Microphysics package with saturation adjustment

.pre-commit-config.yaml

@@ -36,6 +36,13 @@ repos:
         pass_filenames: false
         always_run: true
 
+      - id: run-atmosphere-microphysics-precommit
+        name: Run Model Atmosphere Microphysics Pre-commit
+        entry: pre-commit run --config model/atmosphere/subgrid_scale_physics/microphysics/.pre-commit-config.yaml --all-files
+        language: system
+        pass_filenames: false
+        always_run: true
+
       - id: run-tools-precommit
         name: Run Tools Pre-commit
         entry: pre-commit run --config tools/.pre-commit-config.yaml --all-files

ci/default.yml

@@ -29,5 +29,5 @@ test_model_datatests:
     - tox -r -e run_model_tests -c model/ --verbose -- --backend=$BACKEND $COMPONENT
   parallel:
     matrix:
-    - COMPONENT: [atmosphere/diffusion/tests/diffusion_tests, atmosphere/dycore/tests/dycore_tests, common/tests, driver/tests]
+    - COMPONENT: [atmosphere/diffusion/tests/diffusion_tests, atmosphere/dycore/tests/dycore_tests, atmosphere/subgrid_scale_physics/microphysics/tests, common/tests, driver/tests]
       BACKEND: [gtfn_cpu]

model/README.md

@@ -7,6 +7,7 @@ It includes the following packages:
 - `atmosphere/dycore`: Contains implementations of the dynamical core of the ICON model
 - `atmosphere/diffusion`: Contains the implementation of diffusion in the ICON model
 - `atmosphere/advection`: Contains implementations of the advection component of the ICON model
+- `atmosphere/subgrid_scale_physics/microphysics`: Contains implementations of the microphysics component of the ICON model
 - `common`: Contains shared functionality that is required by multiple components.
 - `driver`: Contains the driving code for the model
 

model/atmosphere/subgrid_scale_physics/microphysics/.bumpversion.cfg

@@ -0,0 +1,10 @@
+[bumpversion]
+current_version = 0.0.6
+parse = (?P<major>\d+)\.(?P<minor>\d+)(\.(?P<patch>\d+))?
+serialize =
+	{major}.{minor}.{patch}
+
+[bumpversion:file:src/icon4py/model/atmosphere/subgrid_scale_physics/microphysics/__init__.py]
+parse = \"(?P<major>\d+)\.(?P<minor>\d+)(\.(?P<patch>\d+))?\"
+serialize =
+	{major}.{minor}.{patch}

model/atmosphere/subgrid_scale_physics/microphysics/.flake8

@@ -0,0 +1,44 @@
+[flake8]
+# Some sane defaults for the code style checker flake8
+max-line-length = 100
+max-complexity = 15
+doctests = true
+extend-ignore =
+    # Do not perform function calls in argument defaults
+    B008,
+    # Public code object needs docstring
+    D1,
+    # Disable dargling errors by default
+    DAR,
+    # Whitespace before ':' (black formatter breaks this sometimes)
+    E203,
+    # Line too long (using Bugbear's B950 warning)
+    E501,
+    # Line break occurred before a binary operator
+    W503,
+    # import statement "abs" is shadowing a Python builtin
+    A004
+
+exclude =
+    .eggs,
+    .gt_cache,
+    .ipynb_checkpoints,
+    .tox,
+    _local_,
+    build,
+    dist,
+    docs,
+    _external_src,
+    tests/_disabled,
+    setup.py
+
+rst-roles =
+    py:mod, mod,
+    py:func, func,
+    py:data, data,
+    py:const, const,
+    py:class, class,
+    py:meth, meth,
+    py:attr, attr,
+    py:exc, exc,
+    py:obj, obj,

model/atmosphere/subgrid_scale_physics/microphysics/.pre-commit-config.yaml

@@ -0,0 +1,80 @@
+# NOTE: pre-commit runs all hooks from the root folder of the repository,
+# as regular git hooks do. Therefore, paths passed as arguments to the plugins
+# should always be relative to the root folder.
+
+default_stages: [commit, push]
+default_language_version:
+  python: python3.10
+minimum_pre_commit_version: 2.20.0
+files: "model/atmosphere/subgrid_scale_physics/microphysics/.*"
+
+repos:
+- repo: meta
+  hooks:
+  - id: check-hooks-apply
+    stages: [manual]
+  - id: check-useless-excludes
+    stages: [manual]
+
+- repo: https://github.com/asottile/setup-cfg-fmt
+  rev: v1.20.1
+  hooks:
+          # Run only manually because it deletes comments
+  - id: setup-cfg-fmt
+    name: format setup.cfg
+    stages: [manual]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks:
+  - id: check-case-conflict
+  - id: check-merge-conflict
+  - id: check-shebang-scripts-are-executable
+  - id: check-symlinks
+  - id: check-yaml
+  - id: debug-statements
+  - id: destroyed-symlinks
+
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.6.0
+  hooks:
+  - id: pretty-format-ini
+    args: [--autofix]
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix, --preserve-quotes, --indent, "2"]
+
+- repo: https://github.com/pre-commit/mirrors-prettier
+  rev: v3.0.0-alpha.4
+  hooks:
+  - id: prettier
+    types_or: [markdown, json]
+
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.3.0
+  hooks:
+  - id: insert-license
+    name: add license for all ICON4Py Python source files
+    types: [python]
+    args: [--comment-style, "|#|", --license-filepath, model/.license_header.txt, --fuzzy-match-generates-todo]
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.2
+  hooks:
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
+
+- repo: local
+  hooks:
+  - id: mypy
+    name: mypy static type checker
+    entry: bash -c 'echo mypy temporarily disabled'
+            #entry: bash -c 'cd model/atmosphere/subgrid_scale_physics/microphysics; mypy src/' --
+    language: system
+    types_or: [python, pyi]
+    always_run: true
+            #pass_filenames: false
+    require_serial: true
+    stages: [commit]

model/atmosphere/subgrid_scale_physics/microphysics/README.md

@@ -0,0 +1,9 @@
+# icon4py-atmosphere-physics-microphysics
+
+## Description
+
+Port of ICON microphysics module 'saturation_adjustment' to gt4py.
+
+## Installation instructions
+
+Check the `README.md` at the root of the `model` folder for installation instructions.

model/atmosphere/subgrid_scale_physics/microphysics/pyproject.toml

@@ -0,0 +1,139 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=61.0", "wheel>=0.40.0"]
+
+[project]
+authors = [
+  {email = "[email protected]"},
+  {name = "ETH Zurich"}
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+  "Operating System :: POSIX",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Topic :: Scientific/Engineering :: Atmospheric Science",
+  "Topic :: Scientific/Engineering :: Mathematics",
+  "Topic :: Scientific/Engineering :: Physics"
+]
+dependencies = [
+  "gt4py>=1.0.1",
+  "icon4py-common>=0.0.5"
+]
+description = "ICON microphysics."
+dynamic = ['version']
+license = {file = "LICENSE"}
+name = "icon4py-atmosphere-subgrid_scale_physics-microphysics"
+readme = "README.md"
+requires-python = ">=3.10"
+
+[project.urls]
+repository = "https://github.com/C2SM/icon4py"
+
+[tool.coverage]
+
+[tool.coverage.html]
+directory = 'tests/_reports/coverage_html'
+
+[tool.coverage.paths]
+source = ['src/icon4py/model/']
+
+[tool.coverage.report]
+exclude_lines = [
+  'raise AssertionError',  # Don't complain if tests don't hit defensive assertion code
+  'raise NotImplementedError',  # Don't complain if tests don't hit defensive assertion code
+  'if 0:',  # Don't complain if non-runnable code isn't run
+  'if __name__ == .__main__.:'  # Don't complain if non-runnable code isn't run
+]
+ignore_errors = true
+
+[tool.coverage.run]
+branch = true
+parallel = true
+source_pkgs = ['microphysics']
+
+[tool.mypy]
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+exclude = [
+  '^tests/*.py'
+]
+ignore_missing_imports = false
+implicit_reexport = true
+install_types = true
+non_interactive = true
+show_column_numbers = true
+show_error_codes = true
+warn_redundant_casts = true
+warn_unused_configs = true
+warn_unused_ignores = true
+
+[tool.pytest]
+
+[tool.pytest.ini_options]
+addopts = ['-p icon4py.model.common.test_utils.pytest_config']
+testpaths = 'tests'
+
+[tool.ruff]
+extend-exclude = [
+  '.eggs',
+  '.gt_cache',
+  '.ipynb_checkpoints',
+  '.tox',
+  '_local_',
+  'build',
+  'dist',
+  'docs',
+  '_external_src',
+  'tests/_disabled',
+  'setup.py'
+]
+indent-width = 4
+line-length = 100
+respect-gitignore = true
+show-fixes = true
+# Assume Python 3.10
+target-version = "py310"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+extend-select = ['E', 'F', 'I', 'B', 'A', 'T10', 'ERA', 'NPY', 'RUF']
+# # Rules sets:
+# E: pycodestyle
+# F: Pyflakes
+# I: isort
+# B: flake8-bugbear
+# A: flake8-builtins
+# T10: flake8-debugger
+# ERA: eradicate
+# NPY: NumPy-specific rules
+# RUF: Ruff-specific rules
+ignore = [
+  'E501',  # Line too long (using Bugbear's B950 warning)
+  'RUF009'  # Do not perform function call in dataclass defaults
+]
+ignore-init-module-imports = true
+
+[tool.ruff.lint.isort]
+combine-as-imports = true
+known-first-party = ['icon4py.model']
+known-third-party = [
+  'gt4py'
+]
+lines-after-imports = 2
+
+[tool.ruff.lint.mccabe]
+max-complexity = 15
+
+[tool.setuptools.dynamic]
+version = {attr = 'icon4py.model.atmosphere.subgrid_scale_physics.microphysics.__init__.__version__'}
+
+[tool.setuptools.package-data]
+'icon4py.model.atmosphere.subgrid_scale_physics.microphysics' = ['py.typed']

model/atmosphere/subgrid_scale_physics/microphysics/requirements-dev.txt

@@ -0,0 +1,3 @@
+-r ../../../../base-requirements-dev.txt
+-e ../../../common
+-e .

model/atmosphere/subgrid_scale_physics/microphysics/requirements.txt

@@ -0,0 +1,3 @@
+-r ../../../../base-requirements.txt
+../../../common
+.

model/atmosphere/subgrid_scale_physics/microphysics/src/icon4py/model/atmosphere/subgrid_scale_physics/microphysics/__init__.py

@@ -0,0 +1,32 @@
+# ICON4Py - ICON inspired code in Python and GT4Py
+#
+# Copyright (c) 2022, ETH Zurich and MeteoSwiss
+# All rights reserved.
+#
+# This file is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or any later
+# version. See the LICENSE.txt file at the top-level directory of this
+# distribution for a copy of the license or check <https://www.gnu.org/licenses/>.
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from typing import Final
+
+from packaging import version as pkg_version
+
+
+__all__ = [
+    "__author__",
+    "__copyright__",
+    "__license__",
+    "__version__",
+    "__version_info__",
+]
+__author__: Final = "ETH Zurich and individual contributors"
+__copyright__: Final = "Copyright (c) 2014-2022 ETH Zurich"
+__license__: Final = "GPL-3.0-or-later"
+
+
+__version__: Final = "0.0.6"
+__version_info__: Final = pkg_version.parse(__version__)