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Remove the dependency of netCDF4#3643

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seisman wants to merge 134 commits intomainGenericMappingTools/pygmt:mainfrom dep/netcdfGenericMappingTools/pygmt:dep/netcdfCopy head branch name to clipboard

+397-105

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Commits on Mar 20, 2024

• Wrap GMT's standard data type GMT_IMAGE for images

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• Initial implementation of to_dataarray method for _GMT_IMAGE class

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Commits on Apr 16, 2024

• pygmt.grdcut: Support both grid and image output

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Commits on Apr 17, 2024

• Merge branch 'main' into datatypes/gmtimage

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Commits on Apr 19, 2024

• Merge branch 'main' into gmtimage

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• Fix

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• Refactor

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• fix

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Commits on Jun 18, 2024

• Merge branch 'main' into datatypes/gmtimage

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• Small typo fixes and add output type-hint for to_dataarray

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• Fix mypy error using np.array([0, 1, 2]) instead of np.arange

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• Parse name and data_attrs from grid/image header

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Commits on Jun 20, 2024

• Transpose array to (band, y, x) order and add doctest for to_dataarray

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• Set registration and gtype from header

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• Print basic shape and padding info in _GMT_IMAGE doctest

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• Only set Conventions = CF-1.7 attribute for NetCDF grid type

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• Merge branch 'main' into datatypes/gmtimage

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• Remove rioxarray import

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• Apply suggestions from code review

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• Merge branch 'main' into gmtimage

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• Address reviewer's comments

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Commits on Jun 21, 2024

• Fix GMT_OUT

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• Merge branch 'main' into gmtimage

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Commits on Jul 7, 2024

• Merge branch 'main' into gmtimage

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• Revert changes for _GMT_IMAGE

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• Use rioxarray.open_rasterio for loading images

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• Check if rioxarray is installed

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• Improve grdcut

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• Fix typos in grdcut

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• Add tests for grdcut images

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• Fix one failing test

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• Fix open_rasterio

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• Fix open_rasterio

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• Make sure the image is loaded

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• Update pygmt/clib/session.py

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Commits on Jul 8, 2024

• Use rioxarray.open_rasterio in a context manager

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• Merge branch 'main' into gmtimage

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• Merge remote-tracking branch 'origin/gmtimage' into gmtimage

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• Fix mypy errors

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• Move grdcut image tests to a separate test file

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• Fix copy & paste errors

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• Run codspeed benchmark for test_grdcut_image_dataarray

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Commits on Jul 27, 2024

• Merge branch 'main' into datatypes/gmtimage

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Commits on Aug 5, 2024

• Merge branch 'main' into gmtimage

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• Add the raster_kind function to determine the raster kind

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• Simplify the grdcut function

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Commits on Sep 19, 2024

• Merge branch 'main' into gmtimage

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• Merge branch 'main' into datatypes/gmtimage

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• Use enum for grid ids

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• Fix the band. Starting from 1

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• Refactor the tests for images

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Commits on Sep 20, 2024

• In np.reshape, a is a position-only parameter

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• Improve tests

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• Fix one failing doctest due to xarray changes

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• The np.reshape's newshape parameter is deprecated

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• Define grid IDs using IntEnum instead of Enum

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• Pass the new shape as a positional parameter

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• Fix failing tests

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• One more fix

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• One more fix

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• Simplify a doctest

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• Improve the tests

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• Merge branch 'datatypes/gmtimage' into gmtimage

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• Remove the workaround for images

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• Convert ctypes array to numpy array using np.ctypeslib.as_array

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• Fix the incorrect value due to floating number conversion in sphinterpolate

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• Merge branch 'ctypesarray' into datatypes/gmtimage

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• Update the to_dataarray method to match the codes in GMT_GRID

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• image data should has uint8 dtype

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Commits on Sep 21, 2024

• Further improve the tests

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• Merge branch 'datatypes/gmtimage' into gmtimage

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Commits on Sep 24, 2024

• Merge branch 'main' into datatypes/gmtimage

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• Add a note that currently only 3-band images are supported

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Commits on Sep 28, 2024

• Apply suggestions from code review

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• Merge branch 'main' into datatypes/gmtimage

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• Remove the old GMTGridID enums from pygmt/datatypes/header.py

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• A minor fix

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• Merge branch 'datatypes/gmtimage' into gmtimage

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Commits on Sep 29, 2024

• Merge branch 'main' into gmtimage

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• Let _raster_kind return grid by default

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• Simplify the grdcut image tests

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• Add one more test for file in & file out

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• Fix typos

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Commits on Sep 30, 2024

• Merge branch 'main' into gmtimage

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• Use the new load_blue_marble function

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• Drop the spatial_ref coord

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Commits on Nov 22, 2024

• Remove netCDF4 to see how if affects our tests

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• Refactor load_static_earth_relief to use GMT for reading, not xarray

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• Merge branch 'main' into gmtimage

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Commits on Nov 25, 2024

• Merge branch 'main' into gmtimage

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• Update _raster_kind

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Commits on Dec 5, 2024

• Add pygmt.read to read a dataset/grid/image into pandas.DataFrame/xarray.DataArray

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• Set GMT accessor

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• Need to set 'source' encoding to make GMT accessor work

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• Merge branch 'main' into feature/read

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• Fix the source encoding

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• No need to set the source encoding in load_remote_dataset.py

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Commits on Dec 6, 2024

• Revert changes in pygmt/datasets/load_remote_dataset.py

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• Improve docstring in pygmt/helpers/testing.py

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• Improve docstrinbgs

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Commits on Dec 8, 2024

• Get rid of decorators

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• Improve comment

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• Get rid of the fmt_docstring alias

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Commits on Dec 9, 2024

• Fix type hints issue with overload

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• Remove the type ignore flag

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• region defaults to None

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• Merge branch 'main' into feature/read

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• Improve type hints and add tests

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• Improve the checking of return value of which

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• Use the read funciton in pygmt/tests/test_datatypes_dataset.py

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• Merge branch 'feature/read' into dep/netcdf

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• Fix merge conflict

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• Use the read function instead of the load_dataarray method

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• Add one test to make sure that read and load_dataarray returns the same DataArray

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• Simplify pygmt/tests/test_clib_read_data.py with read

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• Merge branch 'feature/read' into dep/netcdf

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• Fix a typo

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• Revert "Update _raster_kind"

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• Merge branch 'main' into gmtimage

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• Remove the _raster_kind function

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• Add the 'kind' parameter

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• Minor update

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• Merge branch 'feature/read' into dep/netcdf

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• Merge branch 'gmtimage' into dep/netcdf

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• netCDF now is a package used in testing only

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• Replace xr.open_dataarray with read

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• Avoid keep the file open

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• Fix a typo

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• Remove one unnecessary pytest.skipif marker

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• Add it back because we still need rioxarray

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• Merge branch 'gmtimage' into dep/netcdf

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• Merge branch 'feature/read' into dep/netcdf

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Commits on Dec 19, 2024

• Merge branch 'main' into dep/netcdf

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• Refactor test_accessor to make netCDF4 optional

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