Set up the first pytest test

This is by no means a "nice" test, but it at least checks that the code
runs, and practically speaking will allow me to gauge speed-up if I make
stuff faster. See #4

.github/workflows/build.yml

@@ -34,3 +34,5 @@ jobs:
         run: |
           black --skip-string-normalization --check .
           isort --conda-env infresnel --profile black --check-only .
+      - name: Run tests
+        run: pytest --capture=no

requirements.txt

@@ -3,6 +3,7 @@
 black[jupyter]
 isort
 nbdime
+pytest
 sphinx
 sphinx-rtd-theme
 sphinxcontrib-apidoc

tests/test_grid.py

@@ -1,8 +1,6 @@
 """
 Reproduce Fig. 2B in Fee et al. (2021) (https://doi.org/10.3389/feart.2021.620813) using
 path difference time delays.
-
-TODO: Make this into a proper testing file for use with pytest...
 """
 
 import matplotlib
@@ -13,82 +11,97 @@
 
 from infresnel import calculate_paths_grid
 
+RUN_FULL_SCRIPT = (
+    True  # False  # Toggle running fully to make plot of travel time differences
+)
+
 CELERITY = 343.5  # [m/s] From Fee et al. (2021)
 
 # Full path to DEM_Union_UAV_161116_sm101.tif (121 MB GeoTIFF, get from Liam or David)
-DEM_FILE = '/Users/ldtoney/work/yasur_ml/data/DEM_Union_UAV_161116_sm101.tif'
+# DEM_FILE = '/Users/ldtoney/work/yasur_ml/data/DEM_Union_UAV_161116_sm101.tif'
+DEM_FILE = None  # For running on GitHub Actions
 
 # Load YIF6 coordinates (we are using YIF6 as a source!)
 SRC_URL = 'http://service.iris.edu/fdsnws/station/1/query?net=3E&sta=YIF6&format=geocsv'
 src_ser = pd.read_csv(SRC_URL, sep='|', comment='#').squeeze()
 src_lat, src_lon = src_ser.Latitude, src_ser.Longitude
 
 # Define [gridline-registered] grid of receiver locations
-SPACING = 100  # [m]
+SPACING = 50  # [m]
 X_RADIUS = (450, 1750)  # [m] Hardcoded to match Fig. 2B
 Y_RADIUS = (1200, 200)  # [m] "                        "
 
-# %% Calculate travel time delay grid
+# %% Define test function for pytest
 
-path_length_differences, dem = calculate_paths_grid(
-    src_lat=src_lat,
-    src_lon=src_lon,
-    x_radius=X_RADIUS,
-    y_radius=Y_RADIUS,
-    spacing=SPACING,
-    dem_file=DEM_FILE,
-)
 
-travel_time_delays = path_length_differences.data / CELERITY
+def test_calculate_paths_grid(output=False):
+    path_length_differences, dem = calculate_paths_grid(
+        src_lat=src_lat,
+        src_lon=src_lon,
+        x_radius=X_RADIUS,
+        y_radius=Y_RADIUS,
+        spacing=SPACING,
+        dem_file=DEM_FILE,
+    )
+    if output:
+        return path_length_differences, dem
 
-# %% Plot travel time delay grid
 
-# Convert from pixel registration back to gridline registration for plotting
-xvec, yvec = path_length_differences.x, path_length_differences.y
-spacing = path_length_differences.spacing
-xvec_plot = np.hstack([xvec, xvec[-1] + spacing]) - spacing / 2
-yvec_plot = np.hstack([yvec, yvec[-1] - spacing]) + spacing / 2  # Note sign change!
+# %% Calculate travel time delay grid, if desired
 
-# Make grid corner (0, 0) by applying this simple transform function
-transform = lambda x, y: (x - xvec_plot.min(), y - yvec_plot.min())
+if RUN_FULL_SCRIPT:
+    path_length_differences, dem = test_calculate_paths_grid(output=True)
+    travel_time_delays = path_length_differences.data / CELERITY
 
-fig, ax = plt.subplots(figsize=(8, 4))
-hs = dem.copy()
-hs.data = matplotlib.colors.LightSource().hillshade(
-    dem.data,
-    dx=abs(dem.x.diff('x').mean().values),
-    dy=abs(dem.y.diff('y').mean().values),
-)
-hs['x'], hs['y'] = transform(hs.x, hs.y)
-hs.plot.imshow(ax=ax, cmap='Greys_r', add_colorbar=False)
-im = ax.pcolormesh(
-    *transform(xvec_plot, yvec_plot),
-    travel_time_delays,
-    cmap='magma_r',
-    shading='flat',
-    # vmax=0.42,  # Match Fig. 2B in Fee et al. (2021)
-    alpha=0.8,
-)
-utm_crs = CRS(path_length_differences.rio.crs)
-proj = Transformer.from_crs(utm_crs.geodetic_crs, utm_crs)
-src_utm = proj.transform(src_lat, src_lon)
-ax.scatter(*transform(*src_utm), s=180, marker='v', color='black', lw=0, zorder=2)
-ax.text(
-    *transform(src_utm[0], src_utm[1] + 5),  # [m] Shifting text here
-    src_ser.Station[-1],  # Just use station # here
-    color='white',
-    ha='center',
-    va='center',
-    fontsize=8,
-    weight='bold',
-    zorder=2,
-)
-ax.set_title(f'{SPACING} m spacing')
-ax.set_xlim(0, xvec_plot.max() - xvec_plot.min())
-ax.set_ylim(0, yvec_plot.max() - yvec_plot.min())
-ax.grid(linestyle=':', alpha=0.5)
-ax.set_aspect('equal')
-ax.set_xlabel('X (m)')
-ax.set_ylabel('Y (m)')
-fig.colorbar(im, label='Time (s)')
-fig.show()
+# %% Plot travel time delay grid, if desired
+
+if RUN_FULL_SCRIPT:
+    # Convert from pixel registration back to gridline registration for plotting
+    xvec, yvec = path_length_differences.x, path_length_differences.y
+    spacing = path_length_differences.spacing
+    xvec_plot = np.hstack([xvec, xvec[-1] + spacing]) - spacing / 2
+    yvec_plot = np.hstack([yvec, yvec[-1] - spacing]) + spacing / 2  # Note sign change!
+
+    # Make grid corner (0, 0) by applying this simple transform function
+    transform = lambda x, y: (x - xvec_plot.min(), y - yvec_plot.min())
+
+    fig, ax = plt.subplots(figsize=(8, 4))
+    hs = dem.copy()
+    hs.data = matplotlib.colors.LightSource().hillshade(
+        dem.data,
+        dx=abs(dem.x.diff('x').mean().values),
+        dy=abs(dem.y.diff('y').mean().values),
+    )
+    hs['x'], hs['y'] = transform(hs.x, hs.y)
+    hs.plot.imshow(ax=ax, cmap='Greys_r', add_colorbar=False)
+    im = ax.pcolormesh(
+        *transform(xvec_plot, yvec_plot),
+        travel_time_delays,
+        cmap='magma_r',
+        shading='flat',
+        # vmax=0.42,  # Match Fig. 2B in Fee et al. (2021)
+        alpha=0.8,
+    )
+    utm_crs = CRS(path_length_differences.rio.crs)
+    proj = Transformer.from_crs(utm_crs.geodetic_crs, utm_crs)
+    src_utm = proj.transform(src_lat, src_lon)
+    ax.scatter(*transform(*src_utm), s=180, marker='v', color='black', lw=0, zorder=2)
+    ax.text(
+        *transform(src_utm[0], src_utm[1] + 5),  # [m] Shifting text here
+        src_ser.Station[-1],  # Just use station # here
+        color='white',
+        ha='center',
+        va='center',
+        fontsize=8,
+        weight='bold',
+        zorder=2,
+    )
+    ax.set_title(f'{SPACING} m spacing')
+    ax.set_xlim(0, xvec_plot.max() - xvec_plot.min())
+    ax.set_ylim(0, yvec_plot.max() - yvec_plot.min())
+    ax.grid(linestyle=':', alpha=0.5)
+    ax.set_aspect('equal')
+    ax.set_xlabel('X (m)')
+    ax.set_ylabel('Y (m)')
+    fig.colorbar(im, label='Time (s)')
+    fig.show()