Merge branch 'flax-backend-normalclasses' of github.com:JaxGaussianPr…

…ocesses/GPJax into flax-backend-normalclasses

.github/workflows/build_docs.yml

@@ -52,16 +52,11 @@ jobs:
           virtualenvs-in-project: false
           installer-parallel: true
 
-      - name: Install LaTex
-        run: |
-          sudo apt-get update
-          sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
-
       - name: Build the documentation with MKDocs
         run: |
           poetry install --all-extras --with docs
           conda install pandoc
-          poetry run mkdocs build
+          poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build
 
       - name: Deploy Page 🚀
         uses: JamesIves/github-pages-deploy-action@v4.4.1

.github/workflows/test_docs.yml

@@ -33,20 +33,6 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
 
-      # Install katex for math support
-      - name: Install NPM
-        uses: actions/setup-node@v3
-        with:
-          node-version: 16
-      - name: Install KaTeX
-        run: |
-          npm install katex
-
-      - name: Install LaTex
-        run: |
-          sudo apt-get update
-          sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
-
       # Install Poetry and build the documentation
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
@@ -60,4 +46,4 @@ jobs:
         run: |
           poetry install --all-extras --with docs
           conda install pandoc
-          poetry run python docs/scripts/gen_examples.py && poetry run mkdocs build
+          poetry run python docs/scripts/gen_examples.py --execute && poetry run mkdocs build

README.md

@@ -72,10 +72,9 @@ helped to shape GPJax into the package it is today.
 ## Notebook examples
 
 > - [**Conjugate Inference**](https://docs.jaxgaussianprocesses.com/examples/regression/)
-> - [**Classification with MCMC**](https://docs.jaxgaussianprocesses.com/examples/classification/)
+> - [**Classification**](https://docs.jaxgaussianprocesses.com/examples/classification/)
 > - [**Sparse Variational Inference**](https://docs.jaxgaussianprocesses.com/examples/collapsed_vi/)
 > - [**Stochastic Variational Inference**](https://docs.jaxgaussianprocesses.com/examples/uncollapsed_vi/)
-> - [**BlackJax Integration**](https://docs.jaxgaussianprocesses.com/examples/classification/#mcmc-inference)
 > - [**Laplace Approximation**](https://docs.jaxgaussianprocesses.com/examples/classification/#laplace-approximation)
 > - [**Inference on Non-Euclidean Spaces**](https://docs.jaxgaussianprocesses.com/examples/constructing_new_kernels/#custom-kernel)
 > - [**Inference on Graphs**](https://docs.jaxgaussianprocesses.com/examples/graph_kernels/)

docs/scripts/gen_examples.py

@@ -28,7 +28,7 @@ def process_file(file: Path, out_file: Path | None = None, execute: bool = False
             f"| jupyter nbconvert --to markdown --execute --stdin --output {out_file}"
         )
     else:
-        command = f"jupytext --to markdown {file} --output {out_file}"
+        command += f"jupytext --to markdown {file} --output {out_file}"
 
     subprocess.run(command, shell=True, check=False)
 
@@ -64,21 +64,26 @@ def main(args):
     print(files)
 
     # process files in parallel
-    with ThreadPoolExecutor(max_workers=args.max_workers) as executor:
-        futures = []
-        for file in files:
-            out_file = out_dir / f"{file.stem}.md"
-            futures.append(
-                executor.submit(
-                    process_file, file, out_file=out_file, execute=args.execute
+    if args.parallel:
+        with ThreadPoolExecutor(max_workers=args.max_workers) as executor:
+            futures = []
+            for file in files:
+                out_file = out_dir / f"{file.stem}.md"
+                futures.append(
+                    executor.submit(
+                        process_file, file, out_file=out_file, execute=args.execute
+                    )
                 )
-            )
 
-        for future in as_completed(futures):
-            try:
-                future.result()
-            except Exception as e:
-                print(f"Error processing file: {e}")
+            for future in as_completed(futures):
+                try:
+                    future.result()
+                except Exception as e:
+                    print(f"Error processing file: {e}")
+    else:
+        for file in files:
+            out_file = out_dir / f"{file.stem}.md"
+            process_file(file, out_file=out_file, execute=args.execute)
 
 
 if __name__ == "__main__":
@@ -91,6 +96,7 @@ def main(args):
     parser.add_argument(
         "--outdir", type=Path, default=project_root / "docs" / "_examples"
     )
+    parser.add_argument("--parallel", type=bool, default=False)
     args = parser.parse_args()
 
     main(args)