Merge pull request #22 from ACCESS-NRI/3-Package-model-config-tests

Package model-config-tests

.github/workflows/CD.yml

@@ -0,0 +1,50 @@
+name: CD
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  pypi-build:
+    name: Build package for PyPI
+    if: github.repository == 'access-nri/model-config-tests'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install build dependencies
+        run: python3 -m pip install --upgrade build
+
+      - name: Build distributions
+        run: python3 -m build
+
+      - name: Upload distribution artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: release
+          path: dist
+
+  pypi-publish:
+    # Split build and publish to restrict trusted publishing to just this workflow
+    needs: ['pypi-build']
+    name: Publish to PyPI.org
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: release
+          path: dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@2f6f737ca5f74c637829c0f5c3acd0e29ea5e8bf # v1.8.11

.github/workflows/CI.yml

@@ -0,0 +1,92 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - 'main'
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd #v3.0.1
+
+  pypi-build:
+    name: Build package for PyPI
+    if: github.repository == 'access-nri/model-config-tests'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: 'pip'
+
+      - name: Install build dependencies
+        run: python3 -m pip install --upgrade build
+
+      - name: Build distributions
+        run: python3 -m build
+
+      - name: Upload distribution artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: release
+          path: dist
+
+  install_from_dist:
+    needs: [ 'pypi-build' ]
+    name: Test install from distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download distribution
+        uses: actions/download-artifact@v4
+        with:
+          name: release
+          path: dist
+
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install model_config_tests
+        run: python3 -m pip install ./dist/model_config_tests-*.tar.gz
+
+      - name: Run model-config-tests command
+        run: model-config-tests --collect-only
+
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [ "3.9", "3.10", "3.11" ]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install model_config_tests with test dependencies
+        run: python3 -m pip install -e '.[test]'
+
+      - name: Run tests
+        run: python3 -m pytest -s --cov=./src --cov-report=xml tests
+
+      - name: Upload code coverage
+        uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c #v4.4.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml

.gitignore

@@ -0,0 +1,11 @@
+*.pyc
+/__pycache__
+/build
+/dist
+*.egg-info
+.coverage
+.ipynb_checkpoints
+.vscode
+.idea
+/tests/tmp/
+coverage.xml

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    - id: black
+      language_version: python3

README.md

@@ -8,11 +8,18 @@ The checksum pytests are used for reproducibility CI checks in the [ACCESS-NRI/r
 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
+### 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/ test-code
+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)
@@ -25,17 +32,17 @@ git checkout <branch/tag>
 3. Setup payu
 ```sh
 module use /g/data/vk83/modules
-module load payu/1.1
+module load payu/1.1.3
 ```
 
 4. Run the pytests
 ```sh
-pytest <path/to/test-code>
+model-config-tests
 ```
 
 ### Pytest Options
 
-The output directory for pytests defaults to `/scratch/$PROJECT/$USER/test-model-repro` and contains the following sub-directories:
+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.
 
@@ -44,7 +51,7 @@ This output directory also contains files generated by pytests, including the `C
 To specify a different folder for pytest outputs, use `--output-path` command flag, for example:
 
 ```sh
-pytest <path/to/test-code> --output-path /some/other/path/for/output
+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 
@@ -57,13 +64,13 @@ file which is stored in the control directory.
 To run only CI reproducibility checksum tests, use `-m checksum`, e.g.
 
 ```sh
-pytest <path/to/test-code> -m checksum
+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
-pytest <path/to/test-code> -m "config or access_om2"
+model-config-tests -m "config or access_om2"
 ```

pyproject.toml

@@ -0,0 +1,98 @@
+[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"
+]
+
+[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"]