Fix examples env and links (#52)

Co-authored-by: Lily Wang <lily@macaque.local>
openforcefield · Aug 13, 2023 · 43f3d8a · 43f3d8a
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diff --git a/devtools/conda-envs/examples_env.yaml b/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

diff --git a/devtools/conda-envs/test_env.yaml b/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
diff --git a/examples/README.md b/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://github.com/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://github.com/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://github.com/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