model-config-tests 0.0.1__tar.gz

model_config_tests-0.0.1/LICENSE

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model_config_tests-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: model_config_tests
+Version: 0.0.1
+Summary: Test for ACCESS model (payu) configurations
+Author: ACCESS-NRI
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/ACCESS-NRI/model-config-tests/
+Project-URL: Issues, https://github.com/ACCESS-NRI/model-config-tests/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: f90nml>=0.16
+Requires-Dist: requests
+Requires-Dist: PyYAML
+Requires-Dist: requests
+Requires-Dist: pytest>=8.0.1
+Requires-Dist: ruamel.yaml>=0.18.5
+Requires-Dist: jsonschema>=4.21.1
+Requires-Dist: payu>=1.1.3
+Provides-Extra: test
+Requires-Dist: pytest-cov; extra == "test"
+
+## Model Configuration Pytests
+
+These pytests are used as part CI checks for model configurations.
+
+The checksum pytests are used for reproducibility CI checks in the [ACCESS-NRI/reproducibility](https://github.com/ACCESS-NRI/reproducibility) repository. The quick configuration tests are used in 
+[ACCESS-NRI/access-om2-configs](https://github.com/ACCESS-NRI/access-om2-configs).
+
+Code from these tests is adapted from COSIMAS's ACCESS-OM2's [
+bit reproducibility tests](https://github.com/COSIMA/access-om2/blob/master/test/test_bit_reproducibility.py).
+
+### How to run tests manually (from a local install of model-config-tests)
+
+1. First clone the pytest code into a separate directory.
+```sh
+git clone https://github.com/ACCESS-NRI/model-config-tests/ model-config-tests
+```
+
+2. To create a local install of `model-config-tests`
+```sh
+cd model-config-tests
+pip install --user -e .
+model-config-tests --help # model-config-tests runs the pytest command for tests in the package
+```
+
+2. Checkout an experiment (in this case it is using an ACCESS-OM2 config)
+```sh
+git clone https://github.com/ACCESS-NRI/access-om2-configs/ <experiment>
+cd <experiment>
+git checkout <branch/tag>
+```
+
+3. Setup payu
+```sh
+module use /g/data/vk83/modules
+module load payu/1.1.3
+```
+
+4. Run the pytests
+```sh
+model-config-tests
+```
+
+### 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` file which is used as part of reproducibility CI workflows.
+
+To specify a different folder for pytest outputs, use `--output-path` command flag, for example:
+
+```sh
+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/CHECKSUM`
+file which is stored in the control directory.
+
+To run only CI reproducibility checksum tests, use `-m checksum`, e.g.
+
+```sh
+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.:
+
+```sh
+model-config-tests -m "config or access_om2"
+```

model_config_tests-0.0.1/README.md

@@ -0,0 +1,76 @@
+## Model Configuration Pytests
+
+These pytests are used as part CI checks for model configurations.
+
+The checksum pytests are used for reproducibility CI checks in the [ACCESS-NRI/reproducibility](https://github.com/ACCESS-NRI/reproducibility) repository. The quick configuration tests are used in 
+[ACCESS-NRI/access-om2-configs](https://github.com/ACCESS-NRI/access-om2-configs).
+
+Code from these tests is adapted from COSIMAS's ACCESS-OM2's [
+bit reproducibility tests](https://github.com/COSIMA/access-om2/blob/master/test/test_bit_reproducibility.py).
+
+### How to run tests manually (from a local install of model-config-tests)
+
+1. First clone the pytest code into a separate directory.
+```sh
+git clone https://github.com/ACCESS-NRI/model-config-tests/ model-config-tests
+```
+
+2. To create a local install of `model-config-tests`
+```sh
+cd model-config-tests
+pip install --user -e .
+model-config-tests --help # model-config-tests runs the pytest command for tests in the package
+```
+
+2. Checkout an experiment (in this case it is using an ACCESS-OM2 config)
+```sh
+git clone https://github.com/ACCESS-NRI/access-om2-configs/ <experiment>
+cd <experiment>
+git checkout <branch/tag>
+```
+
+3. Setup payu
+```sh
+module use /g/data/vk83/modules
+module load payu/1.1.3
+```
+
+4. Run the pytests
+```sh
+model-config-tests
+```
+
+### 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` file which is used as part of reproducibility CI workflows.
+
+To specify a different folder for pytest outputs, use `--output-path` command flag, for example:
+
+```sh
+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/CHECKSUM`
+file which is stored in the control directory.
+
+To run only CI reproducibility checksum tests, use `-m checksum`, e.g.
+
+```sh
+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.:
+
+```sh
+model-config-tests -m "config or access_om2"
+```

model_config_tests-0.0.1/pyproject.toml

@@ -0,0 +1,99 @@
+[project]
+name = "model_config_tests"
+version = "0.0.1"
+authors = [
+  { name = "ACCESS-NRI" },
+]
+description = "Test for ACCESS model (payu) configurations"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "Apache-2.0" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: POSIX :: Linux",
+]
+dependencies = [
+    "f90nml >=0.16",
+    "requests",
+    "PyYAML",
+    "requests",
+    "pytest >=8.0.1",
+    "ruamel.yaml >=0.18.5",
+    "jsonschema >=4.21.1",
+    "payu >=1.1.3"
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest-cov"
+]
+
+[project.scripts]
+model-config-tests = "model_config_tests.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/ACCESS-NRI/model-config-tests/"
+Issues = "https://github.com/ACCESS-NRI/model-config-tests/issues"
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools >= 61.0.0",
+]
+
+[tool.ruff]
+target-version = "py39"
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+[tool.ruff.lint]
+# E402: module level import not at top of file
+# E501: line too long - let black worry about that
+ignore = [
+    "E402",
+    "E501",
+]
+select = [
+    # Pyflakes
+    "F",
+    # Pycodestyle
+    "E",
+    "W",
+    # isort
+    "I",
+    # Pyupgrade
+    "UP",
+]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 18
+
+[tool.ruff.lint.isort]
+known-first-party = ["model_config_tests"]

model_config_tests-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

model_config_tests-0.0.1/src/model_config_tests/__main__.py

@@ -0,0 +1,18 @@
+import os
+import sys
+
+# Running pytests using --pyargs does not run pytest_addoption in conftest.py
+# Using workaround as described here:
+# https://stackoverflow.com/questions/41270604/using-command-line-parameters-with-pytest-pyargs
+HERE = os.path.dirname(__file__)
+
+
+def main():
+    import pytest
+
+    errcode = pytest.main([HERE] + sys.argv[1:])
+    sys.exit(errcode)
+
+
+if __name__ == "__main__":
+    main()

model_config_tests-0.0.1/src/model_config_tests/conftest.py

@@ -0,0 +1,110 @@
+# Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0
+
+import os
+from pathlib import Path
+
+import pytest
+import yaml
+from ruamel.yaml import YAML
+
+
+@pytest.fixture(scope="session")
+def output_path(request):
+    """Set the output path: This contains control and lab directories for each
+    test and test output files - e.g. CHECKSUMS
+    """
+    path = request.config.getoption("--output-path")
+    if path is None:
+        # Set default to $TMPDIR/test-model-repro/
+        tmp_dir = os.environ.get("TMPDIR")
+        path = f"{tmp_dir}/test-model-repro"
+    return Path(path)
+
+
+@pytest.fixture(scope="session")
+def control_path(request):
+    """Set the path of the model configuration directory to test"""
+    path = request.config.getoption("--control-path")
+    if path is None:
+        # Set default to current working directory
+        path = Path.cwd()
+    return Path(path)
+
+
+@pytest.fixture(scope="session")
+def checksum_path(request, control_path):
+    """Set the path of the model configuration directory to test"""
+    path = request.config.getoption("--checksum-path")
+    if path is None:
+        # Set default to checksum stored on model configuration
+        path = control_path / "testing" / "checksum" / "historical-3hr-checksum.json"
+    return Path(path)
+
+
+@pytest.fixture(scope="session")
+def metadata(control_path: Path):
+    """Read the metadata file in the control directory"""
+    metadata_path = control_path / "metadata.yaml"
+    # Use ruamel.yaml as that is what is used to read metadata files in Payu
+    # It also errors out if there are duplicate keys in metadata
+    content = YAML().load(metadata_path)
+    return content
+
+
+@pytest.fixture(scope="session")
+def config(control_path: Path):
+    """Read the config file in the control directory"""
+    config_path = control_path / "config.yaml"
+    with open(config_path) as f:
+        config_content = yaml.safe_load(f)
+    return config_content
+
+
+@pytest.fixture(scope="session")
+def target_branch(request):
+    """Set the target branch - i.e., the branch the configuration will be
+    merged into. This used is to infer configuration information, if the
+    configuration branches follow a common naming scheme (e.g. ACCESS-OM2)"""
+    return request.config.getoption("--target-branch")
+
+
+# Set up command line options and default for directory paths
+def pytest_addoption(parser):
+    """Attaches optional command line arguments"""
+    parser.addoption(
+        "--output-path",
+        action="store",
+        help="Specify the output directory path for test output",
+    )
+
+    parser.addoption(
+        "--control-path",
+        action="store",
+        help="Specify the model configuration path to test",
+    )
+
+    parser.addoption(
+        "--checksum-path",
+        action="store",
+        help="Specify the checksum file to compare against",
+    )
+
+    parser.addoption(
+        "--target-branch", action="store", help="Specify the target branch name"
+    )
+
+
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers", "slow: mark tests as slow (deselect with '-m \"not slow\"')"
+    )
+    config.addinivalue_line(
+        "markers", "checksum: mark tests to run as part of reproducibility CI tests"
+    )
+    config.addinivalue_line(
+        "markers", "config: mark as configuration tests in quick QA CI checks"
+    )
+    config.addinivalue_line(
+        "markers", "access_om2: mark as access-om2 specific tests in quick QA CI checks"
+    )