Deprecate pages module and update docs and tests

pyproject.toml

@@ -53,6 +53,7 @@ dev-dependencies = [
     "pip~=24.2",
     "hatch-vcs~=0.4.0",
     "watchfiles~=0.24.0",
+    "pytest-playwright~=0.5.2",
 ]
 
 [project.scripts]

requirements-dev.lock

@@ -115,6 +115,8 @@ geopandas==1.0.1
     # via tseda
 geoviews==1.13.0
     # via tseda
+greenlet==3.1.1
+    # via playwright
 h11==0.14.0
     # via httpcore
 hatch-vcs==0.4.0
@@ -365,6 +367,8 @@ pip==24.2
 platformdirs==4.2.2
     # via jupyter-core
     # via pooch
+playwright==1.48.0
+    # via pytest-playwright
 pluggy==1.5.0
     # via hatchling
     # via pytest
@@ -388,6 +392,8 @@ pycparser==2.22
     # via cffi
 pyct==0.5.0
     # via datashader
+pyee==12.0.0
+    # via playwright
 pygments==2.18.0
     # via ipython
     # via jupyter-console
@@ -407,6 +413,11 @@ pyshp==2.3.1
 pyslim==1.0.4
     # via stdpopsim
 pytest==8.3.2
+    # via pytest-base-url
+    # via pytest-playwright
+pytest-base-url==2.1.0
+    # via pytest-playwright
+pytest-playwright==0.5.2
 python-dateutil==2.9.0.post0
     # via arrow
     # via jupyter-client
@@ -415,6 +426,8 @@ python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
     # via daiquiri
     # via jupyter-events
+python-slugify==8.0.4
+    # via pytest-playwright
 pytz==2024.1
     # via pandas
 pyviz-comms==3.0.3
@@ -443,6 +456,7 @@ requests==2.32.3
     # via jupyterlab-server
     # via panel
     # via pooch
+    # via pytest-base-url
 rfc3339-validator==0.1.4
     # via jsonschema
     # via jupyter-events
@@ -487,6 +501,8 @@ svgwrite==1.4.3
 terminado==0.18.1
     # via jupyter-server
     # via jupyter-server-terminals
+text-unidecode==1.3
+    # via python-slugify
 tinycss2==1.3.0
     # via nbconvert
 toolz==0.12.1
@@ -536,6 +552,7 @@ types-python-dateutil==2.9.0.20240821
     # via arrow
 typing-extensions==4.12.2
     # via panel
+    # via pyee
     # via pyright
 tzdata==2024.1
     # via pandas

src/tseda/__main__.py

@@ -37,34 +37,6 @@ def cli():
     """Command line interface for tseda."""
 
 
-@cli.command()
-@click.argument("path", type=click.Path(exists=True, dir_okay=False))
-@click.option("--port", default=8080, help="Port to serve on")
-@click.option(
-    "--show/--no-show",
-    default=True,
-    help="Launch a web-browser showing the app",
-)
-@click.option("--log-level", default="INFO", help="Logging level")
-@click.option(
-    "--no-log-filter",
-    default=False,
-    is_flag=True,
-    help="Do not filter the output log (advanced debugging only)",
-)
-def serve2(path, port, show, log_level, no_log_filter):
-    """
-    Run the tseda server, obsolete version.
-    """
-    setup_logging(log_level, no_log_filter)
-
-    tsm = model.TSEdaModel(path)
-
-    logger.info("Starting panel server")
-    app_ = app.App(tsm)
-    pn.serve(app_.view(), port=port, show=show, verbose=False)
-
-
 @cli.command()
 @click.argument("tszip_path", type=click.Path(exists=True, dir_okay=False))
 @click.option(

src/tseda/app.py

@@ -1,3 +1,10 @@
+"""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.
+"""
+
 import time
 
 import daiquiri
@@ -7,7 +14,7 @@
 from holoviews import opts
 from panel.viewable import Viewer
 
-from tseda import config, datastore, pages, vpages
+from tseda import config, datastore, vpages
 
 logger = daiquiri.getLogger("tseda")
 
@@ -41,56 +48,14 @@
 )
 
 
-class App:
-    def __init__(self, tsm):
-        self.tsm = tsm
-        t = time.time()
-        logger.info("Initialising pages")
-        self.pages = {page.title: page(tsm) for page in pages.PAGES}
-        self.spinner = pn.indicators.LoadingSpinner(
-            value=True, width=50, height=50
-        )
-        logger.info(f"Initialised pages in {time.time() - t:.2f}s")
-
-    def view(self):
-        page_titles = list(self.pages.keys())
-        header_selector = pn.widgets.RadioButtonGroup(
-            options=page_titles,
-            value=page_titles[0],
-            name="Select Page",
-            button_type="success",
-        )
-
-        @pn.depends(header_selector.param.value)
-        def get_content(selected_page):
-            yield self.spinner
-            yield self.pages[selected_page].content
-
-        @pn.depends(header_selector.param.value)
-        def get_sidebar(selected_page):
-            yield self.spinner
-            yield self.pages[selected_page].sidebar
-
-        template = pn.template.FastListTemplate(
-            title=self.tsm.name[:15] + "..."
-            if len(self.tsm.name) > 15
-            else self.tsm.name,
-            header=[header_selector],
-            sidebar=get_sidebar,
-            main=get_content,
-            raw_css=[RAW_CSS],
-            **DEFAULT_PARAMS,
-        )
-
-        return template
-
-
 class DataStoreApp(Viewer):
+    """Main application class for tseda visualization app."""
+
     datastore = param.ClassSelector(class_=datastore.DataStore)
 
-    title = param.String()
+    title = param.String(doc="Application title")
 
-    views = param.List()
+    views = param.List(doc="What views to show on startup.")
 
     def __init__(self, **params):
         super().__init__(**params)
@@ -116,6 +81,10 @@ def __init__(self, **params):
 
     @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."""
         page_titles = list(self.pages.keys())
         header_selector = pn.widgets.RadioButtonGroup(
             options=page_titles,

src/tseda/main.py

@@ -0,0 +1,46 @@
+"""Helper module for serving the TSEda app from the command line using
+panel serve.
+
+This module is used to serve the TSEda app from the command line using
+panel serve. One use case is for development purposes where the --dev
+argument enables automated reloading of the app when the source code
+changes. To launch the app from the command line run:
+
+    $ panel serve --dev --admin --show --args path/to/tszip_file.zip
+
+See https://panel.holoviz.org/how_to/server/commandline.html for more
+information.
+"""
+
+from tseda import app  # noqa
+from tseda import datastore  # noqa
+from tsbrowse.model import TSModel  # noqa
+import daiquiri
+import sys
+
+daiquiri.setup(level="WARN")  # noqa
+logger = daiquiri.getLogger("tseda")
+
+
+if len(sys.argv) < 2:
+    logger.error(
+        "Please provide the path to a TreeSequence file via the --args option."
+    )
+    sys.exit(1)
+
+path = sys.argv.pop()
+
+tsm = TSModel(path)
+individuals_table, sample_sets_table = datastore.preprocess(tsm)
+
+app_ = app.DataStoreApp(
+    datastore=datastore.DataStore(
+        tsm=tsm,
+        individuals_table=individuals_table,
+        sample_sets_table=sample_sets_table,
+    ),
+    title="TSEda Datastore App",
+    views=[datastore.IndividualsTable],
+)
+
+app_.view().servable()