Merge branch 'develop' into feature/wisc-relocation

Author: emanuel-schmid

.github/workflows/ci.yml

@@ -6,11 +6,11 @@ on: [push]
 # Use bash explicitly for being able to enter the conda environment
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -el {0}
 
 jobs:
   build-and-test:
-    name: Build Env, Install, Unit Tests
+    name: 'Core / Unit Test Pipeline'
     runs-on: ubuntu-latest
     permissions:
       # For publishing results
@@ -41,8 +41,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             make
-          init-shell: >-
-            bash
           # Persist environment for branch, Python version, single day
           cache-environment-key: env-${{ github.ref }}-${{ matrix.python-version }}-${{ steps.date.outputs.date }}
       -
@@ -59,12 +57,22 @@ jobs:
         if: always()
         with:
           junit_files: tests_xml/tests.xml
-          check_name: "Unit Test Results Python ${{ matrix.python-version }}"
+          check_name: "Core / Unit Test Results (${{ matrix.python-version }})"
           comment_mode: "off"
       -
         name: Upload Coverage Reports
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: coverage-report-unittests-py${{ matrix.python-version }}
+          name: coverage-report-core-unittests-py${{ matrix.python-version }}
           path: coverage/
+
+  test-petals:
+    name: Petals Compatibility
+    uses: CLIMADA-project/climada_petals/.github/workflows/testing.yml@develop
+    needs: build-and-test
+    with:
+      core_branch: ${{ github.ref }}
+      petals_branch: develop
+    permissions:
+      checks: write

AUTHORS.md

@@ -29,8 +29,10 @@
 * Raphael Portmann
 * Nicolas Colombi
 * Leonie Villiger
+* Timo Schmid
 * Kam Lam Yeung
 * Sarah Hülsen
 * Timo Schmid
 * Luca Severino
 * Samuel Juhel
+* Valentin Gebhart

CHANGELOG.md

@@ -10,19 +10,54 @@ Code freeze date: YYYY-MM-DD
 
 ### Dependency Changes
 
+### Added
+
+- `climada.util.interpolation` module for inter- and extrapolation util functions used in local exceedance intensity and return period functions [#930](https://github.com/CLIMADA-project/climada_python/pull/930)
+  
 ### 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)
+- 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)
 
 ### 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)
+### Deprecated
+
+### Removed
+
+## 5.0.0
+
+Release date: 2024-07-19
+
+### Dependency Changes
+
+Added:
+
+- `bayesian-optimization`
+- `seaborn` >=0.13
+
+Updated:
+
+- `bottleneck` >=1.3 → >=1.4
+- `cartopy` >=0.22 → >=0.23
+- `contextily` >=1.5 → >=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
 
 ### Added
 
+- GitHub actions workflow for CLIMADA Petals compatibility tests [#855](https://github.com/CLIMADA-project/climada_python/pull/855)
+- `climada.util.calibrate` module for calibrating impact functions [#692](https://github.com/CLIMADA-project/climada_python/pull/692)
+- Method `Hazard.check_matrices` for bringing the stored CSR matrices into "canonical format" [#893](https://github.com/CLIMADA-project/climada_python/pull/893)
 - Generic s-shaped impact function via `ImpactFunc.from_poly_s_shape` [#878](https://github.com/CLIMADA-project/climada_python/pull/878)
 - climada.hazard.centroids.centr.Centroids.get_area_pixel
 - climada.hazard.centroids.centr.Centroids.get_dist_coast
@@ -33,6 +68,31 @@ CLIMADA tutorials. [#872](https://github.com/CLIMADA-project/climada_python/pull
 - climada.hazard.centroids.centr.Centroids.to_default_crs
 - climada.hazard.centroids.centr.Centroids.write_csv
 - climada.hazard.centroids.centr.Centroids.write_excel
+- climada.hazard.local_return_period [#898](https://github.com/CLIMADA-project/climada_python/pull/898)
+- climada.util.plot.subplots_from_gdf [#898](https://github.com/CLIMADA-project/climada_python/pull/898)
+
+### Changed
+
+- Use Geopandas GeoDataFrame.plot() for centroids plotting function [896](https://github.com/CLIMADA-project/climada_python/pull/896)
+- Update SALib sensitivity and sampling methods from newest version (SALib 1.4.7) [#828](https://github.com/CLIMADA-project/climada_python/issues/828)
+- Allow for computation of relative and absolute delta impacts in `CalcDeltaClimate`
+- 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)
+- Update the Holland et al. 2010 TC windfield model and introduce `model_kwargs` parameter to adjust model parameters [#846](https://github.com/CLIMADA-project/climada_python/pull/846)
+- Changed module structure: `climada.hazard.Hazard` has been split into the modules `base`, `io` and `plot` [#871](https://github.com/CLIMADA-project/climada_python/pull/871)
+- Ensure `csr_matrix` stored in `climada.hazard.Hazard` have consistent data format and store no explicit zeros when initializing `ImpactCalc` [#893](https://github.com/CLIMADA-project/climada_python/pull/893)
+- `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)
+
+### 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)
+- Allow downgrading the Python bugfix version to improve environment compatibility [#900](https://github.com/CLIMADA-project/climada_python/pull/900)
+- Fix broken links in `CONTRIBUTING.md` [#900](https://github.com/CLIMADA-project/climada_python/pull/900)
+- When writing `TCTracks` to NetCDF, only apply compression to `float` or `int` data types. This fixes a downstream issue, see [climada_petals#135](https://github.com/CLIMADA-project/climada_petals/issues/135) [#911](https://github.com/CLIMADA-project/climada_python/pull/911)
 
 ### Deprecated
 
@@ -43,6 +103,7 @@ CLIMADA tutorials. [#872](https://github.com/CLIMADA-project/climada_python/pull
 - 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
+- `scheduler` parameter in `climada.util.coordinates.set_df_geometry_points`, as dask is not used anymore, leaving all calculation to shapely [#912](https://github.com/CLIMADA-project/climada_python/pull/912)
 
 ### Removed
 
@@ -153,6 +214,7 @@ Changed:
 
 - `geopandas` >=0.13 &rarr; >=0.14
 - `pandas` >=1.5,<2.0 &rarr; >=2.1
+- `salib` >=1.3.0 &rarr; >=1.4.7
 
 Removed:
 

CONTRIBUTING.md

@@ -22,7 +22,7 @@ Please contact the [lead developers](https://wcr.ethz.ch/research/climada.html)
 
 ## Minimal Steps to Contribute
 
-Before you start, please have a look at our [Developer Guide][devguide].
+Before you start, please have a look at our Developer Guide section in the [CLIMADA Docs][docs].
 
 To contribute follow these steps:
 
@@ -65,21 +65,22 @@ To contribute follow these steps:
 
 ## Resources
 
-The CLIMADA documentation provides a [Developer Guide][devguide].
+The [CLIMADA documentation][docs] provides several Developer Guides.
 Here's a selection of the commonly required information:
 
 * How to use Git and GitHub for CLIMADA development: [Development and Git and CLIMADA](https://climada-python.readthedocs.io/en/latest/guide/Guide_Git_Development.html)
-* Coding instructions for CLIMADA: [Python Dos and Don'ts](https://climada-python.readthedocs.io/en/latest/guide/Guide_PythonDos-n-Donts.html), [Performance Tips](https://climada-python.readthedocs.io/en/latest/guide/Guide_Py_Performance.html), [CLIMADA Conventions](https://climada-python.readthedocs.io/en/latest/guide/Guide_Miscellaneous.html)
-* How to execute tests in CLIMADA: [Testing and Continuous Integration][testing]
+* Coding instructions for CLIMADA: [Python Dos and Don'ts](https://climada-python.readthedocs.io/en/latest/guide/Guide_PythonDos-n-Donts.html), [Performance Tips](https://climada-python.readthedocs.io/en/latest/guide/Guide_Py_Performance.html), [CLIMADA Conventions](https://climada-python.readthedocs.io/en/latest/guide/Guide_CLIMADA_conventions.html)
+* How to execute tests in CLIMADA: [Testing][testing] and [Continuous Integration](https://climada-python.readthedocs.io/en/latest/guide/Guide_continuous_integration_GitHub_actions.html)
 
 ## Pull Requests
 
 After developing a new feature, fixing a bug, or updating the tutorials, you can create a [pull request](https://docs.github.com/en/pull-requests) to have your changes reviewed and then merged into the CLIMADA code base.
 To ensure that your pull request can be reviewed quickly and easily, please have a look at the _Resources_ above before opening a pull request.
-In particular, please check out the [Pull Request instructions](https://climada-python.readthedocs.io/en/latest/guide/Guide_Git_Development.html#Pull-requests).
+In particular, please check out the [Pull Request instructions](https://climada-python.readthedocs.io/en/latest/guide/Guide_Git_Development.html#pull-requests).
 
 We provide a description template for pull requests that helps you provide the essential information for reviewers.
 It also contains a checklist for both pull request authors and reviewers to guide the review process.
 
+[docs]: https://climada-python.readthedocs.io/en/latest/
 [devguide]: https://climada-python.readthedocs.io/en/latest/#developer-guide
-[testing]: https://climada-python.readthedocs.io/en/latest/guide/Guide_Continuous_Integration_and_Testing.html
+[testing]: https://climada-python.readthedocs.io/en/latest/guide/Guide_Testing.html

Makefile

@@ -5,8 +5,8 @@
 PYTEST_JUNIT_ARGS = --junitxml=tests_xml/tests.xml
 
 PYTEST_COV_ARGS = \
-	--cov --cov-config=.coveragerc --cov-report html --cov-report xml \
-	--cov-report term:skip-covered
+	--cov --cov-config=.coveragerc --cov-report html:coverage \
+	--cov-report xml:coverage.xml --cov-report term:skip-covered
 
 PYTEST_ARGS = $(PYTEST_JUNIT_ARGS) $(PYTEST_COV_ARGS)
 

climada/_version.py

@@ -1 +1 @@
-__version__ = '4.1.2-dev'
+__version__ = '5.0.1-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", "hail"],
+        "supported_hazard_types": ["river_flood", "tropical_cyclone", "storm_europe", "relative_cropyield", "wildfire", "earthquake", "flood", "hail", "aqueduct_coastal_flood"],
         "supported_exposures_types": ["litpop", "crop_production", "ssp_population", "crops"]
     }
 }

climada/engine/forecast.py

@@ -186,7 +186,7 @@ def __init__(
         if exposure_name is None:
             try:
                 self.exposure_name = u_coord.country_to_iso(
-                    exposure.gdf.region_id.unique()[0], "name"
+                    exposure.gdf["region_id"].unique()[0], "name"
                 )
             except (KeyError, AttributeError):
                 self.exposure_name = "custom"