Merge branch 'feature/exposures_crs' into feature/wisc-relocation

Author: emanuel-schmid

.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

@@ -10,16 +10,135 @@ Code freeze date: YYYY-MM-DD
 
 ### Dependency Changes
 
-### Added
-
 ### 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
+
+- 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
+- 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)
+- `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
 
 Release date: 2023-09-27

CONTRIBUTING.md

@@ -1,8 +1,26 @@
 # CLIMADA Contribution Guide
 
-Thank you for contributing to CLIMADA!
+We welcome any contribution to CLIMADA and want to express our thanks to everybody who contributes.
 
-## Overview
+## What Warrants a Contribution?
+
+Anything!
+For orientation, these are some categories of possible contributions we can think of:
+
+* **Technical problems and bugs:** Did you encounter a problem when using CLIMADA? Raise an [issue](https://github.com/CLIMADA-project/climada_python/issues) in our repository, providing a description or ideally a code replicating the error. Did you already find a solution to the problem? Please raise a pull request to help us resolve the issue!
+* **Documentation and Tutorial Updates:** Found a typo in the documentation? Is a tutorial lacking some information you find important? Simply fix a line, or add a paragraph. We are happy to incorporate you additions! Please raise a pull request!
+* **New Modules and Utility Functions:** Did you create a function or an entire module you find useful for your work? Maybe you are not the only one! Feel free to simply raise a pull request for functions that improve, e.g., plotting or data handling. As an entire module has to be carefully integrated into the framework, it might help if you talk to us first so we can design the module and plan the next steps. You can do that by raising an issue or starting a [discussion](https://github.com/CLIMADA-project/climada_python/discussions) on GitHub.
+
+A good place to start a personal discussion is our monthly CLIMADA developers call.
+Please contact the [lead developers](https://wcr.ethz.ch/research/climada.html) if you want to join.
+
+## Why Should You Contribute?
+
+* You will be listed as author of the CLIMADA repository in the [AUTHORS](AUTHORS.md) file.
+* You will improve the quality of the CLIMADA software for you and for everybody else using it.
+* You will gain insights into scientific software development.
+
+## Minimal Steps to Contribute
 
 Before you start, please have a look at our [Developer Guide][devguide].
 

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.
@@ -61,7 +62,9 @@ Please use the following logo if you are presenting results obtained with or thr
 
 ## Contributing
 
-See the [Contribution Guide](CONTRIBUTING.md).
+We welcome any contribution to this repository, be it bugfixes and other code changes and additions, documentation improvements, or tutorial updates.
+
+If you would like to contribute, please refer to our [Contribution Guide](CONTRIBUTING.md).
 
 ## Versioning
 

climada/_version.py

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