Merge pull request #933 from FlorianDeconinck/pyMoist_setup

`pyMoist` setup & stub code

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache
+*.egg-info/

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/.pre-commit-config.yaml

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+default_language_version:
+  python: python3
+
+files: pyMoist
+
+repos:
+-   repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+    - id: black
+      additional_dependencies: ["click==8.0.4"]
+
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.4.2
+    hooks:
+    - id: isort
+      args: ["--profile", "black"]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.4.1
+    hooks:
+    - id: mypy
+      name: mypy-pyMoist
+      args: [
+        --ignore-missing-imports,
+        "--follow-imports=normal",
+        --namespace-packages,
+        --no-strict-optional,
+        --warn-unreachable,
+        --explicit-package-bases,
+      ]
+      additional_dependencies: [types-PyYAML]
+      files: pyMoist
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    - id: check-toml
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+    - id: flake8
+      name: flake8
+      language_version: python3
+      args: [
+        "--exclude=docs",
+        "--ignore=W503,E302,E203,F841",
+        "--max-line-length=88"
+      ]
+      exclude: |
+        (?x)^(
+        .*/__init__.py |
+        )$
+    - id: flake8
+      name: flake8 __init__.py files
+      files: "__init__.py"
+      # ignore unused import error in __init__.py files
+      args: [
+        "--exclude=docs",
+        "--ignore=W503,E302,E203,F841,F401",
+        "--max-line-length=88",]

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/README.md

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+# pyMoist
+
+`pyMoist` is the [NDSL](https://github.com/NOAA-GFDL/NDSL) version of the NASA GMAO's GEOS Moist physics and it's required interface to GEOS.
+
+## Testing
+
+The `tests/savepoint` folder contains the numerical regression testing that served to port the code from the original Fortran. It tests that the difference from original Fortran is minimal.
+
+Note: bit to bit equivalence is not possible considering the targeted hardware and the change of compiled language (NDSL uses C).
+
+## Interface
+
+The `interface` sub-directory contain the three-way bridge to and from GEOS.
+
+## Develop
+
+- Run `pre-commit run --all-files` before comitting for code guidelines coherency.

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/interface/README.md

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+# Interface between GEOS and pyMoist
+
+This is the `cffi` based interface between the GEOS Moist grid component and the `pyMoist` NDSL numerical code.

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/radiation_coupling.py

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+from ndsl import QuantityFactory, StencilFactory
+from ndsl.constants import X_DIM, Y_DIM, Z_DIM
+
+
+def _fix_up_clouds_stencil():
+    pass
+
+
+def _radcouple_stencil():
+    pass
+
+
+class RadiationCoupling:
+    def __init__(
+        self,
+        stencil_factory: StencilFactory,
+        quantity_factory: QuantityFactory,
+        do_qa: bool,
+    ) -> None:
+        self._fix_up_clouds = stencil_factory.from_dims_halo(
+            func=_fix_up_clouds_stencil, compute_dims=[X_DIM, Y_DIM, Z_DIM]
+        )
+        self._radcouple = stencil_factory.from_dims_halo(
+            func=_radcouple_stencil, compute_dims=[X_DIM, Y_DIM, Z_DIM]
+        )
+        self.do_qa = do_qa
+
+    def __call__(self) -> None:
+        self._fix_up_clouds()
+        self._radcouple()
+        if self.do_qa:
+            pass

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/pyMoist/wrapper.py

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+"""
+Wraps pyMoist for GEOS interface use.
+"""

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/setup.cfg

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+[bumpversion]
+current_version = 0.2.0
+commit = True
+
+[bdist_wheel]
+universal = 1
+
+[flake8] # WARNING: This configuration is duplicated in pre-commit-config.yaml due to pre-config lack of working dir
+exclude = docs
+ignore = W503,E302,E203,F841
+max-line-length = 88
+
+[aliases]
+
+[tool:isort]
+line_length = 88
+force_grid_wrap = 0
+include_trailing_comma = true
+multi_line_output = 3
+use_parentheses = true
+lines_after_imports = 2
+default_section = THIRDPARTY
+sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+known_first_party = pyMoist,ndsl
+known_third_party = f90nml,pytest,xarray,numpy,mpi4py,gt4py
+
+[mypy] # WARNING: This configuration is duplicated in pre-commit-config.yaml due to pre-config lack of working dir
+ignore_missing_imports = True
+follow_imports = normal
+namespace_packages = True
+strict_optional = False
+warn_unreachable = True
+explicit_package_bases = True
+
+[coverage:run]
+parallel = true
+branch = true
+omit =
+        tests/*
+        *gt_cache*
+        .dacecache*
+        __init__.py
+source_pkgs = pyMoist

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/setup.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""pyMoist is the NDSL version of GEOS Moist physics."""
+
+from setuptools import find_namespace_packages, setup
+
+
+with open("README.md", encoding="utf-8") as readme_file:
+    readme = readme_file.read()
+
+test_requirements = ["pytest", "pytest-subtests", "serialbox", "coverage"]
+ndsl_requirements = ["ndsl @ git+https://github.com/NOAA-GFDL/NDSL.git@2024.04.00"]
+develop_requirements = test_requirements + ndsl_requirements + ["pre-commit"]
+
+extras_requires = {
+    "test": test_requirements,
+    "ndsl": ndsl_requirements,
+    "develop": develop_requirements,
+}
+
+setup(
+    author="NASA",
+    author_email="florian.g.deconinck@nasa.gov",
+    python_requires=">=3.11",
+    classifiers=[
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: Apache 2 License",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3.11",
+    ],
+    description=("pyMoist is the NDSL version of NASA GMAO's GEOS Moist physics."),
+    install_requires=[],
+    extras_require=extras_requires,
+    license="BSD license",
+    long_description=readme,
+    include_package_data=True,
+    name="pyMoist",
+    packages=find_namespace_packages(include=["pyMoist", "pyMoist.*"]),
+    setup_requires=[],
+    test_suite="tests",
+    url="https://github.com/NOAA-GFDL/pyFV3",
+    version="0.0.0",
+    zip_safe=False,
+)

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/conftest.py

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+import savepoint
+
+import ndsl.stencils.testing.conftest
+from ndsl.stencils.testing.conftest import *  # noqa: F403,F401
+
+
+# Point to an __init__.py where all the TestX are improted
+ndsl.stencils.testing.conftest.translate = savepoint  # type: ignore

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/savepoint/__init__.py

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+from .translate_radiation_coupling import TranslateRadiationCoupling

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/savepoint/translate_radiation_coupling.py

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+from ndsl import Namelist, StencilFactory
+from ndsl.stencils.testing.translate import TranslateFortranData2Py
+from pyMoist.radiation_coupling import RadiationCoupling
+
+
+class TranslateRadiationCoupling(TranslateFortranData2Py):
+    def __init__(
+        self,
+        grid,
+        namelist: Namelist,
+        stencil_factory: StencilFactory,
+    ):
+        super().__init__(grid, stencil_factory)
+        self.compute_func = RadiationCoupling(  # type: ignore
+            self.stencil_factory,
+            self.grid.quantity_factory,
+            do_qa=namelist.do_qa,
+        )
+
+        # ADAPT BELOW TO INPUTS
+        #
+        # fillq_info = self.grid.compute_dict()
+        # fillq_info["serialname"] = "fq"
+        # self.in_vars["data_vars"] = {
+        #     "mass": self.grid.compute_dict(),
+        #     "q": self.grid.compute_dict(),
+        #     "fillq": fillq_info,
+        # }
+        # self.out_vars = {
+        #     "fillq": fillq_info,
+        #     "q": self.grid.compute_dict(),
+        # }
+
+    def compute_from_storage(self, inputs):
+        self.compute_func(**inputs)
+        return inputs

GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSmoist_GridComp/pyMoist/tests/test_translate.py

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+from ndsl.stencils.testing.test_translate import *  # noqa: F403,F401