rowan-python 2.1.11__tar.gz → 2.1.12__tar.gz

rowan_python-2.1.12/.github/workflows/build-and-deploy-docs.yml

@@ -0,0 +1,42 @@
+name: Build & Deploy Rowan Python Docs
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-deploy-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: main
+      
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.9.1
+        with:
+          pixi-version: "latest"
+          activate-environment: true
+
+      - name: Build MkDocs site
+        run: pixi run mkdocs-build
+
+      - name: Install SSH Key
+        uses: shimataro/ssh-key-action@v2
+        with:
+          key: ${{ secrets.DOCS_SSH_KEY }}
+          known_hosts: "unnecessary"
+
+      - name: Add server to known_hosts
+        run: ssh-keyscan -H ${{ secrets.DOCS_IP }} >> ~/.ssh/known_hosts
+
+      - name: Deploy with rsync
+        run: |
+          rsync -avz --delete ./ \
+            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:{{ secrets.DOCS_TARGET_DIR }}

{rowan_python-2.1.11 → rowan_python-2.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.11
+Version: 2.1.12
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -11,7 +11,7 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.128
+Requires-Dist: stjames>=0.0.137
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

rowan_python-2.1.12/examples/admet.py

@@ -0,0 +1,12 @@
+import rowan
+
+# rowan.api_key = ""
+
+oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
+
+result = rowan.submit_admet_workflow(
+    initial_smiles=oseltamivir_SMILES,
+    name="Oseltamivir ADMET",
+)
+
+print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.12/examples/membrane_permeability.py

@@ -0,0 +1,12 @@
+import rowan
+
+# rowan.api_key = ""
+
+oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
+
+result = rowan.submit_membrane_permeability_workflow(
+    initial_smiles=oseltamivir_SMILES,
+    name="Oseltamivir Membrane Permeability",
+)
+
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.1.11 → rowan_python-2.1.12}/pixi.lock

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+      - pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
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@@ -1549,10 +1549,10 @@ packages:
 - pypi: ./
   name: rowan-python
   version: 2.1.11
-  sha256: 6a0e2c797288e17fedb71af670d982c56e893cd611b8e5930c9c74ca756de265
+  sha256: 17d8beaef39332f342c634e38512ea7b8be7db261e3e6e43ef173dec0582925e
   requires_dist:
   - httpx
-  - stjames>=0.0.128
+  - stjames>=0.0.137
   - setuptools
   - rdkit
   - nest-asyncio
@@ -1648,10 +1648,10 @@ packages:
   - pygments ; extra == 'tests'
   - littleutils ; extra == 'tests'
   - cython ; extra == 'tests'
-- pypi: https://files.pythonhosted.org/packages/19/d1/4f1b26e50bad8f91c2072c559a4cdd70dff7778043abf1e20f430efd9baf/stjames-0.0.129-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
   name: stjames
-  version: 0.0.129
-  sha256: de6cd8e053aab55bc5a564128fbe3758c23d24a869882b9a22aee92f32669feb
+  version: 0.0.137
+  sha256: cd6f7736aeaea416891eb81c60cfb672afe60be7a99dc0b684a2ce34989d07e0
   requires_dist:
   - pydantic>=2.4
   - numpy

{rowan_python-2.1.11 → rowan_python-2.1.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.11"
+version = "2.1.12"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.128",
+    "stjames>=0.0.137",
     "setuptools",
     "rdkit",
     "nest-asyncio",

{rowan_python-2.1.11 → rowan_python-2.1.12}/rowan/folder.py

@@ -58,7 +58,6 @@ class Folder(BaseModel):
 
         return self
 
-
     def update(
         self,
         name: str | None = None,
@@ -121,6 +120,7 @@ class Folder(BaseModel):
         """
         print_folder_tree(self.uuid, max_depth, show_uuids)
 
+
 def retrieve_folder(uuid: str) -> Folder:
     """
     Retrieves a folder from the API by UUID. Folder UUID can be found in the folder's URL.
@@ -208,6 +208,7 @@ def create_folder(
         folder_data = response.json()
     return Folder(**folder_data)
 
+
 def print_folder_tree(uuid: str, max_depth: int = 10, show_uuids: bool = False) -> None:
     """
     Retrieves a folder tree from the API.

{rowan_python-2.1.11 → rowan_python-2.1.12}/rowan/workflow.py

@@ -242,8 +242,9 @@ class Workflow(BaseModel):
         with open(path / f"{self.name}-msa.tar.gz", "wb") as f:
             f.write(response.content)
 
-    def download_dcd_files(self, replicates: list[int],
-                           name: str | None = None, path: Path | None = None) -> None:
+    def download_dcd_files(
+        self, replicates: list[int], name: str | None = None, path: Path | None = None
+    ) -> None:
         """
         Downloads DCD trajectory files for specified replicates
 
@@ -262,9 +263,7 @@ class Workflow(BaseModel):
         path.mkdir(parents=True, exist_ok=True)
 
         with api_client() as client:
-            response = client.post(
-                f"/trajectory/{self.uuid}/trajectory_dcds", json=replicates
-            )
+            response = client.post(f"/trajectory/{self.uuid}/trajectory_dcds", json=replicates)
             response.raise_for_status()
 
         file_path = path / f"{name or self.name}.tar.gz"
@@ -423,6 +422,7 @@ def retrieve_workflows(uuids: list[str]) -> list[Workflow]:
         response.raise_for_status()
         return [Workflow(**workflow_data) for workflow_data in response.json()]
 
+
 def batch_poll_status(uuids: list[str]) -> list[Workflow]:
     """
     Polls the status of a list of workflows.
@@ -1606,3 +1606,71 @@ def submit_msa_workflow(
         response = client.post("/workflow", json=data)
         response.raise_for_status()
         return Workflow(**response.json())
+
+
+def submit_admet_workflow(
+    initial_smiles: str,
+    name: str = "ADMET Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits an ADMET workflow to the API.
+
+    :param initial_smiles: The molecule used in the workflow.
+    :param name: The name of the workflow.
+    :param folder_uuid: The UUID of the folder to store the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+
+    workflow = stjames.ADMETWorkflow(initial_smiles=initial_smiles)
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "admet",
+        "workflow_data": workflow.model_dump(),
+        "initial_smiles": initial_smiles,
+        "max_credits": max_credits,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())
+
+
+def submit_membrane_permeability_workflow(
+    initial_smiles: str,
+    name: str = "ADMET Workflow",
+    folder_uuid: str | None = None,
+    max_credits: int | None = None,
+) -> Workflow:
+    """
+    Submits a membrane permeability workflow to the API.
+
+    :param initial_smiles: The molecule used in the workflow.
+    :param name: The name of the workflow.
+    :param folder_uuid: The UUID of the folder to store the workflow in.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted workflow.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+
+    workflow = stjames.MembranePermeabilityWorkflow(initial_smiles=initial_smiles)
+
+    data = {
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "workflow_type": "membrane_permeability",
+        "workflow_data": workflow.model_dump(),
+        "initial_smiles": initial_smiles,
+        "max_credits": max_credits,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())