revise set_lines_ids with cKDTree

[davide-f]

Closes #806

Changes proposed in this Pull Request

This PR revise the implementation of set_lines_ids with cKDTree.
Performance speed increases by a factor 10 in the Nigeria case (0.12s vs 1.2s in the standard implementation).
For US, 26s are required vs about 12min in the previous formulation.
Performance speed is expected to be significant with the problem size.

Checklist

• I consent to the release of this PR's code under the AGPLv3 license and non-code contributions under CC0-1.0 and CC-BY-4.0.
• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and doc/requirements.txt.
• Changes in configuration options are added in all of config.default.yaml and config.tutorial.yaml.
• Add a test config or line additions to test/ (note tests are changing the config.tutorial.yaml)
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.

[davide-f]

@mnm-matin FYI :)

[davide-f]

An alternative implementation using only geopandas may be used: https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.sjoin_nearest.html#geopandas.GeoDataFrame.sjoin_nearest
though not sure if it may be more performant

[mnm-matin]

@davide-f the geopandas spatial index uses cKDTree under the hood, so either implementation is equivalent. The geopandas sjoin hides the complexity and reduces per-script dependancies.

[davide-f]

Closing in favor of #845