From d9305cb8bbd036417cd7eb3d521867c2bb810abd Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Fri, 28 Oct 2022 14:17:10 +0100 Subject: [PATCH 01/30] Made a very bare bones start to vr_run function --- virtual_rainforest/main.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 virtual_rainforest/main.py diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py new file mode 100644 index 000000000..0d934600f --- /dev/null +++ b/virtual_rainforest/main.py @@ -0,0 +1,18 @@ +"""TODO - WRITE DOC STRING DESCRIBING MAIN FUNCTION.""" + +from typing import Union + +from virtual_rainforest.core.config import validate_config +from virtual_rainforest.core.logger import LOGGER + + +def vr_run( + cfg_paths: Union[str, list[str]], output_folder: str, out_file_name: str +) -> None: + """TODO - DOCSSTRING FOR FUNCTION.""" + + config = validate_config(cfg_paths, output_folder, out_file_name) + + print(config) + + LOGGER.info("Virtual rainforest model run completed!") From cf8b23034547c414e7b19e5be9bae253a065dde1 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 1 Nov 2022 11:53:13 +0000 Subject: [PATCH 02/30] Wrote actual docstrings for the main function and script --- virtual_rainforest/main.py | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 0d934600f..6f969a682 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -1,4 +1,8 @@ -"""TODO - WRITE DOC STRING DESCRIBING MAIN FUNCTION.""" +"""Defines the function used to run a full simulation of the model. + +As well as setting up the function to run the overall virtual rainforest simulation, +this script also defines the command line entry points for the model. +""" from typing import Union @@ -9,10 +13,23 @@ def vr_run( cfg_paths: Union[str, list[str]], output_folder: str, out_file_name: str ) -> None: - """TODO - DOCSSTRING FOR FUNCTION.""" + """Perform a virtual rainforest simulation. + + This is a high-level function that runs a virtual rainforest simulation. At the + moment this is fairly limited, and just involves validating an input configuration. + Down the line this should be extended to encompass far more steps. + + Args: + cfg_paths: Set of paths to configuration files + output_folder: Folder to save combined configuration to + out_file_name: Name for the combined configuration file + """ config = validate_config(cfg_paths, output_folder, out_file_name) print(config) LOGGER.info("Virtual rainforest model run completed!") + + +# def _vr_run_cli From c9ea1e94a37779abba4ce00980d07398533d1514 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Fri, 4 Nov 2022 07:52:48 +0000 Subject: [PATCH 03/30] Added TODOs to vr_main function --- virtual_rainforest/main.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 6f969a682..192033a70 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -10,6 +10,7 @@ from virtual_rainforest.core.logger import LOGGER +# TODO - Add tests for this function def vr_run( cfg_paths: Union[str, list[str]], output_folder: str, out_file_name: str ) -> None: @@ -27,9 +28,19 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - print(config) + # TODO - Add in additional model details + + # TODO - SELECT MODELS TO BE RUN + + # TODO - Save model state + + # TODO - Add timing loop + # TODO - Find models to update + # TODO - Solve models to steady state + # TODO - Save model state LOGGER.info("Virtual rainforest model run completed!") + print(config) -# def _vr_run_cli +# TODO - Define command line entry point From 6cdfe8fd2ffc87ad3f72419f5b08d461e3557ead Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Fri, 4 Nov 2022 09:53:09 +0000 Subject: [PATCH 04/30] Updating poetry lock to new format --- poetry.lock | 757 ++++++++++++++++++++++++++-------------------------- 1 file changed, 379 insertions(+), 378 deletions(-) diff --git a/poetry.lock b/poetry.lock index 03994750d..74b41099e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -16,7 +16,7 @@ python-versions = "*" [[package]] name = "asttokens" -version = "2.0.8" +version = "2.1.0" description = "Annotate AST trees with source code positions" category = "dev" optional = false @@ -55,7 +55,7 @@ Sphinx = ">=2.2,<6.0" [[package]] name = "babel" -version = "2.10.3" +version = "2.11.0" description = "Internationalization utilities" category = "dev" optional = false @@ -145,15 +145,15 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.5" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" [[package]] name = "contourpy" -version = "1.0.5" +version = "1.0.6" description = "Python library for calculating contours of 2D quadrilateral grids" category = "dev" optional = false @@ -164,7 +164,7 @@ numpy = ">=1.16" [package.extras] bokeh = ["bokeh", "selenium"] -docs = ["docutils (<0.18)", "sphinx", "sphinx-rtd-theme"] +docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"] test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"] test-minimal = ["pytest"] test-no-codebase = ["Pillow", "matplotlib", "pytest"] @@ -249,7 +249,7 @@ python-versions = ">=3.6" [[package]] name = "exceptiongroup" -version = "1.0.0rc9" +version = "1.0.1" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false @@ -260,7 +260,7 @@ test = ["pytest (>=6)"] [[package]] name = "executing" -version = "1.1.1" +version = "1.2.0" description = "Get the currently executing AST node of a frame, and other information" category = "dev" optional = false @@ -319,7 +319,7 @@ pydocstyle = ">=2.1" [[package]] name = "fonttools" -version = "4.37.4" +version = "4.38.0" description = "Tools to manipulate font files" category = "dev" optional = false @@ -341,18 +341,19 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "greenlet" -version = "1.1.3.post0" +version = "2.0.0.post0" description = "Lightweight in-process concurrent programming" category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["Sphinx"] +docs = ["Sphinx", "docutils (<0.18)"] +test = ["faulthandler", "objgraph"] [[package]] name = "hypothesis" -version = "6.56.3" +version = "6.56.4" description = "A library for property-based testing" category = "dev" optional = false @@ -360,7 +361,7 @@ python-versions = ">=3.7" [package.dependencies] attrs = ">=19.2.0" -exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} +exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""} sortedcontainers = ">=2.1.0,<3.0.0" [package.extras] @@ -381,7 +382,7 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2022.5)"] [[package]] name = "identify" -version = "2.5.6" +version = "2.5.8" description = "File identification library for Python" category = "dev" optional = false @@ -432,11 +433,11 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.16.0" +version = "6.17.0" description = "IPython Kernel for Jupyter" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] appnope = {version = "*", markers = "platform_system == \"Darwin\""} @@ -452,11 +453,12 @@ tornado = ">=6.1" traitlets = ">=5.1.0" [package.extras] -test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=6.0)", "pytest-cov", "pytest-timeout"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-cov", "pytest-timeout"] [[package]] name = "ipython" -version = "8.5.0" +version = "8.6.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -477,9 +479,9 @@ stack-data = "*" traitlets = ">=5" [package.extras] -all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"] +all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.20)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] black = ["black"] -doc = ["Sphinx (>=1.3)"] +doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] nbformat = ["nbformat"] @@ -487,7 +489,7 @@ notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] -test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] +test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.20)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] [[package]] name = "isort" @@ -534,7 +536,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" -version = "4.16.0" +version = "4.17.0" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -574,7 +576,7 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma [[package]] name = "jupyter-client" -version = "7.4.3" +version = "7.4.4" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -658,7 +660,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.6.1" +version = "3.6.2" description = "Python plotting package" category = "dev" optional = false @@ -952,7 +954,7 @@ python-versions = "*" [[package]] name = "pillow" -version = "9.2.0" +version = "9.3.0" description = "Python Imaging Library (Fork)" category = "dev" optional = false @@ -1021,7 +1023,7 @@ virtualenv = ">=20.0.8" [[package]] name = "prompt-toolkit" -version = "3.0.31" +version = "3.0.32" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -1173,7 +1175,7 @@ diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyrsistent" -version = "0.18.1" +version = "0.19.2" description = "Persistent/Functional/Immutable data structures" category = "main" optional = false @@ -1181,7 +1183,7 @@ python-versions = ">=3.7" [[package]] name = "pytest" -version = "7.1.3" +version = "7.2.0" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -1190,11 +1192,11 @@ python-versions = ">=3.7" [package.dependencies] attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" -py = ">=1.8.2" -tomli = ">=1.0.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] @@ -1270,7 +1272,7 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.5" +version = "2022.6" description = "World timezone definitions, modern and historical" category = "dev" optional = false @@ -1323,7 +1325,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] -name = 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From: Jacob Cook Date: Mon, 7 Nov 2022 10:31:14 +0000 Subject: [PATCH 05/30] Removed outstanding config OSError --- tests/test_config.py | 2 +- virtual_rainforest/core/config.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_config.py b/tests/test_config.py index 59904579a..ad08ce40a 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -47,7 +47,7 @@ def test_check_outfile(caplog, mocker): mock_content.return_value = [Path(f"{file_name}.toml")] # Check that check_outfile fails as expected - with pytest.raises(OSError): + with pytest.raises(config.ConfigurationError): config.check_outfile(".", file_name) expected_log_entries = ( diff --git a/virtual_rainforest/core/config.py b/virtual_rainforest/core/config.py index 08840ee50..cdecaeeaa 100644 --- a/virtual_rainforest/core/config.py +++ b/virtual_rainforest/core/config.py @@ -158,7 +158,7 @@ def check_outfile(output_folder: str, out_file_name: str) -> None: file to out_file_name: The name to save the outputted complete configuration file under Raises: - OSError: If the final output file already exist. + ConfigurationError: If the final output file already exist. """ # Throw critical error if combined output file already exists @@ -168,7 +168,7 @@ def check_outfile(output_folder: str, out_file_name: str) -> None: f"A config file in the specified configuration folder already makes use" f" of the specified output file name ({out_file_name}.toml), this file " f"should either be renamed or deleted!", - OSError, + ConfigurationError, ) return None From 5a086c2663915fa54837c78e9e4a21e66fb8802a Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 7 Nov 2022 12:03:26 +0000 Subject: [PATCH 06/30] Now setup such that models can be found in the registry --- tests/fixtures/model_init_testing.toml | 7 +++++++ virtual_rainforest/__init__.py | 3 +++ virtual_rainforest/main.py | 19 +++++++++++++++++++ 3 files changed, 29 insertions(+) create mode 100644 tests/fixtures/model_init_testing.toml diff --git a/tests/fixtures/model_init_testing.toml b/tests/fixtures/model_init_testing.toml new file mode 100644 index 000000000..b951c563d --- /dev/null +++ b/tests/fixtures/model_init_testing.toml @@ -0,0 +1,7 @@ +# This toml files is used to test the model initialisation. It needs to exist as a +# separate file because the other files (and the default) are setup to configure the +# plants module, which does not have a Model class defined. Once plants has a Model +# class defined this file should be deleted. + +[core] +modules = ["soil"] \ No newline at end of file diff --git a/virtual_rainforest/__init__.py b/virtual_rainforest/__init__.py index d2dfebb47..65317d397 100644 --- a/virtual_rainforest/__init__.py +++ b/virtual_rainforest/__init__.py @@ -5,4 +5,7 @@ from virtual_rainforest.plants import schema # noqa from virtual_rainforest.soil import schema # noqa +# Import models here so that they also end up in the registry +from virtual_rainforest.soil.model import SoilModel # noqa + __version__ = importlib.metadata.version("virtual_rainforest") diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 192033a70..7adeec562 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -4,10 +4,28 @@ this script also defines the command line entry points for the model. """ +from copy import deepcopy from typing import Union from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER +from virtual_rainforest.core.model import MODEL_REGISTRY + + +# TODO - WORK OUT WHAT THIS FUNCTION SHOULD ACTUALLY RETURN +def select_models(model_list: list[str]) -> None: + """TODO - WRITE A SENSIBLE DOCSTRING!""" + + # Remove "core" from model list as it is not a model + if "core" in model_list: + model_list.remove("core") + + # Then look for each model in the registry + for model in model_list: + print(MODEL_REGISTRY[model]) + + # SOME KIND OF ERROR FOR MODEL NOT FOUND + # IDEALLY CATCH THEM ALL IN ONE # TODO - Add tests for this function @@ -31,6 +49,7 @@ def vr_run( # TODO - Add in additional model details # TODO - SELECT MODELS TO BE RUN + select_models(deepcopy(config["core"]["modules"])) # TODO - Save model state From a14bfb5025ffc3e3cea90198a80eb282baec42c9 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 8 Nov 2022 10:05:42 +0000 Subject: [PATCH 07/30] Added check for missing models in registry --- virtual_rainforest/main.py | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 7adeec562..f8115d6d8 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -5,7 +5,7 @@ """ from copy import deepcopy -from typing import Union +from typing import Any, Optional, Union from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER @@ -13,20 +13,32 @@ # TODO - WORK OUT WHAT THIS FUNCTION SHOULD ACTUALLY RETURN -def select_models(model_list: list[str]) -> None: +# SHOULD BE A LIST But question is what type the list should contain +# TODO - ADD TESTS FOR THIS FUNCTION +def select_models(config: dict[str, Any]) -> Optional[list]: """TODO - WRITE A SENSIBLE DOCSTRING!""" + model_list = deepcopy(config["core"]["modules"]) + # Remove "core" from model list as it is not a model if "core" in model_list: model_list.remove("core") + # Make list of missing models, and return an error if necessary + miss_model = [model for model in model_list if model not in MODEL_REGISTRY.keys()] + if miss_model != []: + LOGGER.error( + f"The following models cannot be configured as they are not found in the " + f"registry: {miss_model}" + ) + return None + # Then look for each model in the registry for model in model_list: + # CAN ALL OF THESE BE DONE IN ONE STEP??? + # OR DOES FACTORY HAVE TO BE DONE ONE BY ONE?? print(MODEL_REGISTRY[model]) - # SOME KIND OF ERROR FOR MODEL NOT FOUND - # IDEALLY CATCH THEM ALL IN ONE - # TODO - Add tests for this function def vr_run( @@ -35,8 +47,9 @@ def vr_run( """Perform a virtual rainforest simulation. This is a high-level function that runs a virtual rainforest simulation. At the - moment this is fairly limited, and just involves validating an input configuration. - Down the line this should be extended to encompass far more steps. + moment this involves validating an input configuration, and using this configuration + to generate a set of configured model objects suitable for downstream use. Down the + line this should be extended to encompass far more steps. Args: cfg_paths: Set of paths to configuration files @@ -46,10 +59,12 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - # TODO - Add in additional model details + # TODO - Extract input data required to initialise the models # TODO - SELECT MODELS TO BE RUN - select_models(deepcopy(config["core"]["modules"])) + select_models(config) + + # TODO - Initialise the set of configured models # TODO - Save model state @@ -59,7 +74,6 @@ def vr_run( # TODO - Save model state LOGGER.info("Virtual rainforest model run completed!") - print(config) # TODO - Define command line entry point From 397cca891ae8015339af73d6aa5622ee4db695d9 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 8 Nov 2022 15:25:19 +0000 Subject: [PATCH 08/30] Added steps to configure the models --- virtual_rainforest/core/model.py | 4 ++-- virtual_rainforest/main.py | 34 ++++++++++++++++++++------------ 2 files changed, 23 insertions(+), 15 deletions(-) diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index 0d345bcfe..0c5283c8d 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -12,13 +12,13 @@ from __future__ import annotations from abc import ABC, abstractmethod -from typing import Any, Callable +from typing import Any, Type from numpy import datetime64, timedelta64 from virtual_rainforest.core.logger import LOGGER -MODEL_REGISTRY: dict[str, Callable] = {} +MODEL_REGISTRY: dict[str, Type[BaseModel]] = {} """A registry for different models.""" diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index f8115d6d8..98dcde672 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -9,14 +9,16 @@ from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER -from virtual_rainforest.core.model import MODEL_REGISTRY +from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel -# TODO - WORK OUT WHAT THIS FUNCTION SHOULD ACTUALLY RETURN -# SHOULD BE A LIST But question is what type the list should contain # TODO - ADD TESTS FOR THIS FUNCTION -def select_models(config: dict[str, Any]) -> Optional[list]: - """TODO - WRITE A SENSIBLE DOCSTRING!""" +def select_models(config: dict[str, Any]) -> Optional[list[BaseModel]]: + """TODO - WRITE A SENSIBLE DOCSTRING! + + EXPLAIN BASIC IDEA, THEN WHAT HAPPENS IF IT SUCCEEDS, AND WHAT HAPPENS IF IT FAILS + EXPLAIN ARGS AND RETURNS. + """ model_list = deepcopy(config["core"]["modules"]) @@ -24,6 +26,8 @@ def select_models(config: dict[str, Any]) -> Optional[list]: if "core" in model_list: model_list.remove("core") + LOGGER.info(f"Attempting to configure the following models: {model_list}") + # Make list of missing models, and return an error if necessary miss_model = [model for model in model_list if model not in MODEL_REGISTRY.keys()] if miss_model != []: @@ -31,13 +35,15 @@ def select_models(config: dict[str, Any]) -> Optional[list]: f"The following models cannot be configured as they are not found in the " f"registry: {miss_model}" ) - return None + return None # Then look for each model in the registry - for model in model_list: - # CAN ALL OF THESE BE DONE IN ONE STEP??? - # OR DOES FACTORY HAVE TO BE DONE ONE BY ONE?? - print(MODEL_REGISTRY[model]) + temp_models = [MODEL_REGISTRY[model] for model in model_list] + + # Use factory methods to configure the following models + confd_models = [model.factory(config) for model in temp_models] + + return confd_models # TODO - Add tests for this function @@ -59,10 +65,12 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - # TODO - Extract input data required to initialise the models - # TODO - SELECT MODELS TO BE RUN - select_models(config) + models = select_models(config) + # LOG INFO ON SUCCESS, OR OTHERWISE END THIS PROGRAM + print(models) + + # TODO - Extract input data required to initialise the models # TODO - Initialise the set of configured models From 1bbd383a4f6bc77039a8004e0a3bc89c7874ae3c Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 9 Nov 2022 08:11:50 +0000 Subject: [PATCH 09/30] Added function docstring --- virtual_rainforest/main.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 98dcde672..019afa639 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -14,10 +14,18 @@ # TODO - ADD TESTS FOR THIS FUNCTION def select_models(config: dict[str, Any]) -> Optional[list[BaseModel]]: - """TODO - WRITE A SENSIBLE DOCSTRING! + """Select the models to be run for a specific virtual rainforest simulation. - EXPLAIN BASIC IDEA, THEN WHAT HAPPENS IF IT SUCCEEDS, AND WHAT HAPPENS IF IT FAILS - EXPLAIN ARGS AND RETURNS. + Based on the configuration this function selects a number of models to configure. + If these models all exist in the model registry and can be configured then this + function returns a list of configured models. Otherwise errors are logged, which + should be handled appropriately downstream. + + Args: + config: The virtual rainforest configuration + + Returns: + confd_models: A set of configured (but not initialised) models """ model_list = deepcopy(config["core"]["modules"]) @@ -65,7 +73,6 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - # TODO - SELECT MODELS TO BE RUN models = select_models(config) # LOG INFO ON SUCCESS, OR OTHERWISE END THIS PROGRAM print(models) From 7ef0455163a91d2e10d28ce195d6382127f00865 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 9 Nov 2022 10:14:00 +0000 Subject: [PATCH 10/30] Split function in two --- virtual_rainforest/main.py | 47 +++++++++++++++++++++++++------------- 1 file changed, 31 insertions(+), 16 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 019afa639..f2ad72dbb 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -5,7 +5,7 @@ """ from copy import deepcopy -from typing import Any, Optional, Union +from typing import Any, Optional, Type, Union from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER @@ -13,23 +13,20 @@ # TODO - ADD TESTS FOR THIS FUNCTION -def select_models(config: dict[str, Any]) -> Optional[list[BaseModel]]: +def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: """Select the models to be run for a specific virtual rainforest simulation. - Based on the configuration this function selects a number of models to configure. - If these models all exist in the model registry and can be configured then this - function returns a list of configured models. Otherwise errors are logged, which + This function looks for models from a list of models, if these models can all be + found in the registry then they are returned. Otherwise an error is logged, which should be handled appropriately downstream. Args: - config: The virtual rainforest configuration + model_list: A list of models to select Returns: - confd_models: A set of configured (but not initialised) models + modules: A set of models to be configured """ - model_list = deepcopy(config["core"]["modules"]) - # Remove "core" from model list as it is not a model if "core" in model_list: model_list.remove("core") @@ -46,12 +43,20 @@ def select_models(config: dict[str, Any]) -> Optional[list[BaseModel]]: return None # Then look for each model in the registry - temp_models = [MODEL_REGISTRY[model] for model in model_list] + modules = [MODEL_REGISTRY[model] for model in model_list] + + return modules - # Use factory methods to configure the following models - confd_models = [model.factory(config) for model in temp_models] - return confd_models +# TODO - ADD TESTS FOR THIS MODULE +def configure_models( + config: dict[str, Any], modules: list[Type[BaseModel]] +) -> Optional[list[BaseModel]]: + """This docstring is wrong?""" + + # Use factory methods to configure the desired models + models_cfd = [model.factory(config) for model in modules] + return models_cfd # TODO - Add tests for this function @@ -73,9 +78,19 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - models = select_models(config) - # LOG INFO ON SUCCESS, OR OTHERWISE END THIS PROGRAM - print(models) + modules = select_models(deepcopy(config["core"]["modules"])) + + if modules is None: + LOGGER.error("Could not find all the desired models, ending the simulation.") + return + else: + LOGGER.info( + "All models found in the registry, now attempting to configure them." + ) + + models_cfd = configure_models(config, modules) + + print(models_cfd) # TODO - Extract input data required to initialise the models From 9d63c39da8fe1533ea9e280303de375c350588f3 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 9 Nov 2022 10:24:57 +0000 Subject: [PATCH 11/30] Wrote a sensible docstring for configure_models --- virtual_rainforest/main.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index f2ad72dbb..ae3d3f122 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -48,11 +48,19 @@ def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: return modules -# TODO - ADD TESTS FOR THIS MODULE +# TODO - ADD TESTS FOR THIS FUNCTION def configure_models( config: dict[str, Any], modules: list[Type[BaseModel]] ) -> Optional[list[BaseModel]]: - """This docstring is wrong?""" + """Configure a set of models for use in a `virtual_rainforest` simulation. + + Args: + config: The full virtual rainforest configuration + modules: A set of models to be configured + + Returns: + models_cfd: A set of configured models + """ # Use factory methods to configure the desired models models_cfd = [model.factory(config) for model in modules] @@ -90,6 +98,8 @@ def vr_run( models_cfd = configure_models(config, modules) + # TODO - DECIDE WHETHER TO CONTINUE HERE + print(models_cfd) # TODO - Extract input data required to initialise the models From 4105791cd456728a9266ff79017ebf74ea0e19e1 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 9 Nov 2022 13:00:30 +0000 Subject: [PATCH 12/30] Switched to raising an exception in vr_run --- virtual_rainforest/core/model.py | 4 ++++ virtual_rainforest/main.py | 9 ++++++--- virtual_rainforest/soil/model.py | 6 +----- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index 0c5283c8d..ea94a35d3 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -22,6 +22,10 @@ """A registry for different models.""" +class InitialisationError(Exception): + """Custom exception class for model initialisation failures.""" + + class BaseModel(ABC): """A superclass for all `vr` models. diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index ae3d3f122..64bfaf125 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -8,8 +8,8 @@ from typing import Any, Optional, Type, Union from virtual_rainforest.core.config import validate_config -from virtual_rainforest.core.logger import LOGGER -from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel +from virtual_rainforest.core.logger import LOGGER, log_and_raise +from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel, InitialisationError # TODO - ADD TESTS FOR THIS FUNCTION @@ -89,7 +89,10 @@ def vr_run( modules = select_models(deepcopy(config["core"]["modules"])) if modules is None: - LOGGER.error("Could not find all the desired models, ending the simulation.") + log_and_raise( + "Could not find all the desired models, ending the simulation.", + InitialisationError, + ) return else: LOGGER.info( diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index c7862acd3..f42e898a3 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -12,11 +12,7 @@ class to be usable to simulate the soil. from pint import Quantity from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import BaseModel - - -class InitialisationError(Exception): - """Custom exception class for model initialisation failures.""" +from virtual_rainforest.core.model import BaseModel, InitialisationError class SoilModel(BaseModel, model_name="soil"): From 77e3dab0976b8da23391756ae7caa12b37c7b457 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 9 Nov 2022 15:44:05 +0000 Subject: [PATCH 13/30] Added test for select_models function --- poetry.lock | 14 +------- tests/test_main.py | 70 ++++++++++++++++++++++++++++++++++++++ virtual_rainforest/main.py | 3 +- 3 files changed, 73 insertions(+), 14 deletions(-) create mode 100644 tests/test_main.py diff --git a/poetry.lock b/poetry.lock index 83b86c6ae..5d9a03516 100644 --- a/poetry.lock +++ b/poetry.lock @@ -215,14 +215,6 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "doctestfn" -version = "1.0.3" -description = "Run doctests for a single function" -category = "dev" -optional = false -python-versions = ">=3.6" - [[package]] name = "docutils" version = "0.17.1" @@ -1764,7 +1756,7 @@ testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools" [metadata] lock-version = "1.1" python-versions = ">=3.9,<3.12" -content-hash = "938ab909c3d78e7f33351ef8254f83dcd361f3b78da29b5beddf149a78f17980" +content-hash = "10a047110b22f122cabbe022d6e18184405fecd0c01f20811e3dcdaa33cc2e58" [metadata.files] alabaster = [ @@ -2059,10 +2051,6 @@ distlib = [ {file = "distlib-0.3.6-py2.py3-none-any.whl", hash = "sha256:f35c4b692542ca110de7ef0bea44d73981caeb34ca0b9b6b2e6d7790dda8f80e"}, {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"}, ] -doctestfn = [ - {file = "doctestfn-1.0.3-py3-none-any.whl", hash = "sha256:bfac02b7912ce0c77e34f329bdf9ac71caea4d274056abcd03328a22d6bbf1df"}, - {file = "doctestfn-1.0.3.tar.gz", hash = "sha256:baca4d0fde8b79e1c32e10425f20773b796ffb9226a313c4fa31761feb95b8a1"}, -] docutils = [ {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"}, {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"}, diff --git a/tests/test_main.py b/tests/test_main.py new file mode 100644 index 000000000..fdfbcef3a --- /dev/null +++ b/tests/test_main.py @@ -0,0 +1,70 @@ +"""Test module for main.py (and associated functionality). + +This module tests both the main simulation function `vr_run` and the other functions +defined in main.py that it calls. +""" + +from logging import ERROR, INFO + +import pytest + +from virtual_rainforest.core.model import BaseModel +from virtual_rainforest.main import select_models + +from .conftest import log_check + + +@pytest.mark.parametrize( + "model_list,no_models,expected_log_entries", + [ + ( + ["soil"], # valid input + 1, + ( + ( + INFO, + "Attempting to configure the following models: ['soil']", + ), + ), + ), + ( + ["soil", "core"], + 1, + ( + ( + INFO, + "Attempting to configure the following models: ['soil']", + ), + ), + ), + ( + ["soil", "freshwater"], # Model that hasn't been defined + 0, + ( + ( + INFO, + "Attempting to configure the following models: ['soil', " + "'freshwater']", + ), + ( + ERROR, + "The following models cannot be configured as they are not found in" + " the registry: ['freshwater']", + ), + ), + ), + ], +) +def test_select_models(caplog, model_list, no_models, expected_log_entries): + """Test the model selecting function.""" + + models = select_models(model_list) + + log_check(caplog, expected_log_entries) + + # Finally check that output is as expected + if no_models > 0: + assert len(models) == no_models + assert all([type(model) == type(BaseModel) for model in models]) + else: + assert models is None diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 64bfaf125..a691ab2e7 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -12,7 +12,6 @@ from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel, InitialisationError -# TODO - ADD TESTS FOR THIS FUNCTION def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: """Select the models to be run for a specific virtual rainforest simulation. @@ -102,6 +101,8 @@ def vr_run( models_cfd = configure_models(config, modules) # TODO - DECIDE WHETHER TO CONTINUE HERE + # IS THIS A POINT FOR A TRY, EXPECT, FINALLY? + # NEED TO CHECK AT A LOWER LEVEL TO SEE IF ERRORS CAN BE BETTER HANDLED print(models_cfd) From d29b752c7463c06acb949cd72cc08212fe71848d Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Thu, 10 Nov 2022 10:43:19 +0000 Subject: [PATCH 14/30] Rethought soil model initilisation error handeling --- tests/test_models.py | 24 +++++++++-------- virtual_rainforest/main.py | 12 ++++----- virtual_rainforest/soil/model.py | 44 +++++++++++++++++--------------- 3 files changed, 43 insertions(+), 37 deletions(-) diff --git a/tests/test_models.py b/tests/test_models.py index 1dcc1d50b..5b86b1e56 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -4,14 +4,13 @@ define models based on the class defined in model.py """ -from contextlib import nullcontext as does_not_raise -from logging import CRITICAL, ERROR, INFO, WARNING +from logging import ERROR, INFO, WARNING import pytest from numpy import datetime64, timedelta64 from virtual_rainforest.core.model import BaseModel -from virtual_rainforest.soil.model import InitialisationError, SoilModel +from virtual_rainforest.soil.model import SoilModel from .conftest import log_check @@ -103,14 +102,14 @@ class NewSoilModel(BaseModel, model_name="soil"): @pytest.mark.parametrize( - "config,raises,expected_log_entries", + "config,valid,expected_log_entries", [ ( {}, - pytest.raises(InitialisationError), + False, ( ( - CRITICAL, + ERROR, "Configuration is missing information required to initialise the " "soil model. The first missing key is 'core'", ), @@ -125,7 +124,7 @@ class NewSoilModel(BaseModel, model_name="soil"): }, "soil": {"no_layers": 2}, }, - does_not_raise(), + True, ( ( INFO, @@ -136,11 +135,14 @@ class NewSoilModel(BaseModel, model_name="soil"): ), ], ) -def test_generate_soil_model(caplog, config, raises, expected_log_entries): +def test_generate_soil_model(caplog, config, valid, expected_log_entries): """Test that the function to initialise the soil model behaves as expected.""" - # Check whether initialising the model fails as expected - with raises: - model = SoilModel.factory(config) + + # Check whether model is initialised (or not) as expected + model = SoilModel.factory(config) + if valid is False: + assert model is None + else: assert model.no_layers == config["soil"]["no_layers"] # Final check that expected logging entries are produced diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index a691ab2e7..59034f764 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -49,8 +49,8 @@ def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: # TODO - ADD TESTS FOR THIS FUNCTION def configure_models( - config: dict[str, Any], modules: list[Type[BaseModel]] -) -> Optional[list[BaseModel]]: + config: dict[str, Any], model_list: list[Type[BaseModel]] +) -> list[BaseModel]: """Configure a set of models for use in a `virtual_rainforest` simulation. Args: @@ -62,7 +62,7 @@ def configure_models( """ # Use factory methods to configure the desired models - models_cfd = [model.factory(config) for model in modules] + models_cfd = [model.factory(config) for model in model_list] return models_cfd @@ -85,9 +85,9 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - modules = select_models(deepcopy(config["core"]["modules"])) + model_list = select_models(deepcopy(config["core"]["modules"])) - if modules is None: + if model_list is None: log_and_raise( "Could not find all the desired models, ending the simulation.", InitialisationError, @@ -98,7 +98,7 @@ def vr_run( "All models found in the registry, now attempting to configure them." ) - models_cfd = configure_models(config, modules) + models_cfd = configure_models(config, model_list) # TODO - DECIDE WHETHER TO CONTINUE HERE # IS THIS A POINT FOR A TRY, EXPECT, FINALLY? diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index f42e898a3..e3b04e859 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -6,13 +6,13 @@ class to be usable to simulate the soil. from __future__ import annotations -from typing import Any +from typing import Any, Optional from numpy import timedelta64 from pint import Quantity -from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import BaseModel, InitialisationError +from virtual_rainforest.core.logger import LOGGER +from virtual_rainforest.core.model import BaseModel class SoilModel(BaseModel, model_name="soil"): @@ -46,19 +46,20 @@ def __init__(self, update_interval: timedelta64, no_layers: int, **kwargs: Any): self._repr.append("no_layers") @classmethod - def factory(cls, config: dict[str, Any]) -> SoilModel: + def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: """Factory function to initialise the soil model. This function unpacks the relevant information from the configuration file, and - then uses it to initialise the model. + then uses it to initialise the model. If any information from the config is + invalid rather than returning an initialised model instance None is returned. Args: config: The complete (and validated) virtual rainforest configuration. - Raises: - InitialisationError: If the information required to initialise the model - either isn't found, or isn't of the correct type. """ + + # Assume input is valid until we learn otherwise + valid_input = True try: raw_interval = Quantity(config["core"]["timing"]["min_time_step"]).to( "minutes" @@ -67,26 +68,29 @@ def factory(cls, config: dict[str, Any]) -> SoilModel: update_interval = timedelta64(int(raw_interval.magnitude), "m") no_layers = config["soil"]["no_layers"] except KeyError as e: - log_and_raise( + valid_input = False + LOGGER.error( f"Configuration is missing information required to initialise the soil " - f"model. The first missing key is {str(e)}.", - InitialisationError, + f"model. The first missing key is {str(e)}." ) except ValueError as e: - log_and_raise( + valid_input = False + LOGGER.error( f"Configuration types appear not to have been properly validated. This " f"problem prevents initialisation of the soil model. The first instance" - f" of this problem is as follows: {str(e)}", - InitialisationError, + f" of this problem is as follows: {str(e)}" ) - # TODO - Add further relevant checks on input here as they become relevant - - LOGGER.info( - "Information required to initialise the soil model successfully extracted." - ) + # TODO - Add further relevant checks on input here as they become necessary - return cls(update_interval, no_layers) + if valid_input: + LOGGER.info( + "Information required to initialise the soil model successfully " + "extracted." + ) + return cls(update_interval, no_layers) + else: + return None # THIS IS BASICALLY JUST A PLACEHOLDER TO DEMONSTRATE HOW THE FUNCTION OVERWRITING # SHOULD WORK From 42d7ca99ded8bd10fe4fd01c42a5cd112650c28a Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Thu, 10 Nov 2022 11:37:53 +0000 Subject: [PATCH 15/30] Validation of core config now logs all errors --- tests/test_config.py | 15 +++++++++++---- virtual_rainforest/core/config.py | 15 +++++++++++++-- 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/tests/test_config.py b/tests/test_config.py index ad08ce40a..2cd2835f3 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -7,7 +7,7 @@ """ from contextlib import nullcontext as does_not_raise -from logging import CRITICAL, INFO +from logging import CRITICAL, ERROR, INFO from pathlib import Path import pytest @@ -366,14 +366,21 @@ def test_extend_with_default(): (), ), ( - {"basybuedb"}, + {"core": {"grid": {"nx": -125, "ny": -10}}}, None, pytest.raises(config.ConfigurationError), ( + ( + ERROR, + "[core][grid][nx]: -125 is less than or equal to the minimum of 0", + ), + ( + ERROR, + "[core][grid][ny]: -10 is less than or equal to the minimum of 0", + ), ( CRITICAL, - "Validation of core configuration files failed: {'basybuedb'} is " - "not of type 'object'", + "Validation of core configuration files failed see above errors", ), ), ), diff --git a/virtual_rainforest/core/config.py b/virtual_rainforest/core/config.py index cdecaeeaa..f05072170 100644 --- a/virtual_rainforest/core/config.py +++ b/virtual_rainforest/core/config.py @@ -309,9 +309,20 @@ def add_core_defaults(config_dict: dict[str, Any]) -> None: ValidatorWithDefaults(core_schema, format_checker=FormatChecker()).validate( config_dict ) - except exceptions.ValidationError as err: + except exceptions.ValidationError: + # Find full set of errors + errors = ValidatorWithDefaults( + core_schema, format_checker=FormatChecker() + ).iter_errors(config_dict) + # Then log all errors in validating core config + for error in errors: + # Construct details of the tag associated with the error + tag = "" + for k in error.path: + tag += f"[{k}]" + LOGGER.error(f"{tag}: {error.message}") log_and_raise( - f"Validation of core configuration files failed: {err.message}", + "Validation of core configuration files failed see above errors", ConfigurationError, ) From f206aea5229838786af331c375c1b85c15df086e Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Thu, 10 Nov 2022 11:55:35 +0000 Subject: [PATCH 16/30] All validation errors for complete schema are now printed --- tests/test_config.py | 15 +++++++++++---- virtual_rainforest/core/config.py | 15 +++++++++++++-- 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/tests/test_config.py b/tests/test_config.py index 2cd2835f3..9d8f9bbe6 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -435,14 +435,21 @@ def test_missing_core_schema(caplog, mocker): (), ), ( - {"basybuedb"}, + {"soil": {"no_layers": -1}}, None, pytest.raises(config.ConfigurationError), ( + ( + ERROR, + "[plants]: 'ftypes' is a required property", + ), + ( + ERROR, + "[soil][no_layers]: -1 is less than or equal to the minimum of 0", + ), ( CRITICAL, - "Validation of configuration files failed: {'basybuedb'} is not of" - " type 'object'", + "Validation of configuration files failed see above errors", ), ), ), @@ -453,7 +460,7 @@ def test_validate_with_defaults( ): """Test that addition of defaults values during configuration works as desired.""" - comb_schema = config.construct_combined_schema(["core", "plants"]) + comb_schema = config.construct_combined_schema(["core", "plants", "soil"]) # Check that find_schema fails as expected with raises: diff --git a/virtual_rainforest/core/config.py b/virtual_rainforest/core/config.py index f05072170..d61bf047e 100644 --- a/virtual_rainforest/core/config.py +++ b/virtual_rainforest/core/config.py @@ -436,9 +436,20 @@ def validate_with_defaults( ValidatorWithDefaults(comb_schema, format_checker=FormatChecker()).validate( config_dict ) - except exceptions.ValidationError as err: + except exceptions.ValidationError: + # Find full set of errors + errors = ValidatorWithDefaults( + comb_schema, format_checker=FormatChecker() + ).iter_errors(config_dict) + # Then log all errors in validating core config + for error in errors: + # Construct details of the tag associated with the error + tag = "" + for k in error.path: + tag += f"[{k}]" + LOGGER.error(f"{tag}: {error.message}") log_and_raise( - f"Validation of configuration files failed: {err.message}", + "Validation of configuration files failed see above errors", ConfigurationError, ) From bb6bee08d90bca4f1b1b054bbf2157cb0476a894 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Thu, 10 Nov 2022 14:29:25 +0000 Subject: [PATCH 17/30] Sorted out model initilisation exceptions --- tests/test_main.py | 90 +++++++++++++++++++++++++++++++- tests/test_models.py | 39 ++++++++------ virtual_rainforest/main.py | 1 - virtual_rainforest/soil/model.py | 34 +++++++----- 4 files changed, 130 insertions(+), 34 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index fdfbcef3a..321738194 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -4,12 +4,12 @@ defined in main.py that it calls. """ -from logging import ERROR, INFO +from logging import CRITICAL, ERROR, INFO import pytest from virtual_rainforest.core.model import BaseModel -from virtual_rainforest.main import select_models +from virtual_rainforest.main import configure_models, select_models from .conftest import log_check @@ -68,3 +68,89 @@ def test_select_models(caplog, model_list, no_models, expected_log_entries): assert all([type(model) == type(BaseModel) for model in models]) else: assert models is None + + +@pytest.mark.parametrize( + "config,output,expected_log_entries", + [ + ( + { # valid config + "soil": {"no_layers": 1}, + "core": {"timing": {"min_time_step": "7 days"}}, + }, + "SoilModel(update_interval = 10080 minutes, no_layers = 1)", + ( + (INFO, "Attempting to configure the following models: ['soil']"), + ( + INFO, + "Information required to initialise the soil model successfully " + "extracted.", + ), + ), + ), + ( + { # missing soil config tag + "soil": {}, + "core": {"timing": {"min_time_step": "7 days"}}, + }, + None, + ( + (INFO, "Attempting to configure the following models: ['soil']"), + ( + ERROR, + "Configuration is missing information required to initialise the " + "soil model. The first missing key is 'no_layers'.", + ), + ), + ), + ( + { # invalid soil config tag + "soil": {"no_layers": -1}, + "core": {"timing": {"min_time_step": "7 days"}}, + }, + None, + ( + (INFO, "Attempting to configure the following models: ['soil']"), + ( + INFO, + "Information required to initialise the soil model successfully " + "extracted.", + ), + ( + CRITICAL, + "There has to be at least one soil layer in the soil model!", + ), + ), + ), + ( + { # min_time_step missing units + "soil": {"no_layers": 1}, + "core": {"timing": {"min_time_step": "7"}}, + }, + None, + ( + (INFO, "Attempting to configure the following models: ['soil']"), + ( + ERROR, + "Configuration types appear not to have been properly validated. " + "This problem prevents initialisation of the soil model. The first " + "instance of this problem is as follows: Cannot convert from " + "'dimensionless' (dimensionless) to 'minute' ([time])", + ), + ), + ), + ], +) +def test_configure_models(caplog, config, output, expected_log_entries): + """Test the function that configures the models.""" + + model_list = select_models(["soil"]) + + models = configure_models(config, model_list) + + if output is None: + assert models == [None] + else: + assert repr(models[0]) == output + + log_check(caplog, expected_log_entries) diff --git a/tests/test_models.py b/tests/test_models.py index 5b86b1e56..1484a3053 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -4,12 +4,13 @@ define models based on the class defined in model.py """ -from logging import ERROR, INFO, WARNING +from contextlib import nullcontext as does_not_raise +from logging import CRITICAL, ERROR, INFO, WARNING import pytest from numpy import datetime64, timedelta64 -from virtual_rainforest.core.model import BaseModel +from virtual_rainforest.core.model import BaseModel, InitialisationError from virtual_rainforest.soil.model import SoilModel from .conftest import log_check @@ -40,46 +41,50 @@ def test_base_model_initialization(caplog, mocker): @pytest.mark.parametrize( - "no_layers,expected_log_entries", + "no_layers,raises,expected_log_entries", [ ( 2, + does_not_raise(), (), ), ( -2, + pytest.raises(InitialisationError), ( ( - ERROR, + CRITICAL, "There has to be at least one soil layer in the soil model!", ), ), ), ( 2.5, + pytest.raises(InitialisationError), ( ( - ERROR, + CRITICAL, "The number of soil layers must be an integer!", ), ), ), ], ) -def test_soil_model_initialization(caplog, no_layers, expected_log_entries): +def test_soil_model_initialization(caplog, no_layers, raises, expected_log_entries): """Test `SoilModel` initialization.""" - # Initialize model - model = SoilModel(timedelta64(1, "W"), no_layers) - - # In cases where it passes then checks that the object has the right properties - assert set(["setup", "spinup", "solve", "cleanup"]).issubset(dir(model)) - assert model.name == "soil" - assert str(model) == "A soil model instance" - assert ( - repr(model) - == f"SoilModel(update_interval = 1 weeks, no_layers = {int(no_layers)})" - ) + with raises: + # Initialize model + model = SoilModel(timedelta64(1, "W"), no_layers) + + # In cases where it passes then checks that the object has the right properties + assert set(["setup", "spinup", "solve", "cleanup"]).issubset(dir(model)) + assert model.name == "soil" + assert str(model) == "A soil model instance" + assert ( + repr(model) + == f"SoilModel(update_interval = 1 weeks, no_layers = {int(no_layers)})" + ) # Final check that expected logging entries are produced log_check(caplog, expected_log_entries) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 59034f764..bc6eefb1f 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -47,7 +47,6 @@ def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: return modules -# TODO - ADD TESTS FOR THIS FUNCTION def configure_models( config: dict[str, Any], model_list: list[Type[BaseModel]] ) -> list[BaseModel]: diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index e3b04e859..3c5252807 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -8,11 +8,11 @@ class to be usable to simulate the soil. from typing import Any, Optional +import pint from numpy import timedelta64 -from pint import Quantity -from virtual_rainforest.core.logger import LOGGER -from virtual_rainforest.core.model import BaseModel +from virtual_rainforest.core.logger import LOGGER, log_and_raise +from virtual_rainforest.core.model import BaseModel, InitialisationError class SoilModel(BaseModel, model_name="soil"): @@ -36,9 +36,14 @@ class SoilModel(BaseModel, model_name="soil"): def __init__(self, update_interval: timedelta64, no_layers: int, **kwargs: Any): if no_layers < 1: - LOGGER.error("There has to be at least one soil layer in the soil model!") + log_and_raise( + "There has to be at least one soil layer in the soil model!", + InitialisationError, + ) elif no_layers != int(no_layers): - LOGGER.error("The number of soil layers must be an integer!") + log_and_raise( + "The number of soil layers must be an integer!", InitialisationError + ) super(SoilModel, self).__init__(update_interval, **kwargs) self.no_layers = int(no_layers) @@ -61,7 +66,7 @@ def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: # Assume input is valid until we learn otherwise valid_input = True try: - raw_interval = Quantity(config["core"]["timing"]["min_time_step"]).to( + raw_interval = pint.Quantity(config["core"]["timing"]["min_time_step"]).to( "minutes" ) # Round raw time interval to nearest minute @@ -73,7 +78,7 @@ def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: f"Configuration is missing information required to initialise the soil " f"model. The first missing key is {str(e)}." ) - except ValueError as e: + except (ValueError, pint.errors.DimensionalityError) as e: valid_input = False LOGGER.error( f"Configuration types appear not to have been properly validated. This " @@ -81,14 +86,15 @@ def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: f" of this problem is as follows: {str(e)}" ) - # TODO - Add further relevant checks on input here as they become necessary - if valid_input: - LOGGER.info( - "Information required to initialise the soil model successfully " - "extracted." - ) - return cls(update_interval, no_layers) + try: + LOGGER.info( + "Information required to initialise the soil model successfully " + "extracted." + ) + return cls(update_interval, no_layers) + except InitialisationError: + return None else: return None From f8ccac5bbef21fcd64d3d65083934c2e9d8a80d4 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 07:43:35 +0000 Subject: [PATCH 18/30] Added a couple of mocked tests of vr_run function --- tests/fixtures/model_init_testing.toml | 7 ---- tests/test_main.py | 52 +++++++++++++++++++++++++- virtual_rainforest/main.py | 16 +++++--- 3 files changed, 60 insertions(+), 15 deletions(-) delete mode 100644 tests/fixtures/model_init_testing.toml diff --git a/tests/fixtures/model_init_testing.toml b/tests/fixtures/model_init_testing.toml deleted file mode 100644 index b951c563d..000000000 --- a/tests/fixtures/model_init_testing.toml +++ /dev/null @@ -1,7 +0,0 @@ -# This toml files is used to test the model initialisation. It needs to exist as a -# separate file because the other files (and the default) are setup to configure the -# plants module, which does not have a Model class defined. Once plants has a Model -# class defined this file should be deleted. - -[core] -modules = ["soil"] \ No newline at end of file diff --git a/tests/test_main.py b/tests/test_main.py index 321738194..2a08bc9f2 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -8,8 +8,8 @@ import pytest -from virtual_rainforest.core.model import BaseModel -from virtual_rainforest.main import configure_models, select_models +from virtual_rainforest.core.model import BaseModel, InitialisationError +from virtual_rainforest.main import configure_models, select_models, vr_run from .conftest import log_check @@ -154,3 +154,51 @@ def test_configure_models(caplog, config, output, expected_log_entries): assert repr(models[0]) == output log_check(caplog, expected_log_entries) + + +def test_vr_run_miss_model(mocker, caplog): + """Test the main `vr_run` function handles missing models correctly.""" + + mock_conf = mocker.patch("virtual_rainforest.main.validate_config") + mock_conf.return_value = {"core": {"modules": ["topsoil"]}} + + with pytest.raises(InitialisationError): + vr_run("tests/fixtures/all_config.toml", ".", "delete_me") + + expected_log_entries = ( + (INFO, "Attempting to configure the following models: ['topsoil']"), + ( + ERROR, + "The following models cannot be configured as they are not found in the " + "registry: ['topsoil']", + ), + (CRITICAL, "Could not find all the desired models, ending the simulation."), + ) + + log_check(caplog, expected_log_entries) + + +def test_vr_run_bad_model(mocker, caplog): + """Test the main `vr_run` function handles bad model configuration correctly.""" + + mock_conf = mocker.patch("virtual_rainforest.main.validate_config") + mock_conf.return_value = {"core": {"modules": ["soil"]}} + mock_cf_mod = mocker.patch("virtual_rainforest.main.configure_models") + mock_cf_mod.return_value = [None] + + with pytest.raises(InitialisationError): + vr_run("tests/fixtures/all_config.toml", ".", "delete_me") + + expected_log_entries = ( + (INFO, "Attempting to configure the following models: ['soil']"), + ( + INFO, + "All models found in the registry, now attempting to configure them.", + ), + ( + CRITICAL, + "Could not configure all the desired models, ending the simulation.", + ), + ) + + log_check(caplog, expected_log_entries) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index bc6eefb1f..a04c7f67e 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -65,7 +65,6 @@ def configure_models( return models_cfd -# TODO - Add tests for this function def vr_run( cfg_paths: Union[str, list[str]], output_folder: str, out_file_name: str ) -> None: @@ -99,11 +98,16 @@ def vr_run( models_cfd = configure_models(config, model_list) - # TODO - DECIDE WHETHER TO CONTINUE HERE - # IS THIS A POINT FOR A TRY, EXPECT, FINALLY? - # NEED TO CHECK AT A LOWER LEVEL TO SEE IF ERRORS CAN BE BETTER HANDLED - - print(models_cfd) + if any(model is None for model in models_cfd): + log_and_raise( + "Could not configure all the desired models, ending the simulation.", + InitialisationError, + ) + return + else: + LOGGER.info( + "All models successfully configured, now attempting to initialise them." + ) # TODO - Extract input data required to initialise the models From 03416c879cfd9ae1b37fb1c1a8da1b05806ba00e Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 10:03:41 +0000 Subject: [PATCH 19/30] Moved error into select models --- tests/test_main.py | 25 ++++++++++++------------- virtual_rainforest/main.py | 25 ++++++++----------------- 2 files changed, 20 insertions(+), 30 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index 2a08bc9f2..01aec3623 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -4,6 +4,7 @@ defined in main.py that it calls. """ +from contextlib import nullcontext as does_not_raise from logging import CRITICAL, ERROR, INFO import pytest @@ -15,11 +16,12 @@ @pytest.mark.parametrize( - "model_list,no_models,expected_log_entries", + "model_list,no_models,raises,expected_log_entries", [ ( ["soil"], # valid input 1, + does_not_raise(), ( ( INFO, @@ -30,6 +32,7 @@ ( ["soil", "core"], 1, + does_not_raise(), ( ( INFO, @@ -40,6 +43,7 @@ ( ["soil", "freshwater"], # Model that hasn't been defined 0, + pytest.raises(InitialisationError), ( ( INFO, @@ -47,7 +51,7 @@ "'freshwater']", ), ( - ERROR, + CRITICAL, "The following models cannot be configured as they are not found in" " the registry: ['freshwater']", ), @@ -55,19 +59,15 @@ ), ], ) -def test_select_models(caplog, model_list, no_models, expected_log_entries): +def test_select_models(caplog, model_list, no_models, raises, expected_log_entries): """Test the model selecting function.""" - models = select_models(model_list) - - log_check(caplog, expected_log_entries) - - # Finally check that output is as expected - if no_models > 0: + with raises: + models = select_models(model_list) assert len(models) == no_models assert all([type(model) == type(BaseModel) for model in models]) - else: - assert models is None + + log_check(caplog, expected_log_entries) @pytest.mark.parametrize( @@ -168,11 +168,10 @@ def test_vr_run_miss_model(mocker, caplog): expected_log_entries = ( (INFO, "Attempting to configure the following models: ['topsoil']"), ( - ERROR, + CRITICAL, "The following models cannot be configured as they are not found in the " "registry: ['topsoil']", ), - (CRITICAL, "Could not find all the desired models, ending the simulation."), ) log_check(caplog, expected_log_entries) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index a04c7f67e..dfc47f792 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -5,14 +5,14 @@ """ from copy import deepcopy -from typing import Any, Optional, Type, Union +from typing import Any, Type, Union from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER, log_and_raise from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel, InitialisationError -def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: +def select_models(model_list: list[str]) -> list[Type[BaseModel]]: """Select the models to be run for a specific virtual rainforest simulation. This function looks for models from a list of models, if these models can all be @@ -22,7 +22,7 @@ def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: Args: model_list: A list of models to select - Returns: + Raises: modules: A set of models to be configured """ @@ -35,13 +35,13 @@ def select_models(model_list: list[str]) -> Optional[list[Type[BaseModel]]]: # Make list of missing models, and return an error if necessary miss_model = [model for model in model_list if model not in MODEL_REGISTRY.keys()] if miss_model != []: - LOGGER.error( + log_and_raise( f"The following models cannot be configured as they are not found in the " - f"registry: {miss_model}" + f"registry: {miss_model}", + InitialisationError, ) - return None - # Then look for each model in the registry + # Then extract each model from the registry modules = [MODEL_REGISTRY[model] for model in model_list] return modules @@ -85,16 +85,7 @@ def vr_run( model_list = select_models(deepcopy(config["core"]["modules"])) - if model_list is None: - log_and_raise( - "Could not find all the desired models, ending the simulation.", - InitialisationError, - ) - return - else: - LOGGER.info( - "All models found in the registry, now attempting to configure them." - ) + LOGGER.info("All models found in the registry, now attempting to configure them.") models_cfd = configure_models(config, model_list) From 10f8a9407c14928cd7215225ba8822d34d1d4505 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 11:02:38 +0000 Subject: [PATCH 20/30] Moved model configure model errors into the function --- tests/test_main.py | 45 ++++++++++++++++++++++++++++---------- virtual_rainforest/main.py | 29 +++++++++++++----------- 2 files changed, 50 insertions(+), 24 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index 01aec3623..9bac425d1 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -71,7 +71,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri @pytest.mark.parametrize( - "config,output,expected_log_entries", + "config,output,raises,expected_log_entries", [ ( { # valid config @@ -79,6 +79,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "core": {"timing": {"min_time_step": "7 days"}}, }, "SoilModel(update_interval = 10080 minutes, no_layers = 1)", + does_not_raise(), ( (INFO, "Attempting to configure the following models: ['soil']"), ( @@ -94,6 +95,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "core": {"timing": {"min_time_step": "7 days"}}, }, None, + pytest.raises(InitialisationError), ( (INFO, "Attempting to configure the following models: ['soil']"), ( @@ -101,6 +103,11 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "Configuration is missing information required to initialise the " "soil model. The first missing key is 'no_layers'.", ), + ( + CRITICAL, + "Could not configure all the desired models, ending the " + "simulation.", + ), ), ), ( @@ -109,6 +116,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "core": {"timing": {"min_time_step": "7 days"}}, }, None, + pytest.raises(InitialisationError), ( (INFO, "Attempting to configure the following models: ['soil']"), ( @@ -120,6 +128,11 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri CRITICAL, "There has to be at least one soil layer in the soil model!", ), + ( + CRITICAL, + "Could not configure all the desired models, ending the " + "simulation.", + ), ), ), ( @@ -128,6 +141,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "core": {"timing": {"min_time_step": "7"}}, }, None, + pytest.raises(InitialisationError), ( (INFO, "Attempting to configure the following models: ['soil']"), ( @@ -137,21 +151,27 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "instance of this problem is as follows: Cannot convert from " "'dimensionless' (dimensionless) to 'minute' ([time])", ), + ( + CRITICAL, + "Could not configure all the desired models, ending the " + "simulation.", + ), ), ), ], ) -def test_configure_models(caplog, config, output, expected_log_entries): +def test_configure_models(caplog, config, output, raises, expected_log_entries): """Test the function that configures the models.""" - model_list = select_models(["soil"]) + with raises: + model_list = select_models(["soil"]) - models = configure_models(config, model_list) + models = configure_models(config, model_list) - if output is None: - assert models == [None] - else: - assert repr(models[0]) == output + if output is None: + assert models == [None] + else: + assert repr(models[0]) == output log_check(caplog, expected_log_entries) @@ -181,9 +201,7 @@ def test_vr_run_bad_model(mocker, caplog): """Test the main `vr_run` function handles bad model configuration correctly.""" mock_conf = mocker.patch("virtual_rainforest.main.validate_config") - mock_conf.return_value = {"core": {"modules": ["soil"]}} - mock_cf_mod = mocker.patch("virtual_rainforest.main.configure_models") - mock_cf_mod.return_value = [None] + mock_conf.return_value = {"core": {"modules": ["soil"]}, "soil": {}} with pytest.raises(InitialisationError): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") @@ -194,6 +212,11 @@ def test_vr_run_bad_model(mocker, caplog): INFO, "All models found in the registry, now attempting to configure them.", ), + ( + ERROR, + "Configuration is missing information required to initialise the soil " + "model. The first missing key is 'timing'.", + ), ( CRITICAL, "Could not configure all the desired models, ending the simulation.", diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index dfc47f792..f0e619d44 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -23,7 +23,7 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: model_list: A list of models to select Raises: - modules: A set of models to be configured + InitialisationError: If one or more models cannot be found in the registry """ # Remove "core" from model list as it is not a model @@ -56,12 +56,19 @@ def configure_models( config: The full virtual rainforest configuration modules: A set of models to be configured - Returns: - models_cfd: A set of configured models + Raises: + InitialisationError: If one or more models cannot be properly configured """ # Use factory methods to configure the desired models models_cfd = [model.factory(config) for model in model_list] + + if any(model is None for model in models_cfd): + log_and_raise( + "Could not configure all the desired models, ending the simulation.", + InitialisationError, + ) + return models_cfd @@ -89,16 +96,12 @@ def vr_run( models_cfd = configure_models(config, model_list) - if any(model is None for model in models_cfd): - log_and_raise( - "Could not configure all the desired models, ending the simulation.", - InitialisationError, - ) - return - else: - LOGGER.info( - "All models successfully configured, now attempting to initialise them." - ) + LOGGER.info( + "All models successfully configured, now attempting to initialise them." + ) + + # This is just a step to pass flake8 checks (DELETE LATER) + print(models_cfd) # TODO - Extract input data required to initialise the models From e2598f7f8516718267fda22c2af625f1a4a6c162 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 14:40:03 +0000 Subject: [PATCH 21/30] Defined FailedModel class --- tests/test_models.py | 4 ++-- virtual_rainforest/core/model.py | 39 ++++++++++++++++++++++++++++++++ virtual_rainforest/main.py | 9 ++++++-- virtual_rainforest/soil/model.py | 10 ++++---- 4 files changed, 53 insertions(+), 9 deletions(-) diff --git a/tests/test_models.py b/tests/test_models.py index 1484a3053..cdda6b87b 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -10,7 +10,7 @@ import pytest from numpy import datetime64, timedelta64 -from virtual_rainforest.core.model import BaseModel, InitialisationError +from virtual_rainforest.core.model import BaseModel, FailedModel, InitialisationError from virtual_rainforest.soil.model import SoilModel from .conftest import log_check @@ -146,7 +146,7 @@ def test_generate_soil_model(caplog, config, valid, expected_log_entries): # Check whether model is initialised (or not) as expected model = SoilModel.factory(config) if valid is False: - assert model is None + assert isinstance(model, FailedModel) else: assert model.no_layers == config["soil"]["no_layers"] diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index ea94a35d3..c80fcc709 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -103,3 +103,42 @@ def __repr__(self) -> str: def __str__(self) -> str: """Inform user what the model type is.""" return f"A {self.name} model instance" + + +# TODO - TEST THIS +class FailedModel(BaseModel, model_name="failed"): + """A class to be returned when a `vr` model fails to be properly constructed.""" + + name = "failed" + + def __init__(self, **kwargs: Any): + # Set to 10000 years to turn update off + update_interval = timedelta64(10000, "Y") + super(FailedModel, self).__init__(update_interval, **kwargs) + + @classmethod + def factory(cls, config: dict[str, Any]) -> FailedModel: + """Factory function informs user that a failed model cannot be configured.""" + + LOGGER.error("Cannot configure a failed model!") + return cls() + + def setup(self) -> None: + """Function to inform user that a failed model cannot be setup.""" + + LOGGER.error("Failed model cannot be setup!") + + def spinup(self) -> None: + """Function to inform user that a failed model cannot be spun up.""" + + LOGGER.error("Failed model cannot be spun up!") + + def solve(self) -> None: + """Function to inform user that a failed model cannot be solved.""" + + LOGGER.error("Failed model cannot be solved!") + + def cleanup(self) -> None: + """Function to inform user that cleanup doesn't work on a failed model.""" + + LOGGER.error("Cleanup doesn't work for failed model!") diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index f0e619d44..21e906faa 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -9,7 +9,12 @@ from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel, InitialisationError +from virtual_rainforest.core.model import ( + MODEL_REGISTRY, + BaseModel, + FailedModel, + InitialisationError, +) def select_models(model_list: list[str]) -> list[Type[BaseModel]]: @@ -63,7 +68,7 @@ def configure_models( # Use factory methods to configure the desired models models_cfd = [model.factory(config) for model in model_list] - if any(model is None for model in models_cfd): + if any([isinstance(model, FailedModel) for model in models_cfd]): log_and_raise( "Could not configure all the desired models, ending the simulation.", InitialisationError, diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index 3c5252807..91d8e8947 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -6,13 +6,13 @@ class to be usable to simulate the soil. from __future__ import annotations -from typing import Any, Optional +from typing import Any, Union import pint from numpy import timedelta64 from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import BaseModel, InitialisationError +from virtual_rainforest.core.model import BaseModel, FailedModel, InitialisationError class SoilModel(BaseModel, model_name="soil"): @@ -51,7 +51,7 @@ def __init__(self, update_interval: timedelta64, no_layers: int, **kwargs: Any): self._repr.append("no_layers") @classmethod - def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: + def factory(cls, config: dict[str, Any]) -> Union[SoilModel, FailedModel]: """Factory function to initialise the soil model. This function unpacks the relevant information from the configuration file, and @@ -94,9 +94,9 @@ def factory(cls, config: dict[str, Any]) -> Optional[SoilModel]: ) return cls(update_interval, no_layers) except InitialisationError: - return None + return FailedModel() else: - return None + return FailedModel() # THIS IS BASICALLY JUST A PLACEHOLDER TO DEMONSTRATE HOW THE FUNCTION OVERWRITING # SHOULD WORK From cde4d179e703f34789a3f12f64fab1e400e0c3ee Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 15:03:27 +0000 Subject: [PATCH 22/30] Added test of FailedModel class --- tests/test_models.py | 35 ++++++++++++++++++++++++++++++++ virtual_rainforest/core/model.py | 15 +++++++------- 2 files changed, 42 insertions(+), 8 deletions(-) diff --git a/tests/test_models.py b/tests/test_models.py index cdda6b87b..da89809e8 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -152,3 +152,38 @@ def test_generate_soil_model(caplog, config, valid, expected_log_entries): # Final check that expected logging entries are produced log_check(caplog, expected_log_entries) + + +# WHAT ELSE TO CHECK +# THAT EACH FUNCTION WARNS THE USER APPROPRIATELY +# CATCH THIS WITH CAPLOG I GUESS +def test_failed_model(caplog): + """Test `FailedModel` initialization and usage.""" + + # Initialise model + model = FailedModel() + + # In cases where it passes then checks that the object has the right properties + assert set(["setup", "spinup", "solve", "cleanup"]).issubset(dir(model)) + assert model.name == "failed" + assert str(model) == "A failed model instance" + assert repr(model) == "FailedModel(update_interval = 320000000000 minutes)" + assert not model.should_update(datetime64("2050-10-28")) + + # Run model functions and check the logging output + model.factory({}) + model.setup() + model.spinup() + model.solve() + model.cleanup() + + expected_log = ( + (WARNING, "Cannot configure a failed model!"), + (WARNING, "Failed model cannot be setup!"), + (WARNING, "Failed model cannot be spun up!"), + (WARNING, "Failed model cannot be solved!"), + (WARNING, "Cleanup doesn't work for failed model!"), + ) + + # Final check that expected (i.e. no) logging entries are produced + log_check(caplog, expected_log) diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index c80fcc709..cc7310bca 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -105,40 +105,39 @@ def __str__(self) -> str: return f"A {self.name} model instance" -# TODO - TEST THIS class FailedModel(BaseModel, model_name="failed"): """A class to be returned when a `vr` model fails to be properly constructed.""" name = "failed" def __init__(self, **kwargs: Any): - # Set to 10000 years to turn update off - update_interval = timedelta64(10000, "Y") + # Set to ~10000 years to turn update off + update_interval = timedelta64(32 * (10**10), "m") super(FailedModel, self).__init__(update_interval, **kwargs) @classmethod def factory(cls, config: dict[str, Any]) -> FailedModel: """Factory function informs user that a failed model cannot be configured.""" - LOGGER.error("Cannot configure a failed model!") + LOGGER.warning("Cannot configure a failed model!") return cls() def setup(self) -> None: """Function to inform user that a failed model cannot be setup.""" - LOGGER.error("Failed model cannot be setup!") + LOGGER.warning("Failed model cannot be setup!") def spinup(self) -> None: """Function to inform user that a failed model cannot be spun up.""" - LOGGER.error("Failed model cannot be spun up!") + LOGGER.warning("Failed model cannot be spun up!") def solve(self) -> None: """Function to inform user that a failed model cannot be solved.""" - LOGGER.error("Failed model cannot be solved!") + LOGGER.warning("Failed model cannot be solved!") def cleanup(self) -> None: """Function to inform user that cleanup doesn't work on a failed model.""" - LOGGER.error("Cleanup doesn't work for failed model!") + LOGGER.warning("Cleanup doesn't work for failed model!") From 5fa88bfbd2dbb009bace5727b49a771a2827a408 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Mon, 14 Nov 2022 15:18:27 +0000 Subject: [PATCH 23/30] Stopped using f-strings in logging --- virtual_rainforest/core/config.py | 7 ++++--- virtual_rainforest/main.py | 2 +- virtual_rainforest/soil/model.py | 12 ++++++------ 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/virtual_rainforest/core/config.py b/virtual_rainforest/core/config.py index d61bf047e..942705cb7 100644 --- a/virtual_rainforest/core/config.py +++ b/virtual_rainforest/core/config.py @@ -320,7 +320,7 @@ def add_core_defaults(config_dict: dict[str, Any]) -> None: tag = "" for k in error.path: tag += f"[{k}]" - LOGGER.error(f"{tag}: {error.message}") + LOGGER.error("%s: %s" % (tag, error.message)) log_and_raise( "Validation of core configuration files failed see above errors", ConfigurationError, @@ -447,7 +447,7 @@ def validate_with_defaults( tag = "" for k in error.path: tag += f"[{k}]" - LOGGER.error(f"{tag}: {error.message}") + LOGGER.error("%s: %s" % (tag, error.message)) log_and_raise( "Validation of configuration files failed see above errors", ConfigurationError, @@ -507,7 +507,8 @@ def validate_config( # Output combined toml file, into the initial config folder LOGGER.info( - f"Saving all configuration details to {output_folder}/{out_file_name}.toml" + "Saving all configuration details to %s/%s.toml" + % (output_folder, out_file_name) ) with open(f"{output_folder}/{out_file_name}.toml", "wb") as toml_file: tomli_w.dump(config_dict, toml_file) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 21e906faa..634c11465 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -35,7 +35,7 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: if "core" in model_list: model_list.remove("core") - LOGGER.info(f"Attempting to configure the following models: {model_list}") + LOGGER.info("Attempting to configure the following models: %s" % model_list) # Make list of missing models, and return an error if necessary miss_model = [model for model in model_list if model not in MODEL_REGISTRY.keys()] diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index 91d8e8947..45a29ee15 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -75,15 +75,15 @@ def factory(cls, config: dict[str, Any]) -> Union[SoilModel, FailedModel]: except KeyError as e: valid_input = False LOGGER.error( - f"Configuration is missing information required to initialise the soil " - f"model. The first missing key is {str(e)}." + "Configuration is missing information required to initialise the soil " + "model. The first missing key is %s." % str(e) ) except (ValueError, pint.errors.DimensionalityError) as e: valid_input = False LOGGER.error( - f"Configuration types appear not to have been properly validated. This " - f"problem prevents initialisation of the soil model. The first instance" - f" of this problem is as follows: {str(e)}" + "Configuration types appear not to have been properly validated. This " + "problem prevents initialisation of the soil model. The first instance" + " of this problem is as follows: %s" % str(e) ) if valid_input: @@ -105,7 +105,7 @@ def factory(cls, config: dict[str, Any]) -> Union[SoilModel, FailedModel]: def setup(self) -> None: """Function to set up the soil model.""" for layer in range(0, self.no_layers): - LOGGER.info(f"Setting up soil layer {layer}") + LOGGER.info("Setting up soil layer %s" % layer) def spinup(self) -> None: """Placeholder function to spin up the soil model.""" From 972ebf3b66d812ba3a02a06f204095bb26b9dd60 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 15 Nov 2022 09:43:49 +0000 Subject: [PATCH 24/30] Using set instead of deepcopying a list --- tests/test_main.py | 20 ++++++++++---------- virtual_rainforest/main.py | 14 ++++++-------- 2 files changed, 16 insertions(+), 18 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index 9bac425d1..3e088a87c 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -25,7 +25,7 @@ ( ( INFO, - "Attempting to configure the following models: ['soil']", + "Attempting to configure the following models: {'soil'}", ), ), ), @@ -36,7 +36,7 @@ ( ( INFO, - "Attempting to configure the following models: ['soil']", + "Attempting to configure the following models: {'soil'}", ), ), ), @@ -47,8 +47,8 @@ ( ( INFO, - "Attempting to configure the following models: ['soil', " - "'freshwater']", + "Attempting to configure the following models: {'freshwater', " + "'soil'}", ), ( CRITICAL, @@ -81,7 +81,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "SoilModel(update_interval = 10080 minutes, no_layers = 1)", does_not_raise(), ( - (INFO, "Attempting to configure the following models: ['soil']"), + (INFO, "Attempting to configure the following models: {'soil'}"), ( INFO, "Information required to initialise the soil model successfully " @@ -97,7 +97,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: ['soil']"), + (INFO, "Attempting to configure the following models: {'soil'}"), ( ERROR, "Configuration is missing information required to initialise the " @@ -118,7 +118,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: ['soil']"), + (INFO, "Attempting to configure the following models: {'soil'}"), ( INFO, "Information required to initialise the soil model successfully " @@ -143,7 +143,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: ['soil']"), + (INFO, "Attempting to configure the following models: {'soil'}"), ( ERROR, "Configuration types appear not to have been properly validated. " @@ -186,7 +186,7 @@ def test_vr_run_miss_model(mocker, caplog): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") expected_log_entries = ( - (INFO, "Attempting to configure the following models: ['topsoil']"), + (INFO, "Attempting to configure the following models: {'topsoil'}"), ( CRITICAL, "The following models cannot be configured as they are not found in the " @@ -207,7 +207,7 @@ def test_vr_run_bad_model(mocker, caplog): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") expected_log_entries = ( - (INFO, "Attempting to configure the following models: ['soil']"), + (INFO, "Attempting to configure the following models: {'soil'}"), ( INFO, "All models found in the registry, now attempting to configure them.", diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 634c11465..9530d00a4 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -4,7 +4,6 @@ this script also defines the command line entry points for the model. """ -from copy import deepcopy from typing import Any, Type, Union from virtual_rainforest.core.config import validate_config @@ -32,14 +31,13 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: """ # Remove "core" from model list as it is not a model - if "core" in model_list: - model_list.remove("core") + model_list_ = set(model_list) - {"core"} - LOGGER.info("Attempting to configure the following models: %s" % model_list) + LOGGER.info("Attempting to configure the following models: %s" % model_list_) # Make list of missing models, and return an error if necessary - miss_model = [model for model in model_list if model not in MODEL_REGISTRY.keys()] - if miss_model != []: + miss_model = [model for model in model_list_ if model not in MODEL_REGISTRY.keys()] + if len(miss_model): log_and_raise( f"The following models cannot be configured as they are not found in the " f"registry: {miss_model}", @@ -47,7 +45,7 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: ) # Then extract each model from the registry - modules = [MODEL_REGISTRY[model] for model in model_list] + modules = [MODEL_REGISTRY[model] for model in model_list_] return modules @@ -95,7 +93,7 @@ def vr_run( config = validate_config(cfg_paths, output_folder, out_file_name) - model_list = select_models(deepcopy(config["core"]["modules"])) + model_list = select_models(config["core"]["modules"]) LOGGER.info("All models found in the registry, now attempting to configure them.") From ec51311f47f0e3c10bcb7e508a6c8e62ef6ac18c Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 15 Nov 2022 10:09:23 +0000 Subject: [PATCH 25/30] Removed FailedModel class --- tests/test_models.py | 51 +++++--------------------------- virtual_rainforest/core/model.py | 38 ------------------------ virtual_rainforest/main.py | 23 +++++++------- virtual_rainforest/soil/model.py | 21 ++++++------- 4 files changed, 29 insertions(+), 104 deletions(-) diff --git a/tests/test_models.py b/tests/test_models.py index da89809e8..14459b0f8 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -10,7 +10,7 @@ import pytest from numpy import datetime64, timedelta64 -from virtual_rainforest.core.model import BaseModel, FailedModel, InitialisationError +from virtual_rainforest.core.model import BaseModel, InitialisationError from virtual_rainforest.soil.model import SoilModel from .conftest import log_check @@ -107,11 +107,11 @@ class NewSoilModel(BaseModel, model_name="soil"): @pytest.mark.parametrize( - "config,valid,expected_log_entries", + "config,raises,expected_log_entries", [ ( {}, - False, + pytest.raises(InitialisationError), ( ( ERROR, @@ -129,7 +129,7 @@ class NewSoilModel(BaseModel, model_name="soil"): }, "soil": {"no_layers": 2}, }, - True, + does_not_raise(), ( ( INFO, @@ -140,50 +140,13 @@ class NewSoilModel(BaseModel, model_name="soil"): ), ], ) -def test_generate_soil_model(caplog, config, valid, expected_log_entries): +def test_generate_soil_model(caplog, config, raises, expected_log_entries): """Test that the function to initialise the soil model behaves as expected.""" # Check whether model is initialised (or not) as expected - model = SoilModel.factory(config) - if valid is False: - assert isinstance(model, FailedModel) - else: + with raises: + model = SoilModel.factory(config) assert model.no_layers == config["soil"]["no_layers"] # Final check that expected logging entries are produced log_check(caplog, expected_log_entries) - - -# WHAT ELSE TO CHECK -# THAT EACH FUNCTION WARNS THE USER APPROPRIATELY -# CATCH THIS WITH CAPLOG I GUESS -def test_failed_model(caplog): - """Test `FailedModel` initialization and usage.""" - - # Initialise model - model = FailedModel() - - # In cases where it passes then checks that the object has the right properties - assert set(["setup", "spinup", "solve", "cleanup"]).issubset(dir(model)) - assert model.name == "failed" - assert str(model) == "A failed model instance" - assert repr(model) == "FailedModel(update_interval = 320000000000 minutes)" - assert not model.should_update(datetime64("2050-10-28")) - - # Run model functions and check the logging output - model.factory({}) - model.setup() - model.spinup() - model.solve() - model.cleanup() - - expected_log = ( - (WARNING, "Cannot configure a failed model!"), - (WARNING, "Failed model cannot be setup!"), - (WARNING, "Failed model cannot be spun up!"), - (WARNING, "Failed model cannot be solved!"), - (WARNING, "Cleanup doesn't work for failed model!"), - ) - - # Final check that expected (i.e. no) logging entries are produced - log_check(caplog, expected_log) diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index cc7310bca..ea94a35d3 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -103,41 +103,3 @@ def __repr__(self) -> str: def __str__(self) -> str: """Inform user what the model type is.""" return f"A {self.name} model instance" - - -class FailedModel(BaseModel, model_name="failed"): - """A class to be returned when a `vr` model fails to be properly constructed.""" - - name = "failed" - - def __init__(self, **kwargs: Any): - # Set to ~10000 years to turn update off - update_interval = timedelta64(32 * (10**10), "m") - super(FailedModel, self).__init__(update_interval, **kwargs) - - @classmethod - def factory(cls, config: dict[str, Any]) -> FailedModel: - """Factory function informs user that a failed model cannot be configured.""" - - LOGGER.warning("Cannot configure a failed model!") - return cls() - - def setup(self) -> None: - """Function to inform user that a failed model cannot be setup.""" - - LOGGER.warning("Failed model cannot be setup!") - - def spinup(self) -> None: - """Function to inform user that a failed model cannot be spun up.""" - - LOGGER.warning("Failed model cannot be spun up!") - - def solve(self) -> None: - """Function to inform user that a failed model cannot be solved.""" - - LOGGER.warning("Failed model cannot be solved!") - - def cleanup(self) -> None: - """Function to inform user that cleanup doesn't work on a failed model.""" - - LOGGER.warning("Cleanup doesn't work for failed model!") diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 9530d00a4..de29a5c13 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -8,12 +8,7 @@ from virtual_rainforest.core.config import validate_config from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import ( - MODEL_REGISTRY, - BaseModel, - FailedModel, - InitialisationError, -) +from virtual_rainforest.core.model import MODEL_REGISTRY, BaseModel, InitialisationError def select_models(model_list: list[str]) -> list[Type[BaseModel]]: @@ -64,11 +59,19 @@ def configure_models( """ # Use factory methods to configure the desired models - models_cfd = [model.factory(config) for model in model_list] - - if any([isinstance(model, FailedModel) for model in models_cfd]): + failed_models = [] + models_cfd = [] + for model in model_list: + try: + models_cfd.append(model.factory(config)) + except InitialisationError: + failed_models.append(model.name) + + # If any models fail to configure inform the user about it + if len(failed_models): log_and_raise( - "Could not configure all the desired models, ending the simulation.", + f"Could not configure all the desired models, ending the simulation. The " + f"following models failed: {failed_models}.", InitialisationError, ) diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index 45a29ee15..0f7a275ed 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -6,13 +6,13 @@ class to be usable to simulate the soil. from __future__ import annotations -from typing import Any, Union +from typing import Any import pint from numpy import timedelta64 from virtual_rainforest.core.logger import LOGGER, log_and_raise -from virtual_rainforest.core.model import BaseModel, FailedModel, InitialisationError +from virtual_rainforest.core.model import BaseModel, InitialisationError class SoilModel(BaseModel, model_name="soil"): @@ -51,7 +51,7 @@ def __init__(self, update_interval: timedelta64, no_layers: int, **kwargs: Any): self._repr.append("no_layers") @classmethod - def factory(cls, config: dict[str, Any]) -> Union[SoilModel, FailedModel]: + def factory(cls, config: dict[str, Any]) -> SoilModel: """Factory function to initialise the soil model. This function unpacks the relevant information from the configuration file, and @@ -87,16 +87,13 @@ def factory(cls, config: dict[str, Any]) -> Union[SoilModel, FailedModel]: ) if valid_input: - try: - LOGGER.info( - "Information required to initialise the soil model successfully " - "extracted." - ) - return cls(update_interval, no_layers) - except InitialisationError: - return FailedModel() + LOGGER.info( + "Information required to initialise the soil model successfully " + "extracted." + ) + return cls(update_interval, no_layers) else: - return FailedModel() + raise InitialisationError() # THIS IS BASICALLY JUST A PLACEHOLDER TO DEMONSTRATE HOW THE FUNCTION OVERWRITING # SHOULD WORK From dc93f27b702c087626a51f331aed829980a77286 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 15 Nov 2022 10:35:57 +0000 Subject: [PATCH 26/30] Changed printing of set (to avoid breaking tests) --- tests/test_main.py | 23 ++++++++++++----------- virtual_rainforest/main.py | 4 +++- 2 files changed, 15 insertions(+), 12 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index 3e088a87c..e4c4591f2 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -25,7 +25,7 @@ ( ( INFO, - "Attempting to configure the following models: {'soil'}", + "Attempting to configure the following models: ['soil']", ), ), ), @@ -36,7 +36,7 @@ ( ( INFO, - "Attempting to configure the following models: {'soil'}", + "Attempting to configure the following models: ['soil']", ), ), ), @@ -47,8 +47,8 @@ ( ( INFO, - "Attempting to configure the following models: {'freshwater', " - "'soil'}", + "Attempting to configure the following models: ['freshwater', " + "'soil']", ), ( CRITICAL, @@ -81,7 +81,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri "SoilModel(update_interval = 10080 minutes, no_layers = 1)", does_not_raise(), ( - (INFO, "Attempting to configure the following models: {'soil'}"), + (INFO, "Attempting to configure the following models: ['soil']"), ( INFO, "Information required to initialise the soil model successfully " @@ -97,7 +97,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: {'soil'}"), + (INFO, "Attempting to configure the following models: ['soil']"), ( ERROR, "Configuration is missing information required to initialise the " @@ -118,7 +118,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: {'soil'}"), + (INFO, "Attempting to configure the following models: ['soil']"), ( INFO, "Information required to initialise the soil model successfully " @@ -143,7 +143,7 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri None, pytest.raises(InitialisationError), ( - (INFO, "Attempting to configure the following models: {'soil'}"), + (INFO, "Attempting to configure the following models: ['soil']"), ( ERROR, "Configuration types appear not to have been properly validated. " @@ -186,7 +186,7 @@ def test_vr_run_miss_model(mocker, caplog): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") expected_log_entries = ( - (INFO, "Attempting to configure the following models: {'topsoil'}"), + (INFO, "Attempting to configure the following models: ['topsoil']"), ( CRITICAL, "The following models cannot be configured as they are not found in the " @@ -207,7 +207,7 @@ def test_vr_run_bad_model(mocker, caplog): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") expected_log_entries = ( - (INFO, "Attempting to configure the following models: {'soil'}"), + (INFO, "Attempting to configure the following models: ['soil']"), ( INFO, "All models found in the registry, now attempting to configure them.", @@ -219,7 +219,8 @@ def test_vr_run_bad_model(mocker, caplog): ), ( CRITICAL, - "Could not configure all the desired models, ending the simulation.", + "Could not configure all the desired models, ending the simulation. The " + "following models failed: ['soil'].", ), ) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index de29a5c13..449bac439 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -28,7 +28,9 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: # Remove "core" from model list as it is not a model model_list_ = set(model_list) - {"core"} - LOGGER.info("Attempting to configure the following models: %s" % model_list_) + LOGGER.info( + "Attempting to configure the following models: %s" % sorted(model_list_) + ) # Make list of missing models, and return an error if necessary miss_model = [model for model in model_list_ if model not in MODEL_REGISTRY.keys()] From d3ab96e202780d2feeddc6bdbc85694dbdd76ca2 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 15 Nov 2022 11:11:18 +0000 Subject: [PATCH 27/30] Made validation error logging a function --- tests/test_config.py | 3 +- virtual_rainforest/core/config.py | 53 +++++++++++++++++++------------ 2 files changed, 34 insertions(+), 22 deletions(-) diff --git a/tests/test_config.py b/tests/test_config.py index 9d8f9bbe6..34aa1048a 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -449,7 +449,8 @@ def test_missing_core_schema(caplog, mocker): ), ( CRITICAL, - "Validation of configuration files failed see above errors", + "Validation of complete configuration files failed see above " + "errors", ), ), ), diff --git a/virtual_rainforest/core/config.py b/virtual_rainforest/core/config.py index 942705cb7..74d1b979a 100644 --- a/virtual_rainforest/core/config.py +++ b/virtual_rainforest/core/config.py @@ -31,6 +31,35 @@ class ConfigurationError(Exception): """Custom exception class for configuration failures.""" +def log_all_validation_errors( + errors: list[exceptions.ValidationError], complete: bool +) -> None: + """Logs all validation errors and raises an exception. + + A tag is constructed to allow the location of each error to be better determined. + For each error this is then printed along with the error message. + + Raises: + ConfigurationError: As at least one validation error has occurred. + """ + if complete: + conf = "complete" + else: + conf = "core" + + for error in errors: + # Construct details of the tag associated with the error + tag = "" + for k in error.path: + tag += f"[{k}]" + LOGGER.error("%s: %s" % (tag, error.message)) + + log_and_raise( + f"Validation of {conf} configuration files failed see above errors", + ConfigurationError, + ) + + def validate_and_add_defaults( validator_class: type[Draft202012Validator], ) -> type[Draft202012Validator]: @@ -315,16 +344,7 @@ def add_core_defaults(config_dict: dict[str, Any]) -> None: core_schema, format_checker=FormatChecker() ).iter_errors(config_dict) # Then log all errors in validating core config - for error in errors: - # Construct details of the tag associated with the error - tag = "" - for k in error.path: - tag += f"[{k}]" - LOGGER.error("%s: %s" % (tag, error.message)) - log_and_raise( - "Validation of core configuration files failed see above errors", - ConfigurationError, - ) + log_all_validation_errors(errors, False) def find_schema(config_dict: dict[str, Any]) -> list[str]: @@ -441,17 +461,8 @@ def validate_with_defaults( errors = ValidatorWithDefaults( comb_schema, format_checker=FormatChecker() ).iter_errors(config_dict) - # Then log all errors in validating core config - for error in errors: - # Construct details of the tag associated with the error - tag = "" - for k in error.path: - tag += f"[{k}]" - LOGGER.error("%s: %s" % (tag, error.message)) - log_and_raise( - "Validation of configuration files failed see above errors", - ConfigurationError, - ) + # Then log all errors in validating complete config + log_all_validation_errors(errors, True) def validate_config( From 8f29bb8b06630fd166de7f2e67d37f26cd6bb814 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Tue, 15 Nov 2022 13:29:37 +0000 Subject: [PATCH 28/30] Updated mypy to fix slow build on 3.11 --- poetry.lock | 442 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 215 insertions(+), 229 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5d9a03516..873292663 100644 --- a/poetry.lock +++ b/poetry.lock @@ -241,7 +241,7 @@ python-versions = ">=3.6" [[package]] name = "exceptiongroup" -version = "1.0.1" +version = "1.0.4" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false @@ -333,7 +333,7 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "greenlet" -version = "2.0.0.post0" +version = "2.0.1" description = "Lightweight in-process concurrent programming" category = "dev" optional = false @@ -341,11 +341,11 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] docs = ["Sphinx", "docutils (<0.18)"] -test = ["faulthandler", "objgraph"] +test = ["faulthandler", "objgraph", "psutil"] [[package]] name = "hypothesis" -version = "6.56.4" +version = "6.57.1" description = "A library for property-based testing" category = "dev" optional = false @@ -357,7 +357,7 @@ exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""} sortedcontainers = ">=2.1.0,<3.0.0" [package.extras] -all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=3.2)", "dpcontracts (>=0.4)", "importlib-metadata (>=3.6)", "lark-parser (>=0.6.5)", "libcst (>=0.3.16)", "numpy (>=1.9.0)", "pandas (>=1.0)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2022.5)"] +all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=3.2)", "dpcontracts (>=0.4)", "importlib-metadata (>=3.6)", "lark-parser (>=0.6.5)", "libcst (>=0.3.16)", "numpy (>=1.9.0)", "pandas (>=1.0)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2022.6)"] cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"] codemods = ["libcst (>=0.3.16)"] dateutil = ["python-dateutil (>=1.4)"] @@ -370,7 +370,7 @@ pandas = ["pandas (>=1.0)"] pytest = ["pytest (>=4.6)"] pytz = ["pytz (>=2014.1)"] redis = ["redis (>=3.0.0)"] -zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2022.5)"] +zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2022.6)"] [[package]] name = "identify" @@ -425,7 +425,7 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.17.0" +version = "6.17.1" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -568,7 +568,7 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma [[package]] name = "jupyter-client" -version = "7.4.4" +version = "7.4.6" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -589,13 +589,14 @@ test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-com [[package]] name = "jupyter-core" -version = "4.11.2" +version = "5.0.0" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] +platformdirs = "*" pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} traitlets = "*" @@ -759,7 +760,7 @@ python-versions = ">=3.7" [[package]] name = "mypy" -version = "0.981" +version = "0.991" description = "Optional static typing for Python" category = "dev" optional = false @@ -772,6 +773,7 @@ typing-extensions = ">=3.10" [package.extras] dmypy = ["psutil (>=4.0)"] +install-types = ["pip"] python2 = ["typed-ast (>=1.4.0,<2)"] reports = ["lxml"] @@ -919,7 +921,7 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.10.1" +version = "0.10.2" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -975,15 +977,15 @@ xarray = ["xarray"] [[package]] name = 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and removed key error handling --- tests/test_main.py | 38 ++++++++++++-------------------- tests/test_models.py | 14 ++++-------- virtual_rainforest/core/model.py | 2 +- virtual_rainforest/main.py | 2 +- virtual_rainforest/soil/model.py | 18 +++++++-------- 5 files changed, 29 insertions(+), 45 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index e4c4591f2..9972e1469 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -89,27 +89,6 @@ def test_select_models(caplog, model_list, no_models, raises, expected_log_entri ), ), ), - ( - { # missing soil config tag - "soil": {}, - "core": {"timing": {"min_time_step": "7 days"}}, - }, - None, - pytest.raises(InitialisationError), - ( - (INFO, "Attempting to configure the following models: ['soil']"), - ( - ERROR, - "Configuration is missing information required to initialise the " - "soil model. The first missing key is 'no_layers'.", - ), - ( - CRITICAL, - "Could not configure all the desired models, ending the " - "simulation.", - ), - ), - ), ( { # invalid soil config tag "soil": {"no_layers": -1}, @@ -201,7 +180,17 @@ def test_vr_run_bad_model(mocker, caplog): """Test the main `vr_run` function handles bad model configuration correctly.""" mock_conf = mocker.patch("virtual_rainforest.main.validate_config") - mock_conf.return_value = {"core": {"modules": ["soil"]}, "soil": {}} + mock_conf.return_value = { + "core": { + "modules": ["soil"], + "timing": { + "start_date": "2020-01-01", + "end_date": "2120-01-01", + "min_time_step": "0.5 martian days", + }, + }, + "soil": {}, + } with pytest.raises(InitialisationError): vr_run("tests/fixtures/all_config.toml", ".", "delete_me") @@ -214,8 +203,9 @@ def test_vr_run_bad_model(mocker, caplog): ), ( ERROR, - "Configuration is missing information required to initialise the soil " - "model. The first missing key is 'timing'.", + "Configuration types appear not to have been properly validated. This " + "problem prevents initialisation of the soil model. The first instance of " + "this problem is as follows: 'martian' is not defined in the unit registry", ), ( CRITICAL, diff --git a/tests/test_models.py b/tests/test_models.py index 14459b0f8..73d080391 100644 --- a/tests/test_models.py +++ b/tests/test_models.py @@ -5,7 +5,7 @@ """ from contextlib import nullcontext as does_not_raise -from logging import CRITICAL, ERROR, INFO, WARNING +from logging import CRITICAL, INFO, WARNING import pytest from numpy import datetime64, timedelta64 @@ -111,14 +111,8 @@ class NewSoilModel(BaseModel, model_name="soil"): [ ( {}, - pytest.raises(InitialisationError), - ( - ( - ERROR, - "Configuration is missing information required to initialise the " - "soil model. The first missing key is 'core'", - ), - ), + pytest.raises(KeyError), + (), # This error isn't handled so doesn't generate logging ), ( { @@ -145,7 +139,7 @@ def test_generate_soil_model(caplog, config, raises, expected_log_entries): # Check whether model is initialised (or not) as expected with raises: - model = SoilModel.factory(config) + model = SoilModel.from_config(config) assert model.no_layers == config["soil"]["no_layers"] # Final check that expected logging entries are produced diff --git a/virtual_rainforest/core/model.py b/virtual_rainforest/core/model.py index ea94a35d3..b8c951f3a 100644 --- a/virtual_rainforest/core/model.py +++ b/virtual_rainforest/core/model.py @@ -67,7 +67,7 @@ def cleanup(self) -> None: @classmethod @abstractmethod - def factory(cls, config: dict[str, Any]) -> Any: + def from_config(cls, config: dict[str, Any]) -> Any: """Factory function to unpack config and initialise a model instance.""" @classmethod diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 449bac439..60008e0e3 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -65,7 +65,7 @@ def configure_models( models_cfd = [] for model in model_list: try: - models_cfd.append(model.factory(config)) + models_cfd.append(model.from_config(config)) except InitialisationError: failed_models.append(model.name) diff --git a/virtual_rainforest/soil/model.py b/virtual_rainforest/soil/model.py index 0f7a275ed..ba856dee7 100644 --- a/virtual_rainforest/soil/model.py +++ b/virtual_rainforest/soil/model.py @@ -51,8 +51,8 @@ def __init__(self, update_interval: timedelta64, no_layers: int, **kwargs: Any): self._repr.append("no_layers") @classmethod - def factory(cls, config: dict[str, Any]) -> SoilModel: - """Factory function to initialise the soil model. + def from_config(cls, config: dict[str, Any]) -> SoilModel: + """Factory function to initialise the soil model from configuration. This function unpacks the relevant information from the configuration file, and then uses it to initialise the model. If any information from the config is @@ -61,6 +61,8 @@ def factory(cls, config: dict[str, Any]) -> SoilModel: Args: config: The complete (and validated) virtual rainforest configuration. + Raises: + InitialisationError: If configuration data can't be properly converted """ # Assume input is valid until we learn otherwise @@ -72,13 +74,11 @@ def factory(cls, config: dict[str, Any]) -> SoilModel: # Round raw time interval to nearest minute update_interval = timedelta64(int(raw_interval.magnitude), "m") no_layers = config["soil"]["no_layers"] - except KeyError as e: - valid_input = False - LOGGER.error( - "Configuration is missing information required to initialise the soil " - "model. The first missing key is %s." % str(e) - ) - except (ValueError, pint.errors.DimensionalityError) as e: + except ( + ValueError, + pint.errors.DimensionalityError, + pint.errors.UndefinedUnitError, + ) as e: valid_input = False LOGGER.error( "Configuration types appear not to have been properly validated. This " From 1c83dd3e2983d09991186eca015f065bd0233ce5 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 16 Nov 2022 11:47:28 +0000 Subject: [PATCH 30/30] Switched to more implict if statement for lists --- virtual_rainforest/main.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/virtual_rainforest/main.py b/virtual_rainforest/main.py index 60008e0e3..530797201 100644 --- a/virtual_rainforest/main.py +++ b/virtual_rainforest/main.py @@ -34,7 +34,7 @@ def select_models(model_list: list[str]) -> list[Type[BaseModel]]: # Make list of missing models, and return an error if necessary miss_model = [model for model in model_list_ if model not in MODEL_REGISTRY.keys()] - if len(miss_model): + if miss_model: log_and_raise( f"The following models cannot be configured as they are not found in the " f"registry: {miss_model}", @@ -70,7 +70,7 @@ def configure_models( failed_models.append(model.name) # If any models fail to configure inform the user about it - if len(failed_models): + if failed_models: log_and_raise( f"Could not configure all the desired models, ending the simulation. The " f"following models failed: {failed_models}.",