations, monitor workflow
+progress, retrieve results, and manage molecules, proteins, folders, and projects through the
+Rowan API.
 
 ## Documentation
 
-The documentation is available [here](https://docs.rowansci.com/python-api).
+Read the [Rowan Python API documentation](https://docs.rowansci.com/python-api).
 
 ## Agent skill
 
@@ -34,6 +41,9 @@ Ships with a [computational chemistry and biology skill](skills/computational-ch
 that helps coding agents choose and run Rowan workflows through either Rowan MCP tools or the
 Rowan Python SDK.
 
+When using Rowan MCP tools, always read and follow this skill and its workflow references first.
+The skill provides the scientific guidance and execution requirements for MCP workflows.
+
 ### Claude Code
 
 ```bash
@@ -74,9 +84,6 @@ and extract it into your agent's skills directory.
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.
 If running the examples in a cloned version of the repository, you can add your api key to a local `.env` file, which will automatically be loaded into the environment by direnv (if installed).
 
-
 ## Issues
 
 To report issues, please use the "Issues" tab above.
-
-*Corin Wagen, 2023*

{rowan_python-3.1.16 → rowan_python-3.2.1}/README.md

@@ -1,16 +1,22 @@
 # Rowan Python Library
 
 [![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
-[![pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
-[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://docs.astral.sh/uv/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Downloads](https://img.shields.io/pypi/dm/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python/)
+[![License](https://img.shields.io/github/license/rowansci/rowan-python)](LICENSE)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/rowansci/rowan-python/test.yml?branch=master&logo=github-actions)](https://github.com/rowansci/rowan-python/actions)
+[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty)
+[![Markdown style: rumdl](https://img.shields.io/badge/md%20style-rumdl-000000.svg)](https://rumdl.dev)
 
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+The Rowan Python library is the Python SDK for running Rowan computational chemistry workflows
+programmatically. Use it from scripts and applications to submit calculations, monitor workflow
+progress, retrieve results, and manage molecules, proteins, folders, and projects through the
+Rowan API.
 
 ## Documentation
 
-The documentation is available [here](https://docs.rowansci.com/python-api).
+Read the [Rowan Python API documentation](https://docs.rowansci.com/python-api).
 
 ## Agent skill
 
@@ -18,6 +24,9 @@ Ships with a [computational chemistry and biology skill](skills/computational-ch
 that helps coding agents choose and run Rowan workflows through either Rowan MCP tools or the
 Rowan Python SDK.
 
+When using Rowan MCP tools, always read and follow this skill and its workflow references first.
+The skill provides the scientific guidance and execution requirements for MCP workflows.
+
 ### Claude Code
 
 ```bash
@@ -58,9 +67,6 @@ and extract it into your agent's skills directory.
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.
 If running the examples in a cloned version of the repository, you can add your api key to a local `.env` file, which will automatically be loaded into the environment by direnv (if installed).
 
-
 ## Issues
 
 To report issues, please use the "Issues" tab above.
-
-*Corin Wagen, 2023*

{rowan_python-3.1.16 → rowan_python-3.2.1}/docs/index.md

@@ -1,7 +1,7 @@
-![Rowan](images/RowanLogoLarge.png){ width="320" }
-
 # Rowan Python API
 
+![Rowan](images/RowanLogoLarge.png){ width="320" }
+
 The `rowan` package is the official Python client for the [Rowan](https://rowansci.com) computational
 chemistry platform. Submit workflows, poll or stream results, and manage
 molecules, proteins, folders, and projects—all from plain Python.
@@ -10,21 +10,21 @@ molecules, proteins, folders, and projects—all from plain Python.
 
 === "pip"
 
-    ```bash
-    pip install rowan-python
-    ```
+```bash
+pip install rowan-python
+```
 
 === "pixi"
 
-    ```bash
-    pixi add --pypi rowan-python
-    ```
+```bash
+pixi add --pypi rowan-python
+```
 
 === "uv"
 
-    ```bash
-    uv add rowan-python
-    ```
+```bash
+uv add rowan-python
+```
 
 ## Authentication
 

{rowan_python-3.1.16 → rowan_python-3.2.1}/docs/workflows/basic-calculation.md

@@ -16,7 +16,7 @@ workflow = rowan.submit_basic_calculation_workflow(
 )
 ```
 
-Pass an [`OptimizationSettings`](settings.md#stjames.opt_settings.OptimizationSettings) object or
+Pass an [`OptimizationSettings`](settings.md) object or
 an equivalent dictionary to `opt_settings`. `optimize_cell` defaults to `False`; set it to `True`
 only when optimizing a periodic cell.
 

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/basic_calculation_with_solvent.py

@@ -18,6 +18,8 @@ def compute_energy_with_solvent_correction(
 
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{opt_workflow.uuid}")
     opt_result = opt_workflow.result()
+    if opt_result.molecule is None:
+        raise ValueError("Optimization returned no molecule")
 
     sp_workflow = rowan.submit_basic_calculation_workflow(
         initial_molecule=opt_result.molecule,
@@ -31,6 +33,8 @@ def compute_energy_with_solvent_correction(
     print(f"View workflow privately at: https://labs.rowansci.com/calculation/{sp_workflow.uuid}")
     sp_result = sp_workflow.result()
 
+    if sp_result.energy is None:
+        raise ValueError("Single-point calculation returned no energy")
     return sp_result.energy
 
 

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/batch_docking.py

@@ -18,7 +18,10 @@ preparation_workflow = rowan.submit_protein_preparation_workflow(
     name="Prepare CDK2",
     folder=folder,
 )
-prepared_protein_uuid = preparation_workflow.result().prepared_protein_uuid
+preparation_result = preparation_workflow.result()
+prepared_protein_uuid = preparation_result.prepared_protein_uuid
+if prepared_protein_uuid is None:
+    raise ValueError("Protein preparation returned no prepared protein")
 
 workflow = rowan.submit_batch_docking_workflow(
     ligands,

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/bde.py

@@ -1,5 +1,4 @@
-"""
-Calculate Bond-Dissociation Energies (BDE) with the Rowan API.
+"""Calculate Bond-Dissociation Energies (BDE) with the Rowan API.
 
 `mode` is a BDE method string (the level of theory):
 - "omol25_conserving_s": neural network potential (default)

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/boltz_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[rowan.MSAFormat.BOLTZ],
+    output_formats={rowan.MSAFormat.BOLTZ},
     name="Boltz Paired MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/boltz_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[rowan.MSAFormat.BOLTZ],
+    output_formats={rowan.MSAFormat.BOLTZ},
     name="Boltz MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/chai_paired_msa.py

@@ -25,7 +25,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[rowan.MSAFormat.CHAI],
+    output_formats={rowan.MSAFormat.CHAI},
     name="CHAI Paired MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/chai_single_msa.py

@@ -22,7 +22,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[rowan.MSAFormat.CHAI],
+    output_formats={rowan.MSAFormat.CHAI},
     name="CHAI MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/cofolding_screen.py

@@ -34,6 +34,8 @@ print(f"View folder privately at: https://labs.rowansci.com/folder/{folder.uuid}
 workflow_results = [(w, w.result()) for w in workflows]
 
 for workflow, result in workflow_results:
+    if result.affinity_score is None:
+        raise ValueError("Cofolding returned no affinity score")
     results[workflow.name] = result.affinity_score.probability_binary
 
 print(results)

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/colabfold_paired_msa.py

@@ -14,7 +14,7 @@ msa_workflow = rowan.submit_msa_workflow(
         "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
         "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH",
     ],
-    output_formats=[rowan.MSAFormat.COLABFOLD],
+    output_formats={rowan.MSAFormat.COLABFOLD},
     name="Colabfold Paired MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/colabfold_single_msa.py

@@ -13,7 +13,7 @@ msa_workflow = rowan.submit_msa_workflow(
     initial_protein_sequences=[
         "HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"
     ],
-    output_formats=[rowan.MSAFormat.COLABFOLD],
+    output_formats={rowan.MSAFormat.COLABFOLD},
     name="Colabfold MSA Example",
     folder=folder,
 )

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/conformer_dependent_redox.py

@@ -15,6 +15,8 @@ redox_potential_workflows = []
 
 for conformer in csearch_result.conformer_uuids[:10]:
     uuid = conformer[0]
+    if uuid is None:
+        raise ValueError("Conformer has no calculation UUID")
     molecule = rowan.retrieve_calculation_molecules(uuid)[0]
     rowan_molecule = rowan.Molecule.model_validate(molecule)
     redox_potential_workflows.append(

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/conformers.py

@@ -1,5 +1,4 @@
-"""
-Calculate the conformers of a molecule using the Rowan API.
+"""Calculate the conformers of a molecule using the Rowan API.
 
 Conformer generation defaults to OpenConf; pass `conf_gen_settings=` to choose a
 different generator (ETKDG, iMTD-GC, MCMM).

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/conformers_screen.py

@@ -1,5 +1,4 @@
-"""
-Rank a conformer ensemble you already have, using the Rowan API (screen-only mode).
+"""Rank a conformer ensemble you already have, using the Rowan API (screen-only mode).
 
 Conformer search normally *generates* conformers and then optimizes, deduplicates,
 and ranks them. If you already have 3D geometries -- from another tool (RDKit,

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/covalent_docking.py

@@ -13,7 +13,8 @@ preparation_workflow = rowan.submit_protein_preparation_workflow(
     name="Prepare TG2",
     folder=folder,
 )
-protein = preparation_workflow.result().get_prepared_protein()
+preparation_result = preparation_workflow.result()
+protein = preparation_result.get_prepared_protein()
 
 center = [-1.079, -3.081, 18.122]
 size = [22.22, 14.08, 21.74]

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/covalent_inhibitor_scan.py

@@ -16,7 +16,8 @@ preparation_workflow = rowan.submit_protein_preparation_workflow(
     name="Prepare BTK inhibitor complex",
     folder=folder,
 )
-protein = preparation_workflow.result().get_prepared_protein()
+preparation_result = preparation_workflow.result()
+protein = preparation_result.get_prepared_protein()
 
 # Protein preparation normalizes 4YHF's residue numbering: Cys481 becomes residue 101,
 # while the retained 4C9 ligand remains residue 701.

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/descriptors.py

@@ -1,5 +1,4 @@
-"""
-Calculate molecular descriptors using the Rowan API.
+"""Calculate molecular descriptors using the Rowan API.
 
 Computes molecular descriptors including COSMO descriptors (surface area,
 screening charge, dielectric energy, polar surface area) in water by default.

{rowan_python-3.1.16 → rowan_python-3.2.1}/examples/docking.py

@@ -14,7 +14,10 @@ preparation_workflow = rowan.submit_protein_preparation_workflow(
     name="Prepare ABL1",
     folder=folder,
 )
-prepared_protein_uuid = preparation_workflow.result().prepared_protein_uuid
+preparation_result = preparation_workflow.result()
+prepared_protein_uuid = preparation_result.prepared_protein_uuid
+if prepared_protein_uuid is None:
+    raise ValueError("Protein preparation returned no prepared protein")
 
 # Pocket is [[center_x, center_y, center_z], [size_x, size_y, size_z]] in Å.
 # For a co-crystal structure, extract these from the bound ligand's position.