Fix examples env and links (#52)

Co-authored-by: Lily Wang <[email protected]>

devtools/conda-envs/examples_env.yaml

@@ -21,18 +21,17 @@ dependencies:
  - rich
 
  # chemistry
- - openff-toolkit ==0.11.1
+ - openff-toolkit >=0.11.1
  - openff-units
- - pydantic
+ - pydantic <3
  - rdkit
  - openeye-toolkits
 
  # database
- - sqlalchemy
- - sqlite
+ - pyarrow
 
  # gcn
- - dglteam::dgl >=0.7
+ - dglteam::dgl >=1.0
  - pytorch
  - pytorch-lightning
  - tensorboard

devtools/conda-envs/test_env.yaml

@@ -13,6 +13,7 @@ dependencies:
  - click
  - click-option-group
  - tqdm
+ - rich
 
  # chemistry
  - openff-recharge
@@ -38,9 +39,7 @@ dependencies:
  - pytest-cov
  - pytest-xdist
  - codecov
- - sqlalchemy <2.0
 
  # Pip-only installs
  - pip:
  - rich
- - mlflow

examples/README.md

@@ -4,5 +4,5 @@ The following examples are available in [the OpenFF NAGL repository](https://git
 
 ## Index of provided examples
 
-* [prepare-dataset](https:/openforcefield/openff-nagl/tree/main/examples/prepare-datset) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openforcefield/openff-nagl/main?labpath=examples%2Fprepare-datset%2Fprepare-datset.ipynb) - Prepare a dataset for training, validating or testing NAGL models from a list of SMILES and the OpenFF Toolkit
+* [prepare-dataset](https:/openforcefield/openff-nagl/tree/main/examples/prepare-dataset) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openforcefield/openff-nagl/main?labpath=examples%2Fprepare-dataset%2Fprepare-dataset.ipynb) - Prepare a dataset for training, validating or testing NAGL models from a list of SMILES and the OpenFF Toolkit
 * [train-gnn-notebook](https:/openforcefield/openff-nagl/tree/main/examples/train-gnn-notebook) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openforcefield/openff-nagl/main?labpath=examples%2Ftrain-gnn-notebook%2Ftrain-gnn-notebook.ipynb) - Architect, train, and use a simple GCN partial charge model on an alkane test dataset