rowan-python 3.0.5__tar.gz → 3.0.6__tar.gz

{rowan_python-3.0.5 → 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-3.0.5 → rowan_python-3.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.5
+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-3.0.5 → rowan_python-3.0.6}/examples/periodic_dft.py

@@ -21,8 +21,8 @@ folder = rowan.get_folder("examples/periodic_dft")
 # 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),
+        (0.0, 2.0230, 2.0230),
+        (2.0230, 0.0, 2.0230),
         (2.0230, 2.0230, 0.0),
     )
 )
@@ -35,10 +35,10 @@ al_fcc = rowan.Molecule.from_atoms(
 
 # 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
+    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
+    degauss=0.01,  # Hartree smearing width
 )
 
 workflow = rowan.submit_basic_calculation_workflow(

{rowan_python-3.0.5 → rowan_python-3.0.6}/pixi.lock

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   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-3.0.5 → rowan_python-3.0.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.0.5"
+version = "3.0.6"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.0.5 → rowan_python-3.0.6}/rowan/molecule.py

@@ -52,28 +52,36 @@ class Molecule(BaseModel):
         return cls(_stjames=stjames.Molecule.from_smiles(smiles))
 
     @classmethod
-    def from_xyz(cls, xyz_string: str, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz(
+        cls, xyz_string: str, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
-        Create molecule from XYZ string.
+        Create Molecule from XYZ string.
 
-        :param xyz_string: XYZ format string.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param xyz_string: XYZ format string
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
-        stj = stjames.Molecule.from_xyz(xyz_string)
-        stj = stjames.Molecule(atoms=stj.atoms, charge=charge, multiplicity=multiplicity)
-        return cls(_stjames=stj)
+        return cls(
+            _stjames=stjames.Molecule.from_xyz(
+                xyz_string,
+                charge=charge,
+                multiplicity=multiplicity,
+            )
+        )
 
     @classmethod
-    def from_xyz_file(cls, path: str | Path, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz_file(
+        cls, path: str | Path, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
         Create molecule from XYZ file.
 
-        :param path: Path to XYZ file.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param path: path to XYZ file
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
         return cls.from_xyz(Path(path).read_text(), charge=charge, multiplicity=multiplicity)
 
@@ -82,8 +90,8 @@ class Molecule(BaseModel):
         """
         Create from stjames.Molecule.
 
-        :param stj: stjames.Molecule instance.
-        :returns: Molecule instance.
+        :param stj: stjames.Molecule
+        :returns: Molecule
         """
         return cls(_stjames=stj)
 

{rowan_python-3.0.5 → rowan_python-3.0.6}/rowan/protein.py

@@ -305,7 +305,7 @@ def list_proteins(
 
 
 def upload_protein(
-    name: str, file_path: Path, project_uuid: str | Project | None = None
+    name: str, file_path: str | Path, project_uuid: str | Project | None = None
 ) -> Protein:
     """
     Uploads a protein from a PDB file to the API.
@@ -315,6 +315,7 @@ def upload_protein(
     :returns: Protein object representing the uploaded protein
     :raises requests.HTTPError: if the request to the API fails
     """
+    file_path = Path(file_path)
     if isinstance(project_uuid, Project):
         project_uuid = project_uuid.uuid
     with api_client() as client:

{rowan_python-3.0.5 → rowan_python-3.0.6}/rowan/workflows/pka.py

@@ -183,8 +183,7 @@ def submit_pka_workflow(
         )
     if method in _PKA_SMILES_METHODS and not initial_smiles:
         raise ValueError(
-            f"{method} requires a SMILES string. "
-            "Provide a SMILES string, not a 3D structure."
+            f"{method} requires a SMILES string. Provide a SMILES string, not a 3D structure."
         )
     if method in _PKA_WATER_ONLY_METHODS and solvent != "water":
         raise ValueError(f"{method} only supports water as solvent.")