Updated GUI to fit COBRA theme

.claude/CLAUDE.md

@@ -66,9 +66,7 @@ pipeline orchestration, and GUI stay in their own packages.
   `uv run ty check`; CI fails on either. Ruff runs with `select = ALL`
   and a curated ignore list in `pyproject.toml` — add to that list only with a
   one-line reason, as the existing entries do.
-- There is no test suite yet (`tests/` is empty, pytest is configured). When
-  adding tests, put them in `tests/`, add `pytest` to the `dev` group, and keep
-  them free of Palace, torch training, and network access.
+- Tests live in `tests/` and run with `uv run pytest` (`pytest` is in the `dev`
 
 ## Simulation and Training
 

.claude/GUI_DESIGN.md

@@ -277,17 +277,16 @@ never the only signal · sentence case, units, tooltip · docs touched.
 
 ## 9. Known deviations in the current GUI
 
-To be resolved in one GUI update step, not incrementally by unrelated changes:
-
-- `theme.py` is light-only with Material-blue literals (the file COBRA's theme
-  started from); it has no tokens, no dark theme, no `ThemeManager`.
-- The stylesheet is applied to the main window (`apply_theme(window)` in
-  `app.py`) rather than the `QApplication`, so dialogs and message boxes miss it.
-- `pipeline_window.py` styles the run button with a per-widget `setStyleSheet`
-  and uses `<h2>` HTML in labels for headings; both become QSS properties
-  (`primaryAction`, `role="heading"`).
-- No `actionState` on the run button, no `progressState` on the progress bar.
-- Pipeline success is announced with a modal `QMessageBox`; it should be the
-  status label plus the `finished` progress state.
-- Labels use trailing colons and Title Case ("Select Geometry:", "Geometry Name:").
-- No icons, no theme toggle, no persisted appearance setting, no `help_texts.py`.
+The GUI update of September 2026 resolved the original list (tokens, both
+themes, `ThemeManager`, application-level stylesheet, QSS properties instead of
+inline styles, no success modal, sentence-case labels, icons, theme toggle,
+`help_texts.py`). What remains, by design rather than by omission:
+
+- No plots, so `theme.py` has no `style_plot` and ORCA does not depend on
+  pyqtgraph. Add both together with the first plot.
+- No pause/stop: `ORCA.run` cannot be interrupted, so the run button only uses
+  the `start` action state and is disabled while a run is in progress.
+- The stage forms are derived from the constructor signatures, so their labels
+  are the parameter names in sentence case without units; a stage option that
+  wants a unit or a friendlier label gets it in its `Args:` docstring, which
+  is what the tooltip shows.

README.md

@@ -155,9 +155,10 @@ orca
 The GUI lets you:
 
 - select a geometry preset or load a custom geometry class,
-- configure pipeline stages and parameters,
-- monitor simulation and training progress in real time,
-- inspect and test the trained model.
+- configure pipeline stages and parameters (each field has a tooltip),
+- monitor simulation and training progress and the log in real time,
+- test the trained model,
+- switch between a light and a dark theme, or follow the system setting.
 
 ### 2. Python script mode
 

docs/running_orca.md

@@ -29,10 +29,12 @@ orca
 
 In GUI mode:
 
-1. Select a geometry class.
-2. Configure pipeline stages and parameters.
-3. Set Palace executable path.
-4. Start the pipeline.
+1. Select a geometry preset, or load a custom `.py` file that defines a `BaseGeometry` subclass. The name field sets the output folder (`output/<name>/`).
+2. Tick the pipeline stages to run and set their parameters. Every field has a tooltip taken from the stage's documentation; leave an optional field empty (or `None`) to use the default.
+3. Set the Palace executable path in the `PalaceSimulator` stage.
+4. Click **Run pipeline**. Progress, the current stage, and the outcome show next to the progress bar (green when finished, red text on an error); the log panel mirrors what ORCA prints on the console. Validation problems, such as no geometry selected, appear inline instead of in a dialog. If the output directory already exists you are asked once before it is overwritten.
+
+The button in the top-right corner switches the appearance between *system* (follows the OS colour scheme), *light* (Sandbank) and *dark* (Deepwater). The choice is remembered across sessions.
 
 ## 3. Run Script Mode
 

pyproject.toml

@@ -63,6 +63,7 @@ dependencies = [
     "tqdm",
     "pandas",
     "PySide6",
+    "qtawesome",
     "colorlog",
     "matplotlib",
     "pebble>=5.2.2",
@@ -89,10 +90,11 @@ cu126 = ["torch"]
 cu130 = ["torch"]
 
 [dependency-groups]
-# Installed by `uv sync` (not by `pip install`): the linters CI runs, pinned by uv.lock.
+# Installed by `uv sync` (not by `pip install`): the linters and test runner CI uses, pinned by uv.lock.
 dev = [
     "ruff",
     "ty",
+    "pytest",
 ]
 
 [tool.uv]

src/orca/gui/README.md

@@ -1,2 +1,2 @@
 ## GUI
-This file contains the GUI of ORCA. It allows the user to use the trained models for inference on new data.
+PySide6 pipeline window of ORCA: pick a geometry, enable and configure the stages, run them, and follow the log.

src/orca/gui/app.py

@@ -2,15 +2,16 @@
 
 from PySide6.QtWidgets import QApplication
 
+from orca.gui import theme
 from orca.gui.pipeline_window import PipelineWindow
-from orca.gui.theme import apply_theme
 
 
 def run_gui():
     app = QApplication(sys.argv)
-
+    app.setOrganizationName("ORCA")
+    app.setApplicationName("ORCA")
+    theme.manager().apply()
     window = PipelineWindow()
-    apply_theme(window)
     window.show()
     sys.exit(app.exec())
 

src/orca/gui/help_texts.py

@@ -0,0 +1,64 @@
+"""Tooltips of the ORCA GUI, in one place so wording stays consistent.
+
+Static controls look their text up by key with :func:`tooltip`; the stage
+parameter forms, which are derived from the stage constructors, take theirs
+from the ``Args:`` section of the constructor docstring via
+:func:`parameter_tooltips`, so a stage documents its options once.
+"""
+
+from __future__ import annotations
+
+import inspect
+import re
+
+TOOLTIPS = {
+    "theme_btn": "Appearance: {mode} ({theme}). Click to switch between system, light and dark.",
+    "run_btn": "Run the enabled stages in order on the selected geometry.",
+    "geometry_combo": "Built-in geometry presets. Loading a custom file replaces the selection.",
+    "geometry_file_btn": "Browse for a Python file that defines a BaseGeometry subclass.",
+    "geometry_name_edit": (
+        "Name of the run. Output goes to output/<name>/; leave the preset name to keep "
+        "its default."
+    ),
+    "stage_group": (
+        "Tick to include this stage in the run. A stage whose inputs are missing "
+        "reports which earlier stage was skipped."
+    ),
+    "log_output": "Messages from the pipeline; the same text ORCA prints on the console.",
+}
+
+#: ``name (type): text`` or ``name: text`` at the start of an Args entry.
+_ARG_LINE = re.compile(r"^(?P<name>\w+)(?:\s*\([^)]*\))?:\s*(?P<text>.*)$")
+
+
+def tooltip(key: str) -> str:
+    return TOOLTIPS.get(key, "")
+
+
+def parameter_tooltips(cls: type) -> dict[str, str]:
+    """Per-parameter descriptions from the ``Args:`` section of ``cls.__init__``'s docstring.
+
+    Continuation lines are joined with spaces; parameters without an entry are
+    absent from the result.
+    """
+    doc = inspect.getdoc(cls.__init__)
+    if not doc:
+        return {}
+    tips: dict[str, str] = {}
+    current: str | None = None
+    in_args = False
+    for raw in doc.splitlines():
+        line = raw.strip()
+        if not in_args:
+            in_args = line == "Args:"
+            continue
+        if not line or (raw and not raw[0].isspace()):
+            # A blank line or a new section heading ends the Args block.
+            break
+        match = _ARG_LINE.match(line)
+        if match and not raw.startswith("        "):
+            current = match.group("name")
+            tips[current] = match.group("text")
+        elif current is not None:
+            tips[current] = f"{tips[current]} {line}".strip()
+    return tips