diff --git a/.github/workflows/deptry.yml b/.github/workflows/deptry.yml new file mode 100644 index 00000000..20a9eb55 --- /dev/null +++ b/.github/workflows/deptry.yml @@ -0,0 +1,17 @@ +name: Deptry Dependency Check + +on: [pull_request] + +jobs: + dependencies: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + # Setup the minimum required python distribution + - uses: actions/setup-python@v5 + with: + python-version: "3.13" + - name: Setup uv + uses: astral-sh/setup-uv@v5 + - run: uv sync --all-extras + - run: uv run deptry . diff --git a/.github/workflows/git-extension.yml b/.github/workflows/git-extension.yml index f99ccf80..f4baae9f 100644 --- a/.github/workflows/git-extension.yml +++ b/.github/workflows/git-extension.yml @@ -1,18 +1,51 @@ -name: Check requirements.txt git URLs are properly formatted - -on: pull_request - -permissions: - contents: read - pull-requests: write +name: Check Git Dependencies +on: + push: + branches: + - master + pull_request: + branches: + - master jobs: - test: + check-git-deps: runs-on: ubuntu-latest + steps: - - uses: actions/checkout@v4 - - run: sed -i '/git\+/ { /\.git$/! s/$/.git/ }' requirements.txt - - uses: parkerbxyz/suggest-changes@v2 - with: - comment: 'Please change the following dependencies for consistency.' - event: 'REQUEST_CHANGES' + - name: Checkout repository + uses: actions/checkout@v4 + + + - name: Set up Python + uses: actions/setup-python@v4 + + - name: Run Git dependency check + run: | + import tomllib + from pathlib import Path + import sys + + pyproject_path = Path("pyproject.toml") + if not pyproject_path.exists(): + print("Error: pyproject.toml not found in the current directory.") + sys.exit(1) + + with open(pyproject_path, "rb") as f: + config = tomllib.load(f) + + issues = [] + for section in ["project", "project.optional-dependencies"]: + if section in config and "dependencies" in config[section]: + deps = config[section]["dependencies"] + for dep in deps: + if "git+https://" in dep and not dep.endswith(".git"): + issues.append(dep) + + if issues: + print("The following git dependencies are missing the .git extension:") + for issue in issues: + print(f" - {issue}") + sys.exit(1) + else: + print("All git dependencies are correctly formatted.") + shell: python diff --git a/.github/workflows/publish-PyPi.yml b/.github/workflows/publish-PyPi.yml deleted file mode 100644 index b5e3e174..00000000 --- a/.github/workflows/publish-PyPi.yml +++ /dev/null @@ -1,62 +0,0 @@ -name: Publish to PyPI -run-name: Publish Python Package to PyPI for release ${{ github.event.release.tag_name }} - -on: - release: - types: [published] - workflow_dispatch: - inputs: - tag_name: - description: 'Git tag to checkout and publish' - required: false - type: string - -jobs: - build: - name: Build distribution 📦 - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - with: - ref: ${{ inputs.tag_name || github.ref }} - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.12" - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: python3 -m build - - name: Store the distribution packages - uses: actions/upload-artifact@v4 - with: - name: python-package-distributions - path: dist/ - publish-to-pypi: - name: Publish to PyPI - needs: - - build - runs-on: ubuntu-latest - - environment: - name: pypi - url: https://pypi.org/p/qcore-utils - - permissions: - id-token: write - - steps: - - name: Download all the dists - uses: actions/download-artifact@v4 - with: - name: python-package-distributions - path: dist/ - - name: Publish distribution to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 00000000..7b177c90 --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,75 @@ +name: Pytest Check + +on: [pull_request] + +jobs: + test: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.13" + - name: Define a cache dependency glob + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Install the project + run: uv sync --all-extras + + - name: Run tests + run: uv run pytest --cov=qcore --cov-report=html tests + + - name: Upload coverage data + uses: actions/upload-artifact@v4 + with: + name: coverage-data + path: .coverage + include-hidden-files: true + if-no-files-found: ignore + + coverage: + needs: test + runs-on: ubuntu-latest + + steps: + - name: Check out the repo + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.13 + + - name: Install dependencies + run: | + python -m pip install --upgrade coverage[toml] + + - name: Download coverage data + uses: actions/download-artifact@v4 + with: + name: coverage-data + + - name: Combine coverage and fail it it’s under 100 % + run: | + python -m coverage html --skip-covered --skip-empty + + # Report and write to summary. + python -m coverage report | sed 's/^/ /' >> $GITHUB_STEP_SUMMARY + + # Report again and fail if under 95%. + python -Im coverage report --fail-under=95 + + - name: Upload HTML report if check failed + uses: actions/upload-artifact@v4 + + with: + name: html-report + path: htmlcov + + if: ${{ failure() }} diff --git a/.gitignore b/.gitignore index 557aca80..20a939bb 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,181 @@ qcore.egg-info .cache/ *.idea/ .pytest_cache + + +# Created by https://www.toptal.com/developers/gitignore/api/python +# Edit at https://www.toptal.com/developers/gitignore?templates=python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +### Python Patch ### +# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration +poetry.toml + +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json + +# End of https://www.toptal.com/developers/gitignore/api/python diff --git a/Jenkinsfile b/Jenkinsfile deleted file mode 100644 index b6b14fe1..00000000 --- a/Jenkinsfile +++ /dev/null @@ -1,45 +0,0 @@ - -pipeline { - agent { - docker { - image 'python:3.13' - // The -u 0 flags means run commands inside the container - // as the user with uid = 0. This user is, by default, the - // root user. So it is effectively saying run the commands - // as root. - args '-u 0:0' - } - } - stages { - stage('Installing OS Dependencies') { - steps { - echo "[[ Install uv ]]" - sh """ - curl -LsSf https://astral.sh/uv/install.sh | sh - """ - } - } - stage('Setting up env') { - steps { - echo "[[ Start virtual environment ]]" - sh """ - source ~/.local/bin/env sh - cd ${env.WORKSPACE} - uv venv - source .venv/bin/activate - uv pip install -e . - """ - } - } - stage('Run regression tests') { - steps { - sh """ - cd ${env.WORKSPACE} - source .venv/bin/activate - cd qcore/test - pytest -s - """ - } - } - } -} diff --git a/MANIFEST.in b/MANIFEST.in index 15be8fff..bc5f914d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1 +1,4 @@ -include qcore/configs/*.json +prune tests +prune .github +prune wiki +prune uv.lock diff --git a/pyproject.toml b/pyproject.toml index 494aaa06..404bbca4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,35 @@ description = "Utils Library" authors = [{ name = "ucgmsim" }] readme = "README.md" requires-python = ">=3.11" -dynamic = ["version", "dependencies"] +dynamic = ["version"] +dependencies = [ + "pandas", + "pyfftw", + "pyproj", + "pooch", + "scipy", + "matplotlib", + "numpy", + "numba>=0.57.0; python_version == '3.11'", + "numba>=0.59.0; python_version == '3.12'", + "numba>=0.61.0; python_version == '3.13'", + "numba>=0.63.0; python_version == '3.14'", + "typer", + "docstring_parser", + "xarray", + "pyyaml", +] + +[project.optional-dependencies] +test = ["pytest", "hypothesis[numpy]", "pytest-cov"] +types = ["pandas-stubs", "scipy-stubs", "types-PyYAML"] +dev = ["ruff", "deptry", "ty"] + +[tool.deptry] +pep621_dev_dependency_groups = ["test", "dev", "types"] + +[tool.coverage.run] +omit = ["qcore/constants.py", "qcore/formats.py"] [tool.setuptools_scm] @@ -16,18 +44,6 @@ dynamic = ["version", "dependencies"] [tool.setuptools.package-dir] qcore = "qcore" -[tool.setuptools.package-data] -"qcore" = [ - "configs/*.json", - "data/*", - "data/*/*", - "data/*/*/*", - "registry/registry.txt", -] - -[tool.setuptools.dynamic] -dependencies = { file = ["requirements.txt"] } - [tool.ruff.lint] extend-select = [ # isort imports diff --git a/qcore/test/__init__.py b/qcore/test/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/runscript.sh b/qcore/test/runscript.sh deleted file mode 100644 index 8a4a6e9a..00000000 --- a/qcore/test/runscript.sh +++ /dev/null @@ -1,11 +0,0 @@ -DIRS='test_*' -curdir=$PWD -for DIR in $DIRS -do -cd ${curdir}/${DIR} -pytest --junitxml ${DIR}.xml -cp -r ./${DIR}.xml /home/tester/.jenkins/workspace/qcore-tests/${DIR}.xml -done -LOG=/home/tester/.jenkins/jobs/qcore-tests/builds/$BUILD_NUMBER/log -sed -i 's/$/
/' ${LOG} - diff --git a/qcore/test/test_geo/__init__.py b/qcore/test/test_geo/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/test_grid/__init__.py b/qcore/test/test_grid/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/test_source_site_dist/__init__.py b/qcore/test/test_source_site_dist/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_locations.npy b/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_locations.npy deleted file mode 100644 index db378edc..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_locations.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_srf_points.npy b/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_srf_points.npy deleted file mode 100644 index c7f7752b..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/input/calc_rrup_rjb_srf_points.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_locations.npy b/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_locations.npy deleted file mode 100644 index db378edc..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_locations.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_header.P b/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_header.P deleted file mode 100644 index de51ca23..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_header.P and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_points.npy b/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_points.npy deleted file mode 100644 index f9c680e0..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/input/calc_rx_ry_srf_points.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rjb.npy b/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rjb.npy deleted file mode 100644 index 821e8344..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rjb.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rrup.npy b/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rrup.npy deleted file mode 100644 index 1b50c24a..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/output/calc_rrup_rjb_rrup.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_rx.npy b/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_rx.npy deleted file mode 100644 index 940b4116..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_rx.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_ry.npy b/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_ry.npy deleted file mode 100644 index 435c4deb..00000000 Binary files a/qcore/test/test_source_site_dist/sample0/output/calc_rx_ry_ry.npy and /dev/null differ diff --git a/qcore/test/test_source_site_dist/test_src_site_dist_calc.py b/qcore/test/test_source_site_dist/test_src_site_dist_calc.py deleted file mode 100644 index 18d28ba1..00000000 --- a/qcore/test/test_source_site_dist/test_src_site_dist_calc.py +++ /dev/null @@ -1,121 +0,0 @@ -""" -Originally written for IM_calculation, but is relocated and modified for qcore. -History of this file: -https://github.com/ucgmsim/IM_calculation/commits/0dac6f172ddbb11e9b4faadf2e3ab27746e8f0d3/IM_calculation/test/test_source_site_dist/test_src_site_dist_calc.py -""" -import os -import pickle - -import numpy as np -import pytest - -from qcore import geo, src_site_dist as ssd - -INPUT = "input" -OUTPUT = "output" - -SAMPLE_NAMES = [("sample0")] - - -@pytest.mark.parametrize("sample_name", SAMPLE_NAMES) -def test_calc_rrub_rjb(sample_name): - function = "calc_rrup_rjb" - - root_path = os.path.join(os.path.dirname(__file__), sample_name) - - srf_points = np.load(os.path.join(root_path, INPUT, function + "_srf_points.npy")) - locations = np.load(os.path.join(root_path, INPUT, function + "_locations.npy")) - - out_rrup = np.load(os.path.join(root_path, OUTPUT, function + "_rrup.npy")) - out_rjb = np.load(os.path.join(root_path, OUTPUT, function + "_rjb.npy")) - - rrup, rjb = ssd.calc_rrup_rjb(srf_points, locations) - - assert np.all(np.isclose(out_rrup, rrup)) - assert np.all(np.isclose(out_rjb, rjb)) - - -BASIC_SRF_POINTS = np.asarray([[0, 0, 0], [1, 0, 0], [0, -1, 1], [1, -1, 1]]) -BASIC_SRF_HEADER = [{"nstrike": 2, "ndip": 2, "strike": 90.0, "length": 2}] -BASIC_STATIONS = np.asarray( - [ - [0, 0, 0], - [0.5, 0, 0], - [*geo.ll_shift(0, 0, 50, 0)[::-1], 0], - [*geo.ll_shift(*geo.ll_shift(0, 0, 50, 270), 100, 0)[::-1], 0], - ] -) -BASIC_RX = np.asarray([0, 0, -50, -100]) -BASIC_RY = np.asarray([-1, geo.ll_dist(0, 0, 0.5, 0) - 1, -1, -51]) - -HOSSACK_SRF_POINTS = np.asarray( - [ - [176.2493, -38.3301, 0.0431], - [176.2202, -38.3495, 0.0431], - [176.2096, -38.3033, 7.886], - [176.1814, -38.3221, 7.886], - ] -) -HOSSACK_SRF_HEADER = [{"nstrike": 2, "ndip": 2, "strike": 230.0, "length": 0.2}] -HOSSACK_STATIONS = np.asarray( - [ - [ - 176.16718461, - -38.27736689, - 0, - ], # location 9.118km down dip of the top centre point - [ - 176.30243581, - -38.40219607, - 0, - ], # location 9.118km up dip of the top centre point - [ - 176.17626422, - -38.35520564, - 0, - ], # Location 3.0383km to the South West of the fault - ] -) -HOSSACK_RX = np.asarray([9.1180, -9.1180, 1.9987]) -HOSSACK_RY = np.asarray([1.56658241, 1.5680196, 6.56920416]) - -RELATIVE_TOLERANCE = 0.001 # 1m tolerance - - -@pytest.mark.parametrize( - ["srf_points", "srf_header", "station_location", "rx_bench", "ry_bench"], - [ - (BASIC_SRF_POINTS, BASIC_SRF_HEADER, BASIC_STATIONS, BASIC_RX, BASIC_RY), - ( - HOSSACK_SRF_POINTS, - HOSSACK_SRF_HEADER, - HOSSACK_STATIONS, - HOSSACK_RX, - HOSSACK_RY, - ), - ], -) -def test_calc_rx_ry_basic(srf_points, srf_header, station_location, rx_bench, ry_bench): - rx, ry = ssd.calc_rx_ry(srf_points, srf_header, station_location) - assert np.all(np.isclose(rx, rx_bench, rtol=RELATIVE_TOLERANCE)) - assert np.all(np.isclose(ry, ry_bench, rtol=RELATIVE_TOLERANCE)) - - -@pytest.mark.parametrize("sample_name", SAMPLE_NAMES) -def test_calc_rx_ry(sample_name): - function = "calc_rx_ry" - - root_path = os.path.join(os.path.dirname(__file__), sample_name) - srf_points = np.load(os.path.join(root_path, INPUT, function + "_srf_points.npy")) - srf_header = pickle.load( - open(os.path.join(root_path, INPUT, function + "_srf_header.P"), "rb") - ) - locations = np.load(os.path.join(root_path, INPUT, function + "_locations.npy")) - - out_rx = np.load(os.path.join(root_path, OUTPUT, function + "_rx.npy")) - out_ry = np.load(os.path.join(root_path, OUTPUT, function + "_ry.npy")) - - rx, ry = ssd.calc_rx_ry(srf_points, srf_header, locations) - - assert np.all(np.isclose(out_rx, rx)) - assert np.all(np.isclose(out_ry, ry)) diff --git a/qcore/test/test_xyts/__init__.py b/qcore/test/test_xyts/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/tool/__init__.py b/qcore/test/tool/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/qcore/test/tool/create_binaryfile.py b/qcore/test/tool/create_binaryfile.py deleted file mode 100644 index 9805aa6f..00000000 --- a/qcore/test/tool/create_binaryfile.py +++ /dev/null @@ -1,45 +0,0 @@ -""" Creates 2 benchmark binary files for testing of the functions srf.srf2llv(srffile) and srf.srf2llv_py(srffile) -First create these binary files and put in the sample output folder, (if you are testing it for a new SRF) -command to run: -python create_binaryfile.py test/test_srf/sample2/input/Tuakana13_HYP01-01_S1244.srf """ - -from qcore import srf -import numpy as np -import sys - -# output for Python and C implementations -OUT_C = "out_array_srf2llv.bin" -OUT_PY = "out_array_srf2llv_py.bin" - - -def srf2bin(srf_file, out_file, py_method=False): - """srffile: path to input srf file - islist: srffile function return a numpy array or a list(of numpy array(s)) - islist is true for srf2llv_py; false for srfllv. default false - """ - - # load data - if py_method: - out_array_list = srf.srf2llv_py(srf_file) - out_array = out_array_list[0] - for array in out_array_list[1:]: - out_array = np.concatenate([out_array, array]) - else: - out_array = srf.srf2llv(srf_file) - - # save data - try: - out_array.astype(np.float32).tofile(out_file) - except Exception as e: - sys.exit(e) - - -# retrieve input srf from command line -try: - srf_file = sys.argv[1] -except IndexError: - sys.exit("Please provide the path to the SRF file as an argument.") - -# produce 2 versions using the different methods -srf2bin(srf_file, OUT_C) -srf2bin(srf_file, OUT_PY, py_method=True) diff --git a/qcore/test/tool/utils.py b/qcore/test/tool/utils.py deleted file mode 100644 index 3121fee8..00000000 --- a/qcore/test/tool/utils.py +++ /dev/null @@ -1,31 +0,0 @@ -""" -Common functions for the test script -""" - -import numpy as np -import os - -ERROR_LIMIT = 1e-06 - - -def compare_np_array(array1, array2, error_limit=ERROR_LIMIT): - """first test if the two numpy arrays are of the same shape - if pass, then test if the relative error between the two arrays are <= the preset error limit - if any of the test fails, assertion error will be raised; - array1: a numpy array from sample output, will be used as the denominator, - array2: a numpy array from test output, makes part of the numerator. - error_limit: preset error_limit to be compared with the relative error (array1-array2)/array1 - """ - - assert array1.shape == array2.shape - assert np.all(np.isclose(array1, array2, rtol=error_limit)) - - -def remove_file(abs_path): - """remove test output file if successfully passed the test - abs_path: abs path of the file to be removed - """ - try: - os.remove(abs_path) - except (IOError, OSError): - raise diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index c5441e1d..00000000 --- a/requirements.txt +++ /dev/null @@ -1,18 +0,0 @@ -pandas -pyfftw -pytest -pytest-black -alphashape -descartes -filelock -pyproj -pooch -requests -shapely -numpy -numba -hypothesis[numpy] -typer -docstring_parser -xarray -pyyaml diff --git a/qcore/test/test_timeseries/R01_seis-00041.e3d b/tests/R01_seis-00041.e3d similarity index 100% rename from qcore/test/test_timeseries/R01_seis-00041.e3d rename to tests/R01_seis-00041.e3d diff --git a/qcore/test/test_siteamp/amp_bandpass_benchmark.pkl b/tests/amp_bandpass_benchmark.pkl similarity index 100% rename from qcore/test/test_siteamp/amp_bandpass_benchmark.pkl rename to tests/amp_bandpass_benchmark.pkl diff --git a/qcore/test/test_siteamp/cb_2014_test.csv b/tests/cb_2014_test.csv similarity index 100% rename from qcore/test/test_siteamp/cb_2014_test.csv rename to tests/cb_2014_test.csv diff --git a/qcore/test/test_siteamp/interpolate_benchmark.pkl b/tests/interpolate_benchmark.pkl similarity index 100% rename from qcore/test/test_siteamp/interpolate_benchmark.pkl rename to tests/interpolate_benchmark.pkl diff --git a/qcore/test/test_geo/sample1/README.md b/tests/sample1/README.md similarity index 58% rename from qcore/test/test_geo/sample1/README.md rename to tests/sample1/README.md index 5104e7da..5879ba4c 100644 --- a/qcore/test/test_geo/sample1/README.md +++ b/tests/sample1/README.md @@ -1,2 +1,2 @@ # readme for test_geo -The sample input and output are self-contained in the test method. So no need to provide any files as sample input or output. \ No newline at end of file +The sample input and output are self-contained in the test method. So no need to provide any files as sample input or output. diff --git a/qcore/test/test_xyts/sample1/output/out_tslice-1 b/tests/sample1/output/out_tslice-1 similarity index 100% rename from qcore/test/test_xyts/sample1/output/out_tslice-1 rename to tests/sample1/output/out_tslice-1 diff --git a/qcore/test/test_xyts/sample1/output/out_tslice0 b/tests/sample1/output/out_tslice0 similarity index 100% rename from qcore/test/test_xyts/sample1/output/out_tslice0 rename to tests/sample1/output/out_tslice0 diff --git a/qcore/test/test_xyts/sample1/output/out_tslice1 b/tests/sample1/output/out_tslice1 similarity index 100% rename from qcore/test/test_xyts/sample1/output/out_tslice1 rename to tests/sample1/output/out_tslice1 diff --git a/qcore/test/test_xyts/sample1/output/out_tslice2 b/tests/sample1/output/out_tslice2 similarity index 100% rename from qcore/test/test_xyts/sample1/output/out_tslice2 rename to tests/sample1/output/out_tslice2 diff --git a/qcore/test/test_xyts/sample1/output/sample_mmiout b/tests/sample1/output/sample_mmiout similarity index 100% rename from qcore/test/test_xyts/sample1/output/sample_mmiout rename to tests/sample1/output/sample_mmiout diff --git a/qcore/test/test_xyts/sample1/output/sample_pgvout b/tests/sample1/output/sample_pgvout similarity index 100% rename from qcore/test/test_xyts/sample1/output/sample_pgvout rename to tests/sample1/output/sample_pgvout diff --git a/tests/test_archive_structure.py b/tests/test_archive_structure.py new file mode 100644 index 00000000..e49aab77 --- /dev/null +++ b/tests/test_archive_structure.py @@ -0,0 +1,34 @@ +from pathlib import Path + +from qcore import archive_structure + + +def test_get_fault_source_dir() -> None: + fault_dir = Path("/path/to/fault") + result = archive_structure.get_fault_source_dir(fault_dir) + assert result == Path("/path/to/fault/Source") + assert isinstance(result, Path) + + +def test_get_fault_im_dir() -> None: + fault_dir = Path("/path/to/fault") + result = archive_structure.get_fault_im_dir(fault_dir) + assert result == Path("/path/to/fault/IM") + assert isinstance(result, Path) + + +def test_get_IM_csv_from_root() -> None: # noqa: N802 + archive_root = Path("/archive/root") + realisation = "SomeFault_REL01" + result = archive_structure.get_IM_csv_from_root(archive_root, realisation) + expected = Path("/archive/root/SomeFault/IM/SomeFault_REL01.csv") + assert result == expected + assert isinstance(result, Path) + + +def test_get_IM_csv_from_root_different_realisation() -> None: # noqa: N802 + archive_root = Path("/archive/root") + realisation = "AlpineF2K3T1_REL03" + result = archive_structure.get_IM_csv_from_root(archive_root, realisation) + expected = Path("/archive/root/AlpineF2K3T1/IM/AlpineF2K3T1_REL03.csv") + assert result == expected diff --git a/qcore/test/test_cli/test_cli.py b/tests/test_cli.py similarity index 54% rename from qcore/test/test_cli/test_cli.py rename to tests/test_cli.py index b25db343..8d9efbb7 100644 --- a/qcore/test/test_cli/test_cli.py +++ b/tests/test_cli.py @@ -1,3 +1,4 @@ +import inspect from typing import Annotated, Optional import pytest @@ -8,7 +9,7 @@ runner = CliRunner() -DOCSTRING = """Example command. +DOCSTRING = inspect.cleandoc("""Example command. Parameters ---------- @@ -16,7 +17,7 @@ This is the first parameter. param2 : Optional[str] This is an optional parameter. -""" +""") def test_from_docstring(capsys: pytest.CaptureFixture[str]): @@ -41,7 +42,8 @@ def example_command( print("Hello World", param1, param2) # Ensure the docstring is unchanged - assert example_command.__doc__ == DOCSTRING + assert example_command.__doc__, "Example command missing docstring." + assert inspect.cleandoc(example_command.__doc__) == DOCSTRING # Run `--help` and check output result = runner.invoke(app, ["--help"]) @@ -57,7 +59,91 @@ def example_command( assert captured.out.strip() == "Hello World 1 c" -def test_from_docstring_kwargs(capsys: pytest.CaptureFixture[str]): +def test_from_docstring_no_docstring_returns_same_function() -> None: + app = typer.Typer() + + def func_no_docstring(x: int): # no docstring! + return x + 1 + + decorated = cli.from_docstring(app)(func_no_docstring) + assert decorated is func_no_docstring + + +def test_from_docstring_oldstyle_and_no_docstring( + capsys: pytest.CaptureFixture[str], +) -> None: + """Test from_docstring with old-style Typer annotations and missing docstring.""" + + app = typer.Typer() + + # --- old-style Typer defaults --- + @cli.from_docstring(app, name="oldstyle_command") + def oldstyle_command( + param1: int = typer.Argument(...), + param2: Optional[str] = typer.Option("a"), + ) -> None: + """Old-style command. + + Parameters + ---------- + param1 : int + This is the first old-style parameter. + param2 : Optional[str] + This is an optional old-style parameter. + """ + print("Old-style", param1, param2) + + # Check help output for the old-style command (should still parse the docstring) + result = runner.invoke(app, ["--help"]) + assert result.exit_code == 0 + assert "Old-style command." in result.output + assert "This is the first old-style parameter." in result.output + assert "This is an optional old-style parameter." in result.output + + # Execute both commands + result = runner.invoke(app, ["5", "--param2", "z"]) + assert result.exit_code == 0 + assert result.stdout.strip() == "Old-style 5 z" + + +def test_from_docstring_implicit_argument_options( + capsys: pytest.CaptureFixture[str], +) -> None: + """Test from_docstring with implicit Typer annotations and missing docstring.""" + + app = typer.Typer() + + # --- Implicit Typer defaults --- + @cli.from_docstring(app, name="implicit_command") + def implicit_command( + param1: int, + param2: str = "a", + ) -> None: + """Implicit command. + + Parameters + ---------- + param1 : int + This is the first implicit parameter. + param2 : Optional[str] + This is an optional implicit parameter. + """ + print("Implicit", param1, param2) + + # Check help output for the implicit command (should still parse the docstring) + result = runner.invoke(app, ["--help"]) + assert result.exit_code == 0 + assert "Implicit command." in result.output + assert "This is the first implicit parameter." in result.output + assert "This is an optional implicit parameter." in result.output + + # Execute both commands + result = runner.invoke(app, ["5", "--param2", "z"]) + assert result.exit_code == 0 + assert result.stdout.strip() == "Implicit 5 z" + + +def test_from_docstring_kwargs(capsys: pytest.CaptureFixture[str]) -> None: """Test the from_docstring decorator passes kwargs correctly.""" pytest.skip("Broken") app = typer.Typer() @@ -95,7 +181,8 @@ def example_command_2( print("Hello World from command 2", param1, param2) # Ensure the docstring is unchanged - assert example_command.__doc__ == DOCSTRING + assert example_command.__doc__, "Example command is missing docstring" + assert inspect.cleandoc(example_command.__doc__) == DOCSTRING # Run `--help` and check output result = runner.invoke(app, ["command_1", "--help"]) diff --git a/qcore/test/test_coordinates/test_coordinates.py b/tests/test_coordinates.py similarity index 84% rename from qcore/test/test_coordinates/test_coordinates.py rename to tests/test_coordinates.py index ff2273b3..41722809 100644 --- a/qcore/test/test_coordinates/test_coordinates.py +++ b/tests/test_coordinates.py @@ -1,4 +1,3 @@ - import numpy as np import pyproj import pytest @@ -9,13 +8,28 @@ def latitude(min_value: float = -90.0, max_value: float = 90.0, **kwargs): - return st.floats(min_value=min_value, max_value=max_value, allow_nan=False, allow_infinity=False, **kwargs) + return st.floats( + min_value=min_value, + max_value=max_value, + allow_nan=False, + allow_infinity=False, + **kwargs, + ) + def longitude(min_value: float = -180.0, max_value: float = 180.0, **kwargs): - return st.floats(min_value=min_value, max_value=max_value, allow_nan=False, allow_infinity=False, **kwargs) + return st.floats( + min_value=min_value, + max_value=max_value, + allow_nan=False, + allow_infinity=False, + **kwargs, + ) + + +GEOD = pyproj.Geod(ellps="sphere", a=R_EARTH * 1000.0, b=R_EARTH * 1000.0) +HALF_SPHERE = R_EARTH * np.pi / 2.0 # Half-circumference of a hemisphere -GEOD = pyproj.Geod(ellps='sphere', a=R_EARTH * 1000.0, b=R_EARTH * 1000.0) -HALF_SPHERE = R_EARTH * np.pi / 2.0 # Half-circumference of a hemisphere @st.composite def points_in_same_hemisphere(draw): @@ -44,7 +58,6 @@ def test_projection_inverse_is_identity(points, mrot): assert pytest.approx(np.array([lat, lon]), rel=1e-4, abs=1e-4) == back - # For this test we must exclude the poles because they don't behave # like the other points wrt. the longitude. Namely the longitude is # always 0 at the poles (because it is undefined), so shifting in @@ -54,7 +67,6 @@ def test_projection_inverse_is_identity(points, mrot): def test_identity_rotation_preserves_axes(mlat, mlon): proj = SphericalProjection(mlon, mlat, 0) - # The coordinate frame of reference is south is y-positive, west # is x-positive. This checks that south is eps = 1e-4 @@ -66,19 +78,18 @@ def test_identity_rotation_preserves_axes(mlat, mlon): assert proj(mlat, mlon - eps)[0] < 0.0 - @given(mlat=latitude(), mlon=longitude(), mrot=st.floats(-360, 360)) def test_center_maps_to_origin(mlat, mlon, mrot): proj = SphericalProjection(mlon, mlat, mrot) out = proj.project(mlat, mlon) - assert pytest.approx(np.zeros_like(out), abs=1e-3) == out + assert pytest.approx(np.zeros_like(out), abs=1e-3) == out @given(points=points_in_same_hemisphere(), mrot=st.floats(-360, 360)) def test_projection_preserves_distance(points, mrot): mlat, mlon, lat, lon = points proj = SphericalProjection(mlon, mlat, mrot) - geod = proj.geod # Pyproj spherical geodesic + geod = proj.geod # Pyproj spherical geodesic dist1 = GEOD.inv(mlon, mlat, lon, lat)[2] / 1000.0 @@ -98,6 +109,7 @@ def test_projection_preserves_depth(): projected = proj.project(lat, lon, depth) assert pytest.approx(projected[2]) == depth # Depth should remain unchanged + def test_inverse_projection_preserves_depth(): # Test that the projection does not change depth proj = SphericalProjection(0, 0, 0) # Centered at the origin @@ -105,4 +117,6 @@ def test_inverse_projection_preserves_depth(): x, y = 10.0, 20.0 # Arbitrary latitude and longitude projected = proj.inverse(x, y, depth) - assert pytest.approx(projected[2], abs=1e-6) == depth # Depth should remain unchanged + assert ( + pytest.approx(projected[2], abs=1e-6) == depth + ) # Depth should remain unchanged diff --git a/qcore/test/test_geo/test_geo.py b/tests/test_geo.py similarity index 100% rename from qcore/test/test_geo/test_geo.py rename to tests/test_geo.py diff --git a/qcore/test/test_grid/test_grid.py b/tests/test_grid.py similarity index 92% rename from qcore/test/test_grid/test_grid.py rename to tests/test_grid.py index 78de8150..1e75e802 100644 --- a/qcore/test/test_grid/test_grid.py +++ b/tests/test_grid.py @@ -6,7 +6,7 @@ from qcore import coordinates, grid -def test_grid_corners(): +def test_grid_corners() -> None: """Test the grid_corners function to verify corner calculations""" centroid = np.array([-43.5, 172.5]) strike = 90 @@ -36,7 +36,7 @@ def test_grid_corners(): assert np.allclose(np.mean(corners, axis=0)[:2], centroid) -def test_coordinate_meshgrid(): +def test_coordinate_meshgrid() -> None: """Test the coordinate_meshgrid function to verify grid creation""" origin = np.array([-43.5, 172.5, 5000]) # (lat, lon, depth in m) x_upper = np.array([-43.45498004, 172.50037108, 5000.0]) @@ -62,7 +62,7 @@ def test_coordinate_meshgrid(): assert np.all(meshgrid[:, :, 2] == pytest.approx(origin[2], rel=1e-2)) -def test_coordinate_meshgrid_x_boundary(): +def test_coordinate_meshgrid_x_boundary() -> None: """Test the coordinate_meshgrid function when you only have one patch in x and y direction""" origin = np.array([-43.5, 172.5, 5000]) # (lat, lon, depth in m) x_upper = np.array([-43.45498004, 172.50037108, 5000.0]) @@ -70,7 +70,7 @@ def test_coordinate_meshgrid_x_boundary(): resolution = coordinates.distance_between_wgs_depth_coordinates( x_upper, origin ) # 1 km resolution - + assert isinstance(resolution, np.floating) meshgrid = grid.coordinate_patchgrid(origin, x_upper, y_bottom, resolution) assert meshgrid.shape[2] == 3 # Should have shape (ny, nx, 3) for (lat, lon, depth) ny, nx = meshgrid.shape[:2] @@ -86,7 +86,7 @@ def test_coordinate_meshgrid_x_boundary(): ) -def test_coordinate_patchgrid_different_nx_ny(): +def test_coordinate_patchgrid_different_nx_ny() -> None: """Test the coordinate_meshgrid function to verify nx/ny parameters""" origin = np.array([-43.5, 172.5, 5000]) # (lat, lon, depth in m) x_upper = np.array([-43.45498004, 172.50037108, 5000.0]) @@ -97,7 +97,7 @@ def test_coordinate_patchgrid_different_nx_ny(): assert meshgrid.shape == (ny, nx, 3) -def test_coordinate_patchgrid(): +def test_coordinate_patchgrid() -> None: """Test the coordinate_meshgrid function to verify grid creation""" origin = np.array([-43.5, 172.5, 5000]) # (lat, lon, depth in m) x_upper = np.array([-43.45498004, 172.50037108, 5000.0]) @@ -119,6 +119,8 @@ def test_coordinate_patchgrid(): ny, nx = meshgrid.shape[:2] width = coordinates.distance_between_wgs_depth_coordinates(y_bottom, origin) length = coordinates.distance_between_wgs_depth_coordinates(x_upper, origin) + assert isinstance(length, np.floating) + assert isinstance(width, np.floating) assert ny == round(length / resolution) assert nx == round(width / resolution) @@ -132,6 +134,8 @@ def test_coordinate_patchgrid(): "length,resolution,expected", [(10, 5, 3), (10, 3, 5), (10000, 1000, 11), (1500, 500, 4)], ) -def test_gridpoint_count_in_length(length: float, resolution: float, expected: int): +def test_gridpoint_count_in_length( + length: float, resolution: float, expected: int +) -> None: """Test gridpoint_count_in_length function""" assert grid.gridpoint_count_in_length(length, resolution) == expected diff --git a/tests/test_nhm.py b/tests/test_nhm.py new file mode 100644 index 00000000..acaabff0 --- /dev/null +++ b/tests/test_nhm.py @@ -0,0 +1,307 @@ +from io import StringIO +from pathlib import Path + +import numpy as np +import pytest + +from qcore import nhm + + +def test_mag2mom_nm() -> None: + # Test magnitude to moment conversion + mw = 7.0 + result = nhm.mag2mom_nm(mw) + + # Expected: 10^(9.05 + 1.5 * 7.0) = 10^19.55 + expected = 10 ** (9.05 + 1.5 * 7.0) + assert result == pytest.approx(expected) + + +def test_mag2mom_nm_small_magnitude() -> None: + mw = 5.0 + result = nhm.mag2mom_nm(mw) + expected = 10 ** (9.05 + 1.5 * 5.0) + assert result == pytest.approx(expected) + + +def test_nhm_fault_creation() -> None: + # Test creating an NHMFault instance + trace = np.array([[172.0, -43.0], [172.1, -43.1]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=0.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + assert fault.name == "TestFault" + assert fault.mw == 7.0 + assert fault.length == 50.0 + assert fault.dip == 45.0 + assert np.array_equal(fault.trace, trace) + + +def test_load_nhm_single_fault(tmp_path: Path): + # Minimal fake NHM content with one fault entry + content = """Header line 1 +Header line 2 +Header line 3 +Header line 4 +Header line 5 +Header line 6 +Header line 7 +Header line 8 +Header line 9 +Header line 10 +Header line 11 +Header line 12 +Header line 13 +Header line 14 +Header line 15 +FakeFault +TECTONIC FAULTTYPE +10.0 0.5 +45.0 5.0 +270.0 +90.0 +15.0 1.0 +5.0 4.0 6.0 +1.2 0.1 +0.9 0.05 +7.1 1200.0 +100.0 200.0 +101.0 201.0""" + + nhm_file = tmp_path / "fake_faults.nhm" + nhm_file.write_text(content) + + # Run loader with skiprows=15 to skip header lines + faults = nhm.load_nhm(str(nhm_file), skiprows=15) + + # Basic structure check + assert isinstance(faults, dict) + assert "FakeFault" in faults + fault = faults["FakeFault"] + assert isinstance(fault, nhm.NHMFault) + + # Sanity check on parsed values + assert np.isclose(fault.length, 10.0) + assert np.isclose(fault.dip, 45.0) + assert fault.trace.shape == (1, 2) + + +def test_nhm_fault_write() -> None: + # Test writing an NHMFault to a file + trace = np.array([[172.0, -43.0], [172.1, -43.1]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=0.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + output = StringIO() + fault.write(output, header=False) + content = output.getvalue() + + # Check that key information is written + assert "TestFault" in content + assert "ACTIVE_SHALLOW" in content + assert "REVERSE" in content + assert "2\n" in content # Number of trace points + + +def test_nhm_fault_write_with_header() -> None: + trace = np.array([[172.0, -43.0]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=0.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + output = StringIO() + fault.write(output, header=True) + content = output.getvalue() + + # Check that header is included + assert "FAULT SOURCES" in content + assert "TestFault" in content + + +def test_nhm_fault_sample_2012() -> None: + # Test sampling/perturbation of fault parameters + np.random.seed(42) # Set seed for reproducibility + + trace = np.array([[172.0, -43.0], [172.1, -43.1]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=2.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + sampled_fault = fault.sample_2012(mw_area_scaling=True, mw_perturbation=True) + + # Check that a new fault is returned + assert isinstance(sampled_fault, nhm.NHMFault) + assert sampled_fault.name == fault.name + + # Sigmas should be set to 0 in sampled fault + assert sampled_fault.length_sigma == 0 + assert sampled_fault.dip_sigma == 0 + assert sampled_fault.dbottom_sigma == 0 + assert sampled_fault.slip_rate_sigma == 0 + assert sampled_fault.coupling_coeff_sigma == 0 + + # Trace should be preserved + assert np.array_equal(sampled_fault.trace, fault.trace) + + +def test_nhm_fault_sample_2012_without_mw_perturbation() -> None: + np.random.seed(42) + + trace = np.array([[172.0, -43.0]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=2.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + sampled_fault = fault.sample_2012(mw_area_scaling=True, mw_perturbation=False) + + # Without perturbation, Mw should remain the same + assert sampled_fault.mw == fault.mw + + +def test_get_fault_header_points() -> None: + # Test getting fault header and points + trace = np.array([[172.0, -43.0], [172.1, -43.1]]) + + fault = nhm.NHMFault( + name="TestFault", + tectonic_type="ACTIVE_SHALLOW", + fault_type="REVERSE", + length=50.0, + length_sigma=5.0, + dip=45.0, + dip_sigma=5.0, + dip_dir=90.0, + rake=90.0, + dbottom=20.0, + dbottom_sigma=2.0, + dtop=0.0, + dtop_min=0.0, + dtop_max=5.0, + slip_rate=5.0, + slip_rate_sigma=1.0, + coupling_coeff=0.9, + coupling_coeff_sigma=0.1, + mw=7.0, + recur_int_median=1000.0, + trace=trace, + ) + + header, points = nhm.get_fault_header_points(fault) + + # Header should be a list of dictionaries + assert isinstance(header, list) + assert len(header) > 0 + assert isinstance(header[0], dict) + assert "nstrike" in header[0] + assert "ndip" in header[0] + + # Points should be a numpy array + assert isinstance(points, np.ndarray) + assert points.shape[1] == 3 # lon, lat, depth diff --git a/tests/test_point_in_polygon.py b/tests/test_point_in_polygon.py new file mode 100644 index 00000000..db4e069d --- /dev/null +++ b/tests/test_point_in_polygon.py @@ -0,0 +1,59 @@ +import numpy as np + +from qcore import point_in_polygon + + +def test_is_inside_postgis_point_inside() -> None: + # Square polygon from (0,0) to (10,10) + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [10.0, 10.0], [0.0, 10.0]]) + point = np.array([5.0, 5.0]) + + result = point_in_polygon.is_inside_postgis(polygon, point) + assert result == 1 + + +def test_is_inside_postgis_point_outside() -> None: + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [10.0, 10.0], [0.0, 10.0]]) + point = np.array([15.0, 15.0]) + + result = point_in_polygon.is_inside_postgis(polygon, point) + assert result == 0 + + +def test_is_inside_postgis_point_on_edge() -> None: + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [10.0, 10.0], [0.0, 10.0]]) + # Use a point that's exactly on an edge with proper alignment + point = np.array([5.0, 0.0]) + + result = point_in_polygon.is_inside_postgis(polygon, point) + assert result == 2 # On edge + + +def test_is_inside_postgis_parallel_single_point() -> None: + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [10.0, 10.0], [0.0, 10.0]]) + points = np.array([[5.0, 5.0]]) + + result = point_in_polygon.is_inside_postgis_parallel(points, polygon) + assert result.shape == (1,) + assert result[0] + + +def test_is_inside_postgis_parallel_multiple_points() -> None: + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [10.0, 10.0], [0.0, 10.0]]) + points = np.array([[5.0, 5.0], [15.0, 15.0], [0.0, 5.0]]) + + result = point_in_polygon.is_inside_postgis_parallel(points, polygon) + assert result.shape == (3,) + assert result[0] # inside + assert not result[1] # outside + assert result[2] # on edge (returns 2, which is truthy) + + +def test_is_inside_postgis_triangle() -> None: + # Triangle polygon + polygon = np.array([[0.0, 0.0], [10.0, 0.0], [5.0, 10.0]]) + point_inside = np.array([5.0, 3.0]) + point_outside = np.array([15.0, 15.0]) # Clearly outside + + assert point_in_polygon.is_inside_postgis(polygon, point_inside) == 1 + assert point_in_polygon.is_inside_postgis(polygon, point_outside) == 0 diff --git a/tests/test_shared.py b/tests/test_shared.py new file mode 100644 index 00000000..5b0d614d --- /dev/null +++ b/tests/test_shared.py @@ -0,0 +1,103 @@ +import tempfile +from pathlib import Path + +import pytest + +from qcore import shared + + +def test_get_stations_without_locations() -> None: + # Create a temporary station file + with tempfile.NamedTemporaryFile(mode="w", delete=False, suffix=".txt") as f: + f.write("# Comment line\n") + f.write("172.5 -43.5 STAT1\n") + f.write("173.0 -44.0 STAT2\n") + f.write("174.5 -45.5 STAT3\n") + station_file = f.name + + try: + result = shared.get_stations(station_file, locations=False) + assert isinstance(result, list) + assert len(result) == 3 + assert result == ["STAT1", "STAT2", "STAT3"] + finally: + Path(station_file).unlink() + + +def test_get_stations_with_locations() -> None: + with tempfile.NamedTemporaryFile(mode="w", delete=False, suffix=".txt") as f: + f.write("172.5 -43.5 STAT1\n") + f.write("173.0 -44.0 STAT2\n") + station_file = f.name + + try: + stations, lats, lons = shared.get_stations(station_file, locations=True) + assert isinstance(stations, list) + assert isinstance(lats, list) + assert isinstance(lons, list) + assert len(stations) == 2 + assert len(lats) == 2 + assert len(lons) == 2 + assert stations == ["STAT1", "STAT2"] + assert lats == pytest.approx([-43.5, -44.0]) + assert lons == pytest.approx([172.5, 173.0]) + finally: + Path(station_file).unlink() + + +def test_get_corners() -> None: + with tempfile.NamedTemporaryFile(mode="w", delete=False, suffix=".txt") as f: + f.write("# Model params\n") + f.write(" c1= 172.164 -41.414\n") + f.write(" c2= 172.500 -41.200\n") + f.write(" c3= 173.000 -41.800\n") + f.write(" c4= 172.700 -42.100\n") + model_params_file = f.name + + try: + result = shared.get_corners(model_params_file, gmt_format=False) + assert isinstance(result, list) + assert len(result) == 4 + assert result[0] == pytest.approx((172.164, -41.414)) + assert result[1] == pytest.approx((172.500, -41.200)) + assert result[2] == pytest.approx((173.000, -41.800)) + assert result[3] == pytest.approx((172.700, -42.100)) + finally: + Path(model_params_file).unlink() + + +def test_get_corners_with_gmt_format() -> None: + with tempfile.NamedTemporaryFile(mode="w", delete=False, suffix=".txt") as f: + f.write(" c1= 172.164 -41.414\n") + f.write(" c2= 172.500 -41.200\n") + f.write(" c3= 173.000 -41.800\n") + f.write(" c4= 172.700 -42.100\n") + model_params_file = f.name + + try: + corners, cnr_str = shared.get_corners(model_params_file, gmt_format=True) + assert isinstance(corners, list) + assert isinstance(cnr_str, str) + assert len(corners) == 4 + assert "172.164 -41.414" in cnr_str + # Check for the coordinate - may be formatted differently (172.5 vs 172.500) + assert "172.5" in cnr_str or "172.500" in cnr_str + assert "-41.2" in cnr_str or "-41.200" in cnr_str + finally: + Path(model_params_file).unlink() + + +@pytest.mark.parametrize( + "station_name,expected", + [ + ("abcdef1", True), + ("1234567", True), + ("abc1234", True), + ("ABCDEF1", False), # Contains capital + ("abc123", False), # Too short (only 6 chars) + ("STAT01", False), # Contains capitals + ], +) +def test_is_virtual_station(station_name: str, expected: bool): + result = shared.is_virtual_station(station_name) + assert result == expected diff --git a/tests/test_simulation_structure.py b/tests/test_simulation_structure.py new file mode 100644 index 00000000..92bedabb --- /dev/null +++ b/tests/test_simulation_structure.py @@ -0,0 +1,122 @@ +import os + +from qcore import simulation_structure + + +def test_get_fault_from_realisation_simple() -> None: + realisation = "AlpineF2K3T1_REL01" + result = simulation_structure.get_fault_from_realisation(realisation) + assert result == "AlpineF2K3T1" + + +def test_get_fault_from_realisation_with_path() -> None: + realisation = "/path/to/simulation/SomeFault_REL05" + result = simulation_structure.get_fault_from_realisation(realisation) + assert result == "SomeFault" + + +def test_get_realisation_name() -> None: + result = simulation_structure.get_realisation_name("MyFault", 3) + assert result == "MyFault_REL03" + + +def test_get_realisation_name_single_digit() -> None: + result = simulation_structure.get_realisation_name("TestFault", 1) + assert result == "TestFault_REL01" + + +def test_get_realisation_name_double_digit() -> None: + result = simulation_structure.get_realisation_name("TestFault", 15) + assert result == "TestFault_REL15" + + +def test_get_srf_info_location() -> None: + realisation = "AlpineF2_REL01" + result = simulation_structure.get_srf_info_location(realisation) + expected = os.path.join("AlpineF2", "Srf", "AlpineF2_REL01.info") + assert result == expected + + +def test_get_srf_dir() -> None: + cybershake_root = "/cybershake" + realisation = "MyFault_REL02" + result = simulation_structure.get_srf_dir(cybershake_root, realisation) + expected = os.path.join("/cybershake", "Data", "Sources", "MyFault", "Srf") + assert result == expected + + +def test_get_srf_location() -> None: + realisation = "TestFault_REL03" + result = simulation_structure.get_srf_location(realisation) + expected = os.path.join("TestFault", "Srf", "TestFault_REL03.srf") + assert result == expected + + +def test_get_srf_path() -> None: + cybershake_root = "/cybershake" + realisation = "AlpineF2_REL01" + result = simulation_structure.get_srf_path(cybershake_root, realisation) + expected = os.path.join( + "/cybershake", "Data", "Sources", "AlpineF2", "Srf", "AlpineF2_REL01.srf" + ) + assert result == expected + + +def test_get_fault_dir() -> None: + cybershake_root = "/cybershake" + fault_name = "MyFault" + result = simulation_structure.get_fault_dir(cybershake_root, fault_name) + expected = os.path.join("/cybershake", "Runs", "MyFault") + assert result == expected + + +def test_get_sim_dir() -> None: + cybershake_root = "/cybershake" + realisation = "MyFault_REL01" + result = simulation_structure.get_sim_dir(cybershake_root, realisation) + expected = os.path.join("/cybershake", "Runs", "MyFault", "MyFault_REL01") + assert result == expected + + +def test_get_im_calc_dir_no_realisation() -> None: + sim_root = "/sim/root" + result = simulation_structure.get_im_calc_dir(sim_root) + assert result == "/sim/root/IM_calc" + + +def test_get_im_calc_dir_with_realisation() -> None: + sim_root = "/sim/root" + realisation = "MyFault_REL01" + result = simulation_structure.get_im_calc_dir(sim_root, realisation) + expected = os.path.join("/sim/root", "Runs", "MyFault", "MyFault_REL01", "IM_calc") + assert result == expected + + +def test_get_IM_csv_from_root() -> None: # noqa: N802 + cybershake_root = "/cybershake" + realisation = "MyFault_REL01" + result = simulation_structure.get_IM_csv_from_root(cybershake_root, realisation) + expected = os.path.join( + "/cybershake", + "Runs", + "MyFault", + "MyFault_REL01", + "IM_calc", + "MyFault_REL01.csv", + ) + assert result == expected + + +def test_get_fault_yaml_path_with_fault() -> None: + sim_root = "/sim/root" + fault_name = "MyFault" + result = simulation_structure.get_fault_yaml_path(sim_root, fault_name) + expected = os.path.join("/sim/root", "MyFault", "fault_params.yaml") + assert result == expected + + +def test_get_fault_yaml_path_without_fault() -> None: + sim_root = "/sim/root" + result = simulation_structure.get_fault_yaml_path(sim_root) + expected = os.path.join("/sim/root", "fault_params.yaml") + assert result == expected diff --git a/qcore/test/test_siteamp/test_siteamp.py b/tests/test_siteamp.py similarity index 85% rename from qcore/test/test_siteamp/test_siteamp.py rename to tests/test_siteamp.py index a74b5ae6..cfa658a2 100644 --- a/qcore/test/test_siteamp/test_siteamp.py +++ b/tests/test_siteamp.py @@ -210,7 +210,7 @@ def test_dc_component_is_unity(basic_setup: dict): np.all(result[:, 0] == 1.0) -def test_single_site(): +def test_single_site() -> None: """Test function with single site (1D amplification array).""" fftfreq = np.logspace(-1, 2, 10) ampv = np.random.uniform(0.5, 2.0, (1, 10)) @@ -221,7 +221,7 @@ def test_single_site(): assert result[0, 0] == 1.0 -def test_multiple_sites(): +def test_multiple_sites() -> None: """Test function with multiple sites.""" fftfreq = np.logspace(-1, 2, 10) ampv = np.random.uniform(0.5, 2.0, (5, 10)) @@ -333,3 +333,44 @@ def test_regression_amp_bandpass(test_df: pd.DataFrame) -> None: interpolated, fmin=0.2, fmidbot=0.5, fhightop=10.0, fmax=15.0, ftfreq=ftfreq ) assert ampv_new == pytest.approx(ampv_old, rel=0.01) + + +def test_cb_2014_siteamp_empty_dataframe() -> None: + """Test that ValueError is raised for empty DataFrame.""" + empty_df = pd.DataFrame() + with pytest.raises(ValueError, match="Input DataFrame is empty"): + siteamp_models.cb_amp_multi(empty_df) + + +def test_cb_2014_siteamp_missing_columns() -> None: + """Test that KeyError is raised for missing required columns.""" + incomplete_df = pd.DataFrame({"vref": [500.0], "vpga": [500.0]}) + with pytest.raises(KeyError, match="Missing required columns"): + siteamp_models.cb_amp_multi(incomplete_df) + + +def test_cb_2014_siteamp_nan_values() -> None: + """Test that ValueError is raised for NaN values.""" + nan_df = pd.DataFrame( + {"vref": [np.nan], "vpga": [500.0], "pga": [0.4], "vsite": [500.0]} + ) + with pytest.raises(ValueError, match="Column 'vref' contains NaN values"): + siteamp_models.cb_amp_multi(nan_df) + + +def test_cb_2014_siteamp_infinite_values() -> None: + """Test that ValueError is raised for infinite values.""" + inf_df = pd.DataFrame( + {"vref": [np.inf], "vpga": [500.0], "pga": [0.4], "vsite": [500.0]} + ) + with pytest.raises(ValueError, match="Column 'vref' contains infinite values"): + siteamp_models.cb_amp_multi(inf_df) + + +def test_cb_2014_siteamp_non_positive_values() -> None: + """Test that ValueError is raised for non-positive values.""" + negative_df = pd.DataFrame( + {"vref": [-500.0], "vpga": [500.0], "pga": [0.4], "vsite": [500.0]} + ) + with pytest.raises(ValueError, match="Column 'vref' contains non-positive values"): + siteamp_models.cb_amp_multi(negative_df) diff --git a/tests/test_src_site_dist.py b/tests/test_src_site_dist.py new file mode 100644 index 00000000..9e8ba7f0 --- /dev/null +++ b/tests/test_src_site_dist.py @@ -0,0 +1,114 @@ +import numpy as np +import pytest + +from qcore import src_site_dist + + +def test_calc_rrup_rjb_single_point() -> None: + # Simple test with a single fault point and a single location + srf_points = np.array([[172.0, -43.0, 5.0]]) + locations = np.array([[172.0, -43.0, 0.0]]) + + out = src_site_dist.calc_rrup_rjb(srf_points, locations) + assert len(out) == 2 + rrup, rjb = out + assert rrup.shape == (1,) + assert rjb.shape == (1,) + assert rrup.dtype == np.float32 + assert rjb.dtype == np.float32 + # Since location is directly above the fault point, rjb should be ~0 + assert rjb[0] == pytest.approx(0.0, abs=1e-2) + # rrup should be approximately the depth difference + assert rrup[0] > 0 + + +def test_calc_rrup_rjb_multiple_points() -> None: + # Multiple fault points and multiple locations + srf_points = np.array( + [ + [172.0, -43.0, 5.0], + [172.1, -43.1, 5.0], + [172.2, -43.2, 5.0], + ] + ) + locations = np.array( + [ + [172.0, -43.0, 0.0], + [172.5, -43.5, 0.0], + ] + ) + + out = src_site_dist.calc_rrup_rjb(srf_points, locations) + assert len(out) == 2 + rrup, rjb = out + + assert rrup.shape == (2,) + assert rjb.shape == (2,) + assert np.all(rrup >= 0) + assert np.all(rjb >= 0) + + +def test_calc_rrup_rjb_with_return_points() -> None: + srf_points = np.array( + [ + [172.0, -43.0, 5.0], + [172.1, -43.1, 5.0], + ] + ) + locations = np.array([[172.0, -43.0, 0.0]]) + + out = src_site_dist.calc_rrup_rjb(srf_points, locations, return_rrup_points=True) + assert len(out) == 3 + + rrup, rjb, rrup_points = out + + assert rrup.shape == (1,) + assert rjb.shape == (1,) + assert rrup_points.shape == (1, 3) + assert rrup_points.dtype == np.float32 + + +def test_calc_rrup_rjb_custom_iterations() -> None: + # Test with custom n_stations_per_iter parameter + srf_points = np.array( + [ + [172.0, -43.0, 5.0], + [172.1, -43.1, 6.0], + ] + ) + locations = np.array( + [ + [172.0, -43.0, 0.0], + [172.05, -43.05, 0.0], + [172.1, -43.1, 0.0], + ] + ) + + out = src_site_dist.calc_rrup_rjb(srf_points, locations, n_stations_per_iter=1) + + assert len(out) == 2 + rrup, rjb = out + + assert rrup.shape == (3,) + assert rjb.shape == (3,) + assert np.all(rrup >= 0) + assert np.all(rjb >= 0) + + +def test_calc_rrup_rjb_rjb_less_than_rrup() -> None: + # rjb should always be <= rrup since rjb is horizontal distance + # and rrup includes vertical component + srf_points = np.array([[172.0, -43.0, 10.0]]) + locations = np.array( + [ + [172.0, -43.0, 0.0], + [172.1, -43.1, 0.0], + ] + ) + + out = src_site_dist.calc_rrup_rjb(srf_points, locations) + assert len(out) == 2 + + rrup, rjb = out + # rjb should be less than or equal to rrup + assert np.all(rjb <= rrup + 1e-5) # Small tolerance for floating point diff --git a/qcore/test/test_timeseries/test_timeseries.py b/tests/test_timeseries.py similarity index 89% rename from qcore/test/test_timeseries/test_timeseries.py rename to tests/test_timeseries.py index 230be9f7..c5b6cb6b 100644 --- a/qcore/test/test_timeseries/test_timeseries.py +++ b/tests/test_timeseries.py @@ -860,3 +860,105 @@ def test_read_lf_seis_file_plural(inputs: list[tuple], tmp_path: Path) -> None: assert dset.attrs["resolution"] == header.resolution assert dset.attrs["rotation"] == header.rotation assert dset.attrs["units"] == "cm/s^2" + + +def test_timeseries_to_text_full(tmp_path: Path) -> None: + """ + Tests the function with a timeseries that is not an even multiple + of values_per_line, ensuring both header and data lines are correct. + """ + test_file = tmp_path / "output.txt" + + test_timeseries = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.123456, 8.987654]) + + params = { + "timeseries": test_timeseries, + "filename": test_file, + "dt": 0.01, + "stat": "TEST", + "comp": "090", + "values_per_line": 6, + "start_hr": 1, + "start_min": 2, + "start_sec": 3.4, + "edist": 100.1, + "az": 45.0, + "baz": 225.0, + "title": "This is a test title", + } + + # Note: We use b"" for a bytes literal because the file is opened in "wb" mode. + expected_output = b"""TEST 090 This is a test title +8 1.00000e-02 1 2 3.40000e+00 1.00100e+02 4.50000e+01 2.25000e+02 + 1.00000e+00 2.00000e+00 3.00000e+00 4.00000e+00 5.00000e+00 6.00000e+00 + 7.12346e+00 8.98765e+00 +""" + + timeseries.timeseries_to_text(**params) # type: ignore + + assert test_file.exists() + actual_output = test_file.read_bytes() + + assert actual_output.strip() == expected_output.strip() + + +def test_timeseries_to_text_empty(tmp_path: Path) -> None: + """ + Tests the function with an empty timeseries to ensure it + writes the header correctly and doesn't crash. + """ + # 1. Arrange + test_file = tmp_path / "empty.txt" + test_timeseries = np.array([]) + + params = { + "timeseries": test_timeseries, + "filename": test_file, + "dt": 0.05, + "stat": "EMPTY", + "comp": "N", + "title": "Empty Test", + } + + # Expected output is just the header + expected_output = b"""EMPTY N Empty Test +0 5.00000e-02 0 0 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 +""" + + timeseries.timeseries_to_text(**params) # type: ignore + + assert test_file.exists() + actual_output = test_file.read_bytes() + + assert actual_output.strip() == expected_output.strip(), ( + f"Expected output differs: {actual_output}" + ) + + +def test_ampdeamp_zero_amplification_factor() -> None: + """Test that ZeroDivisionError is raised when de-amplifying with zero amplification factor.""" + waveform = np.ones(100, dtype=np.float32) + amplification_factor = np.zeros(25, dtype=np.float32) + + with pytest.raises(ZeroDivisionError, match="Would divide by zero in amplification factor"): + timeseries.ampdeamp(waveform, amplification_factor, amplify=False, taper=False) + + +def test_lfseis_parser_invalid_file() -> None: + """Test that ValueError is raised for invalid LFSeis file.""" + invalid_data = b"\x00\x00\x00\x00" * 100 # Create invalid file data + + with tempfile.TemporaryFile() as f: + f.write(invalid_data) + f.seek(0) + with pytest.raises(ValueError, match="Handle does not read from an LFSeis file"): + _ = timeseries.LFSeisParser(f) # Constructor triggers endianness detection + + +def test_read_lfseis_directory_no_files(tmp_path: Path) -> None: + """Test that ValueError is raised when no LF seis files are found.""" + empty_dir = tmp_path / "empty_dir" + empty_dir.mkdir() + + with pytest.raises(ValueError, match="No LF seis files found"): + timeseries.read_lfseis_directory(empty_dir) diff --git a/tests/test_utils.py b/tests/test_utils.py new file mode 100644 index 00000000..d0772dd3 --- /dev/null +++ b/tests/test_utils.py @@ -0,0 +1,24 @@ +import tempfile +from pathlib import Path + +import yaml + +from qcore import utils + + +def test_load_yaml() -> None: + # Create a temporary YAML file + data = {"key1": "value1", "key2": 123, "key3": ["a", "b", "c"]} + + with tempfile.NamedTemporaryFile(mode="w", delete=False, suffix=".yaml") as f: + yaml.safe_dump(data, f) + yaml_file = f.name + + try: + result = utils.load_yaml(yaml_file) # type: ignore + assert result == data + assert result["key1"] == "value1" + assert result["key2"] == 123 + assert result["key3"] == ["a", "b", "c"] + finally: + Path(yaml_file).unlink() diff --git a/qcore/test/test_xyts/test_xyts.py b/tests/test_xyts.py similarity index 91% rename from qcore/test/test_xyts/test_xyts.py rename to tests/test_xyts.py index 08ac3d4e..22008210 100644 --- a/qcore/test/test_xyts/test_xyts.py +++ b/tests/test_xyts.py @@ -68,6 +68,8 @@ def test_corners( expected_array, expected_string = expected_corners computed_array, computed_string = computed_corners + assert isinstance(computed_string, str) 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