Conda test (FlexTRKR#108)

* Updates for compliance.

1. Updated use of np.nan in compliance with NumPy 2.0.
2. Updated quicklook plot codes to use default font.family and fixed a small bug to work with current version of Xarray.
3. Updated demo shell scripts commenting out activating pyflextrkr environments.

* Updated README.md with conda install instructions.

* Updated CI test to use get_basetime_from_string

Author: feng045

.github/workflows/test.yml

@@ -29,6 +29,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
+          pip install -e .
           pip install pytest
 
       - name: Run Tests

Analysis/plot_subset_cell_tracks_ETH_demo.py

@@ -297,7 +297,7 @@ def plot_map(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=300, facecolor='w')
     gs = gridspec.GridSpec(1,2, height_ratios=[1], width_ratios=[1,0.03])
     gs.update(wspace=0.05, hspace=0.05, left=0.1, right=0.9, top=0.92, bottom=0.08)

Analysis/plot_subset_cell_tracks_demo.py

@@ -250,7 +250,7 @@ def plot_map(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=200)
     gs = gridspec.GridSpec(1,2, height_ratios=[1], width_ratios=[1,0.03])
     gs.update(wspace=0.05, hspace=0.05, left=0.1, right=0.9, top=0.92, bottom=0.08)
@@ -374,13 +374,13 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
         map_info['subset'] = subset
 
     # Make dilation structure (larger values make thicker outlines)
-    # perim_thick = 1
-    # dilationstructure = np.zeros((perim_thick+1,perim_thick+1), dtype=int)
-    # dilationstructure[1:perim_thick, 1:perim_thick] = 1
-    # dilationstructure = generate_binary_structure(2,1)
     perim_width = plot_info['perim_width']
-    dilationstructure = np.zeros((perim_width+1,perim_width+1), dtype=int)
-    dilationstructure[1:perim_width, 1:perim_width] = 1
+    if perim_width > 1:
+        dilationstructure = np.zeros((perim_width+1,perim_width+1), dtype=int)
+        dilationstructure[1:perim_width, 1:perim_width] = 1
+    else:
+        dilationstructure = generate_binary_structure(2,1)
+    # import pdb; pdb.set_trace()
 
     # Data variable names
     field_varname = config["field_varname"]
@@ -483,25 +483,26 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
             figsize = [10, 10]
 
     # Specify plotting info
-    # cmap = 'RdBu_r',   # colormap
-    # levels = np.arange(-4, 4.01, 0.2),  # shading levels
-    # cbticks = np.arange(-4, 4.01, 1),  # colorbar ticks
-    # cblabels = 'Z500 Anomaly (m$^{2}$ s$^{-1}$)',  # colorbar label
-    cmap = 'gist_ncar'   # colormap
-    levels = np.arange(0, 70.01, 5)  # shading levels
-    cbticks = np.arange(0, 70.01, 10)  # colorbar ticks
-    cblabels = 'Reflectivity (dBZ)'  # colorbar label
+    cmap = 'RdBu_r'   # colormap
+    levels = np.arange(-4, 4.01, 0.2)  # shading levels
+    cbticks = np.arange(-4, 4.01, 1)  # colorbar ticks
+    cblabels = 'Z500 Anomaly (m$^{2}$ s$^{-1}$)'  # colorbar label
+    # cmap = 'gist_ncar'   # colormap
+    # levels = np.arange(0, 70.01, 5)  # shading levels
+    # cbticks = np.arange(0, 70.01, 10)  # colorbar ticks
+    # cblabels = 'Reflectivity (dBZ)'  # colorbar label
     plot_info = {
         'fontsize': 13,     # plot font size
         'cmap': cmap,
         'levels': levels,
         'cbticks': cbticks, 
         'cblabels': cblabels,
-        'remove_oob_low': True,   # mask out-of-bounds low values (< min(levels))
+        'remove_oob_low': False,   # mask out-of-bounds low values (< min(levels))
         'remove_oob_high': False,  # mask out-of-bounds high values (> max(levels))
         'marker_size': 10,   # track symbol marker size
         'tracknumber_fontsize': 10,
-        'perim_width': 6,  # width of the track feature perimeter (number of pixels)
+        # 'perim_width': 6,  # width of the track feature perimeter (number of pixels)
+        'perim_width': 1,  # width of the track feature perimeter (number of pixels)
         'trackpath_linewidth': 1.5, # track path line width
         'trackpath_color': 'blueviolet',    # track path color
         'map_edgecolor': 'gray',    # background map edge color
@@ -521,7 +522,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
         'lonv': lonv,
         'latv': latv,
         'draw_border': True,
-        'draw_state': True,
+        'draw_state': False,
     }
 
     # Track stats file

Analysis/plot_subset_generic_tracks_demo.py

@@ -235,7 +235,7 @@ def plot_map(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=200)
     gs = gridspec.GridSpec(1,2, height_ratios=[1], width_ratios=[1,0.03])
     gs.update(wspace=0.05, hspace=0.05, left=0.1, right=0.9, top=0.92, bottom=0.08)

Analysis/plot_subset_psi_tracks_demo.py

@@ -232,7 +232,7 @@ def plot_map_2panels(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=300, facecolor='w')
     gs = gridspec.GridSpec(1, 2, height_ratios=[1], width_ratios=[1, 0.03])
     gs.update(wspace=0.05, hspace=0.05, left=0.1, right=0.9, top=0.92, bottom=0.08)
@@ -386,7 +386,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
     if (np.nanmax(tn) > 0):
 
         # Tracknumber color levels for MCS masks (limit to 256 to fit in a colormap)
-        tracknumbers = track_dict['lifetime'].tracks
+        tracknumbers = track_dict['lifetime'].tracks.values
         tn_nlev = np.min([len(tracknumbers), 256])
         tn_levels = np.linspace(np.min(tracknumbers)+1, np.max(tracknumbers)+1, tn_nlev)
         # Add to plot_info dictionary

Analysis/plot_subset_tb_mcs_tracks_demo.py

@@ -274,7 +274,7 @@ def plot_map_2panels(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=dpi, facecolor='w')
 
     # Set GridSpec for left (plot) and right (colorbars)
@@ -455,7 +455,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
     if (np.nanmax(tn) > 0):
 
         # Tracknumber color levels for MCS masks (limit to 256 to fit in a colormap)
-        tracknumbers = track_dict['lifetime'].tracks
+        tracknumbers = track_dict['lifetime'].tracks.values
         tn_nlev = np.min([len(tracknumbers), 256])
         tn_levels = np.linspace(np.min(tracknumbers)+1, np.max(tracknumbers)+1, tn_nlev)
         # Add to plot_info dictionary

Analysis/plot_subset_tbpf_mcs_tracks_1panel_demo.py

@@ -278,7 +278,7 @@ def plot_map_2panels(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=dpi, facecolor='w')
     # vertical: left + right panel
     if panel_orientation == 'vertical':
@@ -513,7 +513,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config, ifile)
     if (np.nanmax(tn) > 0):
 
         # Tracknumber color levels for MCS masks (limit to 256 to fit in a colormap)
-        tracknumbers = track_dict['lifetime'].tracks
+        tracknumbers = track_dict['lifetime'].tracks.values
         tn_nlev = np.min([len(tracknumbers), 256])
         tn_levels = np.linspace(np.min(tracknumbers)+1, np.max(tracknumbers)+1, tn_nlev)
         # Add to plot_info dictionary

Analysis/plot_subset_tbpf_mcs_tracks_demo.py

@@ -255,7 +255,7 @@ def plot_map_1panel(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=300, facecolor='w')
     # gs = gridspec.GridSpec(1, 3, height_ratios=[1], width_ratios=[1, 0.03, 0.03])
     # gs.update(wspace=0.2, hspace=0.05, left=0.05, right=0.95, top=0.92, bottom=0.08)
@@ -438,7 +438,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
     # if (np.nanmax(tn) > 0):
 
     # Tracknumber color levels for MCS masks (limit to 256 to fit in a colormap)
-    tracknumbers = track_dict['lifetime'].tracks
+    tracknumbers = track_dict['lifetime'].tracks.values
     tn_nlev = np.min([len(tracknumbers), 256])
     tn_levels = np.linspace(np.min(tracknumbers)+1, np.max(tracknumbers)+1, tn_nlev)
     # Add to plot_info dictionary

Analysis/plot_subset_tbze_mcs_tracks_1panel_demo.py

@@ -254,7 +254,7 @@ def plot_map_2panels(pixel_dict, plot_info, map_info, track_dict):
 
     # Set up figure
     mpl.rcParams['font.size'] = fontsize
-    mpl.rcParams['font.family'] = 'Helvetica'
+    # mpl.rcParams['font.family'] = 'Helvetica'
     fig = plt.figure(figsize=figsize, dpi=300, facecolor='w')
     # vertical: left + right panel
     if panel_orientation == 'vertical':
@@ -486,7 +486,7 @@ def work_for_time_loop(datafile, track_dict, map_info, plot_info, config):
     # if (np.nanmax(tn) > 0):
 
     # Tracknumber color levels for MCS masks (limit to 256 to fit in a colormap)
-    tracknumbers = track_dict['lifetime'].tracks
+    tracknumbers = track_dict['lifetime'].tracks.values
     tn_nlev = np.min([len(tracknumbers), 256])
     if tn_nlev > 1:
         tn_levels = np.linspace(np.min(tracknumbers)+1, np.max(tracknumbers)+1, tn_nlev)