Merge pull request #49 from hannamlmv/main

Project Work

.vscode/launch.json

@@ -0,0 +1,21 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+      {
+        "name": "Python: tseda serve",
+        "type": "debugpy",
+        "request": "launch",
+        "module": "tseda",  // Use the module 'tseda' directly
+        "args": [
+          "serve", "tests/data/test.trees.tseda"  // Arguments to the module
+        ],
+        "console": "integratedTerminal",
+        "env": {
+          "PYTHONPATH": "${workspaceFolder}"
+        },
+        "justMyCode": true,
+        "python": "${workspaceFolder}/.venv/bin/python"
+      }
+    ]
+  }
+

src/tseda/__main__.py

@@ -49,8 +49,8 @@ def cli():
     ),
 )
 def preprocess(tszip_path, output):
-    """
-    Preprocess a tskit tree sequence or tszip file, producing a .tseda file.
+    """Preprocess a tskit tree sequence or tszip file, producing a .tseda file.
+
     Calls tsbrowse.preprocess.preprocess.
     """
     tszip_path = pathlib.Path(tszip_path)
@@ -79,9 +79,7 @@ def preprocess(tszip_path, output):
     help="Do not filter the output log (advanced debugging only)",
 )
 def serve(path, port, show, log_level, no_log_filter, admin):
-    """
-    Run the tseda datastore server, version based on View base class.
-    """
+    """Run the tseda datastore server, version based on View base class."""
     setup_logging(log_level, no_log_filter)
 
     tsm = TSModel(path)
@@ -91,8 +89,8 @@ def serve(path, port, show, log_level, no_log_filter, admin):
     app_ = app.DataStoreApp(
         datastore=datastore.DataStore(
             tsm=tsm,
-            individuals_table=individuals_table,
             sample_sets_table=sample_sets_table,
+            individuals_table=individuals_table,
         ),
         title="TSEda Datastore App",
         views=[IndividualsTable],

src/tseda/app.py

@@ -1,8 +1,8 @@
 """Main application for tseda.
 
-Provides the DataStoreApp class that is the main application for
-tseda. The DataStoreApp subclasses the Viewer class from panel and
-renders a panel.FastListTemplate object.
+Provides the DataStoreApp class that is the main application for tseda. The
+DataStoreApp subclasses the Viewer class from panel and renders a
+panel.FastListTemplate object.
 """
 
 import time
@@ -20,7 +20,7 @@
 
 RAW_CSS = """
         .sidenav#sidebar {
-            background-color: #15E3AC;
+            background-color: WhiteSmoke;
         }
         .title {
             font-size: var(--type-ramp-plus-2-font-size);
@@ -50,7 +50,20 @@
 
 
 class DataStoreApp(Viewer):
-    """Main application class for tseda visualization app."""
+    """Main application class for tseda visualization app.
+
+    Attributes:
+        datastore (DataStore): The data store instance for accessing and
+        managing data.
+        title (str): The title of the application.
+        views (List[str]): A list of views to show on startup.
+
+    Methods:
+        __init__(**params): Initializes the application, loads pages, and sets
+        up data update listeners.
+        view(): Creates the main application view, including a header selector
+        for switching between different pages.
+    """
 
     datastore = param.ClassSelector(class_=datastore.DataStore)
 
@@ -71,21 +84,28 @@ def __init__(self, **params):
         logger.info(f"Initialised pages in {time.time() - t:.2f}s")
 
         updating = (
-            self.datastore.individuals_table.data.rx.updating()
-            | self.datastore.sample_sets_table.data.rx.updating()
+            self.datastore.sample_sets_table.data.rx.updating()
+            | self.datastore.individuals_table.data.rx.updating()
         )
         updating.rx.watch(
-            lambda updating: pn.state.curdoc.hold()
-            if updating
-            else pn.state.curdoc.unhold()
+            lambda updating: (
+                pn.state.curdoc.hold()
+                if updating
+                else pn.state.curdoc.unhold()
+            )
         )
 
     @param.depends("views")
     def view(self):
-        """Main application view that renders a radio button group on
-        top with links to pages. Each page consists of a main content
-        page with plots and sidebars that provide user options for
-        configuring plots and outputs."""
+        """Creates the main application view. Main application view that
+        renders a radio button group on top with links to pages. Each page
+        consists of a main content page with plots and sidebars that provide
+        user options for configuring plots and outputs.
+
+        Returns:
+            pn.template.FastListTemplate: A Panel template containing the
+            header selector, sidebar, and main content.
+        """
         page_titles = list(self.pages.keys())
         header_selector = pn.widgets.RadioButtonGroup(
             options=page_titles,
@@ -105,9 +125,11 @@ def get_sidebar(selected_page):
             yield self.pages[selected_page].sidebar
 
         self._template = pn.template.FastListTemplate(
-            title=self.datastore.tsm.name[:75] + "..."
-            if len(self.datastore.tsm.name) > 75
-            else self.datastore.tsm.name,
+            title=(
+                self.datastore.tsm.name[:75] + "..."
+                if len(self.datastore.tsm.name) > 75
+                else self.datastore.tsm.name
+            ),
             header=[header_selector],
             sidebar=get_sidebar,
             main=get_content,

src/tseda/cache.py

@@ -1,3 +1,6 @@
+"""This module provides a caching mechanism for the TSeDA application,
+utilizing the `diskcache` library."""
+
 import pathlib
 
 import appdirs
@@ -7,7 +10,14 @@
 logger = daiquiri.getLogger("cache")
 
 
-def get_cache_dir():
+def get_cache_dir() -> pathlib.Path:
+    """Retrieves the user's cache directory for the TSeDA application. Creates
+    the directory if it doesn't exist, ensuring its creation along with any
+    necessary parent directories.
+
+    Returns:
+        pathlib.Path: The path to the cache directory.
+    """
     cache_dir = pathlib.Path(appdirs.user_cache_dir("tseda", "tseda"))
     cache_dir.mkdir(exist_ok=True, parents=True)
     return cache_dir

src/tseda/config.py

@@ -1,3 +1,9 @@
+"""Config file.
+
+This file stores configurations for the entire application such as figure
+dimensions and color schemes.
+"""
+
 import holoviews as hv
 from holoviews.plotting.util import process_cmap
 
@@ -8,9 +14,9 @@
 PLOT_COLOURS = ["#15E3AC", "#0FA57E", "#0D5160"]
 
 # VCard settings
-SIDEBAR_BACKGROUND = "#15E3AC"
+SIDEBAR_BACKGROUND = "#5CB85D"
 VCARD_STYLE = {
-    "background": "#15E3AC",
+    "background": "WhiteSmoke",
 }
 
 # Global color map