From 3d4d7120ac705601717ed9350b18c57f96fcd9d0 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Fri, 14 Jul 2023 07:13:06 -0700 Subject: [PATCH] -n auto is causing issues --- .github/workflows/CI.yaml | 2 +- README.md | 8 +++----- devtools/conda-envs/espaloma.yaml | 1 + 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index dfd2a5bf..524603fc 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -67,7 +67,7 @@ jobs: - name: Run tests run: | - pytest -v -n auto --cov=espaloma --cov-report=xml --color=yes espaloma/ + pytest -v --cov=espaloma --cov-report=xml --color=yes espaloma/ - name: CodeCov uses: codecov/codecov-action@v3 diff --git a/README.md b/README.md index 33625254..a3f62c37 100644 --- a/README.md +++ b/README.md @@ -49,10 +49,6 @@ import os import torch import espaloma as esp -# grab pretrained model -if not os.path.exists("espaloma_model.pt"): - os.system("wget http://data.wangyq.net/espaloma_model.pt") - # define or load a molecule of interest via the Open Force Field toolkit from openff.toolkit.topology import Molecule molecule = Molecule.from_smiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C") @@ -60,8 +56,10 @@ molecule = Molecule.from_smiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C") # create an Espaloma Graph object to represent the molecule of interest molecule_graph = esp.Graph(molecule) +# load pretrained model +espaloma_model = esp.get_model("latest") + # apply a trained espaloma model to assign parameters -espaloma_model = torch.load("espaloma_model.pt") espaloma_model(molecule_graph.heterograph) # create an OpenMM System for the specified molecule diff --git a/devtools/conda-envs/espaloma.yaml b/devtools/conda-envs/espaloma.yaml index 27186486..c000003a 100644 --- a/devtools/conda-envs/espaloma.yaml +++ b/devtools/conda-envs/espaloma.yaml @@ -19,6 +19,7 @@ dependencies: - openmm - openmmforcefields >=0.11.2 - tqdm + - pydantic <2 # We need our deps to fix this # Pytorch - pytorch>=1.8.0 - dgl =0.9.0