Merge branch 'develop' into DahyannAraya-patch-1

.coveragerc

@@ -1,8 +1,9 @@
 # .coveragerc to control coverage.py
 
 [run]
-# Also report branch coverage
-branch = True
+# skip test files
+omit =
+    */test*/*
 # Set concurrency type for correct coverage of multi-processing code
 concurrency = multiprocessing
 
@@ -14,12 +15,3 @@ source = climada/
 exclude_also =
     # Main code is not run
     if __name__ == .__main__.:
-
-    # Abtract methods are not run
-    @(abc\.)?abstractmethod
-
-# Never fail when reporting
-ignore_errors = True
-
-[html]
-directory = coverage

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior/error:
+1. 
+
+Code example:
+```python
+# Your code here
+```
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Climada Version:** [Version or branch]
+
+**System Information (please complete the following information):**
+ - Operating system and version: [e.g. Ubuntu 22.04, macOS 14.3.1, Windows 10]
+ - Python version: [e.g. 3.10] 
+ (to obtain this information execute > import sys  >print(sys.version))
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/code-feature-request.md

@@ -0,0 +1,20 @@
+---
+name: Code feature request
+about: Suggest an idea to improve the code
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
     steps:
       -
         name: Checkout Repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       -
         # Store the current date to use it as cache key for the environment
         name: Get current date
@@ -64,7 +64,7 @@ jobs:
       -
         name: Upload Coverage Reports
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-report-unittests-py${{ matrix.python-version }}
           path: coverage/

.readthedocs.yml

@@ -5,8 +5,13 @@ build:
   tools:
     python: "mambaforge-4.10"
 
+  # Append fixed Python version to requirements
+  jobs:
+    pre_create_environment:
+      - echo "  - python=3.9" >> requirements/env_climada.yml
+
 conda:
-  environment: requirements/env_docs.yml
+  environment: requirements/env_climada.yml
 
 python:
   install:

AUTHORS.md

@@ -29,3 +29,8 @@
 * Raphael Portmann
 * Nicolas Colombi
 * Leonie Villiger
+* Kam Lam Yeung
+* Sarah Hülsen
+* Timo Schmid
+* Luca Severino
+* Samuel Juhel

CHANGELOG.md

@@ -10,20 +10,133 @@ Code freeze date: YYYY-MM-DD
 
 ### Dependency Changes
 
+### Changed
+
+- Remove content tables and make minor improvements (fix typos and readability) in
+CLIMADA tutorials. [#872](https://github.com/CLIMADA-project/climada_python/pull/872)
+- Centroids complete overhaul. Most function should be backward compatible. Internal data is stored in a geodataframe attribute. Raster are now stored as points, and the meta attribute is removed. Several methds were deprecated or removed. [#787](https://github.com/CLIMADA-project/climada_python/pull/787)
+- Improved error messages produced by `ImpactCalc.impact()` in case impact function in the exposures is not found in impf_set [#863](https://github.com/CLIMADA-project/climada_python/pull/863)
+
+### Fixed
+
+- Avoid an issue where a Hazard subselection would have a fraction matrix with only zeros as entries by throwing an error [#866](https://github.com/CLIMADA-project/climada_python/pull/866)
+
 ### Added
 
+- climada.hazard.centroids.centr.Centroids.get_area_pixel
+- climada.hazard.centroids.centr.Centroids.get_dist_coast
+- climada.hazard.centroids.centr.Centroids.get_elevation
+- climada.hazard.centroids.centr.Centroids.get_meta
+- climada.hazard.centroids.centr.Centroids.get_pixel_shapes
+- climada.hazard.centroids.centr.Centroids.to_crs
+- climada.hazard.centroids.centr.Centroids.to_default_crs
+- climada.hazard.centroids.centr.Centroids.write_csv
+- climada.hazard.centroids.centr.Centroids.write_excel
+
+### Deprecated
+
+- climada.hazard.centroids.centr.Centroids.from_lat_lon
+- climada.hazard.centroids.centr.Centroids.def set_area_pixel
+- climada.hazard.centroids.centr.Centroids.def set_area_approx
+- climada.hazard.centroids.centr.Centroids.set_dist_coast
+- climada.hazard.centroids.centr.Centroids.empty_geometry_points
+- climada.hazard.centroids.centr.Centroids.set_meta_to_lat_lon
+- climada.hazard.centroids.centr.Centroids.set_lat_lon_to_meta
+
+### Removed
+
+- climada.hazard.base.Hazard.clear
+- climada.hazard.base.Hazard.raster_to_vector
+- climada.hazard.base.Hazard.read_mat
+- climada.hazard.base.Hazard.reproject_raster
+- climada.hazard.base.Hazard.set_vector
+- climada.hazard.base.Hazard.vector_to_raster
+- climada.hazard.centroids.centr.Centroids.calc_pixels_polygons
+- climada.hazard.centroids.centr.Centroids.check
+- climada.hazard.centroids.centr.Centroids.clear
+- climada.hazard.centroids.centr.Centroids.equal
+- climada.hazard.centroids.centr.Centroids.from_mat
+- climada.hazard.centroids.centr.Centroids.from_base_grid
+- climada.hazard.centroids.centr.Centroids.read_excel
+- climada.hazard.centroids.centr.Centroids.read_hdf5
+- climada.hazard.centroids.centr.Centroids.read_mat
+- climada.hazard.centroids.centr.Centroids.set_elevation
+- climada.hazard.centroids.centr.Centroids.set_geometry_points
+- climada.hazard.centroids.centr.Centroids.set_lat_lon
+- climada.hazard.centroids.centr.Centroids.set_raster_file
+- climada.hazard.centroids.centr.Centroids.set_raster_from_pnt_bounds
+- climada.hazard.centroids.centr.Centroids.set_vector_file
+- climada.hazard.centroids.centr.Centroids.values_from_raster_files
+- climada.hazard.centroids.centr.Centroids.values_from_vector_files
+- climada.hazard.centroids.centr.generate_nat_earth_centroids
+- `requirements/env_docs.yml`. The regular environment specs are now used to build the online documentation [#687](https://github.com/CLIMADA-project/climada_python/pull/687)
+
+## 4.1.1
+
+Release date: 2024-02-21
+
+### Fixed
+
+- Fix `util.coordinates.latlon_bounds` for cases where the specified buffer is very large so that the bounds cover more than the full longitudinal range `[-180, 180]` [#839](https://github.com/CLIMADA-project/climada_python/pull/839)
+- Fix `climada.hazard.trop_cyclone` for TC tracks crossing the antimeridian [#839](https://github.com/CLIMADA-project/climada_python/pull/839)
+
+## 4.1.0
+
+Release date: 2024-02-14
+
+### Dependency Changes
+
+Added:
+
+- `pyproj` >=3.5
+- `numexpr` >=2.9
+
+Updated:
+
+- `contextily` >=1.3 → >=1.5
+- `dask` >=2023 → >=2024
+- `numba` >=0.57 → >=0.59
+- `pandas` >=2.1 &rarr; >=2.1,<2.2
+- `pint` >=0.22 &rarr; >=0.23
+- `scikit-learn` >=1.3 &rarr; >=1.4
+- `scipy` >=1.11 &rarr; >=1.12
+- `sparse` >=0.14 &rarr; >=0.15
+- `xarray` >=2023.8 &rarr; >=2024.1
+- `overpy` =0.6 &rarr; =0.7
+- `peewee` =3.16.3 &rarr; =3.17.1
+
+Removed:
+
+- `proj` (in favor of `pyproj`)
+
+### Added
+
+- Convenience method `api_client.Client.get_dataset_file`, combining `get_dataset_info` and `download_dataset`, returning a single file objet. [#821](https://github.com/CLIMADA-project/climada_python/pull/821)
+- Read and Write methods to and from csv files for the `DiscRates` class. [#818](ttps://github.com/CLIMADA-project/climada_python/pull/818)
+- Add `CalcDeltaClimate` to unsequa module to allow uncertainty and sensitivity analysis of impact change calculations [#844](https://github.com/CLIMADA-project/climada_python/pull/844)
+- Add function `safe_divide` in util which handles division by zero and NaN values in the numerator or denominator [#844](https://github.com/CLIMADA-project/climada_python/pull/844)
+- Add reset_frequency option for the impact.select() function. [#847](https://github.com/CLIMADA-project/climada_python/pull/847)
+
 ### Changed
 
+- Update Developer and Installation Guides for easier accessibility by new developers. [808](https://github.com/CLIMADA-project/climada_python/pull/808)
+- Add `shapes` argument to `geo_im_from_array` to allow flexible turning on/off of plotting coastline in `plot_intensity`. [#805](https://github.com/CLIMADA-project/climada_python/pull/805)
 - Update `CONTRIBUTING.md` to better explain types of contributions to this repository [#797](https://github.com/CLIMADA-project/climada_python/pull/797)
 - The default tile layer in Exposures maps is not Stamen Terrain anymore, but [CartoDB Positron](https://github.com/CartoDB/basemap-styles). Affected methods are `climada.engine.Impact.plot_basemap_eai_exposure`,`climada.engine.Impact.plot_basemap_impact_exposure` and `climada.entity.Exposures.plot_basemap`. [#798](https://github.com/CLIMADA-project/climada_python/pull/798)
+- Recommend using Mamba instead of Conda for installing CLIMADA [#809](https://github.com/CLIMADA-project/climada_python/pull/809)
+- `Hazard.from_xarray_raster` now allows arbitrary values as 'event' coordinates [#837](https://github.com/CLIMADA-project/climada_python/pull/837)
+- `climada.test.get_test_file` now compares the version of the requested test dataset with the version of climada itself and selects the most appropriate dataset. In this way a test file can be updated without the need of changing the code of the unittest. [#822](https://github.com/CLIMADA-project/climada_python/pull/822)
+- Explicitly require `pyproj` instead of `proj` (the latter is now implicitly required) [#845](https://github.com/CLIMADA-project/climada_python/pull/845)
 
 ### Fixed
 
+- `Hazard.from_xarray_raster` now stores strings as default values for `Hazard.event_name` [#795](https://github.com/CLIMADA-project/climada_python/pull/795)
 - Fix the dist_approx util function when used with method="geosphere" and log=True and points that are very close. [#792](https://github.com/CLIMADA-project/climada_python/pull/792)
-
-### Deprecated
-
-### Removed
+- `climada.util.yearsets.sample_from_poisson`: fix a bug ([#819](https://github.com/CLIMADA-project/climada_python/issues/819)) and inconsistency that occurs when lambda events per year (`lam`) are set to 1. [[#823](https://github.com/CLIMADA-project/climada_python/pull/823)]
+- In the TropCyclone class in the Holland model 2008 and 2010 implementation, a doublecounting of translational velocity is removed [#833](https://github.com/CLIMADA-project/climada_python/pull/833)
+- `climada.util.test.test_finance` and `climada.test.test_engine` updated to recent input data from worldbank [#841](https://github.com/CLIMADA-project/climada_python/pull/841)
+- Set `nodefaults` in Conda environment specs because `defaults` are not compatible with conda-forge [#845](https://github.com/CLIMADA-project/climada_python/pull/845)
+- Avoid redundant calls to `np.unique` in `Impact.impact_at_reg` [#848](https://github.com/CLIMADA-project/climada_python/pull/848)
 
 ## 4.0.1
 

README.md

@@ -21,13 +21,14 @@ This is the Python (3.9+) version of CLIMADA - please see [here](https://github.
 ## Getting started
 
 CLIMADA runs on Windows, macOS and Linux.
-The released versions of the CLIMADA core can be installed directly through Anaconda:
+The released versions of CLIMADA are available from [conda-forge](https://anaconda.org/conda-forge/climada).
+Use the [Mamba](https://mamba.readthedocs.io/en/latest/) package manager to install it:
 
 ```shell
-conda install -c conda-forge climada
+mamba install -c conda-forge climada
 ```
 
-It is **highly recommended** to install CLIMADA into a **separate** Anaconda environment.
+It is **highly recommended** to install CLIMADA into a **separate** Conda environment.
 See the [installation guide](https://climada-python.readthedocs.io/en/latest/guide/install.html) for further information.
 
 Follow the [tutorials](https://climada-python.readthedocs.io/en/stable/tutorial/1_main_climada.html) in a Jupyter Notebook to see what can be done with CLIMADA and how.

climada/_version.py

@@ -1 +1 @@
-__version__ = '4.0.2-dev'
+__version__ = '4.1.2-dev'

climada/conf/climada.conf

@@ -67,7 +67,7 @@
         "cache_db": "{local_data.system}/.downloads.db",
         "cache_enabled": true,
         "cache_dir": "{local_data.system}/.apicache",
-        "supported_hazard_types": ["river_flood", "tropical_cyclone", "storm_europe", "relative_cropyield", "wildfire", "earthquake", "flood"],
-        "supported_exposures_types": ["litpop", "crop_production", "ssp_population"]
+        "supported_hazard_types": ["river_flood", "tropical_cyclone", "storm_europe", "relative_cropyield", "wildfire", "earthquake", "flood", "hail"],
+        "supported_exposures_types": ["litpop", "crop_production", "ssp_population", "crops"]
     }
 }

climada/engine/forecast.py

@@ -31,6 +31,7 @@
 from matplotlib.ticker import PercentFormatter, ScalarFormatter
 from matplotlib.colors import ListedColormap, BoundaryNorm
 import cartopy.crs as ccrs
+from matplotlib import colormaps as cm
 import pyproj
 import shapely
 from cartopy.io import shapereader
@@ -88,7 +89,7 @@
 warnprob_colors_extended = np.repeat(warnprob_colors, 10, axis=0)
 CMAP_WARNPROB = ListedColormap(warnprob_colors_extended)
 # colors for impact forecast
-color_map_pre = plt.get_cmap("plasma", 90)
+color_map_pre = cm.get_cmap("plasma").resampled(90)
 impact_colors = color_map_pre(np.linspace(0, 1, 90))
 white_extended = np.repeat([[255 / 255, 255 / 255, 255 / 255, 1]], 10, axis=0)
 impact_colors_extended = np.append(white_extended, impact_colors, axis=0)

climada/engine/impact.py

@@ -451,12 +451,12 @@ def impact_at_reg(self, agg_regions=None):
         at_reg_event = np.hstack(
             [
                 self.imp_mat[:, np.where(agg_regions == reg)[0]].sum(1)
-                for reg in np.unique(agg_reg_unique)
+                for reg in agg_reg_unique
             ]
         )
 
         at_reg_event = pd.DataFrame(
-            at_reg_event, columns=np.unique(agg_reg_unique), index=self.event_id
+            at_reg_event, columns=agg_reg_unique, index=self.event_id
         )
 
         return at_reg_event
@@ -1475,9 +1475,14 @@ def _cen_return_imp(imp, freq, imp_th, return_periods):
 
         return imp_fit
 
-    def select(self,
-               event_ids=None, event_names=None, dates=None,
-               coord_exp=None):
+    def select(
+        self,
+        event_ids=None,
+        event_names=None,
+        dates=None,
+        coord_exp=None,
+        reset_frequency=False
+    ):
         """
         Select a subset of events and/or exposure points from the impact.
         If multiple input variables are not None, it returns all the impacts
@@ -1509,6 +1514,9 @@ def select(self,
         coord_exp : np.array, optional
             Selection of exposures coordinates [lat, lon] (in degrees)
             The default is None.
+        reset_frequency : bool, optional
+            Change frequency of events proportional to difference between first and last
+            year (old and new). Assumes annual frequency values. Default: False.
 
         Raises
         ------
@@ -1580,6 +1588,19 @@ def select(self,
             LOGGER.info("The total value cannot be re-computed for a "
                         "subset of exposures and is set to None.")
 
+        # reset frequency if date span has changed (optional):
+        if reset_frequency:
+            if self.frequency_unit not in ['1/year', 'annual', '1/y', '1/a']:
+                LOGGER.warning("Resetting the frequency is based on the calendar year of given"
+                    " dates but the frequency unit here is %s. Consider setting the frequency"
+                    " manually for the selection or changing the frequency unit to %s.",
+                    self.frequency_unit, DEF_FREQ_UNIT)
+            year_span_old = np.abs(dt.datetime.fromordinal(self.date.max()).year -
+                                   dt.datetime.fromordinal(self.date.min()).year) + 1
+            year_span_new = np.abs(dt.datetime.fromordinal(imp.date.max()).year -
+                                   dt.datetime.fromordinal(imp.date.min()).year) + 1
+            imp.frequency = imp.frequency * year_span_old / year_span_new
+
         # cast frequency vector into 2d array for sparse matrix multiplication
         freq_mat = imp.frequency.reshape(len(imp.frequency), 1)
         # .A1 reduce 1d matrix to 1d array