refactor: remove __file__ (#571)

* refactor: remove __file__

Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>

* refactor: fix cwd to use benchmark_root directly

Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>

---------

Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>

Author: srivarra

benchmarks/utils.py

@@ -6,6 +6,7 @@
 import time
 from contextlib import contextmanager
 from dataclasses import dataclass, field
+from importlib.resources import as_file, files
 from pathlib import Path
 
 import numpy as np
@@ -82,19 +83,17 @@ def save(self, path: Path):
 # --- Metadata collection ---
 
 
-# Path to the waveorder repo root (two levels up from this file)
-_REPO_ROOT = str(Path(__file__).resolve().parent.parent)
-
-
 def _run_git(*args: str) -> str:
     """Run a git command in the waveorder repo and return stripped stdout, or '' on failure."""
     try:
-        result = subprocess.run(
-            ["git", "-C", _REPO_ROOT, *args],
-            capture_output=True,
-            text=True,
-            timeout=5,
-        )
+        with as_file(files("benchmarks")) as benchmark_root:
+            result = subprocess.run(
+                ["git", *args],
+                cwd=benchmark_root,
+                capture_output=True,
+                text=True,
+                timeout=5,
+            )
         return result.stdout.strip()
     except (subprocess.TimeoutExpired, FileNotFoundError):
         return ""

tests/cli_tests/test_settings.py

@@ -1,5 +1,3 @@
-from pathlib import Path
-
 import pytest
 import yaml
 from pydantic import ValidationError
@@ -79,9 +77,8 @@ def test_fluor_tf_settings():
         fluorescence.TransferFunctionSettings(wavelength_emission=0.500, yx_pixel_size=2000)
 
 
-def test_generate_example_settings():
-    project_root = Path(__file__).parent.parent.parent
-    example_path = project_root / "docs" / "examples" / "cli" / "configs"
+def test_generate_example_settings(pytestconfig):
+    example_path = pytestconfig.rootpath / "docs" / "examples" / "cli" / "configs"
 
     # 2D configs override regularization_strength for better 2D defaults
     phase_2d_apply_inverse = phase.ApplyInverseSettings(regularization_strength=1e-2)

tests/test_benchmark_runner.py

@@ -132,11 +132,9 @@ def test_from_dict(self):
 
 
 class TestLoadRegressionExperiment:
-    def test_regression_yml_valid(self):
+    def test_regression_yml_valid(self, pytestconfig):
         """Validate the committed regression.yml experiment."""
-        from pathlib import Path
-
-        regression_path = Path(__file__).parent.parent / "benchmarks" / "experiments" / "regression.yml"
+        regression_path = pytestconfig.rootpath / "benchmarks" / "experiments" / "regression.yml"
         if not regression_path.exists():
             pytest.skip("regression.yml not found")
         exp = load_experiment(regression_path)

tests/test_examples.py

@@ -2,27 +2,43 @@
 import runpy
 import subprocess
 import sys
-from pathlib import Path
 from unittest.mock import patch
 
 import matplotlib.pyplot as plt
 import pytest
 
-DOCS = Path(__file__).parent.parent / "docs"
-EXAMPLES = DOCS / "examples"
+# Examples per test, relative to docs/examples: either explicit files or a glob pattern.
+_EXAMPLES = {
+    "test_maintenance_examples": [
+        "maintenance/QLIPP_simulation/2D_QLIPP_forward.py",
+        "maintenance/QLIPP_simulation/2D_QLIPP_recon.py",
+        "maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py",
+        "maintenance/PTI_simulation/PTI_Simulation_Recon2D.py",
+        "maintenance/PTI_simulation/PTI_Simulation_Recon3D.py",
+    ],
+    "test_demo_examples": [
+        "demos/QPI_defocus/QPI_defocus_simulation.py",
+        "demos/QLIPP/QLIPP_simulation.py",
+    ],
+    "test_api_examples": "api/*.py",
+    "test_cli_examples": "cli/*.sh",
+}
+
+
+def pytest_generate_tests(metafunc):
+    """Resolve repository examples from pytest's configured project root."""
+    entry = _EXAMPLES.get(metafunc.function.__name__)
+    if entry is None:
+        return
+
+    examples_dir = metafunc.config.rootpath / "docs" / "examples"
+    if isinstance(entry, str):
+        examples = sorted(examples_dir.glob(entry))
+    else:
+        examples = [examples_dir / name for name in entry]
+    metafunc.parametrize("example", examples, ids=lambda path: path.name)
 
 
-@pytest.mark.parametrize(
-    "example",
-    [
-        EXAMPLES / "maintenance" / "QLIPP_simulation/2D_QLIPP_forward.py",
-        EXAMPLES / "maintenance" / "QLIPP_simulation/2D_QLIPP_recon.py",
-        EXAMPLES / "maintenance" / "PTI_simulation/PTI_Simulation_Forward_2D3D.py",
-        EXAMPLES / "maintenance" / "PTI_simulation/PTI_Simulation_Recon2D.py",
-        EXAMPLES / "maintenance" / "PTI_simulation/PTI_Simulation_Recon3D.py",
-    ],
-    ids=lambda p: p.name,
-)
 def test_maintenance_examples(example):
     """Test maintenance examples (QLIPP, PTI) with mocked plotting"""
     with (
@@ -39,14 +55,6 @@ def test_maintenance_examples(example):
     plt.close("all")
 
 
-@pytest.mark.parametrize(
-    "example",
-    [
-        EXAMPLES / "demos/QPI_defocus/QPI_defocus_simulation.py",
-        EXAMPLES / "demos/QLIPP/QLIPP_simulation.py",
-    ],
-    ids=lambda p: p.name,
-)
 def test_demo_examples(example):
     """Run Colab demo scripts so renamed APIs in waveorder are caught early.
 
@@ -80,9 +88,9 @@ def test_demo_examples(example):
         "inplane_oriented_thick_pol3d.py",
     ],
 )
-def test_phase_examples(script):
+def test_phase_examples(script, pytestconfig):
     """Test phase model examples"""
-    path = EXAMPLES / "models" / script
+    path = pytestconfig.rootpath / "docs" / "examples" / "models" / script
     # examples needs two <enters>s so send input="e\ne"
     completed_process = subprocess.run(
         [sys.executable, str(path)],
@@ -93,21 +101,11 @@ def test_phase_examples(script):
     assert completed_process.returncode == 0
 
 
-@pytest.mark.parametrize(
-    "example",
-    sorted((EXAMPLES / "api").glob("*.py")),
-    ids=lambda p: p.name,
-)
 def test_api_examples(example):
     """Test API-level examples (no napari, no matplotlib)"""
     runpy.run_path(str(example), run_name="__main__")
 
 
-@pytest.mark.parametrize(
-    "example",
-    sorted((EXAMPLES / "cli").glob("*.sh")),
-    ids=lambda p: p.name,
-)
 def test_cli_examples(example, tmp_path, monkeypatch):
     """Test CLI-level shell script examples (skip 'wo view' lines)."""
     import shlex

waveorder/cli/bench.py

@@ -8,14 +8,13 @@
 import shutil
 import traceback
 from datetime import datetime
+from importlib.resources import as_file, files
 from pathlib import Path
 
 import click
 import numpy as np
 import yaml
 
-_DEFAULT_EXPERIMENT = Path(__file__).parent.parent.parent / "benchmarks" / "experiments" / "regression.yml"
-
 
 def _resolve_output_dir(cli_value: str | None) -> Path:
     """Resolve the output directory.
@@ -102,9 +101,10 @@ def run(experiment, scope, output_dir, save_all):
     from benchmarks.utils import collect_metadata
 
     if experiment is None:
-        experiment = str(_DEFAULT_EXPERIMENT)
-
-    experiment_path = Path(experiment)
+        benchmark_root = click.get_current_context().with_resource(as_file(files("benchmarks")))
+        experiment_path = benchmark_root / "experiments" / "regression.yml"
+    else:
+        experiment_path = Path(experiment)
     output_dir = _resolve_output_dir(output_dir)
     exp = load_experiment(experiment_path)
 

waveorder/plugin/main_widget.py

@@ -4,7 +4,7 @@
 import logging
 import os
 import textwrap
-from os.path import dirname
+from importlib.resources import files
 from pathlib import Path, PurePath
 
 # type hint/check
@@ -52,6 +52,15 @@
     pass
 
 
+def _load_asset_pixmap(name: str) -> QPixmap:
+    """Load a bundled image from ``waveorder/assets`` as a ``QPixmap``."""
+    data = (files("waveorder") / "assets" / name).read_bytes()
+    pixmap = QPixmap()
+    if not pixmap.loadFromData(data):
+        raise ValueError(f"Unable to load bundled image: {name}")
+    return pixmap
+
+
 class MainWidget(QWidget):
     """
     This is the main waveorder widget that houses all of the GUI components of waveorder.
@@ -173,7 +182,6 @@ def __init__(self, napari_viewer: Viewer):
         self.reconstruction_data = None
         self.calib_assessment_level = None
         self.ret_max = 25
-        waveorder_dir = dirname(dirname(dirname(os.path.abspath(__file__))))
         self.worker = None
 
         ## Initialize calibration plot
@@ -185,15 +193,10 @@ def __init__(self, napari_viewer: Viewer):
 
         ## Initialize visuals
         # Initialize GUI Images (plotting legends, waveorder logo)
-        assets_dir = Path(__file__).parent.parent / "assets"
-        jch_legend_path = assets_dir / "JCh_legend.png"
-        hsv_legend_path = assets_dir / "HSV_legend.png"
-        logo_path = assets_dir / "waveorder_plugin_logo.png"
-
-        self.jch_pixmap = QPixmap(str(jch_legend_path))
-        self.hsv_pixmap = QPixmap(str(hsv_legend_path))
+        self.jch_pixmap = _load_asset_pixmap("JCh_legend.png")
+        self.hsv_pixmap = _load_asset_pixmap("HSV_legend.png")
         self.ui.label_orientation_image.setPixmap(self.hsv_pixmap)
-        logo_pixmap = QPixmap(str(logo_path))
+        logo_pixmap = _load_asset_pixmap("waveorder_plugin_logo.png")
         self.ui.label_logo.setPixmap(logo_pixmap)
 
         # Hide UI elements for popups