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First stab at intersections extension module #15

Merged
merged 57 commits into from
Jul 27, 2021
Merged

First stab at intersections extension module #15

merged 57 commits into from
Jul 27, 2021

Commits on Jul 16, 2021

  1. Construct Vec2 from tuple

    @tlestang
    tlestang committed Jul 16, 2021
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  2. Add pybind11 as submodule

    @tlestang
    tlestang committed Jul 16, 2021
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  3. Add base structure for intersections extension module

    @tlestang
    tlestang committed Jul 16, 2021
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  4. Forgot to add intersections module TU

    @tlestang
    tlestang committed Jul 16, 2021
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  5. Intersections wrapper takes raster metadata as argument and computes … 

    …intersections
    @tlestang
    tlestang committed Jul 16, 2021
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  6. Convert C++ vector of linestrings back to vector of python shapely li… 

    …nestrings
    @tlestang
    tlestang committed Jul 16, 2021
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  7. [format] clang-format

    @tlestang
    tlestang committed Jul 16, 2021
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  8. [refactor] Extract conversion of linestring from py to cpp

    @tlestang
    tlestang committed Jul 16, 2021
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  9. [refactor] Exctract conversion of linestring from cpp to py and impor… 

    …t shapely linestring as global variable
    @tlestang
    tlestang committed Jul 16, 2021
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  10. [test] Add test for intersections computation from python

    @tlestang
    tlestang committed Jul 16, 2021
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  11. [refactor] Minor changes in convert py2cpp

    @tlestang
    tlestang committed Jul 16, 2021
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  12. rename function from fun to split

    @tlestang
    tlestang committed Jul 16, 2021
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  13. [setup] Add shapely to install_requires list in setup script

    @tlestang
    tlestang committed Jul 16, 2021
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  14. [CI] Build extension module after setting up python

    @tlestang
    tlestang committed Jul 16, 2021
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Commits on Jul 19, 2021

  1. Build wheel with scikit-build

    @tlestang
    tlestang committed Jul 19, 2021
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  2. Use pip to install package in github workflow

    @tlestang
    tlestang committed Jul 19, 2021
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  3. [test] Import intersections module from snail package

    @tlestang
    tlestang committed Jul 19, 2021
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Commits on Jul 20, 2021

  1. Add initial infrastructure for cli

    @tlestang
    tlestang committed Jul 20, 2021
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  2. Add initial cli structure

    @tlestang
    tlestang committed Jul 20, 2021
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  3. Use geopandas and rasterio to read datasets

    @tlestang
    tlestang committed Jul 20, 2021
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  4. [nonworking] Start on testing cli

    @tlestang
    tlestang committed Jul 20, 2021
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  5. [test] Write test vector data

    @tlestang
    tlestang committed Jul 20, 2021
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  6. Loop over linestrings in a geodataframe an run intersections.split fu… 

    …nction on them
    @tlestang
    tlestang committed Jul 20, 2021
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  7. Write splits in output vector dataset

    @tlestang
    tlestang committed Jul 20, 2021
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  8. [test] Assert that geodataframe of splits compares to expected

    @tlestang
    tlestang committed Jul 20, 2021
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Commits on Jul 21, 2021

  1. Write test raster and vector files inside temporary directory 

    Cannot use tempfile.TemporaryFile() directly since this opens a file and removes it when close. To use rasterio.open I need a filename rather than a file-like obj?
    @tlestang
    tlestang committed Jul 21, 2021
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  2. [refactor] Extract creation of expected geodataframe

    @tlestang
    tlestang committed Jul 21, 2021
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  3. [refactor][test] clean imports

    @tlestang
    tlestang committed Jul 21, 2021
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  4. [setup] Update install requires

    @tlestang
    tlestang committed Jul 21, 2021
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Commits on Jul 22, 2021

  1. Add a function to get cell indices for a split linestring

    @tlestang
    tlestang committed Jul 22, 2021
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  2. Add python function raster2split to attribute raster values to split … 

    …linestrings in geodataframe
    @tlestang
    tlestang committed Jul 22, 2021
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  3. [format] Minor formatting

    @tlestang
    tlestang committed Jul 22, 2021
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  4. Fix definition of bounds for splits

    @tlestang
    tlestang committed Jul 22, 2021
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  5. [test] Fix indices of expected raster values in underlying numpy array

    @tlestang
    tlestang committed Jul 22, 2021
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Commits on Jul 27, 2021

  1. test for exact equality for line indices

    @tlestang
    tlestang committed Jul 27, 2021
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  2. Merge branch 'cli' into raster2vector

    @tlestang
    tlestang committed Jul 27, 2021
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  3. extract splitting of vector data into separate function split

    @tlestang
    tlestang committed Jul 27, 2021
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  4. Move function raster2split to module snail_intersections

    @tlestang
    tlestang committed Jul 27, 2021
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  5. Remove raster2split's side effects. Function takes geodf and raster d… 

    …ataset and returns geodf
    @tlestang
    tlestang committed Jul 27, 2021
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  6. Add new cli function snail_raster2split and corresponding entry point

    @tlestang
    tlestang committed Jul 27, 2021
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  7. Rename cli function main to snail_split

    @tlestang
    tlestang committed Jul 27, 2021
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  8. [test] Test API instead of CLI

    @tlestang
    tlestang committed Jul 27, 2021
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  9. [test] Rename test file

    @tlestang
    tlestang committed Jul 27, 2021
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  10. [test] Don't go through disk for test dataframes

    @tlestang
    tlestang committed Jul 27, 2021
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  11. [test] Move management of test raster dataset into setUp and tearDown… 

    … functions
    @tlestang
    tlestang committed Jul 27, 2021
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  12. [test] Use rasterio.io.MemoryFile to create test dataset object inste… 

    …ad of temporary file.
    @tlestang
    tlestang committed Jul 27, 2021
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  13. [test] Use tuple instead of list to index underlying raster data. 

    This adresses a FutureWarning raised by numpy:

FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
  expected_raster_values = np.tile(raster_data[data_array_indices], 2)
    @tlestang
    tlestang committed Jul 27, 2021
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  14. [format][test] run Black with 79 characters limit.

    @tlestang
    tlestang committed Jul 27, 2021
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  15. Move copy of input gdf at the top of raster2split

    @tlestang
    tlestang committed Jul 27, 2021
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  16. add "inplace" boolean argument in raster2split function

    @tlestang
    tlestang committed Jul 27, 2021
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  17. import "assert_array_almost_equal" as well

    @tlestang
    tlestang committed Jul 27, 2021
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  18. import "assert_array_almost_equal" as well

    @tlestang
    tlestang committed Jul 27, 2021
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  19. Merge branch 'raster2vector' into restructure_python_intersections

    @tlestang
    tlestang committed Jul 27, 2021
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  20. Merge pull request #19 from nismod/restructure_python_intersections 

    Restructure python side of intersection code
    @tlestang
    tlestang authored Jul 27, 2021
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  21. Merge pull request #18 from nismod/raster2vector 

    Raster to vector attribution
    @tlestang
    tlestang authored Jul 27, 2021
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  22. Merge pull request #17 from nismod/cli 

    Add a command line interface to intersections kernel
    @tlestang
    tlestang authored Jul 27, 2021
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  23. Merge pull request #16 from nismod/build_intersections_extension 

    Build intersections extension
    @tlestang
    tlestang authored Jul 27, 2021
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