rowan-python 3.0.4__tar.gz → 3.0.6__tar.gz

{rowan_python-3.0.4 → rowan_python-3.0.6}/.gitignore

@@ -199,9 +199,6 @@ local/
 
 cyp/
 
-# AI agent instructions (not part of the project source)
-AGENTS.md
-
 # MSA download output directories
 msa_directory/
 

rowan_python-3.0.6/AGENTS.md

@@ -0,0 +1,124 @@
+# AI Agent Development Guide
+
+This document provides essential guidance for AI agents working on this repository.
+
+## Repository overview
+
+rowan-python-internal is the private Python SDK for the Rowan computational chemistry platform. It wraps the stjames data model library and provides user-facing workflow submission and result retrieval.
+
+Structure:
+- `rowan/` - source code (flat layout)
+- `rowan/workflows/` - workflow submission functions and result types
+- `examples/` - usage examples for each workflow
+- `docs/` - documentation (mkdocs)
+- `.github/workflows/` - CI/CD configuration
+
+Key relationships:
+- **stjames** (`../stjames`) - data model dependency, imported as `stjames`. Defines workflow models, settings, validation, and engine compatibility.
+- **rowan-python** - public version of this repo. Push via `git push public master` from this repo.
+
+Python version: >=3.12
+
+## Essential commands
+
+```bash
+# Setup
+pixi install                    # Install dependencies
+
+# Code quality (these are the pre-commit hooks)
+pixi run fmt                    # Format code (ruff format)
+pixi run lint                   # Lint code (ruff check --fix)
+pixi run types                  # Type check (mypy)
+
+# Testing
+pixi run test                   # Run tests (pytest with doctests)
+pixi run all                    # Run fmt + lint + types + test
+
+# Run a specific example
+pixi run python examples/basic_calculation.py
+```
+
+## Before every commit
+
+- Run `pixi run fmt`, `pixi run lint`, `pixi run types`
+- Pre-commit hooks (`.pre-commit-config.yaml`) run these automatically on commit
+- No pytest in pre-commit hooks — tests run in CI
+
+## Code conventions
+
+### Docstrings
+
+Format: reStructuredText-style. No types in docstrings, no leading articles.
+
+```python
+def process_data(input_data: list[str], threshold: int = 10) -> dict[str, int]:
+    """Process input data and return summary statistics.
+
+    :param input_data: strings to process
+    :param threshold: minimum count threshold for inclusion
+    :returns: mapping of categories to counts
+    """
+```
+
+### Type annotations
+
+- All functions must have complete type annotations
+- Modern syntax: `list[str]`, `dict[str, int]`, `str | None`
+- Import from `typing` only when necessary
+
+### Code formatting
+
+Via ruff:
+- Line length: 100
+- Indentation: 4 spaces
+
+### Imports
+
+- Absolute imports preferred
+- No wildcard imports except in `__init__.py`
+- Import sorting handled by ruff (isort)
+
+## Workflow development guidelines
+
+### Validation
+- Use stjames validation when possible. Don't duplicate validation that stjames model validators already handle (e.g. engine/method compatibility, solvent checks). Only add rowan-side validation when stjames doesn't cover it.
+
+### stjames type aliasing
+- Users should never need to `import stjames` directly. All user-facing stjames types must be aliased in `rowan/__init__.py`. If an example requires a stjames import, that's a signal the type needs to be aliased.
+
+### Serialization
+- Use `serialize_as_any=True` on `model_dump` when the workflow has union-typed fields (e.g. `ConformerGenSettingsUnion`, `MultiStageOptSettings` containing `Settings` subfields). Without it, pydantic may silently drop subclass-specific fields during serialization.
+
+### Defaults
+- When hardcoding a default value for a stjames field, make sure it matches the corresponding default in the stjames workflow model.
+
+### Type hints in function signatures
+- Don't use pydantic-specific types (`PositiveInt`, `NonNegativeInt`, etc.) in plain function signatures. They don't enforce constraints outside pydantic models and are misleading. Use plain `int`, `float`, etc. — stjames validates downstream when the model is constructed.
+
+### Testing
+- After editing a workflow, run its relevant example before committing (not on every change) to catch breakage early.
+
+## Git authorization policy
+
+**Do not run `git commit`, `git push`, or any other git write commands without explicit permission from the user.**
+
+**Never add yourself as a commit author or co-author.** Do not include `Co-Authored-By:`, `Author:`, or any similar trailer that attributes the commit to an AI model or tool. Commits are attributed solely to the human developer.
+
+## CI/CD
+
+File: `.github/workflows/test.yml`
+
+Triggers: all PRs, pushes to `master`
+
+Checks:
+1. `pixi run fmt` - format check
+2. `pixi run lint` - lint check
+3. `pixi run types` - type check
+
+Matrix: Python 3.14, ubuntu-latest
+
+## Additional resources
+
+- pixi documentation: https://pixi.sh
+- ruff documentation: https://docs.astral.sh/ruff
+- pytest documentation: https://docs.pytest.org

rowan_python-3.0.6/CLAUDE.md

@@ -0,0 +1 @@
+@AGENTS.md

rowan_python-3.0.6/GEMINI.md

@@ -0,0 +1 @@
+@AGENTS.md

{rowan_python-3.0.4 → rowan_python-3.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.4
+Version: 3.0.6
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues

rowan_python-3.0.6/examples/data/Al_FCC.xyz

@@ -0,0 +1,3 @@
+1
+Lattice="0.0 2.0230 2.0230 2.0230 0.0 2.0230 2.0230 2.0230 0.0" Properties=species:S:1:pos:R:3
+Al   0.00000000   0.00000000   0.00000000

rowan_python-3.0.6/examples/periodic_dft.py

@@ -0,0 +1,58 @@
+"""
+Run a periodic DFT energy calculation on bulk aluminium using Quantum ESPRESSO.
+
+Key settings for PBC calculations:
+- ``pw_cutoff``: plane-wave kinetic-energy cutoff in Hartree (higher = more accurate/slower)
+- ``kpoints``: Monkhorst–Pack k-point grid (denser = more accurate/slower)
+- ``smearing``: occupation smearing type — recommended for metals to aid SCF convergence
+- ``degauss``: smearing width in Hartree (typical range: 0.005–0.02)
+
+Periodic molecules are constructed from atomic positions + lattice vectors.
+See documentation at: https://docs.rowansci.com/science/workflows/basic-calculation
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/periodic_dft")
+
+# Build bulk Al FCC primitive cell.
+# Lattice vectors in Angstrom; Al has 13 electrons so multiplicity=2.
+cell = rowan.PeriodicCell(
+    lattice_vectors=(
+        (0.0, 2.0230, 2.0230),
+        (2.0230, 0.0, 2.0230),
+        (2.0230, 2.0230, 0.0),
+    )
+)
+al_fcc = rowan.Molecule.from_atoms(
+    atoms=[rowan.Atom(atomic_number=13, position=(0.0, 0.0, 0.0))],
+    charge=0,
+    multiplicity=2,
+    cell=cell,
+)
+
+# Marzari–Vanderbilt cold smearing is recommended for metals.
+pbc_settings = rowan.PBCDFTSettings(
+    pw_cutoff=7.5,  # Hartree; SSSP efficiency recommends ~7–9 Ha for Al
+    kpoints=(4, 4, 4),  # Monkhorst–Pack grid; increase for production runs
+    smearing=rowan.PBCDFTSmearing.MV,
+    degauss=0.01,  # Hartree smearing width
+)
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=al_fcc,
+    tasks=["energy"],
+    method="PBE",
+    basis_set="SSSP_efficiency",
+    pbc_dft_settings=pbc_settings,
+    name="Al FCC bulk energy",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <BasicCalculationResult energy=-19.725 H>
+print(f"Al FCC energy: {result.energy:.6f} Hartree")

rowan_python-3.0.6/examples/pka.py

@@ -0,0 +1,69 @@
+"""
+Calculate the pKa of phenol using the Rowan API.
+
+Experimental value ≈ 9.99
+
+Four methods are available:
+- aimnet2_wagen2024: AIMNet2-based; requires 3D structure; water only.
+- gxtb_wagen2026: g-xTB-based; requires 3D structure; water only; full periodic table.
+- chemprop_nevolianis2025: Chemprop-based; requires SMILES; several solvents supported.
+- starling: SMILES-based; water only.
+
+See documentation at: https://docs.rowansci.com/science/workflows/pka
+"""
+
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples/pka")
+
+# 3D structure-based methods — pass a Molecule with coordinates
+mol = rowan.Molecule.from_smiles("c1ccccc1O")
+
+workflow = rowan.submit_pka_workflow(
+    initial_molecule=mol,
+    method="aimnet2_wagen2024",
+    name="Phenol pKa (aimnet2_wagen2024)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <pKaResult acid=9.87>
+
+workflow2 = rowan.submit_pka_workflow(
+    initial_molecule=mol,
+    method="gxtb_wagen2026",
+    name="Phenol pKa (gxtb_wagen2026)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow2.uuid}")
+result2 = workflow2.result()
+print(result2)
+# e.g. <pKaResult acid=9.92>
+
+# SMILES-based methods — pass a SMILES string directly
+smiles = "c1ccccc1O"
+
+workflow3 = rowan.submit_pka_workflow(
+    initial_molecule=smiles,
+    method="chemprop_nevolianis2025",
+    name="Phenol pKa (chemprop_nevolianis2025)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow3.uuid}")
+result3 = workflow3.result()
+print(result3)
+# e.g. <pKaResult acid=9.75>
+
+workflow4 = rowan.submit_pka_workflow(
+    initial_molecule=smiles,
+    method="starling",
+    name="Phenol pKa (starling)",
+    folder=folder,
+)
+print(f"View at: https://labs.rowansci.com/pka/{workflow4.uuid}")
+result4 = workflow4.result()
+print(result4)
+# e.g. <pKaResult acid=9.81>

{rowan_python-3.0.4 → rowan_python-3.0.6}/pixi.lock

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-  sha256: 31b5dbb55293c1bd27c0fc813a0d2bb5ceef9d65ac5afa2e58f829dab7921fd5
+  version: 1.20.1
+  sha256: 2c3f6221a76f34d5100c6d35b3ef6b947054123c3f8d6938a4ba00b1308aa572
   requires_dist:
   - typing-extensions>=4.6.0
   - mypy-extensions>=1.0.0
@@ -1140,10 +1140,10 @@ packages:
   purls: []
   size: 3106008
   timestamp: 1775587972483
-- pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/7a/c2/920ef838e2f0028c8262f16101ec09ebd5969864e5a64c4c05fad0617c56/packaging-26.1-py3-none-any.whl
   name: packaging
-  version: '26.0'
-  sha256: b36f1fef9334a5588b4166f8bcd26a14e521f2b55e6b9de3aaa80d3ff7a37529
+  version: '26.1'
+  sha256: 5d9c0669c6285e491e0ced2eee587eaf67b670d94a19e94e3984a481aba6802f
   requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/90/96/04b8e52da071d28f5e21a805b19cb9390aa17a47462ac87f5e2696b9566d/paginate-0.5.7-py2.py3-none-any.whl
   name: paginate
@@ -1289,29 +1289,29 @@ packages:
   sha256: 1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0
   requires_dist:
   - pytest ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/5a/87/b70ad306ebb6f9b585f114d0ac2137d792b48be34d732d60e597c2f8465a/pydantic-2.12.5-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/81/5a/2225f4c176dbfed0d809e848b50ef08f70e61daa667b7fa14b0d311ae44d/pydantic-2.13.1-py3-none-any.whl
   name: pydantic
-  version: 2.12.5
-  sha256: e561593fccf61e8a20fc46dfc2dfe075b8be7d0188df33f221ad1f0139180f9d
+  version: 2.13.1
+  sha256: 9557ecc2806faaf6037f85b1fbd963d01e30511c48085f0d573650fdeaad378a
   requires_dist:
   - annotated-types>=0.6.0
-  - pydantic-core==2.41.5
+  - pydantic-core==2.46.1
   - typing-extensions>=4.14.1
   - typing-inspection>=0.4.2
   - email-validator>=2.0.0 ; extra == 'email'
   - tzdata ; python_full_version >= '3.9' and sys_platform == 'win32' and extra == 'timezone'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/4c/d2/ef2074dc020dd6e109611a8be4449b98cd25e1b9b8a303c2f0fca2f2bcf7/pydantic_core-2.41.5-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/76/fd/19d711e4e9331f9d77f222bffc202bf30ea0d74f6419046376bb82f244c8/pydantic_core-2.46.1-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: pydantic-core
-  version: 2.41.5
-  sha256: 22f0fb8c1c583a3b6f24df2470833b40207e907b90c928cc8d3594b76f874375
+  version: 2.46.1
+  sha256: b83ce9fede4bc4fb649281d9857f06d30198b8f70168f18b987518d713111572
   requires_dist:
   - typing-extensions>=4.14.1
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/74/1a/145646e5687e8d9a1e8d09acb278c8535ebe9e972e1f162ed338a622f193/pydantic_core-2.41.5-cp314-cp314-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/d2/87/e9a905ddfcc2fd7bd862b340c02be6ab1f827922822d425513635d0ac774/pydantic_core-2.46.1-cp314-cp314-macosx_11_0_arm64.whl
   name: pydantic-core
-  version: 2.41.5
-  sha256: 1d1d9764366c73f996edd17abb6d9d7649a7eb690006ab6adbda117717099b14
+  version: 2.46.1
+  sha256: 0e749679ca9f8a9d0bff95fb7f6b57bb53f2207fa42ffcc1ec86de7e0029ab89
   requires_dist:
   - typing-extensions>=4.14.1
   requires_python: '>=3.9'
@@ -1531,8 +1531,8 @@ packages:
   requires_python: '>=3.10'
 - pypi: ./
   name: rowan-python
-  version: 3.0.4
-  sha256: 68bb5250327c5075096e931e0f397030cdb0a64fec9cb12c901fc97caba6f01d
+  version: 3.0.6
+  sha256: 511acf0d60990b7bf5a6ca9567cd6417cc18dd5e2b2cce084394de59e5327a08
   requires_dist:
   - httpx
   - stjames>=0.0.174
@@ -1624,10 +1624,10 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/02/e6/5d6c315b37e517dc93a09665c3e3f88e68f1d2cdd120edf3b093f7d461b2/stjames-0.0.180-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/20/1c/0b3011c55381804e68833f192e398c294846e196efe9f9773dcf9d3b4e33/stjames-0.0.182-py3-none-any.whl
   name: stjames
-  version: 0.0.180
-  sha256: 8224350783a2a7715bcc8bad37d2f345a47c1c3529edc20b8c80b8b7be856aba
+  version: 0.0.182
+  sha256: 4a243ff896e36eecc3cf3ebdd659efe83c60e245aecc00c495fadb4ec1e1255c
   requires_dist:
   - pydantic>=2.4
   - numpy
@@ -1705,17 +1705,17 @@ packages:
   - pysocks>=1.5.6,!=1.5.7,<2.0 ; extra == 'socks'
   - backports-zstd>=1.0.0 ; python_full_version < '3.14' and extra == 'zstd'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/20/0e/f083a76cb590e60dff3868779558eefefb8dfb7c9ed020babc7aa014ccbf/virtualenv-21.2.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/27/8d/edd0bd910ff803c308ee9a6b7778621af0d10252219ad9f19ef4d4982a61/virtualenv-21.2.4-py3-none-any.whl
   name: virtualenv
-  version: 21.2.1
-  sha256: bd16b49c53562b28cf1a3ad2f36edb805ad71301dee70ddc449e5c88a9f919a2
+  version: 21.2.4
+  sha256: 29d21e941795206138d0f22f4e45ff7050e5da6c6472299fb7103318763861ac
   requires_dist:
   - distlib>=0.3.7,<1
   - filelock>=3.24.2,<4 ; python_full_version >= '3.10'
   - filelock>=3.16.1,<=3.19.1 ; python_full_version < '3.10'
   - importlib-metadata>=6.6 ; python_full_version < '3.8'
   - platformdirs>=3.9.1,<5
-  - python-discovery>=1
+  - python-discovery>=1.2.2
   - typing-extensions>=4.13.2 ; python_full_version < '3.11'
   requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/b5/e8/dbf020b4d98251a9860752a094d09a65e1b436ad181faf929983f697048f/watchdog-6.0.0-py3-none-manylinux2014_x86_64.whl

{rowan_python-3.0.4 → rowan_python-3.0.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.0.4"
+version = "3.0.6"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.0.4 → rowan_python-3.0.6}/rowan/__init__.py

@@ -1,17 +1,25 @@
 # ruff: noqa
 from . import constants
 from stjames import (
+    Atom,
     Constraint,
     ConstraintType,
+    ConformerGenSettingsUnion,
     Correction,
     Engine,
+    ETKDGSettings,
+    iMTDSettings,
     Method,
     Mode,
+    MultiStageOptSettings,
     OptimizationSettings,
+    PBCDFTSettings,
+    PeriodicCell,
     Settings,
     SolventSettings,
     Task,
 )
+from stjames.pbc_dft_settings import PBCDFTSmearing
 from stjames.optimization.freezing_string_method import (
     FSMInterpolation,
     FSMOptimizationCoordinates,