Fix tikz/pdf and add latex to devcontainer (#287)

* fix typing issue in plot classes

* add minimal latex installation to dev container

* fix missing tikz-network.sty

* fix tikz backend visualisations

* remove latex packages

* add ghostscript dependency

Author: M-Lampert

.devcontainer/Dockerfile

@@ -6,6 +6,9 @@ RUN apt-get -y install git
 # For signed commits: https://code.visualstudio.com/remote/advancedcontainers/sharing-git-credentials#_sharing-gpg-keys
 RUN apt install gnupg2 -y
 
+# Install dependencies for .svg support in tikz
+RUN apt update && apt install -y ghostscript
+
 # Install dependencies for manim
 RUN apt-get install -y build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg
 

.devcontainer/devcontainer.json

@@ -37,5 +37,12 @@
 		"all"
 	],
 	// Install pathpyG as editable python package
-	"postCreateCommand": "pip install -e '.[dev,test,doc,vis]' && git config --global --add safe.directory /workspaces/pathpyG"
+	"postCreateCommand": "pip install -e '.[dev,test,doc,vis]' && git config --global --add safe.directory /workspaces/pathpyG",
+	"features": {
+		"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"
+		}
+	}
 }

src/pathpyG/core/temporal_graph.py

@@ -89,8 +89,26 @@ def from_edge_list(edge_list, num_nodes: Optional[int] = None, device: Optional[
         )
 
     @property
-    def temporal_edges(self) -> Generator[Tuple[int, int, int], None, None]:
-        """Iterator that yields each edge as a tuple of source and destination node as well as the corresponding timestamp."""
+    def temporal_edges(self) -> list:
+        """Return all temporal edges as a list of tuples (source, destination, timestamp).
+
+        Returns:
+            list: A list of tuples representing temporal edges in the format (source, destination, timestamp).
+
+        Examples:
+            Get the list of temporal edges:
+
+            >>> g = pp.TemporalGraph.from_edge_list([('a', 'b', 1), ('b', 'c', 2), ('c', 'a', 3)])
+            >>> print(g.temporal_edges)
+            [('a', 'b', 1), ('b', 'c', 2), ('c', 'a', 3)]
+
+            Iterate over temporal edges:
+            >>> for edge in g.temporal_edges:
+            >>>     print(edge)
+            ('a', 'b', 1)
+            ('b', 'c', 2)
+            ('c', 'a', 3)
+        """
         return [(*self.mapping.to_ids(e), t.item()) for e, t in zip(self.data.edge_index.t(), self.data.time)]
 
     def to(self, device: torch.device) -> TemporalGraph:

src/pathpyG/visualisations/_tikz/core.py

@@ -28,7 +28,7 @@
 
 
 class TikzPlot(PathPyPlot):
-    """Base class for plotting d3js objects."""
+    """Base class for plotting tikz objects."""
 
     def __init__(self, **kwargs: Any) -> None:
         """Initialize plot class."""
@@ -52,20 +52,30 @@ def save(self, filename: str, **kwargs: Any) -> None:
             shutil.copy(temp_file, filename)
             # remove the temporal directory
             shutil.rmtree(temp_dir)
-
+        elif filename.endswith("svg"):
+            # compile temporary svg
+            temp_file, temp_dir = self.compile_svg()
+            # Copy a file with new name
+            shutil.copy(temp_file, filename)
+            # remove the temporal directory
+            shutil.rmtree(temp_dir)
         else:
             raise NotImplementedError
 
     def show(self, **kwargs: Any) -> None:
         """Show the plot on the device."""
         # compile temporary pdf
-        temp_file, temp_dir = self.compile_pdf()
+        temp_file, temp_dir = self.compile_svg()
 
         if config["environment"]["interactive"]:
-            from IPython.display import IFrame, display
-
-            # open the file in the notebook
-            display(IFrame(temp_file, width=600, height=300))
+            from IPython.display import SVG, display
+
+            # open the file, read the content and display it
+            # workaround because it is not possible to embed files in vs code
+            # https://github.com/microsoft/vscode-jupyter/discussions/13769
+            with open(temp_file, "r") as svg_file:
+                svg = SVG(svg_file.read())
+            display(svg)
         else:
             # open the file in the webbrowser
             webbrowser.open(r"file:///" + temp_file)
@@ -76,33 +86,44 @@ def show(self, **kwargs: Any) -> None:
         # remove the temporal directory
         shutil.rmtree(temp_dir)
 
-    def compile_pdf(self) -> tuple:
-        """Compile pdf from tex."""
-        # basename
-        basename = "default"
-        # get current directory
-        current_dir = os.getcwd()
-
-        # template directory
-        tikz_dir = str(
-            os.path.join(
-                os.path.dirname(os.path.dirname(__file__)),
-                os.path.normpath("templates"),
-                "tikz-network.sty",
-            )
-        )
-
-        # get temporal directory
-        temp_dir = tempfile.mkdtemp()
+    def compile_svg(self) -> tuple:
+        """Compile svg from tex."""
+        temp_dir, current_dir, basename = self.prepare_compile()
 
-        # copy tikz-network to temporal directory
-        shutil.copy(tikz_dir, temp_dir)
+        # latex compiler
+        command = [
+            "latexmk",
+            "--interaction=nonstopmode",
+            basename + ".tex",
+        ]
+        try:
+            subprocess.check_output(command, stderr=subprocess.STDOUT)
+        except subprocess.CalledProcessError as e:
+            logger.error("latexmk compiler failed with output:\n%s", e.output.decode())
+            raise AttributeError from e
+        
+        # dvisvgm command
+        command = [
+            "dvisvgm",
+            basename + ".dvi",
+            "-o",
+            basename + ".svg",
+        ]
+        try:
+            subprocess.check_output(command, stderr=subprocess.STDOUT)
+        except subprocess.CalledProcessError as e:
+            logger.error("dvisvgm command failed with output:\n%s", e.output.decode())
+            raise AttributeError from e
+        finally:
+            # change back to the current directory
+            os.chdir(current_dir)
 
-        # change to output dir
-        os.chdir(temp_dir)
+        # return the name of the folder and temp svg file
+        return os.path.join(temp_dir, basename + ".svg"), temp_dir
 
-        # save the tex file
-        self.save(basename + ".tex")
+    def compile_pdf(self) -> tuple:
+        """Compile pdf from tex."""
+        temp_dir, current_dir, basename = self.prepare_compile()
 
         # latex compiler
         command = [
@@ -115,16 +136,32 @@ def compile_pdf(self) -> tuple:
 
         try:
             subprocess.check_output(command, stderr=subprocess.STDOUT)
-        except Exception:
-            # If compiler does not exist, try next in the list
-            logger.error("No latexmk compiler found")
-            raise AttributeError
+        except subprocess.CalledProcessError as e:
+            logger.error("latexmk compiler failed with output:\n%s", e.output.decode())
+            raise AttributeError from e
         finally:
             # change back to the current directory
             os.chdir(current_dir)
 
         # return the name of the folder and temp pdf file
-        return (os.path.join(temp_dir, basename + ".pdf"), temp_dir)
+        return os.path.join(temp_dir, basename + ".pdf"), temp_dir
+
+    def prepare_compile(self) -> tuple[str, str, str]:
+        """Prepare compilation of tex to pdf or svg by saving the tex file."""
+        # basename
+        basename = "default"
+        # get current directory
+        current_dir = os.getcwd()
+
+        # get temporal directory
+        temp_dir = tempfile.mkdtemp()
+
+        # change to output dir
+        os.chdir(temp_dir)
+
+        # save the tex file
+        self.save(basename + ".tex")
+        return temp_dir, current_dir, basename
 
     def to_tex(self) -> str:
         """Convert data to tex."""
@@ -144,8 +181,8 @@ def to_tex(self) -> str:
         # fill template with data
         tex = Template(tex_template).substitute(
             classoptions=self.config.get("latex_class_options", ""),
-            width=self.config.get("width", "6cm"),
-            height=self.config.get("height", "6cm"),
+            width=self.config.get("width", "12cm"),
+            height=self.config.get("height", "12cm"),
             tikz=data,
         )
 

src/pathpyG/visualisations/_tikz/network_plots.py

@@ -32,12 +32,10 @@ def __init__(self, data: dict, **kwargs: Any) -> None:
         super().__init__()
         self.data = data
         self.config = kwargs
-        self.config["width"] = self.config.pop("width", 6)
-        self.config["height"] = self.config.pop("height", 6)
         self.generate()
 
     def generate(self) -> None:
-        """Clen up data."""
+        """Clean up data."""
         self._compute_node_data()
         self._compute_edge_data()
         self._update_layout()

src/pathpyG/visualisations/_tikz/templates/network.tex

@@ -1,10 +1,12 @@
 \documentclass[$classoptions]{standalone}
 \usepackage[dvipsnames]{xcolor}
 \usepackage{tikz-network}
+\newcommand{\width}{$width}
+\newcommand{\height}{$height}
 \begin{document}
 \begin{tikzpicture}
 \tikzset{every node}=[font=\sffamily\bfseries]
-\clip (0,0) rectangle ($width,$height);
+\clip (-0.5*\width,-0.5*\height) rectangle (0.5*\width,0.5*\height);
 $tikz
 \end{tikzpicture}
 \end{document}

src/pathpyG/visualisations/_tikz/templates/static.tex

@@ -1,10 +1,13 @@
 \documentclass[$classoptions]{standalone}
 \usepackage[dvipsnames]{xcolor}
 \usepackage{tikz-network}
+\newcommand{\width}{$width}
+\newcommand{\height}{$height}
 \begin{document}
 \begin{tikzpicture}
 \tikzset{every node}=[font=\sffamily\bfseries]
-\clip (0,0) rectangle ($width,$height);
+\clip (-0.5*\width,-0.5*\height) rectangle (0.5*\width,0.5*\height);
+\draw[draw,opacity=0] (-0.5*\width,-0.5*\height) rectangle (0.5*\width,0.5*\height);
 $tikz
 \end{tikzpicture}
 \end{document}

src/pathpyG/visualisations/_tikz/templates/temporal.tex

@@ -1,10 +1,12 @@
 \documentclass[$classoptions]{standalone}
 \usepackage[dvipsnames]{xcolor}
 \usepackage{tikz-network}
+\newcommand{\width}{$width}
+\newcommand{\height}{$height}
 \begin{document}
 \begin{tikzpicture}
 \tikzset{every node}=[font=\sffamily\bfseries]
-\clip (0,0) rectangle ($width,$height);
+\clip (-0.5*\width,-0.5*\height) rectangle (0.5*\width,0.5*\height);
 $tikz
 \end{tikzpicture}
 \end{document}

src/pathpyG/visualisations/network_plots.py

@@ -412,15 +412,15 @@ class TemporalNetworkPlot(NetworkPlot):
     """Network plot class for a temporal network."""
 
     _kind = "temporal"
+    network: TemporalGraph
 
     def __init__(self, network: TemporalGraph, **kwargs: Any) -> None:
         """Initialize network plot class."""
         super().__init__(network, **kwargs)
 
     def _get_edge_data(self, edges: dict, attributes: set, attr: defaultdict, categories: set) -> None:
         """Extract edge data from temporal network."""
-        # TODO: Fix typing issue with temporal graphs
-        for u, v, t in self.network.temporal_edges:  # type: ignore
+        for u, v, t in self.network.temporal_edges:
             uid = f"{u}-{v}-{t}"
             edges[uid] = {
                 "uid": uid,

src/pathpyG/visualisations/plot.py

@@ -28,6 +28,7 @@
     ".html": "d3js",
     ".tex": "tikz",
     ".pdf": "tikz",
+    ".svg": "tikz",
     ".png": "matplotlib",
     ".mp4": "manim",
     ".gif": "manim",