Fix pre-commit config to check all model files (#637)

Fix pre-commit config to work on all model files, and not only on `model/common` folder. This PR also includes all the format and linter changes required to make CI pass. Additionally, add the `esbonio` language server for RestructuredText to the`docs` dependency group. Bug originally reported by @havogt --------- Co-authored-by: Nicoletta Farabullini <[email protected]>
C2SM · Jan 9, 2025 · 77a7a68 · 77a7a68
1 parent 5a19c81
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ minimum_pre_commit_version: 3.8.0
 files: |
   (?x)^(
       tools/.*|
-      model/common/.*
+      model/.*
   )$
 
 repos:

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ ICON4Py is licensed under the terms of the BSD-3-Clause.
 
 Since this project is still in a highly experimental state, it is not yet available as a regular Python distribution package through PyPI. The installation procedure involves cloning the [ICON4Py GitHub repository](https://github.com/C2SM/icon4py) and installing it in a Python virtual environment (_venv_).
 
-ICON4Py uses the `uv` tool to manage the development workflow. `uv` is a versatile tool that consolidates functionality previously distributed across different applications into subcommands.
+ICON4Py uses the [`uv`](https://docs.astral.sh/uv/) project manager for development workflow. `uv` is a versatile tool that consolidates functionality previously distributed across different applications into subcommands.
 
 - The `uv pip` subcommand provides a _fast_ Python package manager, emulating [`pip`](https://pip.pypa.io/en/stable/).
 - The `uv export | lock | sync` subcommands manage dependency versions in a manner similar to the [`pip-tools`](https://pip-tools.readthedocs.io/en/stable/) command suite.

diff --git a/model/README.md b/model/README.md
@@ -22,10 +22,12 @@ Until the development reaches a stable state, we recommend you to follow the gen
 See the repository [README](../README.md) for general information.
 
 #### Unit tests for stencils
+
 The `gt4py` stencils in the `icon4py-model` packages are used for integration into Fortran code
 via [icon4pygen](../tools/src/icon4py/icon4pygen). To make integration easier
 unit tests for the stencils need to be placed into
 a `stencil_tests` subfolder of the packages test path. For example
+
 ```
 model/atmosphere/diffusion/tests/stencil_tests
 model/atmosphere/dycore/tests/stencil_tests
@@ -35,10 +37,10 @@ model/common/tests/tests/stencil_tests
 
 #### Data dependent tests
 
-Some test depend on serialized data generated by a full model run. 
-Those test are marked with `pytest.mark.datatest` and are only run when the `--datatest` 
-option is specified. Note that due to `pytests` configuration discovery 
-you need to specify the base a package directory i.e. one that contains a `pyproject.toml` for the 
+Some tests depend on serialized data generated by a full model run.
+Those tests are marked with `pytest.mark.datatest` and are only run when the `--datatest`
+option is specified. Note that due to `pytest` configuration discovery
+you need to specify the base package directory i.e. one that contains a `pyproject.toml` for the
 commandline option to work.
 
 ```bash
@@ -48,6 +50,7 @@ pytest -v --datatest model/atmosphere/diffusion
 ```
 
 #### Testing parallel code
+
 Icon4Py uses GHEX as communication library. It is an optional dependency of the model. In order to install and
 run the parallel version do the following:
 
@@ -56,25 +59,31 @@ run the parallel version do the following:
 ```bash
 sudo apt-get install libopenmpi-dev
 ```
+
 or
+
 ```bash
 sudo apt-get install mpich
 ```
-On MacOS run 
+
+On MacOS run
+
 ```bash
 brew install mpich
 ```
+
 2. Install optional python libraries:
-In the main folder of the repository run
+   In the main folder of the repository, run
+
 ```bash
 pip install -r requirements-dev-opt.txt
 ```
+
 Note that the current Python build for GHEX seems not to run on MacOS.
 
 3. Run parallel tests
-In order to run the parallel tests you need to specify specify the `--with-mpi` option to `pytest`
-and _pass the exact folder location of the tests_ to `pytest`.
-
+   In order to run the parallel tests you need to specify the `--with-mpi` option to `pytest`
+   and _pass the exact folder location of the tests_ to `pytest`.
 
 ```bash
 mpirun -np 4 pytest -v -s --with-mpi --datatest model/atmosphere/diffusion/diffusion_tests/mpi_tests/

diff --git a/...sphere/advection/tests/advection_stencil_tests/test_apply_horizontal_density_increment.py b/...sphere/advection/tests/advection_stencil_tests/test_apply_horizontal_density_increment.py
@@ -45,7 +45,9 @@ def reference(
     @pytest.fixture
     def input_data(self, grid) -> dict:
         p_rhodz_new = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
-        p_mflx_contra_v = data_alloc.random_field(grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1})
+        p_mflx_contra_v = data_alloc.random_field(
+            grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1}
+        )
         deepatmo_divzl = data_alloc.random_field(grid, dims.KDim)
         deepatmo_divzu = data_alloc.random_field(grid, dims.KDim)
         rhodz_ast2 = data_alloc.zero_field(grid, dims.CellDim, dims.KDim)

diff --git a/...e/advection/tests/advection_stencil_tests/test_apply_interpolated_tracer_time_tendency.py b/...e/advection/tests/advection_stencil_tests/test_apply_interpolated_tracer_time_tendency.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestApplyInterpolatedTracerTimeTendency(helpers.StencilTest):
     PROGRAM = apply_interpolated_tracer_time_tendency
     OUTPUTS = ("p_tracer_new",)

diff --git a/...mosphere/advection/tests/advection_stencil_tests/test_apply_vertical_density_increment.py b/...mosphere/advection/tests/advection_stencil_tests/test_apply_vertical_density_increment.py
@@ -14,8 +14,8 @@
 from icon4py.model.atmosphere.advection.stencils.apply_vertical_density_increment import (
     apply_vertical_density_increment,
 )
-from icon4py.model.common.utils import data_allocation as data_alloc
 from icon4py.model.common import dimension as dims
+from icon4py.model.common.utils import data_allocation as data_alloc
 
 
 class TestApplyVerticalDensityIncrement(helpers.StencilTest):
@@ -48,7 +48,9 @@ def reference(
     @pytest.fixture
     def input_data(self, grid) -> dict:
         rhodz_ast = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
-        p_mflx_contra_v = data_alloc.random_field(grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1})
+        p_mflx_contra_v = data_alloc.random_field(
+            grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1}
+        )
         deepatmo_divzl = data_alloc.random_field(grid, dims.KDim)
         deepatmo_divzu = data_alloc.random_field(grid, dims.KDim)
         rhodz_ast2 = data_alloc.zero_field(grid, dims.CellDim, dims.KDim)

diff --git a/...here/advection/tests/advection_stencil_tests/test_average_horizontal_flux_subcycling_2.py b/...here/advection/tests/advection_stencil_tests/test_average_horizontal_flux_subcycling_2.py
@@ -18,7 +18,6 @@
 from icon4py.model.common.utils import data_allocation as data_alloc
 
 
-
 class TestAverageHorizontalFluxSubcycling2(helpers.StencilTest):
     PROGRAM = average_horizontal_flux_subcycling_2
     OUTPUTS = ("p_out_e",)

diff --git a/...here/advection/tests/advection_stencil_tests/test_average_horizontal_flux_subcycling_3.py b/...here/advection/tests/advection_stencil_tests/test_average_horizontal_flux_subcycling_3.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestAverageHorizontalFluxSubcycling3(helpers.StencilTest):
     PROGRAM = average_horizontal_flux_subcycling_3
     OUTPUTS = ("p_out_e",)

diff --git a/...ction/tests/advection_stencil_tests/test_compute_antidiffusive_cell_fluxes_and_min_max.py b/...ction/tests/advection_stencil_tests/test_compute_antidiffusive_cell_fluxes_and_min_max.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_antidiffusive_cell_fluxes_and_min_max import (
     compute_antidiffusive_cell_fluxes_and_min_max,
 )

diff --git a/...sphere/advection/tests/advection_stencil_tests/test_compute_barycentric_backtrajectory.py b/...sphere/advection/tests/advection_stencil_tests/test_compute_barycentric_backtrajectory.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_barycentric_backtrajectory import (
     compute_barycentric_backtrajectory,
 )

diff --git a/...re/advection/tests/advection_stencil_tests/test_compute_barycentric_backtrajectory_alt.py b/...re/advection/tests/advection_stencil_tests/test_compute_barycentric_backtrajectory_alt.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_barycentric_backtrajectory_alt import (
     compute_barycentric_backtrajectory_alt,
 )

diff --git a/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ffsl_backtrajectory.py b/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ffsl_backtrajectory.py
@@ -10,13 +10,13 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_ffsl_backtrajectory import (
     compute_ffsl_backtrajectory,
 )
 from icon4py.model.common import dimension as dims
-from icon4py.model.common.utils import data_allocation as data_alloc
+
 
 class TestComputeFfslBacktrajectory(helpers.StencilTest):
     PROGRAM = compute_ffsl_backtrajectory

diff --git a/...ts/advection_stencil_tests/test_compute_ffsl_backtrajectory_counterclockwise_indicator.py b/...ts/advection_stencil_tests/test_compute_ffsl_backtrajectory_counterclockwise_indicator.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputeFfslBacktrajectoryCounterclockwiseIndicator(helpers.StencilTest):
     PROGRAM = compute_ffsl_backtrajectory_counterclockwise_indicator
     OUTPUTS = ("lvn_sys_pos",)

diff --git a/...ts/advection_stencil_tests/test_compute_horizontal_tracer_flux_from_cubic_coefficients.py b/...ts/advection_stencil_tests/test_compute_horizontal_tracer_flux_from_cubic_coefficients.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputeHorizontalTracerFluxFromCubicCoefficients(helpers.StencilTest):
     PROGRAM = compute_horizontal_tracer_flux_from_cubic_coefficients
     OUTPUTS = ("p_out_e_hybrid_2",)

diff --git a/...s/advection_stencil_tests/test_compute_horizontal_tracer_flux_from_linear_coefficients.py b/...s/advection_stencil_tests/test_compute_horizontal_tracer_flux_from_linear_coefficients.py
@@ -19,7 +19,6 @@
 from icon4py.model.common.utils import data_allocation as data_alloc
 
 
-
 class TestComputeHorizontalTracerFluxFromLinearCoefficients(helpers.StencilTest):
     PROGRAM = compute_horizontal_tracer_flux_from_linear_coefficients
     OUTPUTS = ("p_out_e",)

diff --git a/...vection_stencil_tests/test_compute_horizontal_tracer_flux_from_linear_coefficients_alt.py b/...vection_stencil_tests/test_compute_horizontal_tracer_flux_from_linear_coefficients_alt.py
@@ -18,6 +18,7 @@
 from icon4py.model.common.grid import horizontal as h_grid
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputeHorizontalTracerFluxFromLinearCoefficientsAlt(helpers.StencilTest):
     PROGRAM = compute_horizontal_tracer_flux_from_linear_coefficients_alt
     OUTPUTS = ("p_out_e",)

diff --git a/...ion_stencil_tests/test_compute_positive_definite_horizontal_multiplicative_flux_factor.py b/...ion_stencil_tests/test_compute_positive_definite_horizontal_multiplicative_flux_factor.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_positive_definite_horizontal_multiplicative_flux_factor import (
     compute_positive_definite_horizontal_multiplicative_flux_factor,
 )

diff --git a/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_all_face_values.py b/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_all_face_values.py
@@ -14,10 +14,8 @@
 from icon4py.model.atmosphere.advection.stencils.compute_ppm_all_face_values import (
     compute_ppm_all_face_values,
 )
-from icon4py.model.common.utils import data_allocation as data_alloc
-
 from icon4py.model.common import dimension as dims
-
+from icon4py.model.common.utils import data_allocation as data_alloc
 
 
 class TestComputePpmAllFaceValues(helpers.StencilTest):
@@ -55,7 +53,7 @@ def input_data(self, grid) -> dict:
         p_cellhgt_mc_now = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
         p_face_in = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
         p_face = data_alloc.zero_field(grid, dims.CellDim, dims.KDim)
-        k  = data_alloc.allocate_indices(dims.KDim, grid, is_halfdim=False, dtype=gtx.int32)
+        k = data_alloc.allocate_indices(dims.KDim, grid, is_halfdim=False, dtype=gtx.int32)
         slev = gtx.int32(1)
         slevp1 = gtx.int32(2)
         elev = gtx.int32(k[-3].as_scalar())

diff --git a/...osphere/advection/tests/advection_stencil_tests/test_compute_ppm_quadratic_face_values.py b/...osphere/advection/tests/advection_stencil_tests/test_compute_ppm_quadratic_face_values.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 outslice = (slice(None), slice(1, None))
 
 

diff --git a/...tmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_quartic_face_values.py b/...tmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_quartic_face_values.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputePpmQuarticFaceValues(helpers.StencilTest):
     PROGRAM = compute_ppm_quartic_face_values
     OUTPUTS = (helpers.Output("p_face", gtslice=(slice(None), slice(2, None))),)

diff --git a/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_slope.py b/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_ppm_slope.py
@@ -9,7 +9,6 @@
 import gt4py.next as gtx
 import numpy as np
 import pytest
-from gt4py.next import as_field
 
 import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.compute_ppm_slope import (
@@ -18,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputePpmSlope(helpers.StencilTest):
     PROGRAM = compute_ppm_slope
     OUTPUTS = (

diff --git a/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_tendency.py b/model/atmosphere/advection/tests/advection_stencil_tests/test_compute_tendency.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestComputeTendency(helpers.StencilTest):
     PROGRAM = compute_tendency
     OUTPUTS = ("opt_ddt_tracer_adv",)

diff --git a/...ere/advection/tests/advection_stencil_tests/test_integrate_tracer_density_horizontally.py b/...ere/advection/tests/advection_stencil_tests/test_integrate_tracer_density_horizontally.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestIntegrateTracerDensityHorizontally(helpers.StencilTest):
     PROGRAM = integrate_tracer_density_horizontally
     OUTPUTS = (

diff --git a/.../atmosphere/advection/tests/advection_stencil_tests/test_integrate_tracer_horizontally.py b/.../atmosphere/advection/tests/advection_stencil_tests/test_integrate_tracer_horizontally.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.integrate_tracer_horizontally import (
     integrate_tracer_horizontally,
 )

diff --git a/model/atmosphere/advection/tests/advection_stencil_tests/test_integrate_tracer_vertically.py b/model/atmosphere/advection/tests/advection_stencil_tests/test_integrate_tracer_vertically.py
@@ -9,7 +9,6 @@
 import gt4py.next as gtx
 import numpy as np
 import pytest
-from gt4py.next import as_field
 
 import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.integrate_tracer_vertically import (
@@ -61,12 +60,14 @@ def reference(
     def input_data(self, grid) -> dict:
         tracer_now = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
         rhodz_now = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
-        p_mflx_tracer_v = data_alloc.random_field(grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1})
+        p_mflx_tracer_v = data_alloc.random_field(
+            grid, dims.CellDim, dims.KDim, extend={dims.KDim: 1}
+        )
         deepatmo_divzl = data_alloc.random_field(grid, dims.KDim)
         deepatmo_divzu = data_alloc.random_field(grid, dims.KDim)
         rhodz_new = data_alloc.random_field(grid, dims.CellDim, dims.KDim)
         tracer_new = data_alloc.zero_field(grid, dims.CellDim, dims.KDim)
-        k = data_alloc.allocate_indices(dims.KDim, grid, is_halfdim=False,dtype=gtx.int32 )
+        k = data_alloc.allocate_indices(dims.KDim, grid, is_halfdim=False, dtype=gtx.int32)
         p_dtime = np.float64(5.0)
         ivadv_tracer = 1
         iadv_slev_jt = 4

diff --git a/...e/advection/tests/advection_stencil_tests/test_limit_vertical_slope_semi_monotonically.py b/...e/advection/tests/advection_stencil_tests/test_limit_vertical_slope_semi_monotonically.py
@@ -10,7 +10,6 @@
 import numpy as np
 import pytest
 
-
 import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.limit_vertical_slope_semi_monotonically import (
     limit_vertical_slope_semi_monotonically,

diff --git a/...n/tests/advection_stencil_tests/test_postprocess_antidiffusive_cell_fluxes_and_min_max.py b/...n/tests/advection_stencil_tests/test_postprocess_antidiffusive_cell_fluxes_and_min_max.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestPostprocessAntidiffusiveCellFluxesAndMinMax(helpers.StencilTest):
     PROGRAM = postprocess_antidiffusive_cell_fluxes_and_min_max
     OUTPUTS = ("z_tracer_new_low", "z_tracer_max", "z_tracer_min")

diff --git a/...phere/advection/tests/advection_stencil_tests/test_prepare_ffsl_flux_area_patches_list.py b/...phere/advection/tests/advection_stencil_tests/test_prepare_ffsl_flux_area_patches_list.py
@@ -10,8 +10,8 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.prepare_ffsl_flux_area_patches_list import (
     prepare_ffsl_flux_area_patches_list,
 )

diff --git a/...dvection_stencil_tests/test_prepare_numerical_quadrature_list_for_cubic_reconstruction.py b/...dvection_stencil_tests/test_prepare_numerical_quadrature_list_for_cubic_reconstruction.py
@@ -17,6 +17,7 @@
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.utils import data_allocation as data_alloc
 
+
 class TestPrepareNumericalQuadratureListForCubicReconstruction(helpers.StencilTest):
     PROGRAM = prepare_numerical_quadrature_list_for_cubic_reconstruction
     OUTPUTS = (

diff --git a/...sphere/advection/tests/advection_stencil_tests/test_reconstruct_cubic_coefficients_svd.py b/...sphere/advection/tests/advection_stencil_tests/test_reconstruct_cubic_coefficients_svd.py
@@ -10,14 +10,15 @@
 import numpy as np
 import pytest
 
-import icon4py.model.testing.helpers as helpers
 import icon4py.model.common.utils.data_allocation as data_alloc
+import icon4py.model.testing.helpers as helpers
 from icon4py.model.atmosphere.advection.stencils.reconstruct_cubic_coefficients_svd import (
     reconstruct_cubic_coefficients_svd,
 )
 from icon4py.model.common import dimension as dims
 from icon4py.model.common.grid import horizontal as h_grid
 
+
 class TestReconstructCubicCoefficientsSvd(helpers.StencilTest):
     PROGRAM = reconstruct_cubic_coefficients_svd
     OUTPUTS = (
Original file line number	Diff line number	Diff line change
Expand Up		@@ -17,6 +17,7 @@
		from icon4py.model.common import dimension as dims
		from icon4py.model.common.utils import data_allocation as data_alloc


		outslice = (slice(None), slice(1, None))


Expand Down