CSET 0.1.0__tar.gz

CSET-0.1.0/LICENCE

@@ -0,0 +1,202 @@
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CSET-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: CSET
+Version: 0.1.0
+Summary: Convective Scale Evaluation Tool for evaluation and investigation of regional models.
+Author: Met Office, NIWA
+License: Apache-2.0
+Project-URL: Documentation, https://metoffice.github.io/CSET
+Project-URL: Source, https://github.com/MetOffice/CSET
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Topic :: Scientific/Engineering :: GIS
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENCE
+
+# CSET
+
+CSET is a tool to aid in evaluating regional model configurations. It aims to
+replace the collection of bespoke scripts littering people’s home directories,
+reducing effort wasted on duplicating already existing code. This centralisation
+of diagnostics should also make evaluations more consistent and comparable.
+Development takes place in the CSET repository on GitHub.
+
+Please read [the documentation](https://metoffice.github.io/CSET) to learn more
+about CSET, and how to use it.
+
+## Contributing
+
+Contributions are readily welcomed! To get started with developing CSET visit
+the [Working
+Practices](https://metoffice.github.io/CSET/working-practices/#getting-started)
+section of the documentation.
+
+In addition to reading the working practices, the key
+recommendation is early communication. Open an [issue on
+Github](https://github.com/MetOffice/CSET/issues) with your proposed change or
+addition in the design phase, and then others can provide guidance early.
+
+## Licence
+
+Copyright © 2022-2023 Met Office and contributors.
+
+Licensed under the [Apache License, Version 2.0](LICENCE) (the "License"); You
+may obtain a copy of the License at
+
+<http://www.apache.org/licenses/LICENSE-2.0>
+
+Unless required by applicable law or agreed to in writing, software distributed
+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.

CSET-0.1.0/README.md

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+# CSET
+
+CSET is a tool to aid in evaluating regional model configurations. It aims to
+replace the collection of bespoke scripts littering people’s home directories,
+reducing effort wasted on duplicating already existing code. This centralisation
+of diagnostics should also make evaluations more consistent and comparable.
+Development takes place in the CSET repository on GitHub.
+
+Please read [the documentation](https://metoffice.github.io/CSET) to learn more
+about CSET, and how to use it.
+
+## Contributing
+
+Contributions are readily welcomed! To get started with developing CSET visit
+the [Working
+Practices](https://metoffice.github.io/CSET/working-practices/#getting-started)
+section of the documentation.
+
+In addition to reading the working practices, the key
+recommendation is early communication. Open an [issue on
+Github](https://github.com/MetOffice/CSET/issues) with your proposed change or
+addition in the design phase, and then others can provide guidance early.
+
+## Licence
+
+Copyright © 2022-2023 Met Office and contributors.
+
+Licensed under the [Apache License, Version 2.0](LICENCE) (the "License"); You
+may obtain a copy of the License at
+
+<http://www.apache.org/licenses/LICENSE-2.0>
+
+Unless required by applicable law or agreed to in writing, software distributed
+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.

CSET-0.1.0/pyproject.toml

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+[project]
+name = "CSET"
+version = "0.1.0"
+description = "Convective Scale Evaluation Tool for evaluation and investigation of regional models."
+authors = [{ name = "Met Office" }, { name = "NIWA" }]
+readme = "README.md"
+license = { text = "Apache-2.0" }
+requires-python = ">=3.8"
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Scientific/Engineering :: GIS",
+]
+dependencies = [
+    "numpy",
+    "scitools-iris",
+    "tomli >= 1.1.0 ; python_version < '3.11'",
+    "importlib_resources >= 3.0.0 ; python_version < '3.9'",
+]
+
+[project.urls]
+Documentation = "https://metoffice.github.io/CSET"
+Source = "https://github.com/MetOffice/CSET"
+
+[project.scripts]
+cset = "CSET:main"
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+addopts = ["--import-mode=importlib", "--verbose", "--cov"]
+pythonpath = ["src"]
+filterwarnings = ['ignore::DeprecationWarning:pytest']
+
+[tool.coverage.run]
+branch = true
+relative_files = true
+source = ["src"]
+
+[tool.coverage.report]
+# This should be steadily increased to ~95% as we add more tests.
+fail_under = 80.0
+
+[tool.tox]
+legacy_tox_ini = '''
+[tox]
+requires = tox-conda
+isolated_build = True
+envlist =
+    coverage-clean
+    py310-linux-tests
+    py310-linux-docs
+
+[testenv:py{38,39,310,311}-lock]
+allowlist_externals = cp
+conda_channels = conda-forge
+conda_create_args = --override-channels
+conda_deps =
+    pip
+    conda-lock
+description = Create explicit environment specification conda lock files for CSET dependencies.
+skip_install = true
+setenv =
+    LOCKDIR = {toxinidir}{/}requirements{/}locks{/}
+    TMPFILE = {envtmpdir}{/}environment.yml
+    YMLFILE = {toxinidir}{/}requirements{/}environment.yml
+commands =
+    cp "{env:YMLFILE}" "{env:TMPFILE}"
+    # Hacky script to avoid having to have per-python-version yaml files.
+    python3 -c 'from sys import version_info as v; fh = open("{env:TMPFILE}", "a"); fh.write(f"\n  - python =\{v.major\}.\{v.minor\}\n")'
+    conda-lock --channel conda-forge --kind explicit --file {env:TMPFILE} --platform linux-64 --filename-template "{env:LOCKDIR}{envname}-\{platform\}.txt" {posargs}
+
+[testenv:py{38,39,310,311}-{linux,osx,win}-tests]
+description = Run unit and integration tests with PyTest.
+conda_spec =
+    py38-linux: {toxinidir}{/}requirements{/}locks{/}py38-lock-linux-64.txt
+    py39-linux: {toxinidir}{/}requirements{/}locks{/}py39-lock-linux-64.txt
+    py310-linux: {toxinidir}{/}requirements{/}locks{/}py310-lock-linux-64.txt
+    py311-linux: {toxinidir}{/}requirements{/}locks{/}py311-lock-linux-64.txt
+usedevelop = true
+depends = coverage-clean
+commands = pytest --cov-append {posargs}
+
+[testenv:py{38,39,310,311}-{linux,osx,win}-docs]
+description = Invoke sphinx-build to build the HTML docs.
+conda_spec =
+    py38-linux: {toxinidir}{/}requirements{/}locks{/}py38-lock-linux-64.txt
+    py39-linux: {toxinidir}{/}requirements{/}locks{/}py39-lock-linux-64.txt
+    py310-linux: {toxinidir}{/}requirements{/}locks{/}py310-lock-linux-64.txt
+    py311-linux: {toxinidir}{/}requirements{/}locks{/}py311-lock-linux-64.txt
+usedevelop = true
+commands = sphinx-build -d "docs/build/doctree" docs/source "docs/build/html" --color -W -bhtml {posargs}
+
+[testenv:build-package]
+description = Build sdist and wheel packages.
+deps = build
+skip_install = true
+commands = python3 -m build
+
+[testenv:coverage-clean]
+deps = coverage
+skip_install = true
+commands = coverage erase
+'''

CSET-0.1.0/setup.cfg

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+[flake8]
+max-line-length = 88
+max-complexity = 19
+docstring-convention = numpy
+select = C,D,E,F,W,B,B950
+ignore = 
+	E203,
+	E226,
+	E231,
+	E402,
+	E501,
+	E731,
+	W503,
+	W504
+exclude = 
+	.eggs
+	_build
+	cli.py
+per-file-ignores = 
+	__init__.py: F401
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

CSET-0.1.0/src/CSET/__init__.py

@@ -0,0 +1,65 @@
+# Copyright 2022-2023 Met Office and contributors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+CSET: Convective Scale Evaluation Tool
+"""
+
+import argparse
+import logging
+from pathlib import Path
+
+
+def main():
+    """CLI entrypoint."""
+    parser = argparse.ArgumentParser(
+        prog="cset", description="Convective Scale Evaluation Tool."
+    )
+    parser.add_argument(
+        "--verbose",
+        "-v",
+        action="count",
+        default=0,
+        help="increase output verbosity, may be specified multiple times",
+    )
+    # https://docs.python.org/3/library/argparse.html#sub-commands
+    subparsers = parser.add_subparsers(title="subcommands", dest="subparser")
+
+    # Run operator chain
+    parser_operators = subparsers.add_parser(
+        "operators", help="run a chain of operators"
+    )
+    parser_operators.add_argument("input_file", type=Path, help="input file to read")
+    parser_operators.add_argument("output_file", type=Path, help="output file to write")
+    parser_operators.add_argument(
+        "recipe_file", type=Path, help="recipe file to execute"
+    )
+    parser_operators.set_defaults(func=_run_operators)
+    args = parser.parse_args()
+    # Logging verbosity
+    if args.verbose >= 2:
+        logging.basicConfig(level=logging.DEBUG)
+    elif args.verbose >= 1:
+        logging.basicConfig(level=logging.INFO)
+
+    if args.subparser:
+        args.func(args)
+    else:
+        parser.print_help()
+
+
+def _run_operators(args):
+    from .operators import execute_recipe
+
+    execute_recipe(args.recipe_file, args.input_file, args.output_file)

CSET-0.1.0/src/CSET/__main__.py

@@ -0,0 +1,18 @@
+# Copyright 2022-2023 Met Office and contributors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import sys  # pragma: no cover
+from . import main  # pragma: no cover
+
+sys.exit(main())  # pragma: no cover

CSET-0.1.0/src/CSET/operators/RECIPES/__init__.py

@@ -0,0 +1,25 @@
+# Copyright 2022-2023 Met Office and contributors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+This module has an attribute for each recipe, holding the Path to that recipe.
+"""
+try:
+    from importlib.resources import files
+except ImportError:
+    # importlib has the files API from python 3.9
+    from importlib_resources import files
+import CSET.operators.RECIPES as recipes
+
+extract_instant_air_temp = files(recipes).joinpath("extract_instant_air_temp.toml")

CSET-0.1.0/src/CSET/operators/__init__.py

@@ -0,0 +1,22 @@
+# Copyright 2022-2023 Met Office and contributors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""This subpackage contains all of CSET's operators."""
+from . import RECIPES, constraints, read, write, filters, plot, misc
+from ._internal import execute_recipe
+
+# Stop iris giving a warning whenever it loads something.
+from iris import FUTURE
+
+FUTURE.datum_support = True

CSET-0.1.0/src/CSET/operators/_internal.py

@@ -0,0 +1,121 @@
+# Copyright 2022-2023 Met Office and contributors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Internal functions used to run operators."""
+
+import logging
+from pathlib import Path
+
+try:
+    import tomllib
+except ModuleNotFoundError:
+    # tomllib is in standard library from 3.11.
+    import tomli as tomllib
+
+import CSET.operators
+
+
+def get_operator(name: str):
+    """
+    Gets an operator by its name.
+
+    Parameters
+    ----------
+    name: str
+        The name of the desired operator.
+
+    Returns
+    -------
+    function
+        The named operator.
+
+    Raises
+    ------
+    ValueError
+        If name is not an operator.
+
+    Examples
+    --------
+    >>> CSET.operators.get_operator("read.read_cubes")
+    <function read_cubes at 0x7fcf9353c8b0>
+    """
+
+    try:
+        name_sections = name.split(".")
+        operator = CSET.operators
+        for section in name_sections:
+            operator = getattr(operator, section)
+        if callable(operator):
+            return operator
+        else:
+            raise AttributeError
+    except (AttributeError, TypeError):
+        raise ValueError(f"Unknown operator: {name}")
+
+
+def execute_recipe(recipe_file: Path, input_file: Path, output_file: Path) -> None:
+    """Parses and executes a recipe file.
+
+    Parameters
+    ----------
+    recipe_file: Path
+        Pathlike to a configuration file indicating the operators that need
+        running.
+
+    input_file: Path
+        Pathlike to netCDF (or something else that iris read) file to be used as
+        input.
+
+    output_file: Path
+        Pathlike indicating desired location of output.
+
+    Raises
+    ------
+    FileNotFoundError
+        The recipe or input file cannot be found.
+
+    ValueError
+        The recipe file is not well formed.
+    """
+
+    def step_parser(step, step_io, output_file_path: Path) -> str:
+        if "input" in step:
+            if type(step["input"]) == dict:
+                logging.debug(f"Recursing into input: {step['input']}")
+                step_io = step_parser(step["input"], step_io, output_file_path)
+            else:
+                step_io = step["input"]
+        kwargs = {}
+        if "args" in step:
+            for key in step["args"].keys():
+                if type(step["args"][key]) == dict:
+                    logging.debug(f"Recursing into args: {step['args']}")
+                    kwargs[key] = step_parser(
+                        step["args"][key], step_io, output_file_path
+                    )
+                elif step["args"][key] == "MAGIC_OUTPUT_PATH":
+                    kwargs[key] = output_file_path
+                else:
+                    kwargs[key] = step["args"][key]
+        operator = get_operator(step["operator"])
+        logging.info(f"operator = {step['operator']}")
+        logging.debug(f"step_input = {step_io}")
+        logging.debug(f"args = {kwargs}")
+        return operator(step_io, **kwargs)
+
+    with open(recipe_file, "rb") as f:
+        recipe = tomllib.load(f)
+    step_io = input_file
+    for step in recipe["steps"]:
+        step_io = step_parser(step, step_io, output_file)