fix merge conflicts

Author: NicolasColombi

.github/CODEOWNERS

@@ -0,0 +1,7 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence, they will
+# be requested for review when someone opens a pull request.
+*       @emanuel-schmid @chahank @peanutfun

.github/pull_request_template.md

@@ -19,10 +19,10 @@ This PR fixes #
 ### PR Reviewer Checklist
 
 - [ ] Read the [Contribution Guide][contrib]
-- [ ] [CLIMADA Reviewer Checklist](https://climada-python.readthedocs.io/en/latest/guide/Guide_Reviewer_Checklist.html) passed
+- [ ] [CLIMADA Reviewer Checklist](https://climada-python.readthedocs.io/en/latest/development/Guide_Review.html) passed
 - [ ] [Tests][testing] passing
 - [ ] No new [linter issues][linter]
 
 [contrib]: https://github.com/CLIMADA-project/climada_python/blob/main/CONTRIBUTING.md
-[testing]: https://climada-python.readthedocs.io/en/latest/guide/Guide_Continuous_Integration_and_Testing.html
-[linter]: https://climada-python.readthedocs.io/en/stable/guide/Guide_Continuous_Integration_and_Testing.html#3.C.--Static-Code-Analysis
+[testing]: https://climada-python.readthedocs.io/en/latest/development/Guide_continuous_integration_GitHub_actions.html
+[linter]: https://climada-python.readthedocs.io/en/latest/development/Guide_continuous_integration_GitHub_actions.html#static-code-analysis

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       # Do not abort other tests if only a single one fails
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       -
@@ -47,7 +47,7 @@ jobs:
       -
         name: Install CLIMADA
         run: |
-          python -m pip install ".[test]"
+          python -m pip install "./[dev]"
       -
         name: Run Unit Tests
         run: |

.github/workflows/pull-request.yml

@@ -16,7 +16,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
       -
         name: Checkout target commit
-        run: git -c protocol.version=2 fetch --no-tags --prune --no-recurse-submodules --depth=1 origin ${{ github.event.pull_request.base.ref }}
+        run: git -c protocol.version=2 fetch --no-tags --prune --no-recurse-submodules --depth=50 origin ${{ github.event.pull_request.base.ref }}
       -
         name: Set up Python 3.11
         uses: actions/setup-python@v5

.gitignore

@@ -183,3 +183,5 @@ results/
 !.pylintrc
 !.readthedocs.yml
 !.github
+climada_petals/
+climada_python/

.readthedocs.yml

@@ -25,3 +25,6 @@ python:
 
 formats:
   - pdf
+
+sphinx:
+  configuration: doc/conf.py

.zenodo.json

@@ -119,6 +119,9 @@
     },
     {
       "name": "Valentin Gebhart"
+    },
+    {
+      "name": "Dahyann Araya"
     }
   ]
 }

AUTHORS.md

@@ -36,3 +36,4 @@
 * Luca Severino
 * Samuel Juhel
 * Valentin Gebhart
+* Dahyann Araya

CHANGELOG.md

@@ -10,16 +10,52 @@ Code freeze date: YYYY-MM-DD
 
 ### Dependency Changes
 
+Added:
+
+- `fiona` >=1.10
+
+Updated:
+
+- `geopandas` >=0.14,<1.0 → >=0.14
+- `pandas` >=2.1,<2.2 → >=2.1
+
+Removed:
+
+- `pandas-datareader`
+
 ### Added
 
+- Added optional parameter to `geo_im_from_array`, `plot_from_gdf`, `plot_rp_imp`, `plot_rp_intensity`,
+`plot_intensity`, `plot_fraction`, `_event_plot` to mask plotting when regions are too far from data points [#1047](https://github.com/CLIMADA-project/climada_python/pull/1047). To recreate previous plots (no masking), the parameter can be set to None.
+- Added instructions to install Climada petals on Euler cluster in `doc.guide.Guide_Euler.ipynb` [#1029](https://github.com/CLIMADA-project/climada_python/pull/1029)
+
+- `ImpactFunc` and `ImpactFuncSet` now support equality comparisons via `==` [#1027](https://github.com/CLIMADA-project/climada_python/pull/1027)
+
 ### Changed
 
+- Changed the default mask_distance in `util.plot.geo_im_from_array` to 0.03 to avoid white gaps in gridded hazard data with comparably low resolution (>80 centroids per axis) [#1073](https://github.com/CLIMADA-project/climada_python/pull/1073)
+- Increased speed of `util.plot.add_shapes` by avoiding for loops, substantially speeding up `Hazard.plot_intensity` and other functions. [#1073](https://github.com/CLIMADA-project/climada_python/pull/1073)
+- `Hazard.local_exceedance_intensity`, `Hazard.local_return_period` and `Impact.local_exceedance_impact`, `Impact.local_return_period`, using the `climada.util.interpolation` module: New default (no binning), binning on decimals, and faster implementation [#1012](https://github.com/CLIMADA-project/climada_python/pull/1012)
+- World Bank indicator data is now downloaded directly from their API via the function `download_world_bank_indicator`, instead of relying on the `pandas-datareader` package [#1033](https://github.com/CLIMADA-project/climada_python/pull/1033)
+- `Exposures.write_hdf5` pickles geometry data in WKB format, which is faster and more sustainable. [#1051](https://github.com/CLIMADA-project/climada_python/pull/1051)
+- The online documentation has been completely overhauled, now uses PyData theme: [#977](https://github.com/CLIMADA-project/climada_python/pull/977)
+- Add `climada.hazard.xarray` module with helper structures for reading Hazard objects from `xarray` data [#1063](https://github.com/CLIMADA-project/climada_python/pull/1063)
+
 ### Fixed
 
+- NaN plotting issues in `geo_im_from_array`[#1038](https://github.com/CLIMADA-project/climada_python/pull/1038)
+- Broken ECMWF links in pydoc of `climada.hazard.storm_europe` relocated. [#944](https://github.com/CLIMADA-project/climada_python/pull/944)
+
 ### Deprecated
 
+- `Hazard.from_xarray_raster_file`. Use `Hazard.from_xarray_raster` and pass the file path as `data` argument [#1063](https://github.com/CLIMADA-project/climada_python/pull/1063)
+
 ### Removed
 
+- `climada.util.interpolation.round_to_sig_digits` [#1012](https://github.com/CLIMADA-project/climada_python/pull/1012)
+- `intensity_thres` of `Hazard`, `StormEurope`, and `TropCyclones` object [#1065](https://github.com/CLIMADA-project/climada_python/pull/1065)
+- Deprecated method `climada.hazard.trop_cyclone.trop_cyclone.TropCyclone.set_from_tracks` [#1065](https://github.com/CLIMADA-project/climada_python/pull/1065)
+
 ## 6.0.1
 
 Release date: 2025-03-13
@@ -41,42 +77,43 @@ Added:
 
 Updated:
 
-- `cartopy` >=0.23 &rarr; >=0.24
-- `cfgrib` >=0.9.9,<0.9.10 &rarr; >=0.9
-- `dask` >=2024.2,<2024.3 &rarr; >=2025.2
-- `eccodes` >=2.27,<2.28 &rarr; >=2.40
-- `gdal` >=3.6 &rarr; >=3.10
-- `geopandas` >=0.14 &rarr; >=0.14,<1.0
-- `h5py` >=3.8 &rarr; >=3.12
-- `haversine` >=2.8 &rarr; >=2.9
-- `matplotlib-base` >=3.9 &rarr; >=3.10
-- `netcdf4` >=1.6 &rarr; >=1.7
-- `numba` >=0.60 &rarr; >=0.61
-- `pillow` =9.4 &rarr; =11.1
-- `pyproj` >=3.5 &rarr; >=3.7
-- `pytables` >=3.7 &rarr; >=3.10
-- `python` =3.9 &rarr; =3.11
-- `rasterio` >=1.3 &rarr; >=1.4
-- `scikit-learn` >=1.5 &rarr; >=1.6
-- `scipy` >=1.13 &rarr; >=1.14,<1.15
-- `tqdm` >=4.66 &rarr; >=4.67
-- `xarray` >=2024.6 &rarr; >=2025.1
-- `xlsxwriter` >=3.1 &rarr; >=3.2
+- `cartopy` >=0.23 → >=0.24
+- `cfgrib` >=0.9.9,<0.9.10 → >=0.9
+- `dask` >=2024.2,<2024.3 → >=2025.2
+- `eccodes` >=2.27,<2.28 → >=2.40
+- `gdal` >=3.6 → >=3.10
+- `geopandas` >=0.14 → >=0.14,<1.0
+- `h5py` >=3.8 → >=3.12
+- `haversine` >=2.8 → >=2.9
+- `matplotlib-base` >=3.9 → >=3.10
+- `netcdf4` >=1.6 → >=1.7
+- `numba` >=0.60 → >=0.61
+- `pillow` =9.4 → =11.1
+- `pyproj` >=3.5 → >=3.7
+- `pytables` >=3.7 → >=3.10
+- `python` =3.9 → =3.11
+- `rasterio` >=1.3 → >=1.4
+- `scikit-learn` >=1.5 → >=1.6
+- `scipy` >=1.13 → >=1.14,<1.15
+- `tqdm` >=4.66 → >=4.67
+- `xarray` >=2024.6 → >=2025.1
+- `xlsxwriter` >=3.1 → >=3.2
 
 Removed:
 
 - `pyepsg`
 
 ### Added
 
+- `climada.entity.impact_funcs.trop_cyclone.ImpfSetTropCyclone.get_impf_id_regions_per_countries` function [#1034](https://github.com/CLIMADA-project/climada_python/pull/1034)
 - `climada.hazard.tc_tracks.TCTracks.subset_years` function [#1023](https://github.com/CLIMADA-project/climada_python/pull/1023)
 -`climada.hazard.tc_tracks.compute_track_density` function, `climada.hazard.tc_tracks.compute_genesis_density` function,
  `climada.util.coordinates.compute_grid_cell_area` function, `climada.util.coordinates.compute_grid_cell_area_validation` function,
  `climada.hazard.tc_tracks.normalize_hist` function, `climada.hazard.plot.plot_track_density` function
  [#1003](https://github.com/CLIMADA-project/climada_python/pull/1003)
 -`climada.hazard.tc_tracks.TCTracks.from_FAST` function, add Australia basin (AU) [#993](https://github.com/CLIMADA-project/climada_python/pull/993)
 - 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
+- `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)
@@ -108,8 +145,8 @@ Removed:
 - the _geometry_ column of the inherent `GeoDataFrame` is set up at initialization
 - 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)
+- 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
 
@@ -143,20 +180,20 @@ Added:
 
 Updated:
 
-- `bottleneck` >=1.3 &rarr; >=1.4
-- `cartopy` >=0.22 &rarr; >=0.23
-- `contextily` >=1.5 &rarr; >=1.6
-- `dask` >=2024.1,<2024.3 &rarr; >=2024.2,<2024.3
-- `matplotlib-base` >=3.8 &rarr; >=3.9
-- `numba` >=0.59 &rarr; >=0.60
-- `numexpr` >=2.9 &rarr; >=2.10
-- `pint` >=0.23 &rarr; >=0.24
-- `pycountry` >=22.3 &rarr; >=24.6
-- `requests` >=2.31 &rarr; >=2.32
-- `salib` >=1.4 &rarr; >=1.5
-- `scikit-learn` >=1.4 &rarr; >=1.5
-- `scipy` >=1.12 &rarr; >=1.13
-- `xarray` >=2024.2 &rarr; >=2024.6
+- `bottleneck` >=1.3 → >=1.4
+- `cartopy` >=0.22 → >=0.23
+- `contextily` >=1.5 → >=1.6
+- `dask` >=2024.1,<2024.3 → >=2024.2,<2024.3
+- `matplotlib-base` >=3.8 → >=3.9
+- `numba` >=0.59 → >=0.60
+- `numexpr` >=2.9 → >=2.10
+- `pint` >=0.23 → >=0.24
+- `pycountry` >=22.3 → >=24.6
+- `requests` >=2.31 → >=2.32
+- `salib` >=1.4 → >=1.5
+- `scikit-learn` >=1.4 → >=1.5
+- `scipy` >=1.12 → >=1.13
+- `xarray` >=2024.2 → >=2024.6
 
 ### Added
 
@@ -191,6 +228,8 @@ CLIMADA tutorials. [#872](https://github.com/CLIMADA-project/climada_python/pull
 - `Impact.from_hdf5` now calls `str` on `event_name` data that is not strings, and issue a warning then [#894](https://github.com/CLIMADA-project/climada_python/pull/894)
 - `Impact.write_hdf5` now throws an error if `event_name` is does not contain strings exclusively [#894](https://github.com/CLIMADA-project/climada_python/pull/894)
 - Split `climada.hazard.trop_cyclone` module into smaller submodules without affecting module usage [#911](https://github.com/CLIMADA-project/climada_python/pull/911)
+- `yearly_steps` parameter of `TropCyclone.apply_climate_scenario_knu` has been made explicit [#991](https://github.com/CLIMADA-project/climada_python/pull/991)
+- `Hazard.write_hdf5` writes centroids as x,y columns (or as wkb in case of polygons) at a compression level of 9, not as pickled `Shapely` objects anymore, which reduces the size of the files significantly.
 
 ### Fixed
 
@@ -261,17 +300,17 @@ Added:
 
 Updated:
 
-- `contextily` >=1.3 &rarr; >=1.5
-- `dask` >=2023 &rarr; >=2024
-- `numba` >=0.57 &rarr; >=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
+- `contextily` >=1.3 → >=1.5
+- `dask` >=2023 → >=2024
+- `numba` >=0.57 → >=0.59
+- `pandas` >=2.1 → >=2.1,<2.2
+- `pint` >=0.22 → >=0.23
+- `scikit-learn` >=1.3 → >=1.4
+- `scipy` >=1.11 → >=1.12
+- `sparse` >=0.14 → >=0.15
+- `xarray` >=2023.8 → >=2024.1
+- `overpy` =0.6 → =0.7
+- `peewee` =3.16.3 → =3.17.1
 
 Removed:
 
@@ -280,7 +319,7 @@ Removed:
 ### 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)
+- Read and Write methods to and from csv files for the `DiscRates` class. [#818](https://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)
@@ -314,13 +353,13 @@ Release date: 2023-09-27
 
 Added:
 
-- `matplotlib-base` None &rarr; >=3.8
+- `matplotlib-base` None → >=3.8
 
 Changed:
 
-- `geopandas` >=0.13 &rarr; >=0.14
-- `pandas` >=1.5,<2.0 &rarr; >=2.1
-- `salib` >=1.3.0 &rarr; >=1.4.7
+- `geopandas` >=0.13 → >=0.14
+- `pandas` >=1.5,<2.0 → >=2.1
+- `salib` >=1.3.0 → >=1.4.7
 
 Removed:
 
@@ -349,37 +388,37 @@ Added:
 
 Changed:
 
-- `cartopy` >=0.20.0,<0.20.3 &rarr; >=0.21
-- `cfgrib` >=0.9.7,<0.9.10 &rarr; =0.9.9
-- `contextily` >=1.0 &rarr; >=1.3
-- `dask` >=2.25 &rarr; >=2023
-- `eccodes` [auto] &rarr; =2.27
-- `gdal` !=3.4.1 &rarr; >=3.6
-- `geopandas` >=0.8 &rarr; >=0.13
-- `h5py` >=2.10 &rarr; >=3.8
-- `haversine` >=2.3 &rarr; >=2.8
-- `matplotlib` >=3.2,< 3.6 &rarr; >=3.7
-- `netcdf4` >=1.5 &rarr; >=1.6
-- `numba` >=0.51,!=0.55.0 &rarr; >=0.57
-- `openpyxl` >=3.0 &rarr; >=3.1
-- `pandas-datareader` >=0.9 &rarr; >=0.10
-- `pathos` >=0.2 &rarr; >=0.3
-- `pint` >=0.15 &rarr; >=0.22
-- `proj` !=9.0.0 &rarr; >=9.1
-- `pycountry` >=20.7 &rarr; >=22.3
-- `pytables` >=3.6 &rarr; >=3.7
-- `rasterio` >=1.2.7,<1.3 &rarr; >=1.3
-- `requests` >=2.24 &rarr; >=2.31
-- `salib` >=1.3.0 &rarr; >=1.4
-- `scikit-learn` >=1.0 &rarr; >=1.2
-- `scipy` >=1.6 &rarr; >=1.10
-- `sparse` >=0.13 &rarr; >=0.14
-- `statsmodels` >=0.11 &rarr; >=0.14
-- `tabulate` >=0.8 &rarr; >=0.9
-- `tqdm` >=4.48 &rarr; >=4.65
-- `xarray` >=0.13 &rarr; >=2023.5
-- `xlrd` >=1.2 &rarr; >=2.0
-- `xlsxwriter` >=1.3 &rarr; >=3.1
+- `cartopy` >=0.20.0,<0.20.3 → >=0.21
+- `cfgrib` >=0.9.7,<0.9.10 → =0.9.9
+- `contextily` >=1.0 → >=1.3
+- `dask` >=2.25 → >=2023
+- `eccodes` [auto] → =2.27
+- `gdal` !=3.4.1 → >=3.6
+- `geopandas` >=0.8 → >=0.13
+- `h5py` >=2.10 → >=3.8
+- `haversine` >=2.3 → >=2.8
+- `matplotlib` >=3.2,< 3.6 → >=3.7
+- `netcdf4` >=1.5 → >=1.6
+- `numba` >=0.51,!=0.55.0 → >=0.57
+- `openpyxl` >=3.0 → >=3.1
+- `pandas-datareader` >=0.9 → >=0.10
+- `pathos` >=0.2 → >=0.3
+- `pint` >=0.15 → >=0.22
+- `proj` !=9.0.0 → >=9.1
+- `pycountry` >=20.7 → >=22.3
+- `pytables` >=3.6 → >=3.7
+- `rasterio` >=1.2.7,<1.3 → >=1.3
+- `requests` >=2.24 → >=2.31
+- `salib` >=1.3.0 → >=1.4
+- `scikit-learn` >=1.0 → >=1.2
+- `scipy` >=1.6 → >=1.10
+- `sparse` >=0.13 → >=0.14
+- `statsmodels` >=0.11 → >=0.14
+- `tabulate` >=0.8 → >=0.9
+- `tqdm` >=4.48 → >=4.65
+- `xarray` >=0.13 → >=2023.5
+- `xlrd` >=1.2 → >=2.0
+- `xlsxwriter` >=1.3 → >=3.1
 
 Removed: