update visualisation-module

.devcontainer/devcontainer.json

@@ -45,7 +45,7 @@
 		"ghcr.io/prulloac/devcontainer-features/latex:1": {
 			"scheme": "minimal",
 			"mirror": "https://mirror.ctan.org/systems/texlive/tlnet/",
-			"packages": "tikz-network,standalone,xcolor,xifthen,tools,ifmtarg,pgf,datatool,etoolbox,tracklang,amsmath,trimspaces,epstopdf-pkg,dvisvgm"
+			"packages": "tikz-network,standalone,xcolor,xifthen,tools,ifmtarg,pgf,datatool,etoolbox,tracklang,amsmath,trimspaces,epstopdf-pkg,dvisvgm,preview,babel-english"
 		}
 	}
 }

.github/actions/setup/action.yml

@@ -1,6 +1,6 @@
 name: Setup # Inspired by https://github.com/pyg-team/pytorch_geometric/blob/737707c37fc2bd712a2289b683ec14549926ff49/.github/actions/setup/action.yml
 
-description: Set up Python, PyTorch and PyTorch Geometric.
+description: Set up environment with dependencies
 
 inputs: # defaults are set to the version used in the dev container
   python-version:
@@ -26,6 +26,12 @@ runs:
         python-version: ${{ inputs.python-version }}
         activate-environment: true
 
+    - name: Cache uv virtual environment
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: uv-venv-${{ runner.os }}-py-${{ inputs.python-version }}-cuda-${{ inputs.cuda-version }}
+
     - name: Install pathpyG
       run: |
         uv sync --frozen --extra ${{ inputs.cuda-version }}
@@ -38,9 +44,48 @@ runs:
         uv run python -c "import torch; print('CUDA:', torch.version.cuda)"
       shell: bash
 
+    - name: Set up TeX Live
+      if: ${{ inputs.full_install == 'true' }}
+      uses: TeX-Live/setup-texlive-action@v3
+      with:
+        cache: true
+        packages: |
+          scheme-basic
+          latexmk
+          tikz-network
+          standalone
+          xcolor
+          xifthen
+          tools
+          ifmtarg
+          pgf
+          datatool
+          etoolbox
+          tracklang
+          amsmath
+          trimspaces
+          epstopdf-pkg
+          dvisvgm
+          preview
+          babel-english
+
     - name: Install extension packages
       if: ${{ inputs.full_install == 'true' }}
-      run: | # ToDo: Add LaTeX installation
-        sudo apt-get update && sudo apt-get install -y build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg
+      uses: awalsh128/cache-apt-pkgs-action@v1
+      with:
+        execute_install_scripts: true
+        packages: |
+          build-essential
+          python3-dev
+          libcairo2-dev
+          libpango1.0-dev
+
+    - name: Install ffmpeg
+      if: ${{ inputs.full_install == 'true' }}
+      uses: FedericoCarboni/setup-ffmpeg@v3
+
+    - name: Install optional Python dependencies
+      if: ${{ inputs.full_install == 'true' }}
+      run: |
         uv sync --frozen --extra vis --extra ${{ inputs.cuda-version }}
       shell: bash

docs/gen_ref_pages.py

@@ -12,7 +12,7 @@
 ignored_modules = yaml.safe_load(ignored_modules_path.read_text("utf-8"))
 
 for path in sorted(Path("src").rglob("*.py")):
-    if str(path.relative_to(".")) in ignored_modules:
+    if ignored_modules and str(path.relative_to(".")) in ignored_modules:
         print(f"Skipping {path} as it is in the ignored modules list.")
         continue
     module_path = path.relative_to("src").with_suffix("")
@@ -28,7 +28,14 @@
     elif parts[-1] == "__main__":
         continue
 
-    nav[(part.split("_")[-1] for part in parts)] = doc_path.as_posix()
+    parts_list = []
+    for part in parts:
+        if part.startswith("_"):
+            parts_list.append(part.split("_")[-1])
+        else:
+            parts_list.append(part)
+
+    nav[tuple(parts_list)] = doc_path.as_posix()
 
     print(f"Checking {full_doc_path}")
     if not (Path("docs") / full_doc_path).exists():

docs/getting_started.md

@@ -47,10 +47,22 @@ pip install git+https://github.com/pathpy/pathpyG.git
 
 ### Optional Visualisation Backends
 
-We provide multiple visualisation backends for PathpyG. The default backend [D3.js](https://d3js.org/) does not require any additional dependencies. We further provide a [Matplotlib](https://matplotlib.org/) backend that is installed by default. Additionally, we implemented a [Manim](https://www.manim.community/) backend that is not installed by default due to its dependencies that are required for installation. Please refer to the [Manim installation instructions](https://docs.manim.community/en/stable/installation/uv.html) for more information. Once installed, you can use the Manim backend for visualisation by setting the `backend` in the `PathpyG.plot` function to `manim`: 
-```python
-import pathpyg as pp
+We provide multiple visualisation backends for PathpyG. The default backend [D3.js](https://d3js.org/) does not require any additional dependencies. We further provide a [Matplotlib](https://matplotlib.org/) backend that is installed by default. Additionally, we implemented a [tikz](https://tikz.dev/) and a [Manim](https://www.manim.community/) backend that are not installed by default due to their dependencies that are required for installation. You can use the tikz backend if you have a LaTeX distribution installed on your system. 
 
-t_graph = TemporalGraph.from_edge_list([('a', 'b', 1),('b', 'a', 3), ('b', 'c', 3)])
-pp.plot(t_graph, backend='manim')
-```
+To use the Manim backend, please refer to the [Manim installation instructions](https://docs.manim.community/en/stable/installation/uv.html) for more information. Once installed, you can use the backends for visualisation by setting the `backend` in the `PathpyG.plot` function to `tikz` or `manim`:
+
+??? example "Using the TikZ Backend"
+    ```python
+    import pathpyg as pp
+
+    g = pp.Graph.from_edge_list([('a', 'b'),('b', 'c'),('c', 'a')])
+    pp.plot(g, backend='tikz')
+    ```
+
+??? example "Using the Manim Backend"
+    ```python
+    import pathpyg as pp
+
+    t_graph = TemporalGraph.from_edge_list([('a', 'b', 1),('b', 'a', 3), ('b', 'c', 3)])
+    pp.plot(t_graph, backend='manim')
+    ```