Bugfix for shapefile reader (#147)

* Change `Speed` to `WindSpeed` in track interpolation
* Remove deprecated Basemap references
* Update conda environment file
* Update actions/checkout to v3, setup-miniconda to v2.2
* Remove deprecated Basemap references
* #145 replace shapefile with pyshp module (#146)

Author: wcarthur

.github/workflows/tcrm-pylint.yml

@@ -1,6 +1,6 @@
-name: Pylint tests for TCRM 
+name: Pylint tests for TCRM
 
-on: 
+on:
   push:
     branches:  [ master, develop ]
 
@@ -12,17 +12,18 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up environment
-      uses: conda-incubator/setup-miniconda@v2.0.0
-      with: 
-        python-version: 3.7
-        mamba-version: "*"
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: 3.9
+        miniforge-variant: Mambaforge
         channels: conda-forge,defaults
         channel-priority: true
         activate-environment: tcrm
         environment-file: tcrmenv.yml
         auto-activate-base: false
         use-only-tar-bz2: true
-        
+
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -32,7 +33,7 @@ jobs:
         pylint --rcfile pylintrc --fail-under=7 `find -regextype egrep -regex '(.*.py)$'` |
         tee pylint.txt
     - name: Upload pylint.txt as artifact
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: pylint report
         path: pylint.txt

.github/workflows/tcrm-tests.yml

@@ -15,20 +15,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.9', '3.10']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up environment
-      uses: conda-incubator/setup-miniconda@v2.0.0
+      uses: conda-incubator/setup-miniconda@v2
       with:
+        miniforge-variant: MambaForge
         python-version: ${{ matrix.python-version }}
-        mamba-version: "*"
         channels: conda-forge,defaults
         channel-priority: true
         activate-environment: tcrm
         environment-file: tcrmenv.yml
         auto-activate-base: false
-        use-only-tar-bz2: true
+        use-only-tar-bz2: tru
+
 
     - name: Test with pytest
       env:

Evaluate/evaluate.py

@@ -32,7 +32,8 @@
 
 from matplotlib import pyplot, cm
 from matplotlib.dates import date2num
-from mpl_toolkits.basemap import Basemap
+from cartopy import crs as ccrs
+from cartopy import feature as cfeature
 from scipy.stats import scoreatpercentile as percentile
 from datetime import datetime
 
@@ -76,7 +77,7 @@
 [ProcessMultipliers]
 MaxWorkingThreads = 4
 ProcessMultiVersion = 2
-ProcessingSegmentSize = 256 
+ProcessingSegmentSize = 256
 WarpMemoryLimit = 500
 
 [Logging]
@@ -169,57 +170,49 @@ def plotDensity(x, y, data, llLon=None, llLat=None, urLon=None, urLat=None,
     else:
         urcrnrlat = y.max()
 
-    meridians = np.arange(dl * np.floor(llcrnrlon / dl),
-                          dl * np.ceil(urcrnrlon / dl), dl)
-    parallels = np.arange(dl * np.floor(llcrnrlat / dl),
-                          dl * np.ceil(urcrnrlat / dl), dl)
-
-    m = Basemap(projection='cyl',
-                resolution=res,
-                llcrnrlon=llcrnrlon,
-                urcrnrlon=urcrnrlon,
-                llcrnrlat=llcrnrlat,
-                urcrnrlat=urcrnrlat)
 
     # Set the colour map:
     if hasattr(cm, cmap):
         cmap = getattr(cm, cmap)
     else:
         cmap = colours.colourMap(cmap, 'stretched')
 
-    if maskocean:
-        try:
-            from mpl_toolkits.basemap import maskoceans
-        except ImportError:
-            log.debug("Maskoceans module unavailable, skipping this command")
-        else:
-            datam = maskoceans(xx, yy, data, inlands=False)
-            m.pcolormesh(xx, yy, datam, edgecolors='None',
-                         vmin=datarange[0], vmax=datarange[1],
-                         cmap=cmap)
-    else:
-        m.pcolormesh(xx, yy, data, edgecolors='None',
-                     vmin=datarange[0], vmax=datarange[1],
-                     cmap=cmap)
+    ax = pyplot.axes(projection=ccrs.PlateCarree())
+    pyplot.pcolormesh(xx, yy, data, edgecolors='None',
+                      vmin=datarange[0], vmax=datarange[1],
+                      cmap=cmap, transfom=ccrs.PlateCarree())
 
-    m.drawcoastlines(linewidth=0.5)
     if maskland:
-        m.fillcontinents(color='white')
+        ax.add_feature(cfeature.LAND, zorder=100, edgecolor='k')
+
+    if maskocean:
+        ax.add_feature(cfeature.OCEAN, zorder=100, edgecolor='k')
+
+    ax.coastlines(linewidth=0.5)
+    gl = ax.gridlines(draw_labels=True, crs=ccrs.PlateCarree(), linewidth=0.2)
+    gl.top_labels = False
+    gl.right_labels = False
+
+    ax.set_extent([llcrnrlon, urcrnrlon,
+                   llcrnrlat, urcrnrlat])
+
+    cb = pyplot.colorbar(shrink=0.5, aspect=30,
+                         orientation='horizontal',
+                         extend='max', pad=0.1)
+
+    if cb.orientation == 'horizontal':
+        for t in cb.ax.get_xticklabels():
+            t.set_fontsize(8)
 
-    m.drawparallels(parallels, labels=[1, 0, 0, 0],
-                    fontsize=7.5, linewidth=0.2)
-    m.drawmeridians(meridians, labels=[0, 0, 0, 1],
-                    fontsize=7.5, linewidth=0.2)
+    if clabel:
+        cb.set_label(clabel)
     if ylab:
         pyplot.ylabel(ylab, fontsize=7.5)
     if xlab:
         pyplot.xlabel(xlab, fontsize=7.5)
     if title:
         pyplot.title(title)
 
-    pyplot.grid(True)
-    pyplot.tick_params(direction='out', right='off', top='off')
-
     cb = pyplot.colorbar(shrink=0.5, aspect=30,
                          orientation='horizontal',
                          extend='max', pad=0.1)

Evaluate/interpolateTracks.py

@@ -73,7 +73,7 @@ def interpolate(track, delta, interpolation_type=None):
                                           track.Minute)]
     else:
         day_ = track.Datetime
-    
+
     timestep = timedelta(delta/24.)
     try:
         time_ = np.array([d.toordinal() + (d.hour + d.minute/60.)/24.0
@@ -104,7 +104,7 @@ def interpolate(track, delta, interpolation_type=None):
         idx[0] = 1
         # TODO: Possibly could change `np.mean(dt)` to `dt`?
         track.WindSpeed = maxWindSpeed(idx, np.mean(dt), track.Longitude,
-                                       track.Latitude, track.CentralPressure, 
+                                       track.Latitude, track.CentralPressure,
                                        track.EnvPressure)
     # Find the indices of valid pressure observations:
     validIdx = np.where(track.CentralPressure < sys.maxsize)[0]
@@ -182,7 +182,7 @@ def interpolate(track, delta, interpolation_type=None):
                                      kind='linear')(newtime[firsttime:lasttime])
 
                 _nwSpd = interp1d(timestep[validIdx],
-                                  track.Speed[validIdx],
+                                  track.WindSpeed[validIdx],
                                   kind='linear')(newtime[firsttime:lasttime])
 
                 npCentre[firsttime:lasttime] = _npCentre