Model Configuration Pytests and CI

This repository houses pytests that are used as part CI checks for model configurations, as well as reusable components of model configuration CI.

The checksum pytests are used for reproducibility CI checks in this repository. The quick configuration tests are used in any repository that calls config-pr-1-ci.yml or is templated by `ACCESS-NRI/model-configs-template. For example, ACCESS-NRI/access-om2-configs.

Code from these pytests is adapted from COSIMAS's ACCESS-OM2's bit reproducibility tests.

Pytests

How to run pytests manually on NCI

Load payu module - this provides the dependencies needed to run the model
```
module use /g/data/vk83/modules
module load payu/1.1.4
```

Create and activate a python virtual environment for installing and running tests

python3 -m venv <path/to/test-venv> --system-site-packages
source <path/to/test-venv>/bin/activate

Either pip install a released version of model-config-tests,
```
pip install model-config-tests==0.0.1
```
Or to install model-config-tests in "editable" mode, first clone the repository, and then run pip install from the repository. This means any changes to the code are reflected in the installed package.
```
git clone https://github.com/ACCESS-NRI/model-config-tests/ <path/to/model-config-tests>
pip install -e <path/to/model-config-tests>
```

Checkout an experiment (in this case it is using an ACCESS-OM2 config)

git clone https://github.com/ACCESS-NRI/access-om2-configs/ <path/to/experiment>
cd <path/to/experiment>
git checkout <branch/tag>

Run the pytests
```
model-config-tests
```
Once done with testing, deactivate the virtual environment, and if the environment is no longer needed, remove the environment
```
deactivate
rm -rf <path/to/test-venv> # Deletes the test environment
```

Pytest Options

The output directory for pytests defaults to $TMPDIR/test-model-repro and contains the following subdirectories:

control - contains copies of the model configuration used for each experiment run in the tests.
lab - contains payu model output directories containing work and archive sub-directories.

This output directory also contains files generated by pytests, including the checksum directory which is used as part of reproducibility CI workflows.

To specify a different folder for pytest outputs, use --output-path command flag, for example:

model-config-tests --output-path /some/other/path/for/output

By default, the control directory, e.g. the model configuration to test, is the current working directory. This can be set similarly to above by using the --control-path command flag.

The path containing the checksum file to check against can also be set using --checksum-path command flag. The default is the testing/checksum/historical-<default-model-runtime>hr-checksums.json file which is stored in the control directory.

To run only CI reproducibility checksum tests, use -m checksum, e.g.

model-config-tests -m checksum

To run quick configuration tests, use the config marker. To additionally run ACCESS-OM2 specific quick configuration tests, use access_om2 marker, e.g.:

model-config-tests -m "config or access_om2"

CI/CD

The .github directory contains many different workflows and actions. This section describes how they are used.

CI/CD For This Repository

CI.yml and CD.yml are used to test, package and upload the model-config-tests package that is used by model-configs-style repositories across the ACCESS-NRI. These are the only workflows that run on this repository. The others are reusable workflows called by model-configs-style repositories, among others.

Reusable CI

The config-*.yml, generate-checksums.yml and test-repro.yml workflows are called by model-configs-style repositories to test model configurations. They are stored in this repository to allow a central place to update generic CI used by all model configuration repositories.

Repos That Use Reusable CI

Currently, these repositories make use of the reusable CI:

Below is information on the use of these workflows.

`config-pr-*.yml` Pipeline

The config-pr-* Pipeline is a series of workflows that govern the testing, ChatOps and merging procedures of pull requests for model configuration repositories, such as ACCESS-NRI/access-om2-configs.

Essentially, these files work on two types of configuration branch pull requests in the model configuration repository. More information on the terminology used in model configuration repositories can be found in the README.md of the ACCESS-NRI/model-configs-template repository. The types of pull requests are:

Pull requests into dev-*: Allows quick checks of configuration metadata and common mistakes in configurations during PRs into the dev-* configuration branches.
Pull requests from dev-* into release-*: Allows both quick checks, as well as a longer, more comprehensive check on the reproducibility of the changes being brought into the release-* configuration branch, compared to the previous release-* commit. It also acts on 'comment commands' run during the pull request, like !bump for updating the version of the configuration (see the 'Config Tags' section in the ACCESS-NRI/model-configs-template repository for more). It is also responsible for the creation of the final config tag and release, once merged.

`config-schedule-*.yml` Pipeline

The config-schedule-* Pipeline is a series of workflows used to check the reproducibility of certain config tags against themselves, every month. This is used as a kind of canary to make sure that we continue to get the same results on the same deployment targets.

`generate-checksums` Reusable Workflow

This workflow is used to easily generate the checksums used in the reproducibility checks, for a specific branch of a model configuration repository, if they don't already exist. This is most often used for the initial commit of a checksum to the release-* configuration branch.

`test-repro` Reusable Workflow

This workflow is used to test the reproducibility of a given model repository against historical checksums, and can be used as a standalone workflow.

Using it has some requirements outside of just filling in the inputs: One must have a valid GitHub Environment (specified by the environment-name input) in the calling repository, that has the following secrets and vars defined:

secrets.SSH_HOST - hostname for the deployment target
secrets.SSH_HOST_DATA - hostname for the data mover on the deployment target (if it exists)
secrets.SSH_KEY - private key for access to the deployment target
secrets.SSH_USER - username for access to the deployment target
vars.EXPERIMENTS_LOCATION - directory on the deployment target that will contain all the experiments used during testing of reproducibility across multiple runs of this workflow (ex. /scratch/some/directory/experiments)
vars.MODULE_LOCATION - directory on the deployment target that contains module files for payu used during reproducibility testing (ex. /g/data/vk83/modules)
vars.PRERELEASE_MODULE_LOCATION - directory on the deployment target that contains module files for development version of payu (ex. /g/data/vk83/prerelease/modules)

`config-comment-test` Reusable Workflow

This comment command allows a repro check from any branch, rather than just the dev-* -> release-* PR pipeline.

It requires all the secrets/vars defined on the caller (as above), as well as vars.CONFIG_CI_SCHEMA_VERSION.

Usage is as follows:

!test TYPE [commit]

Where TYPE is a test suite that we support. Currently, this consists of repro.

The commands are all case sensitive and require lower case.

Using commit as an option will commit the result of the test to the PR, provided the commenter has at least write permission, and the checksums differ.

`!test repro`

!test repro: will compare the HEAD of the current PR source branch against the common ancestor on the target branch. For example, in the below diagram we would be comparing generated checksums in C against checksums already stored at A:

D   (PR Target Branch)
|
| C (PR Source Branch)
| |
| B
|/
A   (Common Ancestor)

CI Configuration File

Each model configuration repository requires a config/ci.json file for defining CI test configuration. This file specifies what scheduled tests to run, and what tests to run for a given git branch (or tag) and test type.

Test types

The different types of test are defined as:

scheduled: Scheduled reproducibility tests run on NCI. These are typically scheduled to run monthly but this can re-configured by modifying the cron in the .github/workflows/schedule.yml workflow. The keys under these tests are released tags or branches to run the scheduled tests.
reproducibility: Reproducibility tests run on NCI as part of pull requests (PRs). These are automatically run for PRs from development (dev-) branches to released (release-) branches. These tests can also be triggered manually in a PR using the !test repro command. The keys under these tests represent the target branches into which PRs are being merged.
qa - Quick quality assurance tests are run locally on a GitHub Runner as part of PRs. These are consistency checks which run without needing to run the model. These are run automatically for any PR being merged into development or released branches. The keys under these tests represent the target branches into which PRs are being merged.

Test Configuration Settings

The configuration properties needed to run the tests are:

Name	Type	Description	Example
markers	`string`	Markers used for pytest, in the Python format	`checksum`
model-config-tests-version	`string`	The version of the model-config-tests	`0.0.1`
python-version	`string`	The python version used to create test virtual environment on GitHub hosted tests	`3.11.0`
payu-version	`string`	The Payu version used to run the model	`1.1.5`

Pytest markers select what pytests to run in model-config-tests. Current markers include:

checksum: Historical reproducibility test that runs a model and compares checksums with a stored previous result.
checksum_slow: Restart reproducibility tests. These include model determinism, by repeating running a configuration from initial conditions to check it reproduces the same output, and checking reproducibility by confirming two short consecutive model runs give the same result as a longer single model run.
dev_config: General configuration QA tests.
config: Configuration QA tests for released branches. This includes the dev_config tests.

There are also model-specific markers for configuration QA tests, e.g., access_om2, access_esm1p5, access_om3 and access_esm1p6.

To select a combination of tests, use the or keyword, e.g. "markers": "access_om2 or config".

The Payu version is the module version loaded on NCI to build the base of the test virtual environment and is only relevant for tests run on NCI. To use the development Payu module which has all the latest changes in Payu repository, set "payu-version": "dev".

A git branch, tag, or commit of the model-config-tests repository can be used for model-config-tests-version, and the CI will install from Github if the package can't be installed from PyPI. For development model configuration branches it may be useful to use the most recent code in the model-config-tests repository. Using the main branch will achieve this. This is good for continuous integration, however it is recommended to use released versions of model-config-tests and payu for the released model configurations so that tests are stable.

File Structure

The schema for this file is found in ACCESS-NRI/schema. As most of the tests use the same test and python versions, and similar markers, there are two levels of defaults. There's a default at the test type level which is useful for defining test markers - this selects certain pytests to run in model-config-tests. There is an outer global default, which is used if a property is not defined for a given branch/tag, and it is not defined for the test default. The parse-ci-config action applies this fall-back default logic.

There is also support for using regex patterns for the git branches for qa and reproducibility tests, e.g. dev-.* will match all development branches. If there are multiple regex patterns, priority will be given to the order so more specific patterns should be higher in the list, e.g. dev-1deg-.* before dev-.*. Note that regex patterns are currently not supported for scheduled tests so every tag that requires a scheduled test needs to be defined.

For example, given the following config/ci.json file:

{
    "$schema": "<https://github.com/ACCESS-NRI/schema/tree/main/au.org.access-nri/model/configuration/ci/2-0-0.json>",
    "scheduled": {
        "release-1deg_jra55_ryf-2.0": {},
        "default": {
            "markers": "checksum"
        },
    },
    "reproducibility": {
        "dev-1deg_jra55do_ryf": {
            "markers": "checksum or checksum_slow"
        },
        "release-1deg_jra55do_ryf": {
            "markers": "checksum or checksum_slow"
        },
        "dev-example-branch": {
            "payu-version": "dev",
            "model-config-tests-version": "main"
        },
        "default": {
            "markers": "checksum"
        },
    },
    "qa": {
        "dev-example-branch": {
            "model-config-tests-version": "main"
        },
        "dev-.*": {
            "markers": "dev_config"
        },
        "default": {
            "markers": "config"
        }
    },
    "default": {
        "model-config-tests-version": "0.0.11",
        "python-version": "3.11.0",
        "payu-version": "1.1.6"
    }
}

The above configuration triggers monthly scheduled tests for release-1deg_jra55_ryf-2.0 GitHub tag. This scheduled test will run with checksum test marker, and the top-level defaults for model-config-tests-version, python-version and payu-version.

If a PR was being merged into a release-1deg_jra55do_ryf branch, the QA tests run on the GitHub runner would use the config or dev_config test markers and the repro tests on NCI, would select the checksum or checksum_slow tests.

If a PR was being merged into a dev-example-branch, the QA tests that run automatically would use the dev_config tests and if repro tests were triggered manually, then it would use the checksum tests. For both test types, it would use the latest changes in the model-config-tests repository. For repro tests, it would use the payu/dev module on NCI for running the model.

Name		Name	Last commit message	Last commit date
Latest commit History 220 Commits
.github		.github
src/model_config_tests		src/model_config_tests
tests		tests
.gitattributes		.gitattributes
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
.zenodo.json		.zenodo.json
COPYRIGHT.txt		COPYRIGHT.txt
LICENSE		LICENSE
README.md		README.md
pyproject.toml		pyproject.toml
setup.py		setup.py

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Model Configuration Pytests and CI

Pytests

How to run pytests manually on NCI

Pytest Options

CI/CD

CI/CD For This Repository

Reusable CI

Repos That Use Reusable CI

`config-pr-*.yml` Pipeline

`config-schedule-*.yml` Pipeline

`generate-checksums` Reusable Workflow

`test-repro` Reusable Workflow

`config-comment-test` Reusable Workflow

`!test repro`

CI Configuration File

Test types

Test Configuration Settings

File Structure

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Model Configuration Pytests and CI

Pytests

How to run pytests manually on NCI

Pytest Options

CI/CD

CI/CD For This Repository

Reusable CI

Repos That Use Reusable CI

config-pr-*.yml Pipeline

config-schedule-*.yml Pipeline

generate-checksums Reusable Workflow

test-repro Reusable Workflow

config-comment-test Reusable Workflow

!test repro

CI Configuration File

Test types

Test Configuration Settings

File Structure

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`config-pr-*.yml` Pipeline

`config-schedule-*.yml` Pipeline

`generate-checksums` Reusable Workflow

`test-repro` Reusable Workflow

`config-comment-test` Reusable Workflow

`!test repro`

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