Fix numpy deprecation warnings (#195)

* Fix coveralls upload

* Fix use of removed xarray functions

* Fix numpy deprecation warnings

* Force up-to-date versions in rc ci environment

.github/workflows/run-tests.yml

@@ -56,6 +56,7 @@ jobs:
       - name: Upload Coverage
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_SERVICE_NAME: github
           COVERALLS_PARALLEL: true
         run: coveralls
   finish-coveralls:
@@ -67,6 +68,7 @@ jobs:
     - name: Coveralls Finished
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_SERVICE_NAME: github
       run: |
         pip3 install --upgrade coveralls &&
         coveralls --finish

ci/requirements-py38-all-rc.yml

@@ -11,9 +11,9 @@ dependencies:
   - joblib
   - netCDF4
   - shapely
-  - geopandas
+  - geopandas>=0.8
   - rasterio
-  - pandas
+  - pandas>=1.2
   - xarray
   - dask
   - matplotlib

salem/gis.py

@@ -277,14 +277,14 @@ def _check_input(self, **kwargs):
         else:
             raise ValueError('Input params not compatible')
 
-        self._nx = np.int(nx)
-        self._ny = np.int(ny)
+        self._nx = int(nx)
+        self._ny = int(ny)
         if (self._nx <= 0) or (self._ny <= 0):
             raise ValueError('nxny not valid')
-        self._dx = np.float(dx)
-        self._dy = np.float(dy)
-        self._x0 = np.float(x0)
-        self._y0 = np.float(y0)
+        self._dx = float(dx)
+        self._dy = float(dy)
+        self._x0 = float(x0)
+        self._y0 = float(y0)
         self._origin = origin
 
         # Check for pixel ref
@@ -712,8 +712,8 @@ def transform(self, x, y, z=None, crs=wgs84, nearest=False, maskout=False):
         # See if we need to round
         if nearest:
             f = np.rint if self.pixel_ref == 'center' else np.floor
-            x = f(x).astype(np.int)
-            y = f(y).astype(np.int)
+            x = f(x).astype(int)
+            y = f(y).astype(int)
 
         # Mask?
         if maskout:
@@ -840,7 +840,7 @@ def lookup_transform(self, data, grid=None, method=np.mean, lut=None,
         out_shape[-2:] = [self.ny, self.nx]
 
         if data.dtype.kind == 'i':
-            out_data = np.zeros(out_shape, dtype=np.float) * np.NaN
+            out_data = np.zeros(out_shape, dtype=float) * np.NaN
         else:
             out_data = np.zeros(out_shape, dtype=data.dtype) * np.NaN
 
@@ -863,7 +863,7 @@ def _2d_trafo(ind, outd):
         # prepare output
         if method is len:
             out_data[~np.isfinite(out_data)] = 0
-            out_data = out_data.astype(np.int)
+            out_data = out_data.astype(int)
         else:
             out_data = np.ma.masked_invalid(out_data)
 
@@ -958,7 +958,7 @@ def map_gridded_data(self, data, grid=None, interp='nearest',
                 # We dont do integer arithmetics other than nearest
                 out_data = np.ma.masked_all(out_shape, dtype=data.dtype)
             elif data.dtype.kind == 'i':
-                out_data = np.ma.masked_all(out_shape, dtype=np.float)
+                out_data = np.ma.masked_all(out_shape, dtype=float)
             else:
                 out_data = np.ma.masked_all(out_shape, dtype=data.dtype)
 

salem/sio.py

@@ -19,7 +19,6 @@
 
 import xarray as xr
 from xarray.backends.netCDF4_ import NetCDF4DataStore
-from xarray.backends.api import _MultiFileCloser
 from xarray.core import dtypes
 try:
     from xarray.backends.locks import (NETCDFC_LOCK, HDF5_LOCK, combine_locks)
@@ -1176,18 +1175,29 @@ def open_mf_wrf_dataset(paths, chunks=None,  compat='no_conflicts', lock=None,
         lock = NETCDF4_PYTHON_LOCK
     datasets = [open_wrf_dataset(p, chunks=chunks or {}, lock=lock)
                 for p in paths]
-    file_objs = [ds._file_obj for ds in datasets]
+    orig_datasets = datasets
+
+    def ds_closer():
+        for ods in orig_datasets:
+            ods.close()
 
     if preprocess is not None:
         datasets = [preprocess(ds) for ds in datasets]
+
     try:
         combined = xr.combine_nested(datasets, concat_dim='time',
                                      compat=compat)
     except AttributeError:
         combined = xr.auto_combine(datasets, concat_dim='time', compat=compat)
-    combined._file_obj = _MultiFileCloser(file_objs)
     combined.attrs = datasets[0].attrs
 
+    try:
+        combined.set_close(ds_closer)
+    except AttributeError:
+        from xarray.backends.api import _MultiFileCloser
+        mfc = _MultiFileCloser([ods._file_obj for ods in orig_datasets])
+        combined._file_obj = mfc
+
     # drop accumulated vars if needed (TODO: make this not hard coded)
     vns = ['PRCP', 'PRCP_C', 'PRCP_NC']
     vns = [vn for vn in vns if vn in combined.variables]

salem/tests/test_gis.py

@@ -705,7 +705,7 @@ def test_map_gridded_data_over(self):
 
         for proj in projs:
             nx, ny = (4, 5)
-            data = np.arange(nx * ny).reshape((ny, nx)).astype(np.float)
+            data = np.arange(nx * ny).reshape((ny, nx)).astype(float)
 
             in_data = data * np.NaN
             in_data[0, :] = 78

salem/utils.py

@@ -278,7 +278,7 @@ def read_colormap(name):
             line = line.split('(')[-1].split(')')[0]
             out.append([float(n) for n in line.split(',')])
 
-    return np.asarray(out).astype(np.float) / 256.
+    return np.asarray(out).astype(float) / 256.
 
 
 @memory.cache

salem/wrftools.py

@@ -590,7 +590,7 @@ def _ncl_slp(z, t, p, q):
 
     p0 = p[0, ...]
 
-    level = np.zeros((ny, nx), dtype=np.int) - 1
+    level = np.zeros((ny, nx), dtype=int) - 1
     for k in np.arange(nz):
         pok = np.nonzero((p[k, ...] < (p0 - pconst)) & (level == -1))
         level[pok] = k
@@ -604,8 +604,8 @@ def _ncl_slp(z, t, p, q):
     if np.any((klo - khi) == 0):
         raise RuntimeError('Trapping levels are weird.')  # pragma: no cover
 
-    x, y = np.meshgrid(np.arange(nx, dtype=np.int),
-                       np.arange(ny, dtype=np.int))
+    x, y = np.meshgrid(np.arange(nx, dtype=int),
+                       np.arange(ny, dtype=int))
 
     plo = p[klo, y, x]
     phi = p[khi, y, x]