Refactor polygon_query() (#422)

* wip

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* wip

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix 2d/3d bb for raster data

* support for 2d/3d bb for 2d/3d points

* better tests

* implemented tests, need to make them pass

* fix test raster

* wip

* polygon_query for points working

* validate against negative radii; all tests passing

* tests multipolygon; cleanup

* renamed tests, wip test query with affine

* test query point partitions, wip tests query transformations

* tests query affine transformation

* fix tests

* test more robust

* improved comments

* fix tuple from list

* wip

* addressing review comments

* fixed tests

* addressed all the review comments

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