Fix docs toc (#1315)

zulissimeta · web-flow · commit f3e978992421 · 2025-06-27T08:37:45.000-07:00
* small toc fix

* fix code to code-cell
diff --git a/docs/_toc.yml b/docs/_toc.yml
@@ -23,9 +23,9 @@ parts:
     - file: core/common_tasks/fine_tuning
     - file: core/common_tasks/workflows
     - file: core/uma_faq
-  - file: core/uma_tutorials/summary
+  - file: uma_tutorials/summary
     sections:
-    - file: core/uma_tutorials/uma_tutorial
+    - file: uma_tutorials/uma_tutorial
   - file: core/uma_examples/summary
     sections:
     - file: core/uma_examples/uma_tutorial
diff --git a/docs/catalysts/examples_tutorials/OCP-introduction.md b/docs/catalysts/examples_tutorials/OCP-introduction.md
@@ -62,7 +62,7 @@ The first step is getting a checkpoint for the model we want to use. UMA is curr
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -74,7 +74,7 @@ The first step is getting a checkpoint for the model we want to use. UMA is curr
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/catalysts/examples_tutorials/adsorbml_walkthrough.md b/docs/catalysts/examples_tutorials/adsorbml_walkthrough.md
@@ -22,7 +22,7 @@ The latest UMA models are now total-energy models, and the results for the adsor
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -34,7 +34,7 @@ The latest UMA models are now total-energy models, and the results for the adsor
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/catalysts/examples_tutorials/adsorption_energies/adsorption_energies.md b/docs/catalysts/examples_tutorials/adsorption_energies/adsorption_energies.md
@@ -22,7 +22,7 @@ One of the most common tasks in computational catalysis is calculating the bindi
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -34,7 +34,7 @@ One of the most common tasks in computational catalysis is calculating the bindi
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/catalysts/examples_tutorials/cattsunami_tutorial.md b/docs/catalysts/examples_tutorials/cattsunami_tutorial.md
@@ -35,7 +35,7 @@ else:
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -47,7 +47,7 @@ else:
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/catalysts/examples_tutorials/ocpapi.md b/docs/catalysts/examples_tutorials/ocpapi.md
@@ -21,7 +21,7 @@ Python library for programmatic use of the [Open Catalyst Demo](https://open-cat
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -33,7 +33,7 @@ Python library for programmatic use of the [Open Catalyst Demo](https://open-cat
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/core/common_tasks/ase_calculator.md b/docs/core/common_tasks/ase_calculator.md
@@ -32,7 +32,7 @@ calc = FAIRChemCalculator(predictor, task_name="oc20")
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -44,7 +44,7 @@ calc = FAIRChemCalculator(predictor, task_name="oc20")
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/core/common_tasks/batch_inference.md b/docs/core/common_tasks/batch_inference.md
@@ -5,7 +5,7 @@
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -17,7 +17,7 @@
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/core/quickstart.md b/docs/core/quickstart.md
@@ -30,7 +30,7 @@ appropriate task name for domain specific prediction.
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -42,7 +42,7 @@ appropriate task name for domain specific prediction.
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/dac/examples_tutorials/adsorption_energy.md b/docs/dac/examples_tutorials/adsorption_energy.md
@@ -29,7 +29,7 @@ Each term on the right-hand side represents the energy of the relaxed state of t
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -41,7 +41,7 @@ Each term on the right-hand side represents the energy of the relaxed state of t
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/index.md b/docs/index.md
@@ -41,7 +41,7 @@ If you want to explore model capabilities check out our
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -53,7 +53,7 @@ If you want to explore model capabilities check out our
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/inorganic_materials/examples_tutorials/bulk_stability.md b/docs/inorganic_materials/examples_tutorials/bulk_stability.md
@@ -23,7 +23,7 @@ We're going to start simple here - let's run a local relaxation (optimize the un
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -35,7 +35,7 @@ We're going to start simple here - let's run a local relaxation (optimize the un
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
diff --git a/docs/inorganic_materials/examples_tutorials/elastic.md b/docs/inorganic_materials/examples_tutorials/elastic.md
@@ -29,9 +29,10 @@ For more documentation, see the quacc docs for [quacc.recipes.mlp.elastic_tensor
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
+
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
 ```
 
@@ -41,9 +42,10 @@ For more documentation, see the quacc docs for [quacc.recipes.mlp.elastic_tensor
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
+
 # Login using the huggingface-cli utility
 ! huggingface-cli login
 
diff --git a/docs/inorganic_materials/examples_tutorials/phonons.md b/docs/inorganic_materials/examples_tutorials/phonons.md
@@ -66,7 +66,7 @@ Congratulations, you ran your first phonon calculation!
 
 
 1. Install the necessary packages using pip, uv etc
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 ! pip install fairchem-core fairchem-data-oc fairchem-applications-cattsunami
@@ -78,7 +78,7 @@ Congratulations, you ran your first phonon calculation!
     * Create a Huggingface token at https://huggingface.co/settings/tokens/ with the permission "Permissions: Read access to contents of all public gated repos you can access"
     * Add the token as an environment variable using `huggingface-cli login` or by setting the HF_TOKEN environment variable. 
 
-```{code}
+```{code-cell} ipython3
 :tags: [skip-execution]
 
 # Login using the huggingface-cli utility
