Cleanup: Restructure docs

.github/workflows/docs.yml

@@ -16,9 +16,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          lfs: "true"
-          fetch-depth: 0 # fetch all commits/branches
       - name: Configure Git Credentials
         run: |
           git config user.name github-actions[bot]

.github/workflows/publish.yml

@@ -13,8 +13,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          lfs: "true"
       - name: Setup Python
         uses: actions/setup-python@v5
         with:

.github/workflows/test.yml

@@ -64,7 +64,7 @@ jobs:
           sudo apt install libglu1
       - name: Test notebooks
         run: |
-          pytest --nbmake examples/
+          pytest --nbmake docs/**/*ipynb
 
   # upload code coverage report
   code-coverage:

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Add `branch_network` and `trunk_network` arguments to `DeepONet` to allow for custom network architectures.
 - Add `MaskedOperator` base class.
 - Add `DeepCatOperator`.
+- Restructure documentation, separating notebooks into tutorials and how-to guides.
 
 ## 0.1.0
 

CONTRIBUTING.md

@@ -51,8 +51,7 @@ pre-commit install
 
 ## Build documentation
 
-API documentation and examples from notebooks are built with
-[mkdocs](https://www.mkdocs.org/).
+API documentation is built with [mkdocs](https://www.mkdocs.org/).
 Notebooks are an integral part of the documentation as well.
 
 You can use this command to continuously rebuild documentation
@@ -92,15 +91,9 @@ pytest -m "not slow"
 
 ## Notebooks
 
-We use notebooks both as documentation (copied over to `docs/examples`) and as
-integration tests. All notebooks in the `examples` directory are executed
-during the test run.
-
+We use notebooks both as documentation and as integration tests.
 Because we want documentation to include the full dataset, we commit notebooks
-with their outputs running with full datasets to the repo. The notebooks are
-then added by CI to the section
-[Examples](https://aai-institute.github.io/continuiti/examples.html) of the
-documentation.
+with their outputs running with full datasets to the repo.
 
 ### Hiding cells in notebooks
 
@@ -135,6 +128,16 @@ To only hide the input and
 ```
 for hiding the output only.
 
+If a cell should be skipped in CI (e.g. because the full data set is missing),
+you can use:
+
+```yaml
+"tags": [
+  "skip-execution"
+]
+```
+
+
 ### Plots in Notebooks
 If you add a plot to a notebook, which should also render nicely in browser
 dark mode, add the tag *invertible-output*, i.e.

README.md

@@ -33,8 +33,9 @@ pip install -e .[dev]
 
 ## Usage
 Our [Documentation](https://aai-institute.github.io/continuiti/) contains a
-verbose introduction to operator learning, a collection of examples using
-continuiti, and a class documentation.
+collection of tutorials on how to learn operators using continuiti,
+a collection of how-to guides to solve specific problems, more background,
+and a class documentation.
 
 In general, the operator syntax in **continuiti** is
 ```python

build_scripts/copy_benchmarks.py

@@ -32,11 +32,11 @@ def on_pre_build(config):
         )
         target_filepath.symlink_to(file)
 
-    logger.info("Finished copying notebooks to examples directory")
+    logger.info("Finished copying notebooks to benchmarks directory")
 
 
 @mkdocs.plugins.event_priority(-100)
 def on_shutdown():
-    logger.info("Removing temporary examples directory")
+    logger.info("Removing temporary benchmarks directory")
     for file in docs_benchmarks_dir.glob("*.json"):
         file.unlink()