rowan-python 0.0.1__tar.gz → 0.0.3__tar.gz

rowan-python-0.0.3/LICENSE

@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) Rowan (https://rowansci.com)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

rowan-python-0.0.3/PKG-INFO

@@ -0,0 +1,32 @@
+Metadata-Version: 2.1
+Name: rowan-python
+Version: 0.0.3
+Summary: Rowan Python Library
+Author-email: Corin Wagen <corin@rowansci.com>
+Project-URL: Homepage, https://github.com/rowansci/rowan-client
+Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cctk>=0.2.18
+Requires-Dist: httpx>=0.25
+Requires-Dist: numpy>=1.24
+Requires-Dist: stjames>=0.0.23
+
+# Rowan Python Library
+
+[![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+
+The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+
+## Documentation
+
+The documentation is available [here](https://docs.rowansci.com/python-api).
+
+
+## Issues
+
+To report issues, please use the "Issues" tab above.
+
+*Corin Wagen, 2023*

rowan-python-0.0.3/README.md

@@ -0,0 +1,17 @@
+# Rowan Python Library
+
+[![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+
+The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+
+## Documentation
+
+The documentation is available [here](https://docs.rowansci.com/python-api).
+
+
+## Issues
+
+To report issues, please use the "Issues" tab above.
+
+*Corin Wagen, 2023*

{rowan-python-0.0.1 → rowan-python-0.0.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "0.0.1"
+version = "0.0.3"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -12,7 +12,7 @@ dependencies = [
     "cctk>=0.2.18",
     "httpx>=0.25",
     "numpy>=1.24",
-    "stjames>=0.0.5",
+    "stjames>=0.0.23",
 ]
 
 [build-system]

rowan-python-0.0.3/rowan/client.py

@@ -0,0 +1,152 @@
+from __future__ import annotations
+
+import cctk
+import httpx
+from typing import Optional
+import stjames
+from dataclasses import dataclass, field
+import time
+
+import rowan
+
+API_URL = "https://api.rowansci.com"
+
+
+@dataclass
+class Client:
+    blocking: bool = True
+    print: bool = True
+    ping_interval: int = 5
+    delete_when_finished: bool = False
+
+    headers: dict = field(init=False)
+
+    def __post_init__(self):
+        self.headers = {"X-API-Key": rowan.utils.get_api_key()}
+
+        if not self.blocking and self.delete_when_finished:
+            print("Warning: ``delete_when_finished`` has no effect when ``blocking`` is False. To delete calculations, call ``Client.delete()`` manually.")
+
+    def compute(
+        self,
+        type: Optional[str] = "calculation",
+        input_mol: Optional[cctk.Molecule] = None,
+        input_smiles: Optional[str] = None,
+        name: Optional[str] = None,
+        folder_uuid: Optional[str] = None,
+        engine: str = "peregrine",
+        **options,
+    ) -> dict | str:
+        if (input_mol is None) == (input_smiles is None):
+            raise ValueError("Must specify exactly one of ``input_smiles`` and ``input_mol``!")
+
+        if input_mol is None:
+            input_mol = cctk.Molecule.new_from_smiles(input_smiles)
+
+        molecule = rowan.utils.cctk_to_stjames(input_mol)
+
+        with httpx.Client() as client:
+            if type == "calculation":
+                settings = stjames.Settings(**options)
+                calc = stjames.Calculation(molecules=[molecule], name=name, engine=engine, settings=settings)
+
+                response = client.post(
+                    f"{API_URL}/calculation",
+                    headers=self.headers,
+                    json={
+                        "json_data": calc.model_dump(mode="json"),
+                        "folder_uuid": folder_uuid,
+                    },
+                )
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.post(
+                    f"{API_URL}/workflow",
+                    headers=self.headers,
+                    json={
+                        "initial_molecule": molecule.model_dump(mode="json"),
+                        "workflow_type": type,
+                        "name": name,
+                        "folder_uuid": folder_uuid,
+                        "workflow_data": options,
+                    },
+                )
+
+            response.raise_for_status()
+            response_dict = response.json()
+            calc_uuid = response_dict["uuid"]
+
+        if self.blocking:
+            while not self.is_finished(calc_uuid, type):
+                time.sleep(self.ping_interval)
+            result = self.get(calc_uuid, type)
+
+            if self.delete_when_finished:
+                self.delete(calc_uuid, type)
+
+            return result
+
+        else:
+            return calc_uuid
+
+    def is_finished(self, calc_uuid: str, type: str = "calculation") -> bool:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.get(f"{API_URL}/calculation/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                status = response_dict["status"]
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.get(f"{API_URL}/workflow/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                status = response_dict["object_status"]
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")
+
+        return status in [2, 3, 4]
+
+    def get(self, calc_uuid: str, type: str = "calculation") -> dict:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.get(f"{API_URL}/calculation/{calc_uuid}/stjames", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                return response_dict
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.get(f"{API_URL}/workflow/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                return response_dict["object_data"]
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")
+
+    def stop(self, calc_uuid: str, type: str = "calculation") -> None:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.post(f"{API_URL}/calculation/{calc_uuid}/stop", headers=self.headers)
+                response.raise_for_status()
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.post(f"{API_URL}/workflow/{calc_uuid}/stop", headers=self.headers)
+                response.raise_for_status()
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")
+
+    def delete(self, calc_uuid: str, type: str = "calculation") -> None:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.delete(f"{API_URL}/calculation/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.delete(f"{API_URL}/folder/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")

rowan-python-0.0.3/rowan/utils.py

@@ -0,0 +1,33 @@
+import os
+import cctk
+import stjames
+import numpy as np
+
+import rowan
+
+
+def get_api_key() -> str:
+    api_key = os.environ.get("ROWAN_API_KEY")
+    if api_key is not None:
+        return api_key
+    elif hasattr(rowan, "api_key"):
+        return rowan.api_key
+    else:
+        raise ValueError(
+            "No API key provided. You can set your API key using 'rowan.api_key = <API-KEY>', or you can set the environment variable ROWAN_API_KEY=<API-KEY>)."
+        )
+
+
+def cctk_to_stjames(molecule: cctk.Molecule) -> stjames.Molecule:
+    atomic_numbers = molecule.atomic_numbers.view(np.ndarray)
+    geometry = molecule.geometry.view(np.ndarray)
+
+    atoms = list()
+    for i in range(molecule.num_atoms()):
+        atoms.append(stjames.Atom(atomic_number=atomic_numbers[i], position=geometry[i]))
+
+    return stjames.Molecule(
+        atoms=atoms,
+        charge=molecule.charge,
+        multiplicity=molecule.multiplicity,
+    )

rowan-python-0.0.3/rowan_python.egg-info/PKG-INFO

@@ -0,0 +1,32 @@
+Metadata-Version: 2.1
+Name: rowan-python
+Version: 0.0.3
+Summary: Rowan Python Library
+Author-email: Corin Wagen <corin@rowansci.com>
+Project-URL: Homepage, https://github.com/rowansci/rowan-client
+Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cctk>=0.2.18
+Requires-Dist: httpx>=0.25
+Requires-Dist: numpy>=1.24
+Requires-Dist: stjames>=0.0.23
+
+# Rowan Python Library
+
+[![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+
+The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+
+## Documentation
+
+The documentation is available [here](https://docs.rowansci.com/python-api).
+
+
+## Issues
+
+To report issues, please use the "Issues" tab above.
+
+*Corin Wagen, 2023*

{rowan-python-0.0.1 → rowan-python-0.0.3}/rowan_python.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+LICENSE
 README.md
 pyproject.toml
 rowan/__init__.py

{rowan-python-0.0.1 → rowan-python-0.0.3}/rowan_python.egg-info/requires.txt

@@ -1,4 +1,4 @@
 cctk>=0.2.18
 httpx>=0.25
 numpy>=1.24
-stjames>=0.0.5
+stjames>=0.0.23

rowan-python-0.0.1/PKG-INFO

@@ -1,78 +0,0 @@
-Metadata-Version: 2.1
-Name: rowan-python
-Version: 0.0.1
-Summary: Rowan Python Library
-Author-email: Corin Wagen <corin@rowansci.com>
-Project-URL: Homepage, https://github.com/rowansci/rowan-client
-Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-Requires-Dist: cctk>=0.2.18
-Requires-Dist: httpx>=0.25
-Requires-Dist: numpy>=1.24
-Requires-Dist: stjames>=0.0.5
-
-# Rowan Python Library
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
-
-## Documentation
-
-The documentation is available [here](https://docs.rowansci.com).
-
-## Installation
-
-To install, run `pip install rowan-python`.
-
-## Usage
-
-Rowan can be run in either blocking (wait until job is complete) or non-blocking (don't wait) modes.
-Both modes require generation of an API key at [labs.rowansci.com](https://labs.rowansci.com/account/api-keys).
-
-For now, molecules are specified through [*cctk*](https://cctk.rtfd.io). Additional ways to specify molecules will be added in the future.
-
-Results are returned as dictionaries in the [*stjames*](https://github.com/rowansci/stjames) format.
-
-### Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client()
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# run calculation remotely and return result
-result = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-print(result)
-```
-
-### Non-Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client(blocking=False)
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# start calculation and return id
-calc_id = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-
-# retrieve result (and status)
-result = client.get(calc_id)
-print(result)
-
-# alternately, cancel queued or running calculation
-client.stop(calc_id)
-```
-
-## Issues
-
-To report issues, please use the "Issues" tab above.
-
-*Corin Wagen, 2023*

rowan-python-0.0.1/README.md

@@ -1,64 +0,0 @@
-# Rowan Python Library
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
-
-## Documentation
-
-The documentation is available [here](https://docs.rowansci.com).
-
-## Installation
-
-To install, run `pip install rowan-python`.
-
-## Usage
-
-Rowan can be run in either blocking (wait until job is complete) or non-blocking (don't wait) modes.
-Both modes require generation of an API key at [labs.rowansci.com](https://labs.rowansci.com/account/api-keys).
-
-For now, molecules are specified through [*cctk*](https://cctk.rtfd.io). Additional ways to specify molecules will be added in the future.
-
-Results are returned as dictionaries in the [*stjames*](https://github.com/rowansci/stjames) format.
-
-### Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client()
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# run calculation remotely and return result
-result = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-print(result)
-```
-
-### Non-Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client(blocking=False)
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# start calculation and return id
-calc_id = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-
-# retrieve result (and status)
-result = client.get(calc_id)
-print(result)
-
-# alternately, cancel queued or running calculation
-client.stop(calc_id)
-```
-
-## Issues
-
-To report issues, please use the "Issues" tab above.
-
-*Corin Wagen, 2023*

rowan-python-0.0.1/rowan/client.py

@@ -1,107 +0,0 @@
-from __future__ import annotations
-
-import cctk
-import httpx
-from typing import Optional
-import numpy as np
-import stjames
-from dataclasses import dataclass, field
-import time
-
-import rowan
-
-API_URL = "https://api.rowansci.com/calculation"
-
-# cf. /opt/miniconda3/envs/openai/lib/python3.9/site-packages/openai/__init__.py
-
-@dataclass
-class Client:
-    blocking: bool = True
-    print: bool = True
-    ping_interval: int = 5
-
-    headers: dict = field(init=False)
-
-    def __post_init__(self):
-        self.headers = {"X-API-Key": rowan.utils.get_api_key()}
-
-    def compute(
-        self,
-        input_molecule: cctk.Molecule,
-        name: Optional[str] = None,
-        folder_id: Optional[str] = None,
-        **options,
-    ) -> stjames.Calculation | int:
-        atomic_numbers = input_molecule.atomic_numbers.view(np.ndarray)
-        geometry = input_molecule.geometry.view(np.ndarray)
-
-        atoms = list()
-        for i in range(input_molecule.num_atoms()):
-            atoms.append(
-                stjames.Atom(atomic_number=atomic_numbers[i], position=geometry[i])
-            )
-
-        molecule = stjames.Molecule(
-            atoms=atoms,
-            charge=input_molecule.charge,
-            multiplicity=input_molecule.multiplicity,
-        )
-        settings = stjames.Settings(**options)
-        calc = stjames.Calculation(molecules=[molecule], name=name, settings=settings)
-
-        with httpx.Client() as client:
-            response = client.post(
-                f"{API_URL}",
-                headers=self.headers,
-                json={
-                    "json_data": calc.model_dump(mode="json"),
-                    "folder_id": folder_id,
-                },
-            )
-            response.raise_for_status()
-            response_dict = response.json()
-            calc_id = response_dict["id"]
-
-            if self.print:
-                print(f"Calculation {calc_id} submitted")
-
-            if self.blocking:
-                while not response_dict["is_finished"]:
-                    time.sleep(self.ping_interval)
-                    response = client.get(f"{API_URL}/{calc_id}", headers=self.headers)
-                    response_dict = response.json()
-                    if not response.status_code == 200:
-                        raise ValueError(
-                            f"Error {response.status_code}: {response.reason}"
-                        )
-
-                # we finished! get proper schema
-                response = client.get(
-                    f"{API_URL}/{calc_id}/stjames", headers=self.headers
-                )
-                response_dict = response.json()
-
-                if self.print:
-                    print(
-                        f"Calculation {calc_id} completed after {response_dict['elapsed']:.1f} s of CPU time"
-                    )
-                    print(
-                        f"(View the results at labs.rowansci.com/calculations/{calc_id})"
-                    )
-
-                return stjames.Calculation.model_validate(response_dict)
-
-            else:
-                return calc_id
-
-    def get(self, calc_id: int) -> stjames.Calculation:
-        with httpx.Client() as client:
-            response = client.get(f"{API_URL}/{calc_id}/stjames", headers=self.headers)
-            response.raise_for_status()
-            response_dict = response.json()
-            return stjames.Calculation.model_validate(response_dict)
-
-    def stop(self, calc_id: int) -> None:
-        with httpx.Client() as client:
-            response = client.post(f"{API_URL}/{calc_id}/stop", headers=self.headers)
-            response.raise_for_status()

rowan-python-0.0.1/rowan/utils.py

@@ -1,15 +0,0 @@
-import os
-
-import rowan
-
-
-def get_api_key() -> str:
-    api_key = os.environ.get("ROWAN_API_KEY")
-    if api_key is not None:
-        return api_key
-    elif hasattr(rowan, "api_key"):
-        return rowan.api_key
-    else:
-        raise ValueError(
-            "No API key provided. You can set your API key using 'rowan.api_key = <API-KEY>', or you can set the environment variable ROWAN_API_KEY=<API-KEY>)."
-        )

rowan-python-0.0.1/rowan_python.egg-info/PKG-INFO

@@ -1,78 +0,0 @@
-Metadata-Version: 2.1
-Name: rowan-python
-Version: 0.0.1
-Summary: Rowan Python Library
-Author-email: Corin Wagen <corin@rowansci.com>
-Project-URL: Homepage, https://github.com/rowansci/rowan-client
-Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-Requires-Dist: cctk>=0.2.18
-Requires-Dist: httpx>=0.25
-Requires-Dist: numpy>=1.24
-Requires-Dist: stjames>=0.0.5
-
-# Rowan Python Library
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
-
-## Documentation
-
-The documentation is available [here](https://docs.rowansci.com).
-
-## Installation
-
-To install, run `pip install rowan-python`.
-
-## Usage
-
-Rowan can be run in either blocking (wait until job is complete) or non-blocking (don't wait) modes.
-Both modes require generation of an API key at [labs.rowansci.com](https://labs.rowansci.com/account/api-keys).
-
-For now, molecules are specified through [*cctk*](https://cctk.rtfd.io). Additional ways to specify molecules will be added in the future.
-
-Results are returned as dictionaries in the [*stjames*](https://github.com/rowansci/stjames) format.
-
-### Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client()
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# run calculation remotely and return result
-result = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-print(result)
-```
-
-### Non-Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client(blocking=False)
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# start calculation and return id
-calc_id = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-
-# retrieve result (and status)
-result = client.get(calc_id)
-print(result)
-
-# alternately, cancel queued or running calculation
-client.stop(calc_id)
-```
-
-## Issues
-
-To report issues, please use the "Issues" tab above.
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-*Corin Wagen, 2023*