Fixes to docs and an example (#73)

* Switch to Forge DGL in examples and docs environments

* Update train-gnn-notebook.ipynb with new version argument

* Fix API docs and upgrade to Sphinx 6

* Fix notebook in train-multi-objective-gnn

"No... There is another" - Yoda

devtools/conda-envs/docs_env.yaml

@@ -1,6 +1,5 @@
 name: openff-nagl-docs
 channels:
-  - dglteam
   - openeye
   - conda-forge
   - defaults
@@ -26,7 +25,7 @@ dependencies:
   - pyarrow
 
   # gcn
-  - dglteam::dgl >=0.7
+  - dgl >=1.0
   - pytorch
   - pytorch-lightning
 
@@ -43,7 +42,7 @@ dependencies:
   - myst-nb
   - myst-parser>=0.16
   - docutils
-  - sphinx<5
+  - sphinx=6
   - sphinx-notfound-page
   - autodoc-pydantic
   - sphinx-click

devtools/conda-envs/examples_env.yaml

@@ -1,6 +1,5 @@
 name: openff-nagl-test
 channels:
-  - dglteam
   - openeye
   - conda-forge
   - defaults
@@ -23,6 +22,7 @@ dependencies:
   # chemistry
   - openff-toolkit >=0.11.1
   - openff-units
+  - openff-recharge
   - pydantic <3
   - rdkit
   - openeye-toolkits
@@ -31,7 +31,7 @@ dependencies:
   - pyarrow
 
   # gcn
-  - dglteam::dgl >=1.0
+  - dgl >=1.0
   - pytorch
   - pytorch-lightning
   - tensorboard

docs/_templates/autosummary/module.rst

@@ -13,17 +13,30 @@
 .. automodule:: {{ fullname }}
 
    {% block modules %}
-   {% if modules %}
+
+   {%- set doc_modules = [] -%}
+   {%- for item in all_modules -%}
+      {%- if item.startswith(fullname) -%}
+         {%- set item = item[fullname | length+1:] -%}
+      {%- endif -%}
+      {%- if not (
+         item.startswith('_')
+         or item in exclude_modules
+         or fullname + "." + item in exclude_modules
+      ) -%}
+         {%- set _ = doc_modules.append(item) -%}
+      {%- endif -%}
+   {%- endfor %}
+
+   {% if doc_modules %}
    .. rubric:: Modules
 
    .. autosummary::
       :caption: Modules
       :toctree:
       :recursive:
-   {% for item in modules %}
-   {%- if item not in exclude_modules %}
+   {% for item in doc_modules %}
       ~{{ item }}
-   {% endif -%}
    {%- endfor %}
 
    {% endif %}

docs/cli.md

@@ -1,5 +1,7 @@
-:::{eval-rst}
+# CLI Reference
+
+```{eval-rst}
 .. click:: openff.nagl._cli:cli
     :prog: openff-nagl
     :nested: full
-:::
+```

docs/designing.md

@@ -67,12 +67,12 @@ bond_features:
 
 ```
 
-And then loaded with the [`GNNModel.from_yaml_file()`] method:
+And then loaded with the [`GNNModel.from_yaml()`] method:
 
 ```python
 from openff.nagl import GNNModel
 
-model = GNNModel.from_yaml_file("model.yml")
+model = GNNModel.from_yaml("model.yml")
 ```
 
 Here we'll go through each option, what it means, and where to find the available choices.

docs/index.md

@@ -91,7 +91,7 @@ cli.md
 The autosummary directive renders to rST,
 so we must use eval-rst here
 -->
-:::{eval-rst}
+```{eval-rst}
 .. raw:: html
 
     <div style="display: None">
@@ -107,4 +107,4 @@ so we must use eval-rst here
 .. raw:: html
 
     </div>
-:::
+```

docs/installation.md

@@ -9,7 +9,7 @@ mamba create -n nagl -c conda-forge openff-nagl
 conda activate nagl
 ```
 
-If you do not have Conda or Mamba installed, see the [OpenFF installation documentation](openff.docs:install).
+If you do not have Conda or Mamba installed, see the [OpenFF installation documentation](inv:openff.docs#install).
 
 We recommend keeping environments minimal, and only installing packages you use together. Environments can be safely discarded when you no longer need them. This avoids dependency conflicts common to large Python environments. If you prefer, NAGL may be installed into the current environment:
 
@@ -30,7 +30,7 @@ conda config --env --set channel_priority strict
 
 In environments with this configuration, the `-c conda-forge` switch is unnecessary. Other channels, like `psi4` and `bioconda`, can still be used in the usual way.
 
-More information on installing OpenFF packages can be found in the [OpenFF installation documentation](openff.docs:install).
+More information on installing OpenFF packages can be found in the [OpenFF installation documentation](inv:openff.docs#install).
 
 ## Installation from source
 

docs/theory.md

@@ -94,8 +94,8 @@ Molecular graphs are provided to NAGL via the [`Molecule`] class of the [OpenFF
 [`Molecule`]: openff.toolkit.topology.Molecule
 [SMILES string]: openff.toolkit.topology.Molecule.from_smiles
 [.SDF file]: openff.toolkit.topology.Molecule.from_file
-[OpenFF Toolkit]: openff.toolkit:index
-[variety of ways]: openff.toolkit:users/molecule_cookbook
+[OpenFF Toolkit]: inv:openff.toolkit#index
+[variety of ways]: inv:openff.toolkit#users/molecule_cookbook
 [`GNNModel.compute_property()`]: openff.nagl.GNNModel.compute_property
 [`MoleculeRecord.from_openff()`]: openff.nagl.storage.record.MoleculeRecord.from_openff
 [`MoleculeRecord.from_precomputed_openff()`]: openff.nagl.storage.record.MoleculeRecord.from_precomputed_openff

docs/training.md

@@ -94,4 +94,4 @@ trainer.test(model, data_module)
 model.save("model.pt")
 ```
 
-[`Trainer`]: pytorch_lightning:common/trainer
+[`Trainer`]: inv:pytorch_lightning#common/trainer