Merge branch 'develop' into feature/climada_osmflex

.github/workflows/ci.yml

@@ -74,6 +74,6 @@ jobs:
     needs: build-and-test
     with:
       core_branch: ${{ github.ref }}
-      petals_branch: feature/exposures_crs
+      petals_branch: develop
     permissions:
       checks: write

CHANGELOG.md

@@ -14,6 +14,9 @@ Code freeze date: YYYY-MM-DD
 
 - Add `osm-flex` package to CLIMADA core [#981](https://github.com/CLIMADA-project/climada_python/pull/981)
 - `doc.tutorial.climada_entity_Exposures_osm.ipynb` tutorial explaining how to use `osm-flex`with CLIMADA
+- `climada.util.coordinates.bounding_box_global` function [#980](https://github.com/CLIMADA-project/climada_python/pull/980)
+- `climada.util.coordinates.bounding_box_from_countries` function [#980](https://github.com/CLIMADA-project/climada_python/pull/980)
+- `climada.util.coordinates.bounding_box_from_cardinal_bounds` function [#980](https://github.com/CLIMADA-project/climada_python/pull/980)
 - `climada.engine.impact.Impact.local_return_period` method [#971](https://github.com/CLIMADA-project/climada_python/pull/971)
 - `doc.tutorial.climada_util_local_exceedance_values.ipynb` tutorial explaining `Hazard.local_exceedance_intensity`, `Hazard.local_return_period`, `Impact.local_exceedance_impact`, and `Impact.local_return_period` methods [#971](https://github.com/CLIMADA-project/climada_python/pull/971)
 - `Hazard.local_exceedance_intensity`, `Hazard.local_return_period` and `Impact.local_exceedance_impact`, that all use the `climada.util.interpolation` module [#918](https://github.com/CLIMADA-project/climada_python/pull/918)
@@ -30,6 +33,8 @@ Code freeze date: YYYY-MM-DD
 
 ### Changed
 
+- `Centroids.append` now takes multiple arguments and provides a performance boost when doing so [#989](https://github.com/CLIMADA-project/climada_python/pull/989)
+- `climada.util.coordinates.get_country_geometries` function: Now throwing a ValueError if unregognized ISO country code is given (before, the invalid ISO code was ignored) [#980](https://github.com/CLIMADA-project/climada_python/pull/980)
 - Improved scaling factors implemented in `climada.hazard.trop_cyclone.apply_climate_scenario_knu` to model the impact of climate changes to tropical cyclones [#734](https://github.com/CLIMADA-project/climada_python/pull/734)
 - In `climada.util.plot.geo_im_from_array`, NaNs are plotted in gray while cells with no centroid are not plotted [#929](https://github.com/CLIMADA-project/climada_python/pull/929)
 - Renamed `climada.util.plot.subplots_from_gdf` to `climada.util.plot.plot_from_gdf` [#929](https://github.com/CLIMADA-project/climada_python/pull/929)
@@ -39,9 +44,13 @@ Code freeze date: YYYY-MM-DD
   - latitude and longitude column are no longer present there (the according arrays can be retrieved as properties of the Exposures object: `exp.latitude` instead of `exp.gdf.latitude.values`).
   - `Exposures.gdf` has been renamed to `Exposures.data` (it still works though, as it is a property now pointing to the latter)
   - the `check` method does not add a default "IMPF_" column to the GeoDataFrame anymore
+- Updated IBTrACS version from v4.0 to v4.1 ([#976](https://github.com/CLIMADA-project/climada_python/pull/976)
+    - Fix xarray future warning in TCTracks for .dims to .sizes
+    - Fix hazard.concatenate type test for pathos pools
 
 ### Fixed
 
+- Resolved an issue where windspeed computation was much slower than in Climada v3 [#989](https://github.com/CLIMADA-project/climada_python/pull/989)
 - File handles are being closed after reading netcdf files with `climada.hazard` modules [#953](https://github.com/CLIMADA-project/climada_python/pull/953)
 - Avoids a ValueError in the impact calculation for cases with a single exposure point and MDR values of 0, by explicitly removing zeros in `climada.hazard.Hazard.get_mdr` [#933](https://github.com/CLIMADA-project/climada_python/pull/948)
 

Makefile

@@ -29,11 +29,11 @@ install_test : ## Test installation was successful
 
 .PHONY : data_test
 data_test : ## Test data APIs
-	python script/jenkins/test_data_api.py
+	pytest $(PYTEST_JUNIT_ARGS) script/jenkins/test_data_api.py
 
 .PHONY : notebook_test
 notebook_test : ## Test notebooks in doc/tutorial
-	python script/jenkins/test_notebooks.py report
+	pytest $(PYTEST_JUNIT_ARGS) script/jenkins/test_notebooks.py
 
 .PHONY : integ_test
 integ_test : ## Integration tests execution with xml reports

climada/engine/impact.py

@@ -107,8 +107,8 @@ def __init__(
         crs=DEF_CRS,
         eai_exp=None,
         at_event=None,
-        tot_value=0,
-        aai_agg=0,
+        tot_value=0.,
+        aai_agg=0.,
         unit="",
         imp_mat=None,
         haz_type="",

climada/entity/exposures/base.py

@@ -132,12 +132,40 @@ def gdf(self):
     @property
     def latitude(self):
         """Latitude array of exposures"""
-        return self.data.geometry.y.values
+        try:
+            return self.data.geometry.y.values
+        except ValueError as valerr:
+            nonpoints = list(
+                self.data[
+                    self.data.geometry.type != "Point"
+                ].geometry.type.drop_duplicates()
+            )
+            if nonpoints:
+                raise ValueError(
+                    "Can only calculate latitude from Points."
+                    f" GeoDataFrame contains {', '.join(nonpoints)}."
+                    " Please see the lines_polygons module tutorial."
+                ) from valerr
+            raise
 
     @property
     def longitude(self):
         """Longitude array of exposures"""
-        return self.data.geometry.x.values
+        try:
+            return self.data.geometry.x.values
+        except ValueError as valerr:
+            nonpoints = list(
+                self.data[
+                    self.data.geometry.type != "Point"
+                ].geometry.type.drop_duplicates()
+            )
+            if nonpoints:
+                raise ValueError(
+                    "Can only calculate longitude from Points."
+                    f" GeoDataFrame contains {', '.join(nonpoints)}."
+                    " Please see the lines_polygons module tutorial."
+                ) from valerr
+            raise
 
     @property
     def geometry(self):

climada/entity/exposures/test/test_base.py

@@ -27,7 +27,7 @@
 import rasterio
 import scipy as sp
 from rasterio.windows import Window
-from shapely.geometry import Point
+from shapely.geometry import MultiPolygon, Point, Polygon
 from sklearn.metrics import DistanceMetric
 
 import climada.util.coordinates as u_coord
@@ -652,6 +652,39 @@ def test_to_crs_epsg_crs(self):
             Exposures.to_crs(self, crs="GCS", epsg=26915)
         self.assertEqual("one of crs or epsg must be None", str(cm.exception))
 
+    def test_latlon_with_polygons(self):
+        """Check for proper error message if the data frame contains non-Point shapes"""
+        poly = Polygon(
+            [(10.0, 0.0), (10.0, 1.0), (11.0, 1.0), (11.0, 0.0), (10.0, 0.0)]
+        )
+        point = Point((1, -1))
+        multi = MultiPolygon(
+            [
+                (
+                    ((0.0, 0.0), (0.0, 1.0), (1.0, 1.0), (1.0, 0.0)),
+                    [((0.1, 1.1), (0.1, 1.2), (0.2, 1.2), (0.2, 1.1))],
+                )
+            ]
+        )
+        poly = Polygon()
+        exp = Exposures(geometry=[poly, point, multi, poly])
+        with self.assertRaises(ValueError) as valer:
+            exp.latitude
+        self.assertEqual(
+            "Can only calculate latitude from Points."
+            " GeoDataFrame contains Polygon, MultiPolygon."
+            " Please see the lines_polygons module tutorial.",
+            str(valer.exception),
+        )
+        with self.assertRaises(ValueError) as valer:
+            exp.longitude
+        self.assertEqual(
+            "Can only calculate longitude from Points."
+            " GeoDataFrame contains Polygon, MultiPolygon."
+            " Please see the lines_polygons module tutorial.",
+            str(valer.exception),
+        )
+
 
 class TestImpactFunctions(unittest.TestCase):
     """Test impact function handling"""

climada/hazard/base.py

@@ -936,8 +936,7 @@ def append(self, *others):
                 "The hazards are incompatible and cannot be concatenated."
             )
         self.haz_type = haz_types.pop()
-
-        haz_classes = {type(haz) for haz in haz_list}
+        haz_classes = {haz.__class__.__name__ for haz in haz_list}
         if len(haz_classes) > 1:
             raise TypeError(
                 f"The given hazards are of different classes: {haz_classes}. "

climada/hazard/centroids/centr.py

@@ -331,11 +331,16 @@ def from_pnt_bounds(cls, points_bounds, res, crs=DEF_CRS):
             }
         )
 
-    def append(self, centr):
-        """Append Centroids
+    def append(self, *centr):
+        """Append Centroids to the current centroid object for concatenation.
+
+        This method checks that all centroids use the same CRS, appends the list of centroids to
+        the initial Centroid object and eventually concatenates them to create a single centroid
+        object with the union of all centroids.
 
         Note that the result might contain duplicate points if the object to append has an overlap
-        with the current object.
+        with the current object. Remove duplicates by either using :py:meth:`union`
+        or calling :py:meth:`remove_duplicate_points` after appending.
 
         Parameters
         ----------
@@ -351,22 +356,25 @@ def append(self, centr):
         union : Union of Centroid objects.
         remove_duplicate_points : Remove duplicate points in a Centroids object.
         """
-        if not u_coord.equal_crs(self.crs, centr.crs):
-            raise ValueError(
-                f"The given centroids use different CRS: {self.crs}, {centr.crs}. "
-                "The centroids are incompatible and cannot be concatenated."
-            )
-        self.gdf = pd.concat([self.gdf, centr.gdf])
+        for other in centr:
+            if not u_coord.equal_crs(self.crs, other.crs):
+                raise ValueError(
+                    f"The given centroids use different CRS: {self.crs}, {other.crs}. "
+                    "The centroids are incompatible and cannot be concatenated."
+                )
+        self.gdf = pd.concat([self.gdf] + [other.gdf for other in centr])
 
     def union(self, *others):
-        """Create the union of Centroids objects
+        """Create the union of the current Centroids object with one or more other centroids
+        objects by passing the list of centroids to :py:meth:`append` for concatenation and then
+        removes duplicates.
 
         All centroids must have the same CRS. Points that are contained in more than one of the
         Centroids objects will only be contained once (i.e. duplicates are removed).
 
         Parameters
         ----------
-        others : list of Centroids
+        others : Centroids
             Centroids contributing to the union.
 
         Returns
@@ -375,8 +383,8 @@ def union(self, *others):
             Centroids object containing the union of all Centroids.
         """
         centroids = copy.deepcopy(self)
-        for cent in others:
-            centroids.append(cent)
+        centroids.append(*others)
+
         return centroids.remove_duplicate_points()
 
     def remove_duplicate_points(self):

climada/hazard/centroids/test/test_centr.py

@@ -816,6 +816,20 @@ def test_append_dif_crs(self):
         with self.assertRaises(ValueError):
             self.centr.append(centr2)
 
+    def test_append_multiple_arguments(self):
+        """Test passing append() multiple arguments in the form of a list of Centroids."""
+        # create a single centroid
+        lat, lon = np.array([1, 2]), np.array([1, 2])
+        centr = Centroids(lat=lat, lon=lon)
+        # create a list of centroids
+        coords = [(np.array([3, 4]), np.array([3, 4]))]
+        centroids_list = [Centroids(lat=lat, lon=lon) for lat, lon in coords]
+
+        centr.append(*centroids_list)
+
+        np.testing.assert_array_equal(centr.lat, [1, 2, 3, 4])
+        np.testing.assert_array_equal(centr.lon, [1, 2, 3, 4])
+
     def test_remove_duplicate_pass(self):
         """Test remove_duplicate_points"""
         centr = Centroids(

climada/hazard/tc_tracks.py

@@ -84,13 +84,13 @@
 IBTRACS_URL = (
     "https://www.ncei.noaa.gov/data/"
     "international-best-track-archive-for-climate-stewardship-ibtracs/"
-    "v04r00/access/netcdf"
+    "v04r01/access/netcdf"
 )
 """Site of IBTrACS netcdf file containing all tracks v4.0,
 s. https://www.ncdc.noaa.gov/ibtracs/index.php?name=ib-v4-access"""
 
-IBTRACS_FILE = "IBTrACS.ALL.v04r00.nc"
-"""IBTrACS v4.0 file all"""
+IBTRACS_FILE = "IBTrACS.ALL.v04r01.nc"
+"""IBTrACS v4.1 file all"""
 
 IBTRACS_AGENCIES = [
     "usa",
@@ -376,7 +376,7 @@ def from_ibtracs_netcdf(
         correct_pres=False,
         discard_single_points=True,
         additional_variables=None,
-        file_name="IBTrACS.ALL.v04r00.nc",
+        file_name=IBTRACS_FILE,
     ):
         """Create new TCTracks object from IBTrACS databse.
 
@@ -485,7 +485,7 @@ def from_ibtracs_netcdf(
             compatiblity with other functions such as `equal_timesteps`. Default: True.
         file_name : str, optional
             Name of NetCDF file to be dowloaded or located at climada/data/system.
-            Default: 'IBTrACS.ALL.v04r00.nc'
+            Default: 'IBTrACS.ALL.v04r01.nc'
         additional_variables : list of str, optional
             If specified, additional IBTrACS data variables are extracted, such as "nature" or
             "storm_speed". Only variables that are not agency-specific are supported.
@@ -731,7 +731,7 @@ def from_ibtracs_netcdf(
                     )
                     ibtracs_ds = ibtracs_ds.sel(storm=valid_storms_mask)
 
-            if ibtracs_ds.dims["storm"] == 0:
+            if ibtracs_ds.sizes["storm"] == 0:
                 LOGGER.info(
                     "After discarding IBTrACS events without valid values by the selected "
                     "reporting agencies, there are no tracks left that match the specified "
@@ -2576,7 +2576,7 @@ def ibtracs_fit_param(explained, explanatory, year_range=(1980, 2019), order=1):
             raise KeyError("Unknown ibtracs variable: %s" % var)
 
     # load ibtracs dataset
-    fn_nc = SYSTEM_DIR.joinpath("IBTrACS.ALL.v04r00.nc")
+    fn_nc = SYSTEM_DIR.joinpath(IBTRACS_FILE)
     with xr.open_dataset(fn_nc) as ibtracs_ds:
         # choose specified year range
         years = ibtracs_ds.sid.str.slice(0, 4).astype(int)

climada/hazard/test/__init__.py

@@ -28,7 +28,7 @@
 
 
 def download_ibtracs():
-    """This makes sure a IBTrACS.ALL.v04r00.nc file is present in SYSTEM_DIR
+    """This makes sure a IBTrACS.ALL.v04r01.nc file is present in SYSTEM_DIR
     First, downloading from the original sources is attempted. If that fails an old version
     is downloaded from the CLIMADA Data API
     """
@@ -44,9 +44,9 @@ def download_ibtracs():
     ):  # plan b: download an old version of that file from the climada api
         client = Client()
         dsinfo = client.get_dataset_info(
-            name="IBTrACS", version="v04r00", status="external"
+            name="IBTrACS", version="v04r01", status="external"
         )
         [fileinfo] = [
-            fi for fi in dsinfo.files if fi.file_name == "IBTrACS.ALL.v04r00.nc"
+            fi for fi in dsinfo.files if fi.file_name == "IBTrACS.ALL.v04r01.nc"
         ]
         client._download_file(local_path=SYSTEM_DIR, fileinfo=fileinfo)