Restructuring of the documentation #977

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Merged

spjuhel merged 62 commits into develop from feature/documentation-restructuring

Jun 4, 2025

.readthedocs.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -25,3 +25,6 @@ python: @@
     formats:
       - pdf
+    sphinx:
+      configuration: doc/conf.py

CHANGELOG.md

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -26,6 +26,7 @@ Removed:
  
    - `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)

    ### Fixed

    @@ -59,27 +60,27 @@ 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:

    @@ -90,7 +91,7 @@ Removed:
  
    - `climada.hazard.tc_tracks.TCTracks.subset_years` function [#1023](https://github.com/CLIMADA-project/climada_python/pull/1023)

    - `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)

    @@ -122,8 +123,8 @@ 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

    @@ -157,20 +158,20 @@ 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

    @@ -276,17 +277,17 @@ 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:

    @@ -295,7 +296,7 @@ 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)

    @@ -329,13 +330,13 @@ 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:

    @@ -364,37 +365,37 @@ 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:

CONTRIBUTING.md

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -12,11 +12,11 @@ For orientation, these are some categories of possible contributions we can thin
  
    * **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.

    Please contact the [lead developers](https://climada.ethz.ch/team/) 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 be listed as author of the CLIMADA repository in the [AUTHORS][authors] 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.

    @@ -40,7 +40,7 @@ To contribute follow these steps:
  
        ```bash

        pylint

        ```

    6. Add your name to the [AUTHORS](AUTHORS.md) file.

    6. Add your name to the [AUTHORS][authors] file.

    7. Push your updates to the remote repository:

        ```bash

    @@ -83,4 +83,5 @@ It also contains a checklist for both pull request authors and reviewers to guid
  
    [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_Testing.html

    [testing]: https://climada-python.readthedocs.io/en/latest/development/Guide_Testing.html

    [authors]: https://github.com/CLIMADA-project/climada_python/blob/main/AUTHORS.md

climada/engine/unsequa/calc_base.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -223,15 +223,15 @@ def make_sample(self, N, sampling_method="saltelli", sampling_kwargs=None):
  
            The 'ff' sampling method does not require a value for the N parameter.

            The inputed N value is hence ignored in the sampling process in the case

            of this method.

            The 'ff' sampling method requires a number of uncerainty parameters to be

            The 'ff' sampling method requires a number of uncertainty parameters to be

            a power of 2. The users can generate dummy variables to achieve this

            requirement. Please refer to https://salib.readthedocs.io/en/latest/api.html

            for more details.

            See Also

            --------

            SALib.sample: sampling methods from SALib SALib.sample

                https://salib.readthedocs.io/en/latest/api.html

            https://salib.readthedocs.io/en/latest/api.html

            """

climada/engine/unsequa/calc_cost_benefit.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -53,8 +53,7 @@ @@
     class CalcCostBenefit(Calc):
-        """
-        Cost Benefit uncertainty analysis class
+        """Cost Benefit uncertainty analysis class
         This is the base class to perform uncertainty analysis on the outputs of
         climada.engine.costbenefit.CostBenefit().
@@ Expand Down @@

climada/engine/unsequa/unc_output.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -84,20 +84,9 @@ @@
         samples_df : pandas.DataFrame
             Values of the sampled uncertainty parameters. It has n_samples rows
             and one column per uncertainty parameter.
-        sampling_method : str
-            Name of the sampling method from SAlib.
-            https://salib.readthedocs.io/en/latest/api.html#
-        n_samples : int
-            Effective number of samples (number of rows of samples_df)
-        param_labels : list
-            Name of all the uncertainty parameters
         distr_dict : dict
             Comon flattened dictionary of all the distr_dict of all input variables.
             It represents the distribution of all the uncertainty parameters.
-        problem_sa : dict
-            The description of the uncertainty variables and their
-            distribution as used in SALib.
-            https://salib.readthedocs.io/en/latest/basics.html.
         """
         _metadata = [
@@ Expand Down Expand Up / @@ -192,6 +181,7 @@ @@
         def sampling_method(self):
             """
             Returns the sampling method used to generate self.samples_df
+            See: https://salib.readthedocs.io/en/latest/api.html#
             Returns
             -------
@@ Expand Down Expand Up / @@ -644,7 +634,7 @@ @@
                         color="green",
                         linestyle="dotted",
                         linewidth=2,
                         label="orig=%.2f%s" % (orig_plot, m_unit),
                     )
                 if log:
                     std_m, std_p = np.log10(avg - std), np.log10(avg + std)
@@ Expand Down @@

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