rowan-python 2.0.1__py3-none-any.whl → 2.0.3__py3-none-any.whl

rowan/rowan_rdkit/chem_utils.py

@@ -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/utils.py

@@ -19,10 +19,10 @@ def get_api_key() -> str:
 
     :return: The API key.
     """
-    if (api_key := os.environ.get("ROWAN_API_KEY")) is not None:
-        return api_key
-    elif hasattr(rowan, "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:
+        return api_key
 
     raise ValueError(
         "No API key provided. You can set your API key using 'rowan.api_key = <API-KEY>',"

rowan/workflow.py

@@ -52,7 +52,7 @@ class Workflow(BaseModel):
     starred: bool
     public: bool
     workflow_type: str = Field(alias="object_type")
-    data: dict[str, Any] = Field(default={}, alias="object_data")
+    data: dict[str, Any] | None = Field(default=None, alias="object_data")
     email_when_complete: bool
     max_credits: int | None = None
     elapsed: float | None = None
@@ -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.dist-info → rowan_python-2.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.1
+Version: 2.0.3
 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-2.0.1.dist-info → rowan_python-2.0.3.dist-info}/RECORD

@@ -4,11 +4,11 @@ rowan/folder.py,sha256=n9WkjHMweQLtVcWUvCttOrmezvUdbFxam_eDEMzLF_A,6791
 rowan/protein.py,sha256=TOCsN50RaYh3Ja4GBxzH6R7qUk-Y9Xv7y1WU3buPFis,7778
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/user.py,sha256=Dl--NPUPATKCs2VmILsW8HnLiunG0Lxr0n6mKuHm21U,3891
-rowan/utils.py,sha256=SyKvrvlgZ2BKZKRKziZdVZvV_Y4Hld77Bris0lerA9o,3296
-rowan/workflow.py,sha256=2TbNFkd91crmWmUgXfmeD8HD4Yv90GMdfPlKeAzYiDk,39467
+rowan/utils.py,sha256=907lV0fEP6BnjOWyisd3Uh8Mk5JuQMOX9QEjGi_mdew,3314
+rowan/workflow.py,sha256=LwU1iaweXseQENOHYAOQqvjNkwITZn82JHeSr4xZiTc,39505
 rowan/rowan_rdkit/__init__.py,sha256=EATX2VRzywzKxqkpCUMTf7RNQLkWsfi5VcCNDW6EIiw,503
-rowan/rowan_rdkit/chem_utils.py,sha256=1WAczzwNzIlghgP7eT2l2LhWW4yUpND5XC475q2lXaA,35044
-rowan_python-2.0.1.dist-info/METADATA,sha256=fGZm8-J4yLkXIBZPFYvgarnzE3aYpwp-sQEyzZMshtw,1598
-rowan_python-2.0.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rowan_python-2.0.1.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-rowan_python-2.0.1.dist-info/RECORD,,
+rowan/rowan_rdkit/chem_utils.py,sha256=i7-EmAcmvHYtc9NiZblLY_k2DoQKofAZo5KT2qtkUCI,34775
+rowan_python-2.0.3.dist-info/METADATA,sha256=-RDgaRghr3pWuUCJp7GTdGzoo1PnggTEsb8uIVrz8mU,1598
+rowan_python-2.0.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rowan_python-2.0.3.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+rowan_python-2.0.3.dist-info/RECORD,,