Test for saving edges in compact ("split") format

An example of how you might address #187

Author: hyanwong

tskit_arg_visualizer/__init__.py

@@ -301,15 +301,18 @@ def from_json(cls, json):
         nodes = pd.DataFrame(json["data"]["nodes"])
         nodes["x_pos_01"] = (nodes["x"] - x_shift) / (width-100)
         if json["plot_type"] == "full":
-            samples = nodes.loc[bool(nodes["ts_flags"] & tskit.NODE_IS_SAMPLE),["id", "fx"]]
+            samples = nodes.loc[(nodes["ts_flags"] & tskit.NODE_IS_SAMPLE) != 0,["id", "fx"]]
             num_samples = samples.shape[0]
             sample_order = [sample for _, sample in sorted(zip(samples["fx"], samples["id"]))]
         else:
             num_samples = -1
             sample_order = []
         return cls(
             nodes=nodes,
-            edges=pd.DataFrame(json["data"]["links"]),
+            edges=pd.DataFrame(
+                json["data"]["links"]["data"],
+                columns=json["data"]["links"]["columns"],
+            ),
             mutations=pd.DataFrame(json["data"]["mutations"]),
             breakpoints=pd.DataFrame(json["data"]["breakpoints"]),
             num_samples=num_samples,
@@ -1065,7 +1068,6 @@ def _prepare_json(
         transformed_bps["x_pos"] = transformed_bps["x_pos_01"] * width + y_axis_left_spacing
         transformed_bps["width"] = transformed_bps["width_01"] * width
         transformed_bps["included"] = "true"
-        transformed_bps = transformed_bps.to_dict("records")
 
         if shift_for_y_axis:
             width += 50
@@ -1078,9 +1080,9 @@ def _prepare_json(
         arg = {
             "data":{
                 "nodes":transformed_nodes,
-                "links":edges.to_dict("records"),
+                "links":edges.to_dict("split"),
                 "mutations":transformed_muts,
-                "breakpoints":transformed_bps,
+                "breakpoints":transformed_bps.to_dict("records"),
                 "evenly_distributed_positions":sample_positions,
             },
             "width":width,

tskit_arg_visualizer/visualizer.js

@@ -104,6 +104,11 @@ function main_visualizer(
     var stepAfter = d3.line().curve(d3.curveStepAfter);
     var stepBefore = d3.line().curve(d3.curveStepBefore);
 
+    var links = graph.links.data.map(array => {
+        let obj = {}; // New object will have column names as keys
+        graph.links.columns.forEach((colName, index) => {obj[colName] = array[index];});
+        return obj;
+    });
 
     // https://gist.github.com/Rokotyan/0556f8facbaf344507cdc45dc3622177
     // Below are the functions that handle actual exporting:
@@ -347,7 +352,7 @@ function main_visualizer(
             .forceSimulation(graph.nodes)
             .force("link", d3.forceLink()
                 .id(d => d.id)
-                .links(graph.links)
+                .links(links)
             )
             //.force("center", d3.forceCenter(275,250).strength(-10))
             .force("charge", d3.forceManyBody().strength(-100))
@@ -357,11 +362,10 @@ function main_visualizer(
             .append("g")
             .attr("class", "links")
             .selectAll("path")
-            .data(graph.links)
+            .data(links)
             .enter()
             .append("g")
-            .attr("bounds", d => d.bounds);
-
+            .attr("bounds", d => d.bounds)
         if ((edge_styles.type == "ortho") & eval(edge_styles.include_underlink)) {
             var underlink = link_container
                 .append("path")