Merge branch 'develop' into main

Author: schmide

climada/entity/exposures/gpw_import.py

@@ -7,7 +7,7 @@
 import logging
 import subprocess
 
-import gdal
+from osgeo import gdal
 import pandas as pd
 from scipy import ndimage as nd
 import numpy as np

climada/entity/exposures/litpop.py

@@ -30,7 +30,7 @@
 import shapefile
 from matplotlib import pyplot as plt
 from iso3166 import countries as iso_cntry
-import gdal
+from osgeo import gdal
 from cartopy.io import shapereader
 
 from climada import CONFIG
@@ -1892,7 +1892,7 @@ def to_sparse_dataframe(ndarr):
     ----------
     ndarr : numpy.ndarray
         2 dimensional
-    
+
     Returns
     -------
     sparse dataframe : pandas.DataFrame

climada/hazard/test/test_tc_surge_bathtub.py

@@ -44,7 +44,7 @@ def __init__(self, bounds, res_deg):
         res_deg : float
             Resolution in degrees
         """
-        lat = np.arange(bounds[1] + 0.5 * res_deg, bounds[3], res_deg)
+        lat = np.arange(bounds[3] - 0.5 * res_deg, bounds[1], -res_deg)
         lon = np.arange(bounds[0] + 0.5 * res_deg, bounds[2], res_deg)
         self.shape = (lat.size, lon.size)
         self.transform = rasterio.Affine(res_deg, 0, bounds[0], 0, -res_deg, bounds[3])
@@ -69,9 +69,9 @@ def __enter__(self):
             'nodata': -32767.0,
         }
 
-        # In Windows, unlike Unix, the temporary file cannot be opened before it is closed
+        # In Windows, unlike Unix, the temporary file cannot be opened before it is closed.
         # Therefore it is closed right after creation and only the path/name is kept.
-        tmpfile = tempfile.NamedTemporaryFile()
+        tmpfile = tempfile.NamedTemporaryFile(delete=False)
         self.topo_path = tmpfile.name
         tmpfile.close()
         with rasterio.open(self.topo_path, 'w', **dst_meta) as dst:
@@ -107,14 +107,14 @@ def test_fraction_on_land(self):
 
         # check valid range and order of magnitude
         self.assertTrue(np.all((fraction >= 0) & (fraction <= 1)))
-        np.testing.assert_array_equal(fraction[dist_coast > 4000], 0)
-        np.testing.assert_array_equal(fraction[dist_coast < -2000], 1)
+        np.testing.assert_array_equal(fraction[dist_coast > 1000], 0)
+        np.testing.assert_array_equal(fraction[dist_coast < -1000], 1)
 
         # check individual known pixel values
-        self.assertEqual(fraction[28, 13], 0.0)
-        self.assertEqual(fraction[26, 11], 0.0625)
-        self.assertEqual(fraction[26, 12], 0.7)
-        self.assertEqual(fraction[23, 14], 1.0)
+        self.assertAlmostEqual(fraction[24, 10], 0.0)
+        self.assertAlmostEqual(fraction[22, 11], 0.21)
+        self.assertAlmostEqual(fraction[22, 12], 0.93)
+        self.assertAlmostEqual(fraction[21, 14], 1.0)
 
 
     def test_surge_from_track(self):
@@ -172,13 +172,14 @@ def test_surge_from_track(self):
                 fraction = surge_haz.fraction.toarray().reshape(shape)
 
                 # check valid range and order of magnitude
-                self.assertTrue(np.all(inten >= 0))
-                self.assertTrue(np.all(inten <= 10))
-                self.assertTrue(np.all((fraction >= 0) & (fraction <= 1)))
+                np.testing.assert_array_equal(inten >= 0, True)
+                np.testing.assert_array_equal(inten <= 10, True)
+                np.testing.assert_array_equal((fraction >= 0) & (fraction <= 1), True)
+                np.testing.assert_array_equal(inten[fraction == 0], 0)
 
                 # check individual known pixel values
-                self.assertAlmostEqual(inten[14, 26], max(-0.125 + slr, 0), places=2)
-                self.assertAlmostEqual(inten[14, 34] - slr, 0.592, places=2)
+                self.assertAlmostEqual(inten[9, 31], max(-0.391 + slr, 0), places=2)
+                self.assertAlmostEqual(inten[14, 34] - slr, 3.637, places=2)
 
 
 # Execute Tests

climada/util/__init__.py

@@ -18,6 +18,7 @@
 
 init util
 """
+import logging
 from pint import UnitRegistry
 
 from .config import *
@@ -26,3 +27,37 @@
 from .save import *
 
 ureg = UnitRegistry()
+
+class log_level:
+    """Context manager that sets all loggers with names starting with
+    name_prefix (default is "") to a given specified level.
+
+    Examples
+    --------
+    Set ALL loggers temporarily to the level 'WARNING'
+    >>> with log_level(level='WARNING'):
+    >>>     ...
+
+    Set all the climada loggers temporarily to the level 'ERROR'
+    >>> with log_level(level='ERROR', name_prefix='climada'):
+    >>>     ...
+
+    """
+
+    def __init__(self, level, name_prefix=""):
+        self.level = level
+        self.loggers = {
+            name: (logger, logger.level)
+            for name, logger in logging.root.manager.loggerDict.items()
+            if isinstance(logger, logging.Logger) and name.startswith(name_prefix)
+            }
+        if name_prefix == "":
+            self.loggers[""] = (logging.getLogger(), logging.getLogger().level)
+
+    def __enter__(self):
+        for logger, _ in self.loggers.values():
+            logger.setLevel(self.level)
+
+    def __exit__(self, exception_type, exception, traceback):
+        for logger, previous_level in self.loggers.values():
+            logger.setLevel(previous_level)

climada/util/plot.py

@@ -343,7 +343,7 @@ def add_shapes(axis):
                                          name='admin_0_countries')
     shp = shapereader.Reader(shp_file)
     for geometry in shp.geometries():
-        axis.add_geometries([geometry], crs=ccrs.PlateCarree(), facecolor='',
+        axis.add_geometries([geometry], crs=ccrs.PlateCarree(), facecolor='none',
                             edgecolor='black')
 
 def add_populated_places(axis, extent, proj=ccrs.PlateCarree()):

climada/util/test/test__init__.py

@@ -0,0 +1,47 @@
+"""
+This file is part of CLIMADA.
+
+Copyright (C) 2017 ETH Zurich, CLIMADA contributors listed in AUTHORS.
+
+CLIMADA is free software: you can redistribute it and/or modify it under the
+terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, version 3.
+
+CLIMADA is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along
+with CLIMADA. If not, see <https://www.gnu.org/licenses/>.
+
+---
+
+Test config module.
+"""
+import unittest
+import logging
+
+from climada.util import log_level
+
+class TestUtilInit(unittest.TestCase):
+    """Test util __init__ methods"""
+
+    def test_log_level_pass(self):
+        """Test log level context manager passes"""
+        #Check loggers are set to level
+        with self.assertLogs('climada', level='INFO') as cm:
+             with log_level('WARNING'):
+                logging.getLogger('climada').info('info')
+                logging.getLogger('climada').error('error')
+                self.assertEqual(cm.output, ['ERROR:climada:error'])
+        #Check if only climada loggers level change
+        with self.assertLogs('matplotlib', level='DEBUG') as cm:
+            with log_level('ERROR', name_prefix='climada'):
+                logging.getLogger('climada').info('info')
+            logging.getLogger('matplotlib').debug('debug')
+            self.assertEqual(cm.output, ['DEBUG:matplotlib:debug'])
+
+# Execute Tests
+if __name__ == "__main__":
+    TESTS = unittest.TestLoader().loadTestsFromTestCase(TestUtilInit)
+    unittest.TextTestRunner(verbosity=2).run(TESTS)

requirements/env_docs.yml

@@ -208,9 +208,12 @@ dependencies:
   - zipp=3.4.1=pyhd8ed1ab_0
   - zlib=1.2.11=h516909a_1010
   - zstd=1.4.9=ha95c52a_0
+  - nb_conda
+  - nb_conda_kernels
   - pip:
     - bitstring==3.1.7
     - overpy==0.4
     - pybufrkit==0.2.18
+    - ipython
     - nbsphinx