Move Harmonica to a src layout

.gitignore

@@ -18,6 +18,6 @@ doc/sg_execution_times.rst
 MANIFEST
 dask-worker-space
 .coverage.*
-harmonica/_version.py
+src/harmonica/_version.py
 .DS_Store
-.spyproject/*
+.spyproject/*

MANIFEST.in

@@ -3,6 +3,7 @@
 prune .github
 prune doc
 prune env
+prune test
 exclude .*.yml
 exclude .*rc
 exclude .gitignore

Makefile

@@ -1,7 +1,6 @@
 # Build, package, test, and clean
 PROJECT=harmonica
-TESTDIR=tmp-test-dir-with-unique-name
-STYLE_CHECK_FILES=$(PROJECT) doc
+STYLE_CHECK_FILES=src/$(PROJECT) test doc
 GITHUB_ACTIONS=.github/workflows
 
 .PHONY: build install test test_coverage test_numba format check check-format check-style check-actions clean
@@ -28,18 +27,10 @@ install:
 test: test_coverage test_numba
 
 test_coverage:
-	# Run a tmp folder to make sure the tests are run on the installed version.
-	# Need to specify configuration file for coverage since we change directiory.
-	mkdir -p $(TESTDIR)
-	cd $(TESTDIR); NUMBA_DISABLE_JIT=1 MPLBACKEND='agg' pytest --verbose --cov --cov-config="../pyproject.toml" --doctest-modules --doctest-continue-on-failure ../$(PROJECT)
-	cp $(TESTDIR)/.coverage* .
-	rm -rvf $(TESTDIR)
+	NUMBA_DISABLE_JIT=1 MPLBACKEND='agg' pytest --verbose --cov --cov-config="pyproject.toml" --doctest-modules --doctest-continue-on-failure src/$(PROJECT) test
 
 test_numba:
-	# Run a tmp folder to make sure the tests are run on the installed version
-	mkdir -p $(TESTDIR)
-	cd $(TESTDIR); NUMBA_DISABLE_JIT=0 MPLBACKEND='agg' pytest --verbose --doctest-modules --doctest-continue-on-failure -m use_numba ../$(PROJECT)
-	rm -rvf $(TESTDIR)
+	NUMBA_DISABLE_JIT=0 MPLBACKEND='agg' pytest --verbose --doctest-modules --doctest-continue-on-failure -m use_numba src/$(PROJECT) test
 
 format:
 	ruff check --select I --fix $(STYLE_CHECK_FILES) # fix isort errors
@@ -62,4 +53,4 @@ clean:
 	find . -name "*.pyc" -exec rm -v {} \;
 	find . -name ".coverage.*" -exec rm -v {} \;
 	rm -rvf build dist MANIFEST *.egg-info __pycache__ .coverage .cache .pytest_cache $(PROJECT)/_version.py
-	rm -rvf $(TESTDIR) dask-worker-space
+	rm -rvf dask-worker-space

pyproject.toml

@@ -58,7 +58,7 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 version_scheme = "post-release"
 local_scheme = "node-and-date"
-version_file = "harmonica/_version.py"
+version_file = "src/harmonica/_version.py"
 
 [tool.pytest.ini_options]
 doctest_optionflags = "NUMBER"
@@ -80,7 +80,7 @@ line-length = 88
 exclude = [
     "doc/_build",
     "doc/gallery",
-    "harmonica/_version.py",
+    "src/harmonica/_version.py",
 ]
 
 [tool.ruff.lint]
@@ -124,7 +124,7 @@ ignore = [
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]  # disable unused-imports errors on __init__.py
 "_kernels.py" = ["ARG001"]  # disable unused arguments in kernel files
-"harmonica/tests/**" = [
+"test/**" = [
     "T20", # allow print statements in tests
     "D",   # ignore pydocstyle warnings in tests
     "RUF012", # ignore undecorated mutable class attributes
@@ -151,7 +151,7 @@ relative_files = true
 
 [tool.coverage.paths]
 source = [
-    "harmonica",
+    "src/harmonica",
     "*/harmonica",
     "*\\harmonica",
 ]

harmonica/tests/test_dipole.py → test/test_dipole.py

@@ -20,8 +20,9 @@
 except ImportError:  # pragma: no cover
     ProgressBar = None
 
-from .. import dipole_magnetic
-from .._forward.dipole import VALID_FIELDS
+from harmonica import dipole_magnetic
+from harmonica._forward.dipole import VALID_FIELDS
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_eq_sources_cartesian.py → test/test_eq_sources_cartesian.py

@@ -16,9 +16,10 @@
 import verde as vd
 import verde.base as vdb
 
-from .. import EquivalentSources, point_gravity
-from .._equivalent_sources.cartesian import greens_func_cartesian
-from .._equivalent_sources.utils import jacobian_numba_serial
+from harmonica import EquivalentSources, point_gravity
+from harmonica._equivalent_sources.cartesian import greens_func_cartesian
+from harmonica._equivalent_sources.utils import jacobian_numba_serial
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_eq_sources_spherical.py → test/test_eq_sources_spherical.py

@@ -13,7 +13,8 @@
 import pytest
 import verde as vd
 
-from .. import EquivalentSourcesSph, point_gravity
+from harmonica import EquivalentSourcesSph, point_gravity
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_eq_sources_utils.py → test/test_eq_sources_utils.py

@@ -14,7 +14,7 @@
 import pytest
 from verde import scatter_points
 
-from .._equivalent_sources.utils import cast_fit_input, pop_extra_coords
+from harmonica._equivalent_sources.utils import cast_fit_input, pop_extra_coords
 
 
 def test_pop_extra_coords():

harmonica/tests/test_euler_deconvolution.py → test/test_euler_deconvolution.py

@@ -7,15 +7,15 @@
 import numpy.testing as npt
 import verde as vd
 
-from .. import (
+from harmonica import (
     EulerDeconvolution,
     derivative_easting,
     derivative_northing,
     derivative_upward,
     dipole_magnetic,
     magnetic_angles_to_vec,
 )
-from .._forward.point import point_gravity
+from harmonica._forward.point import point_gravity
 
 
 def test_euler_with_numeric_derivatives():

harmonica/tests/test_filters.py → test/test_filters.py

@@ -17,8 +17,8 @@
 import xarray.testing as xrt
 from verde import grid_coordinates, make_xarray_grid
 
-from ..filters._fft import fft, ifft
-from ..filters._filters import (
+from harmonica.filters._fft import fft, ifft
+from harmonica.filters._filters import (
     derivative_easting_kernel,
     derivative_northing_kernel,
     derivative_upward_kernel,
@@ -27,7 +27,7 @@
     reduction_to_pole_kernel,
     upward_continuation_kernel,
 )
-from ..filters._utils import apply_filter
+from harmonica.filters._utils import apply_filter
 
 # -------------------------------
 # Fixtures

harmonica/tests/test_forward_utils.py → test/test_forward_utils.py

@@ -15,7 +15,11 @@
 import numpy.testing as npt
 import pytest
 
-from .._forward.utils import check_coordinate_system, distance, initialize_progressbar
+from harmonica._forward.utils import (
+    check_coordinate_system,
+    distance,
+    initialize_progressbar,
+)
 
 try:
     from numba_progress import ProgressBar

harmonica/tests/test_gradient_boosted_eqs.py → test/test_gradient_boosted_eqs.py

@@ -13,8 +13,9 @@
 import pytest
 import verde as vd
 
-from .. import EquivalentSourcesGB, point_gravity
-from .._equivalent_sources.gradient_boosted import _get_region_data_sources
+from harmonica import EquivalentSourcesGB, point_gravity
+from harmonica._equivalent_sources.gradient_boosted import _get_region_data_sources
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_gravity_corrections.py → test/test_gravity_corrections.py

@@ -12,8 +12,8 @@
 import numpy.testing as npt
 import xarray as xr
 
-from .. import bouguer_correction
-from ..constants import GRAVITATIONAL_CONST
+from harmonica import bouguer_correction
+from harmonica.constants import GRAVITATIONAL_CONST
 
 
 def test_bouguer_correction():

harmonica/tests/test_icgem.py → test/test_icgem.py

@@ -14,7 +14,7 @@
 import numpy.testing as npt
 import pytest
 
-from .. import load_icgem_gdf
+from harmonica import load_icgem_gdf
 
 MODULE_DIR = Path(__file__).parent
 TEST_DATA_DIR = MODULE_DIR / "data"

harmonica/tests/test_igrf.py → test/test_igrf.py

@@ -14,7 +14,7 @@
 import pytest
 import verde as vd
 
-from .._spherical_harmonics.igrf import (
+from harmonica._spherical_harmonics.igrf import (
     IGRF14,
     interpolate_coefficients,
     load_igrf,

harmonica/tests/test_isostasy.py → test/test_isostasy.py

@@ -13,7 +13,7 @@
 import pytest
 import xarray as xr
 
-from .. import isostatic_moho_airy
+from harmonica import isostatic_moho_airy
 
 
 @pytest.mark.parametrize("reference_depth", [0, 30e3])

harmonica/tests/test_legendre.py → test/test_legendre.py

@@ -13,14 +13,15 @@
 import numpy as np
 import pytest
 
-from .._spherical_harmonics.legendre import (
+from harmonica._spherical_harmonics.legendre import (
     associated_legendre,
     associated_legendre_derivative,
     associated_legendre_full,
     associated_legendre_full_derivative,
     associated_legendre_schmidt,
     associated_legendre_schmidt_derivative,
 )
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_oasis.py → test/test_oasis.py

@@ -16,8 +16,8 @@
 import xarray as xr
 import xarray.testing as xrt
 
-from .. import load_oasis_montaj_grid
-from .._io.oasis_montaj_grd import _check_ordering, _check_sign_flag
+from harmonica import load_oasis_montaj_grid
+from harmonica._io.oasis_montaj_grd import _check_ordering, _check_sign_flag
 
 MODULE_DIR = Path(__file__).parent
 TEST_DATA_DIR = MODULE_DIR / "data"

harmonica/tests/test_point_gravity.py → test/test_point_gravity.py

@@ -28,9 +28,10 @@
     gravity_uu,
 )
 
-from .._forward.point import point_gravity
-from .._forward.utils import distance_cartesian
-from ..constants import GRAVITATIONAL_CONST
+from harmonica._forward.point import point_gravity
+from harmonica._forward.utils import distance_cartesian
+from harmonica.constants import GRAVITATIONAL_CONST
+
 from .utils import run_only_with_numba
 
 MODULE_DIR = Path(__file__).parent

harmonica/tests/test_prism.py → test/test_prism.py

@@ -33,8 +33,13 @@
 except ImportError:  # pragma: no cover
     ProgressBar = None
 
-from .. import bouguer_correction
-from .._forward.prism_gravity import _check_prisms, _discard_null_prisms, prism_gravity
+from harmonica import bouguer_correction
+from harmonica._forward.prism_gravity import (
+    _check_prisms,
+    _discard_null_prisms,
+    prism_gravity,
+)
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_prism_layer.py → test/test_prism_layer.py

@@ -17,8 +17,8 @@
 import verde as vd
 import xarray as xr
 
-from .. import prism_gravity, prism_layer
-from .._forward.prism_layer import _discard_thin_prisms
+from harmonica import prism_gravity, prism_layer
+from harmonica._forward.prism_layer import _discard_thin_prisms
 
 try:
     import pyvista

harmonica/tests/test_prism_magnetic.py → test/test_prism_magnetic.py

@@ -20,8 +20,9 @@
 except ImportError:  # pragma: no cover
     ProgressBar = None
 
-from .. import prism_magnetic
-from .._forward.prism_magnetic import VALID_FIELDS
+from harmonica import prism_magnetic
+from harmonica._forward.prism_magnetic import VALID_FIELDS
+
 from .utils import run_only_with_numba
 
 

harmonica/tests/test_tesseroid.py → test/test_tesseroid.py

@@ -18,22 +18,23 @@
 import verde as vd
 from verde import grid_coordinates
 
-from .._forward._tesseroid_utils import (
+from harmonica._forward._tesseroid_utils import (
     _discard_null_tesseroids,
     _distance_tesseroid_point,
     _longitude_continuity,
     _split_tesseroid,
     _tesseroid_dimensions,
 )
-from .._forward.tesseroid_gravity import (
+from harmonica._forward.tesseroid_gravity import (
     MAX_DISCRETIZATIONS,
     STACK_SIZE,
     _adaptive_discretization,
     _check_tesseroids,
     check_points_outside_tesseroids,
     tesseroid_gravity,
 )
-from ..constants import GRAVITATIONAL_CONST
+from harmonica.constants import GRAVITATIONAL_CONST
+
 from .utils import run_only_with_numba
 
 try:

harmonica/tests/test_tesseroid_layer.py → test/test_tesseroid_layer.py

@@ -18,8 +18,8 @@
 import verde as vd
 import xarray as xr
 
-from .. import tesseroid_gravity, tesseroid_layer
-from .._forward.tesseroid_layer import _discard_thin_tesseroids
+from harmonica import tesseroid_gravity, tesseroid_layer
+from harmonica._forward.tesseroid_layer import _discard_thin_tesseroids
 
 try:
     from numba_progress import ProgressBar

harmonica/tests/test_tesseroid_variable_density.py → test/test_tesseroid_variable_density.py

@@ -18,15 +18,15 @@
 from verde import grid_coordinates
 
 import harmonica
-
-from .. import tesseroid_gravity
-from .._forward._tesseroid_variable_density import (
+from harmonica import tesseroid_gravity
+from harmonica._forward._tesseroid_variable_density import (
     _density_based_discretization,
     density_minmax,
     maximum_absolute_diff,
     straight_line,
 )
-from ..constants import GRAVITATIONAL_CONST
+from harmonica.constants import GRAVITATIONAL_CONST
+
 from .utils import run_only_with_numba
 
 try:

harmonica/tests/test_transformations.py → test/test_transformations.py

@@ -18,13 +18,13 @@
 import xarray as xr
 import xarray.testing as xrt
 
-from .. import (
+from harmonica import (
     dipole_magnetic,
     magnetic_angles_to_vec,
     point_gravity,
     total_field_anomaly,
 )
-from .._transformations import (
+from harmonica._transformations import (
     _get_dataarray_coordinate,
     derivative_easting,
     derivative_northing,
@@ -36,6 +36,7 @@
     total_gradient_amplitude,
     upward_continuation,
 )
+
 from .utils import root_mean_square_error
 
 MODULE_DIR = Path(__file__).parent