test, don't merge

src/tseda/datastore.py

@@ -14,6 +14,7 @@
 
 logger = daiquiri.getLogger("tseda")
 
+# test comment 
 
 def make_individuals_table(tsm):
     result = []
@@ -107,7 +108,6 @@ class IndividualsTable(Viewer):
             "type": "tickCross",
             "tristate": True,
             "indeterminateValue": None,
-            "placeholder": "Enter True/False",
         },
     }
 
@@ -136,10 +136,6 @@ def tooltip(self):
             ),
         )
 
-    def sample_set_indices(self):
-        """Return indices of sample groups."""
-        return sorted(self.data.rx.value["sample_set_id"].unique().tolist())
-
     def sample_sets(self):
         sample_sets = {}
         samples = []
@@ -161,6 +157,14 @@ def get_sample_sets(self, indexes=None):
             return [sample_sets[i] for i in indexes]
         return [sample_sets[i] for i in sample_sets]
 
+    def sample_set_indices(self):
+        """Return indices of sample groups."""
+        return sorted(self.data.rx.value["sample_set_id"].unique().tolist())
+
+    def selected_sample_set_indices(self):
+        samples, sample_sets = self.sample_sets()
+        return list(sample_sets.keys())
+
     @property
     def sample2ind(self):
         """Map sample (tskit node) ids to individual ids"""
@@ -183,16 +187,14 @@ def loc(self, i):
 
     @pn.depends("page_size", "sample_select.value", "mod_update_button.value")
     def __panel__(self):
-        self.data.rx.value["selected"] = False
-        if (
-            isinstance(self.sample_select.value, list)
-            and self.sample_select.value
-        ):
+        if isinstance(self.sample_select.value, list):
+            self.data.rx.value["selected"] = False
             for sample_set_id in self.sample_select.value:
                 self.data.rx.value.loc[
                     self.data.rx.value.sample_set_id == sample_set_id,
                     "selected",
                 ] = True
+
         if self.sample_set_to is not None:
             if self.population_from is not None:
                 try:

src/tseda/vpages/individuals.py

@@ -21,13 +21,13 @@
 class IndividualsPage(View):
     key = "individuals"
     title = "Individuals"
-    geomap = param.ClassSelector(class_=GeoMap)
     data = param.ClassSelector(class_=IndividualsTable)
+    geomap = param.ClassSelector(class_=GeoMap)
 
     def __init__(self, **params):
         super().__init__(**params)
-        self.geomap = GeoMap(datastore=self.datastore)
         self.data = self.datastore.individuals_table
+        self.geomap = GeoMap(datastore=self.datastore)
 
     def __panel__(self):
         return pn.Column(self.geomap, self.data)

src/tseda/vpages/map.py

@@ -14,6 +14,7 @@
 
 import geopandas
 import hvplot.pandas  # noqa
+import pandas as pd
 import panel as pn
 import param
 import xyzservices.providers as xyz
@@ -34,17 +35,15 @@
 
 
 class GeoMap(View):
-    height = param.Integer(default=400, doc="Height of the map")
-    width = param.Integer(default=1200, doc="Width of the map")
-
     tiles_selector = param.Selector(
         default="WorldPhysical",
         objects=list(tiles_options.keys()),
         doc="Select XYZ tiles for map",
     )
     tiles = tiles_options[tiles_selector.default]
+    refresh_button = pn.widgets.Button(name="Refresh map")
 
-    @pn.depends("tiles_selector", "height", "width")
+    @pn.depends("refresh_button.value")
     def __panel__(self):
         self.tiles = tiles_options[self.tiles_selector]
         df = self.datastore.individuals_table.data.rx.value
@@ -56,24 +55,45 @@ def __panel__(self):
         )
         color = color.loc[~gdf.geometry.is_empty.values]
         gdf = gdf[~gdf.geometry.is_empty]
-        return gdf.hvplot.points(
+
+        kw = {
+            "geo": True,
+            "tiles": self.tiles,
+            "tiles_opts": {"alpha": 0.5},
+            "responsive": True,
+            "max_height": 200,
+            "min_height": 199,
+            "xlim": (-180, 180),
+            "ylim": (-60, 70),
+            "tools": ["wheel_zoom", "box_select", "tap", "pan", "reset"],
+        }
+
+        if gdf.empty:
+            gdf = geopandas.GeoDataFrame(
+                pd.DataFrame(index=[0]),
+                geometry=geopandas.points_from_xy([0.0], [0.0]),
+            )
+            return gdf.hvplot(
+                **kw,
+                hover_cols=None,
+                size=100,
+                color=None,
+                fill_alpha=0.0,
+                line_color=None,
+            )
+        return gdf.hvplot(
+            **kw,
             hover_cols=["name", "population", "sample_set_id"],
-            geo=True,
-            tiles=self.tiles,
-            tiles_opts={"alpha": 0.5},
-            max_height=self.height,
-            min_height=self.height,
             size=100,
             color=color,
-            tools=["wheel_zoom", "box_select", "tap", "pan", "reset"],
             fill_alpha=0.5,
             line_color="black",
-            responsive=True,
         )
 
     def sidebar(self):
         return pn.Card(
             self.param.tiles_selector,
+            self.refresh_button,
             collapsed=False,
             title="Map options",
             header_background=config.SIDEBAR_BACKGROUND,

src/tseda/vpages/stats.py

@@ -9,6 +9,7 @@
 """
 
 import ast
+import itertools
 
 import holoviews as hv
 import pandas as pd
@@ -25,9 +26,10 @@
 
 
 # TODO: make sure this is safe
-def eval_sample_sets(sample_sets):
-    """Evaluate sample sets parameter."""
-    return ast.literal_eval(sample_sets)
+def eval_comparisons(comparisons):
+    """Evaluate comparisons parameter."""
+    evaluated = ast.literal_eval(str(comparisons).replace("-", ","))
+    return [tuple(map(int, item.split(","))) for item in evaluated]
 
 
 def eval_indexes(indexes):
@@ -37,9 +39,10 @@ def eval_indexes(indexes):
 
 class OnewayStats(View):
     mode = param.Selector(
-        objects=["branch", "site"],
+        objects=["site"],
         default="site",
-        doc="Select mode for statistics.",
+        doc="""Select mode (site or branch) for statistics. 
+        Branch mode is only available for calibrated data.""",
     )
     statistic = param.Selector(
         objects=["Tajimas_D", "diversity"],
@@ -49,9 +52,11 @@ class OnewayStats(View):
     window_size = param.Integer(
         default=10000, bounds=(1, None), doc="Size of window"
     )
-    sample_sets = param.String(
-        default="[0,1]",
-        doc="Comma-separated list of sample sets (0-indexed) to plot.",
+
+    sample_select_warning = pn.pane.Alert(
+        """Select at least 1 sample set to see this plot.
+        Sample sets are selected on the Individuals page""",
+        alert_type="warning",
     )
 
     @property
@@ -63,19 +68,23 @@ def tooltip(self):
             )
         )
 
-    @param.depends("mode", "statistic", "window_size", "sample_sets")
+    def __init__(self, **params):
+        super().__init__(**params)
+        if self.datastore.tsm.ts.time_units != "uncalibrated":
+            self.param.mode.objects = ["branch", "site"]
+
+    @param.depends("mode", "statistic", "window_size")
     def __panel__(self):
         data = None
         windows = make_windows(
             self.window_size, self.datastore.tsm.ts.sequence_length
         )
-        sample_sets_list = eval_sample_sets(self.sample_sets)
-        try:
-            sample_sets = self.datastore.individuals_table.get_sample_sets(
-                sample_sets_list
-            )
-        except KeyError:
-            return pn.pane.Alert("Sample set error. Check sample set indexes.")
+        sample_sets_list = (
+            self.datastore.individuals_table.selected_sample_set_indices()
+        )
+        if len(sample_sets_list) < 1:
+            return self.sample_select_warning
+        sample_sets = self.datastore.individuals_table.get_sample_sets()
 
         if self.statistic == "Tajimas_D":
             data = self.datastore.tsm.ts.Tajimas_D(
@@ -120,7 +129,6 @@ def sidebar(self):
             self.param.mode,
             self.param.statistic,
             self.param.window_size,
-            self.param.sample_sets,
             collapsed=False,
             title="Oneway statistics plotting options",
             header_background=config.SIDEBAR_BACKGROUND,
@@ -131,9 +139,10 @@ def sidebar(self):
 
 class MultiwayStats(View):
     mode = param.Selector(
-        objects=["branch", "site"],
+        objects=["site"],
         default="site",
-        doc="Select mode for statistics.",
+        doc="""Select mode (site or branch) for statistics. 
+        Branch mode is only available for calibrated data.""",
     )
     statistic = param.Selector(
         objects=["Fst", "divergence"],
@@ -143,16 +152,14 @@ class MultiwayStats(View):
     window_size = param.Integer(
         default=10000, bounds=(1, None), doc="Size of window"
     )
-    sample_sets = param.String(
-        default="[0,1,2]",
-        doc="Comma-separated list of sample sets (0-indexed) to compare.",
+    comparisons = pn.widgets.MultiChoice(
+        name="Comparisons", description="Choose indexes to compare."
     )
-    indexes = param.String(
-        default="[(0,1), (0,2), (1,2)]",
-        doc=(
-            "Comma-separated list of tuples of sample sets "
-            "(0-indexed) indexes to compare."
-        ),
+
+    sample_select_warning = pn.pane.Alert(
+        """Select at least 2 sample sets to see this plot.
+        Sample sets are selected on the Individuals page""",
+        alert_type="warning",
     )
     cmaps = {
         cm.name: cm
@@ -167,6 +174,11 @@ class MultiwayStats(View):
         doc="Holoviews colormap for sample set pairs",
     )
 
+    def __init__(self, **params):
+        super().__init__(**params)
+        if self.datastore.tsm.ts.time_units != "uncalibrated":
+            self.param.mode.objects = ["branch", "site"]
+
     @property
     def tooltip(self):
         return pn.widgets.TooltipIcon(
@@ -176,42 +188,49 @@ def tooltip(self):
             )
         )
 
+    def set_multichoice_options(self):
+        all_comparisons = list(
+            f"{x}-{y}"
+            for x, y in itertools.combinations(
+                self.datastore.individuals_table.selected_sample_set_indices(),
+                2,
+            )
+        )
+        self.comparisons.options = all_comparisons
+        if self.comparisons.value == [] and all_comparisons != []:
+            self.comparisons.value = [all_comparisons[0]]
+
     @pn.depends(
-        "mode",
-        "statistic",
-        "window_size",
-        "sample_sets",
-        "indexes",
-        "colormap",
+        "mode", "statistic", "window_size", "colormap", "comparisons.value"
     )
     def __panel__(self):
+        self.set_multichoice_options()
+
         data = None
         tsm = self.datastore.tsm
-        sample_sets_list = []
         windows = []
-        indexes_list = []
         colormap_list = []
         windows = make_windows(self.window_size, tsm.ts.sequence_length)
-        sample_sets_list = eval_sample_sets(self.sample_sets)
-        indexes_list = eval_indexes(self.indexes)
-        try:
-            sample_sets = self.datastore.individuals_table.get_sample_sets(
-                sample_sets_list
-            )
-        except KeyError:
-            return pn.pane.Alert("Sample set error. Check sample set indexes.")
+        comparisons = eval_comparisons(self.comparisons.value)
+
+        sample_sets_list = (
+            self.datastore.individuals_table.selected_sample_set_indices()
+        )
+        if len(sample_sets_list) < 2:
+            return self.sample_select_warning
+        sample_sets = self.datastore.individuals_table.get_sample_sets()
         if self.statistic == "Fst":
             data = tsm.ts.Fst(
                 sample_sets,
                 windows=windows,
-                indexes=indexes_list,
+                indexes=comparisons,
                 mode=self.mode,
             )
         elif self.statistic == "divergence":
             data = tsm.ts.divergence(
                 sample_sets,
                 windows=windows,
-                indexes=indexes_list,
+                indexes=comparisons,
                 mode=self.mode,
             )
         else:
@@ -226,7 +245,7 @@ def __panel__(self):
                         sample_sets_table.loc(j)["name"],
                     ]
                 )
-                for i, j in indexes_list
+                for i, j in comparisons
             ],
         )
         position = hv.Dimension(
@@ -255,8 +274,7 @@ def sidebar(self):
             self.param.mode,
             self.param.statistic,
             self.param.window_size,
-            self.param.sample_sets,
-            self.param.indexes,
+            self.comparisons,
             self.param.colormap,
             collapsed=False,
             title="Multiway statistics plotting options",