PyPI - rowan-python - Versions diffs - 2.0.1__tar.gz → 2.0.2__tar.gz - Mend

rowan-python 2.0.1tar.gz → 2.0.2tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (44) hide show

{rowan_python-2.0.1 → rowan_python-2.0.2}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.1
+Version: 2.0.2
 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-2.0.2/examples/basic_calculation_from_json.py ADDED Viewed

@@ -0,0 +1,21 @@
+import json
+import rowan
+# rowan.api_key = ""
+with open("examples/data/workflow_example.json") as f:
+    workflow_data = json.load(f)
+result = (
+    rowan.submit_workflow(
+        workflow_type="basic_calculation",
+        workflow_data=workflow_data,
+        name="basic calculation from json",
+        initial_molecule=workflow_data["initial_molecule"],
+    )
+    .wait_for_result()
+    .fetch_latest()
+)
+print(result)

{rowan_python-2.0.1 → rowan_python-2.0.2}/pixi.lock RENAMED Viewed

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+  version: 2025.3.5
+  sha256: b564067066c97136c448c58ac796c66010d041a5fd5dccf8997461a1846e63b7
   requires_dist:
   - numpy
   - pillow
@@ -1548,8 +1494,8 @@ packages:
   requires_python: '>=3.8'
 - pypi: ./
   name: rowan-python
-  version: 2.0.1
-  sha256: 538deecdcbfe274e9b6bd98bc1db5ff036d409d503774710ad34fb5aeda726e0
+  version: 2.0.2
+  sha256: 1be16d4b806a376989c925f8c8770bbd1b855b7f8a05a82094f070138d766353
   requires_dist:
   - httpx
   - stjames>=0.0.83
@@ -1558,15 +1504,15 @@ packages:
   - nest-asyncio
   requires_python: '>=3.9'
   editable: true
-- pypi: https://files.pythonhosted.org/packages/64/f4/e3cd7f7bda646526f09693e2e02bd83d85fff8a8222c52cf9681c0d30843/ruff-0.12.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/55/bf/9cb1ea5e3066779e42ade8d0cd3d3b0582a5720a814ae1586f85014656b6/ruff-0.12.7-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: ruff
-  version: 0.12.4
-  sha256: 2abc48f3d9667fdc74022380b5c745873499ff827393a636f7a59da1515e7c57
+  version: 0.12.7
+  sha256: 06bfb01e1623bf7f59ea749a841da56f8f653d641bfd046edee32ede7ff6c606
   requires_python: '>=3.7'
-- pypi: https://files.pythonhosted.org/packages/d6/8d/756d780ff4076e6dd035d058fa220345f8c458391f7edfb1c10731eedc75/ruff-0.12.4-py3-none-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/a8/c9/3e24a8472484269b6b1821794141f879c54645a111ded4b6f58f9ab0705f/ruff-0.12.7-py3-none-macosx_11_0_arm64.whl
   name: ruff
-  version: 0.12.4
-  sha256: a8224cc3722c9ad9044da7f89c4c1ec452aef2cfe3904365025dd2f51daeae0e
+  version: 0.12.7
+  sha256: 2e1c2a3b8626339bb6369116e7030a4cf194ea48f49b64bb505732a7fce4f4e3
   requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
   name: setuptools
@@ -1648,10 +1594,10 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/e8/c2/72c3a4876e5dd8e13844c65ae6ff4002d436688b97d551f8f8ab9c3c9434/stjames-0.0.93-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/a0/ff/be39dd5325ae00c8b36e903512b5a62cae40ea3205deb7517de753c9fcad/stjames-0.0.96-py3-none-any.whl
   name: stjames
-  version: 0.0.93
-  sha256: cf73b3b84f27150faed20d776a9dee896cbcd3e805fedba3e1a2e5f4f2021c4a
+  version: 0.0.96
+  sha256: dbf8ade7834fb5c883c30539bd5eb923f1924cbf53a0c1ecc924e30b94893685
   requires_dist:
   - pydantic>=2.4
   - numpy
@@ -1727,10 +1673,10 @@ packages:
   - pysocks>=1.5.6,!=1.5.7,<2.0 ; extra == 'socks'
   - zstandard>=0.18.0 ; extra == 'zstd'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/5c/c6/f8f28009920a736d0df434b52e9feebfb4d702ba942f15338cb4a83eafc1/virtualenv-20.32.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/ca/ff/ded57ac5ff40a09e6e198550bab075d780941e0b0f83cbeabd087c59383a/virtualenv-20.33.1-py3-none-any.whl
   name: virtualenv
-  version: 20.32.0
-  sha256: 2c310aecb62e5aa1b06103ed7c2977b81e042695de2697d01017ff0f1034af56
+  version: 20.33.1
+  sha256: 07c19bc66c11acab6a5958b815cbcee30891cd1c2ccf53785a28651a0d8d8a67
   requires_dist:
   - distlib>=0.3.7,<1
   - filelock>=3.12.2,<4

{rowan_python-2.0.1 → rowan_python-2.0.2}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.0.1"
+version = "2.0.2"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"

{rowan_python-2.0.1 → rowan_python-2.0.2}/rowan/rowan_rdkit/chem_utils.py RENAMED Viewed

@@ -97,24 +97,24 @@ apply_nest_asyncio()
 def _get_rdkit_mol_from_uuid(calculation_uuid: str) -> RdkitMol:
     stjames_mol_dict = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
-    return Chem.MolFromXYZBlock(stjames.Molecule(**stjames_mol_dict).to_xyz())  # type: ignore [attr-defined]
+    return Chem.MolFromXYZBlock(stjames.Molecule(**stjames_mol_dict).to_xyz())
 def _embed_rdkit_mol(rdkm: RdkitMol) -> RdkitMol:
     try:
-        AllChem.SanitizeMol(rdkm)
+        AllChem.SanitizeMol(rdkm)  # type: ignore [attr-defined]
     except Exception as e:
         raise ValueError("Molecule could not be generated -- invalid chemistry!") from e
-    rdkm = AllChem.AddHs(rdkm)
+    rdkm = AllChem.AddHs(rdkm)  # type: ignore [attr-defined]
     try:
-        assert AllChem.EmbedMolecule(rdkm, maxAttempts=200) >= 0
+        assert AllChem.EmbedMolecule(rdkm, maxAttempts=200) >= 0  # type: ignore [attr-defined]
     except AssertionError as e:
-        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)
+        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)  # type: ignore [attr-defined]
         if status1 < 0:
             raise ValueError("Cannot embed molecule!") from e
     try:
-        assert AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200) >= 0  # type: ignore    [call-arg]
+        assert AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200) >= 0  # type: ignore [attr-defined]
     except AssertionError:
         pass
@@ -477,9 +477,9 @@ async def _single_energy(
     get_api_key()
     method = stjames.Method(method)
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
     if method not in FAST_METHODS:
@@ -489,7 +489,7 @@ async def _single_energy(
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
         stjames_mol = _rdkit_to_stjames(mol, cid)
         post = rowan.submit_workflow(
             name=name,
@@ -623,9 +623,9 @@ async def _single_optimize(
     get_api_key()
     method = stjames.Method(method)
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
     if method not in FAST_METHODS:
@@ -637,7 +637,7 @@ async def _single_optimize(
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
         stjames_mol = _rdkit_to_stjames(mol, cid)
         post = rowan.submit_workflow(
@@ -677,7 +677,7 @@ async def _single_optimize(
     energies = [cacluation[-1]["energy"] for cacluation in calculations]
     for i, conformer in enumerate(optimized_mol.GetConformers()):
-        conformer.SetPositions(np.array(optimized_positions[i]))  # type: ignore  [attr-defined]
+        conformer.SetPositions(np.array(optimized_positions[i]))
     return {
         "molecule": mol,
@@ -796,9 +796,9 @@ async def _single_conformers(
     get_api_key()
     method = stjames.Method(method)
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
     if method not in FAST_METHODS:
@@ -858,12 +858,12 @@ async def _single_conformers(
     lowest_n_uuids = [item[1][0] for item in sorted_data[:num_conformers]]
     lowest_energies = [item[0] for item in sorted_data[:num_conformers]]
-    AllChem.EmbedMultipleConfs(mol, numConfs=num_conformers)
+    AllChem.EmbedMultipleConfs(mol, numConfs=num_conformers)  # type: ignore [attr-defined]
     for i, conformer in enumerate(mol.GetConformers()):
         atoms = rowan.retrieve_calculation_molecules(lowest_n_uuids[i])[-1]["atoms"]
         pos = [atom["position"] for atom in atoms]
-        conformer.SetPositions(np.array(pos))  # type: ignore  [attr-defined]
+        conformer.SetPositions(np.array(pos))
     return {
         "molecule": mol,
@@ -959,9 +959,9 @@ async def _single_charges(
     get_api_key()
     method = stjames.Method(method)
-    if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+    if mol.GetNumConformers() == 0:
         mol = _embed_rdkit_mol(mol)
-        if mol.GetNumConformers() == 0:  # type: ignore    [call-arg]
+        if mol.GetNumConformers() == 0:
             raise NoConformersError("This molecule has no conformers")
     if method not in FAST_METHODS:
@@ -971,7 +971,7 @@ async def _single_charges(
     workflow_uuids = []
     for conformer in mol.GetConformers():
-        cid = conformer.GetId()  # type: ignore    [call-arg]
+        cid = conformer.GetId()
         post = rowan.submit_workflow(
             name=name,

{rowan_python-2.0.1 → rowan_python-2.0.2}/rowan/workflow.py RENAMED Viewed

@@ -416,7 +416,7 @@ def submit_conformer_search_workflow(
     conf_gen_mode: str = "rapid",
     final_method: stjames.Method | str = "aimnet2_wb97md3",
     solvent: str | None = None,
-    transistion_state: bool = False,
+    transition_state: bool = False,
     name: str = "Conformer Search Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
@@ -433,7 +433,7 @@ def submit_conformer_search_workflow(
     for options.
     :param solvent: The solvent to use for the final optimization. See [the list of available solvents](https://github.com/rowansci/stjames-public/blob/master/stjames/solvent.py)
         for valid values. Be aware that not all methods support solvents.
-    :param transistion_state: Whether to optimize the transition state.
+    :param transition_state: Whether to optimize the transition state.
     :param name: The name of the workflow.
     :param folder_uuid: The UUID of the folder to place the workflow in.
     :param max_credits: The maximum number of credits to use for the workflow.
@@ -457,7 +457,7 @@ def submit_conformer_search_workflow(
         tasks=["optimize"],
         mode=stjames.Mode.AUTO,
         solvent_settings={"solvent": solvent, "model": solvent_model} if solvent else None,
-        opt_settings={"transition_state": transistion_state, "constraints": []},
+        opt_settings={"transition_state": transition_state, "constraints": []},
     )
     msos = stjames.MultiStageOptSettings(
@@ -471,7 +471,7 @@ def submit_conformer_search_workflow(
         "conf_gen_mode": conf_gen_mode,
         "mso_mode": "manual",
         "solvent": solvent,
-        "transistion_state": transistion_state,
+        "transition_state": transition_state,
     }
     data = {
@@ -644,7 +644,7 @@ def submit_fukui_workflow(
     optimization_method: str = "gfn2_xtb",
     fukui_method: str = "gfn1_xtb",
     solvent_settings: dict[str, str] | None = None,
-    name: str = "Redox Potential Workflow",
+    name: str = "Fukui Workflow",
     folder_uuid: str | None = None,
     max_credits: int | None = None,
 ) -> Workflow:
@@ -652,9 +652,9 @@ def submit_fukui_workflow(
     Submits a fukui workflow to the API.
     :param initial_molecule: The molecule to calculate the fukui indices of.
-    :optimization_method: The method to use for the optimization.
-    :fukui_method: The method to use for the fukui calculation.
-    :solvent_settings: The solvent settings to use for the fukui calculation.
+    :param optimization_method: The method to use for the optimization.
+    :param fukui_method: The method to use for the fukui calculation.
+    :param solvent_settings: The solvent settings to use for the fukui calculation.
     :param name: The name of the workflow.
     :param folder_uuid: The UUID of the folder to place the workflow in.
     :param max_credits: The maximum number of credits to use for the workflow.
@@ -670,9 +670,9 @@ def submit_fukui_workflow(
     fukui_settings = stjames.Settings(method=fukui_method, solvent_settings=solvent_settings)
     workflow_data = {
-        "opt_settings": optimization_settings,
+        "opt_settings": optimization_settings.model_dump(),
         "opt_engine": stjames.Method(optimization_method).default_engine(),
-        "fukui_settings": fukui_settings,
+        "fukui_settings": fukui_settings.model_dump(),
         "fukui_engine": stjames.Method(fukui_method).default_engine(),
     }

rowan_python-2.0.1/examples/basic_calculation_from_json.py DELETED Viewed

@@ -1,20 +0,0 @@
-import json
-import rowan
-# rowan.api_key = ""
-with open("examples/data/workflow_example.json", "r") as f:
-    workflow_data = json.load(f)
-result = rowan.submit_workflow(
-    workflow_type="basic_calculation",
-    workflow_data=workflow_data,
-    name="basic calculation from json",
-    initial_molecule=workflow_data["initial_molecule"],
-)
-result.wait_for_result()
-result.fetch_latest(in_place=True)
-print(result)