rowan-python 2.1.10__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-2.1.10 → rowan_python-2.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.10
+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-2.1.10 → rowan_python-2.1.12}/pixi.lock

@@ -51,7 +51,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/1a/a1/72ac8a3015cd55b4c14e882507adcd61957426fb0a60688ae1f824f4cdef/stjames-0.0.128-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/dc/9b/47798a6c91d8bdb567fe2698fe81e0c6b7cb7ef4d13da4114b41d239f65d/typing_inspection-0.4.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a7/c2/fe1e52489ae3122415c51f387e221dd0773709bad6c6cdaa599e8a2c5185/urllib3-2.5.0-py3-none-any.whl
@@ -92,7 +92,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/1a/a1/72ac8a3015cd55b4c14e882507adcd61957426fb0a60688ae1f824f4cdef/stjames-0.0.128-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/dc/9b/47798a6c91d8bdb567fe2698fe81e0c6b7cb7ef4d13da4114b41d239f65d/typing_inspection-0.4.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a7/c2/fe1e52489ae3122415c51f387e221dd0773709bad6c6cdaa599e8a2c5185/urllib3-2.5.0-py3-none-any.whl
@@ -140,7 +140,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/67/ff/f6b948ca32e4f2a4576aa129d8bed61f2e0543bf9f5f2b7fc3758ed005c9/charset_normalizer-3.4.4-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/98/78/01c019cdb5d6498122777c1a43056ebb3ebfeef2076d9d026bfe15583b2b/click-8.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/20/1d/784b87270784b0b88e4beec9d028e8d58f73ae248032579c63ad2ac6f69a/coverage-7.11.3-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/d9/1d/9529d9bd44049b6b05bb319c03a3a7e4b0a8a802d28fa348ad407e10706d/coverage-7.12.0-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/4e/8c/f3147f5c4b73e7550fe5f9352eaa956ae838d5c51eb58e7a25b9f3e2643b/decorator-5.2.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/33/6b/e0547afaf41bf2c42e52430072fa5658766e3d65bd4b03a563d1b6336f57/distlib-0.4.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl
@@ -205,7 +205,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/f1/7b/ce1eafaf1a76852e2ec9b22edecf1daa58175c090266e9f6c64afcd81d91/stack_data-0.6.3-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/1a/a1/72ac8a3015cd55b4c14e882507adcd61957426fb0a60688ae1f824f4cdef/stjames-0.0.128-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/dc/9b/47798a6c91d8bdb567fe2698fe81e0c6b7cb7ef4d13da4114b41d239f65d/typing_inspection-0.4.2-py3-none-any.whl
@@ -242,7 +242,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/2a/35/7051599bd493e62411d6ede36fd5af83a38f37c4767b92884df7301db25d/charset_normalizer-3.4.4-cp314-cp314-macosx_10_13_universal2.whl
       - pypi: https://files.pythonhosted.org/packages/98/78/01c019cdb5d6498122777c1a43056ebb3ebfeef2076d9d026bfe15583b2b/click-8.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/28/76/1079547f9d46f9c7c7d0dad35b6873c98bc5aa721eeabceafabd722cd5e7/coverage-7.11.3-cp314-cp314-macosx_11_0_arm64.whl
+      - pypi: https://files.pythonhosted.org/packages/1f/c1/ce3e525d223350c6ec16b9be8a057623f54226ef7f4c2fee361ebb6a02b8/coverage-7.12.0-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/4e/8c/f3147f5c4b73e7550fe5f9352eaa956ae838d5c51eb58e7a25b9f3e2643b/decorator-5.2.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/33/6b/e0547afaf41bf2c42e52430072fa5658766e3d65bd4b03a563d1b6336f57/distlib-0.4.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl
@@ -307,7 +307,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/f1/7b/ce1eafaf1a76852e2ec9b22edecf1daa58175c090266e9f6c64afcd81d91/stack_data-0.6.3-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/1a/a1/72ac8a3015cd55b4c14e882507adcd61957426fb0a60688ae1f824f4cdef/stjames-0.0.128-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/dc/9b/47798a6c91d8bdb567fe2698fe81e0c6b7cb7ef4d13da4114b41d239f65d/typing_inspection-0.4.2-py3-none-any.whl
@@ -451,17 +451,17 @@ packages:
   version: 0.4.6
   sha256: 4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6
   requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*'
-- pypi: https://files.pythonhosted.org/packages/20/1d/784b87270784b0b88e4beec9d028e8d58f73ae248032579c63ad2ac6f69a/coverage-7.11.3-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/1f/c1/ce3e525d223350c6ec16b9be8a057623f54226ef7f4c2fee361ebb6a02b8/coverage-7.12.0-cp314-cp314-macosx_11_0_arm64.whl
   name: coverage
-  version: 7.11.3
-  sha256: 9061a3e3c92b27fd8036dafa26f25d95695b6aa2e4514ab16a254f297e664f83
+  version: 7.12.0
+  sha256: 8787b0f982e020adb732b9f051f3e49dd5054cebbc3f3432061278512a2b1360
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/28/76/1079547f9d46f9c7c7d0dad35b6873c98bc5aa721eeabceafabd722cd5e7/coverage-7.11.3-cp314-cp314-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/d9/1d/9529d9bd44049b6b05bb319c03a3a7e4b0a8a802d28fa348ad407e10706d/coverage-7.12.0-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: coverage
-  version: 7.11.3
-  sha256: fe3425dc6021f906c6325d3c415e048e7cdb955505a94f1eb774dafc779ba203
+  version: 7.12.0
+  sha256: fdba9f15849534594f60b47c9a30bc70409b54947319a7c4fd0e8e3d8d2f355d
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
   requires_python: '>=3.10'
@@ -1548,11 +1548,11 @@ packages:
   requires_python: '>=3.9'
 - pypi: ./
   name: rowan-python
-  version: 2.1.10
-  sha256: 1ba305d3b9b98cce45fe2c3ab1d0925bc9b7fac2aa16c664cc827dd2d9e502e9
+  version: 2.1.11
+  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/1a/a1/72ac8a3015cd55b4c14e882507adcd61957426fb0a60688ae1f824f4cdef/stjames-0.0.128-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/99/0c/d3f6549fcb16cb9fc3ef5740125ae13c966f05d0aa81fdc447472e95c35b/stjames-0.0.137-py3-none-any.whl
   name: stjames
-  version: 0.0.128
-  sha256: 2bc1f56ae4b3f4d350498ec42ec408d829da51c78f5d024cd1bc8dacbff1e982
+  version: 0.0.137
+  sha256: cd6f7736aeaea416891eb81c60cfb672afe60be7a99dc0b684a2ce34989d07e0
   requires_dist:
   - pydantic>=2.4
   - numpy

{rowan_python-2.1.10 → rowan_python-2.1.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.10"
+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-2.1.10 → 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-2.1.10 → rowan_python-2.1.12}/rowan/workflow.py

@@ -43,6 +43,7 @@ class Workflow(BaseModel):
     :var max_credits: The maximum number of credits to use for the workflow.
     :var elapsed: The elapsed time of the workflow.
     :var credits_charged: The number of credits charged for the workflow.
+    :var logfile: The workflow's logfile.
     ...
     """
 
@@ -63,6 +64,7 @@ class Workflow(BaseModel):
     max_credits: int | None = None
     elapsed: float | None = None
     credits_charged: float
+    logfile: str = Field(alias="object_logfile")
 
     class Config:  # noqa: D106
         validate_by_name = True
@@ -240,8 +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
 
@@ -260,9 +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"
@@ -421,6 +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.
@@ -1604,3 +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())