diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..5171767 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,11 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + target-branch: "develop" + schedule: + interval: "monthly" + groups: + github-actions: + patterns: + - "*" \ No newline at end of file diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml new file mode 100644 index 0000000..4fd795a --- /dev/null +++ b/.github/workflows/publish-to-pypi.yml @@ -0,0 +1,150 @@ +name: Build, test, and deploy + +on: + push: + branches: [develop, main] + pull_request: + branches: [develop, main] + release: + types: [published] + workflow_dispatch: + +permissions: + contents: read + +jobs: + lint: + name: Lint and check formatting + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v7 + with: + persist-credentials: false + + - name: Check code with ruff + uses: astral-sh/ruff-action@v3 + with: + version: "0.16.9" + args: check + + - name: Check formatting with ruff + uses: astral-sh/ruff-action@v3 + with: + version: "0.16.9" + args: format --check + + build: + name: Build distributions + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v7 + with: + persist-credentials: false + + - uses: actions/setup-python@v7 + with: + python-version: "3.14" + + - name: Check release tag matches package version + if: github.event_name == 'release' + shell: bash + run: | + version=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])") + tag="${GITHUB_REF_NAME#v}" + if [ "$tag" != "$version" ]; then + echo "::error::Release tag ($GITHUB_REF_NAME) does not match version in pyproject.toml ($version)" + exit 1 + fi + + - name: Build sdist and wheel + run: pipx run build + + - name: Check distribution metadata + run: pipx run twine check --strict dist/* + + - uses: actions/upload-artifact@v7 + with: + name: dist + path: dist/ + + test: + name: Test on ${{ matrix.os }} with Python ${{ matrix.python-version }} + needs: build + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + # macos-15-intel is an Intel runner, macos-15 is Apple silicon + os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-15] + python-version: ["3.10", "3.15"] + exclude: + # NumPy and SciPy do not provide Windows ARM64 packages for Python 3.10 + - os: windows-11-arm + python-version: "3.10" + include: + # Test the intermediate Python versions on Linux only + - os: ubuntu-latest + python-version: "3.11" + - os: ubuntu-latest + python-version: "3.12" + - os: ubuntu-latest + python-version: "3.13" + - os: ubuntu-latest + python-version: "3.14" + + steps: + # Checkout is only needed for the tests and sample data; the package is + # installed from the built wheel so the tests check what gets published + - uses: actions/checkout@v7 + with: + persist-credentials: false + + - uses: actions/setup-python@v7 + with: + python-version: ${{ matrix.python-version }} + + - uses: actions/download-artifact@v8 + with: + name: dist + path: dist + + - name: Install tcplotter wheel and test dependencies + shell: bash + run: | + python -m pip install --upgrade pip + python -m pip install dist/*.whl pytest + + - name: Run tests + run: python -m pytest -v + + upload_testpypi: + name: Publish to TestPyPI + needs: [lint, build, test] + runs-on: ubuntu-latest + environment: testpypi + permissions: + id-token: write + if: github.event_name == 'workflow_dispatch' + steps: + - uses: actions/download-artifact@v8 + with: + name: dist + path: dist + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ + + upload_pypi: + name: Publish to PyPI + needs: [lint, build, test] + runs-on: ubuntu-latest + environment: pypi + permissions: + id-token: write + if: github.event_name == 'release' && github.event.action == 'published' + steps: + - uses: actions/download-artifact@v8 + with: + name: dist + path: dist + - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.gitignore b/.gitignore index e946c42..2820620 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,9 @@ __pycache__ .pixi/* !.pixi/config.toml .DS_Store + +# Build and test output +build/ +dist/ +*.egg-info/ +.pytest_cache/ diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ade0e40..1b00017 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ version: 2 # Set the OS, Python version and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: python: "3.12" diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..c401af6 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,38 @@ +cff-version: 1.2.0 +message: "If you use tcplotter in your work, please cite it as below." +type: software +title: "tcplotter: a Python package for creating and customizing thermochronometer age and closure temperature plots" +authors: + - family-names: Whipp + given-names: David M. + affiliation: University of Helsinki, Finland + - family-names: Ketcham + given-names: Richard A. + affiliation: University of Texas at Austin, USA +version: 0.5.0 +doi: 10.5281/zenodo.5958939 +license: GPL-3.0-or-later +repository-code: "https://github.com/HUGG/tcplotter" +url: "https://tcplotter.readthedocs.io/" +keywords: + - thermochronology + - geology + - geophysics +references: + - type: article + title: "Short communication: Modeling competing effects of cooling rate, grain size, and radiation damage in low-temperature thermochronometers" + authors: + - family-names: Whipp + given-names: David M. + - family-names: Kellett + given-names: Dawn A. + - family-names: Coutand + given-names: Isabelle + - family-names: Ketcham + given-names: Richard A. + journal: Geochronology + volume: 4 + start: 143 + end: 152 + year: 2022 + doi: 10.5194/gchron-4-143-2022 \ No newline at end of file diff --git a/LICENSE b/LICENSE index 12beda5..f288702 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,674 @@ -MIT License - -Copyright (c) 2021-2022 David Whipp - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index 5c954cd..43ea5ab 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,13 @@ # Tcplotter code description and instructions for use [![DOI](https://zenodo.org/badge/444915688.svg)](https://zenodo.org/badge/latestdoi/444915688) +[![Build, test, and deploy](https://github.com/HUGG/tcplotter/actions/workflows/publish-to-pypi.yml/badge.svg)](https://github.com/HUGG/tcplotter/actions/workflows/publish-to-pypi.yml) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![Python versions](https://img.shields.io/pypi/pyversions/tcplotter)](https://pypi.org/project/tcplotter/) [![PyPI - Version](https://img.shields.io/pypi/v/tcplotter)](https://pypi.org/project/tcplotter/) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/tcplotter/badges/version.svg)](https://anaconda.org/conda-forge/tcplotter) [![Documentation Status](https://readthedocs.org/projects/tcplotter/badge/?version=latest)](https://tcplotter.readthedocs.io/en/latest/?badge=latest) -[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) +[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/HUGG/tcplotter/HEAD?urlpath=lab/tree/notebooks/tcplotter.ipynb) Tcplotter is a Python package for creating and customizing thermochronometer age and closure temperature plots presented in the article [Short communication: Modelling competing effects of cooling rate, grain size and radiation damage in low temperature thermochronometers](https://doi.org/10.5194/gchron-2021-29) by D. Whipp, D. Kellett, I. Coutand, and R. Ketcham. @@ -26,7 +29,9 @@ pip install tcplotter You can also find installation instructions on the [Tcplotter documentation page](https://tcplotter.readthedocs.io/en/latest/installation.html#installing-the-latest-version-of-t-sub-c-sub-plotter-from-github). -**Note**: In order for Tcplotter to work properly you will also need to install the thermochronometer age prediction programs available in the [Tccore package](https://github.com/HUGG/Tc_core/). +Installing Tcplotter also installs [Tcages](https://github.com/HUGG/tcages), which provides the thermochronometer age prediction codes. Pre-built packages are available for Linux, macOS and Windows, so no compilers are needed. + +**Note**: Tcplotter versions up to 0.4.0 required installing separate age prediction programs from the Tccore package. This is no longer necessary from version 0.5.0 onwards. ## Usage @@ -91,7 +96,11 @@ You're also welcome to cite the manuscript related to Tcplotter when ### How to cite related articles -The age prediction software used for calculating apatite and zircon (U-Th)/He and apatite fission-track ages was written by Richard Ketcham at the University of Texas, USA. Results published using this software should also cite the articles below: +The age prediction software used for calculating apatite and zircon (U-Th)/He and apatite fission-track ages (provided by [Tcages](https://github.com/HUGG/tcages)) was written by Richard Ketcham at the University of Texas, USA. Results published using this software should also cite the articles below: + +- Flowers, R. M., Ketcham, R. A., Shuster, D. L., and Farley, K. A.: Apatite (U-Th)/He thermochronometry using a radiation damage accumulation and annealing model, Geochimica et Cosmochimica Acta, 73, 2347–2365, doi: [10.1016/j.gca.2009.01.015](https://doi.org/10.1016/j.gca.2009.01.015), 2009. + +- Guenthner, W. R., Reiners, P. W., Ketcham, R. A., Nasdala, L., and Giester, G.: Helium diffusion in natural zircon: Radiation damage, anisotropy, and the interpretation of zircon (U-Th)/He thermochronology, American Journal of Science, 313, 145–198, doi: [10.2475/03.2013.01](https://doi.org/10.2475/03.2013.01), 2013. - Ketcham, R. A., Donelick, R. A., & Carlson, W. D.: Variability of apatite fission-track annealing kinetics III: Extrapolation to geological time scales. American Mineralogist, 84, 1235-1255, doi: [10.2138/am-1999-0903](https://doi.org/10.2138/am-1999-0903), 1999. @@ -99,4 +108,5 @@ The age prediction software used for calculating apatite and zircon (U-Th)/He an ## License -The Tcplotter software is licensed under an MIT License: [Tcplotter software license](LICENSE) +Tcplotter is distributed under the [GNU General Public License v3.0 or later](LICENSE). +Versions up to 0.4.0 were released under the MIT License. diff --git a/docs/conf.py b/docs/conf.py index 95b17e9..566e618 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -14,12 +14,18 @@ # import sys # sys.path.insert(0, os.path.abspath('.')) +import tcplotter + # -- Project information ----------------------------------------------------- -project = 'tcplotter' -copyright = '2022, David Whipp, University of Helsinki' -author = 'David Whipp' +project = "tcplotter" +copyright = "2022-2026, David Whipp, University of Helsinki" +author = "David Whipp" + +# Version info +release = tcplotter.__version__ +version = release # -- General configuration --------------------------------------------------- @@ -35,7 +41,7 @@ ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -47,12 +53,12 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_book_theme' +html_theme = "sphinx_book_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -#html_static_path = ['_static'] +# html_static_path = ['_static'] # HTML theme options html_theme_options = { @@ -72,7 +78,7 @@ } # HTML context -#html_context = { +# html_context = { # # Enable the "Edit in GitHub link within the header of each page. # "display_github": True, # # Set the following variables to generate the resulting github URL for each page. @@ -81,7 +87,7 @@ # "github_repo": "pyrosm", # "github_version": "master/", # "conf_py_path": "/docs/", -#} +# } # The master toctree document. master_doc = "index" @@ -96,10 +102,10 @@ pygments_style = "sphinx" # Allow errors -execution_allow_errors = True +nb_execution_allow_errors = True # Do not execute cells -jupyter_execute_notebooks = "off" +nb_execution_mode = "off" # Allow myst admonition style myst_admonition_enable = True diff --git a/docs/installation.ipynb b/docs/installation.ipynb index 495871c..e3940c3 100644 --- a/docs/installation.ipynb +++ b/docs/installation.ipynb @@ -13,48 +13,37 @@ "pip install tcplotter\n", "```\n", "\n", - "**Note**: In order for Tcplotter to work properly you will also need to install the thermochronometer age prediction programs available in the [Tccore package](https://github.com/HUGG/Tc_core/).\n", + "This also installs [Tcages](https://github.com/HUGG/tcages), which provides the thermochronometer age prediction codes used by Tcplotter. Pre-built packages are available for Linux, macOS and Windows, so no compilers are needed.\n", "\n", - "## Installing the latest version of Tcplotter from GitHub (not recommended)\n", + "**Note**: Tcplotter versions up to 0.4.0 required installing separate age prediction programs. This is no longer necessary from version 0.5.0 onwards.\n", "\n", - "Below you will find the steps to install the latest version of the Tcplotter package from GitHub. If you have difficulty with the installation, we recommend [using Binder](https://mybinder.org/v2/gh/HUGG/tcplotter/HEAD?urlpath=lab/tree/notebooks/tcplotter.ipynb) to create and save plots using Tcplotter.\n", + "## Installing the latest version of Tcplotter from GitHub\n", "\n", - "1. First, you will need the several items in order to compile the software used for thermochronometer age and closure temperature calculations.\n", + "You can install the latest development version of Tcplotter directly from GitHub using `pip`:\n", "\n", - " - [cmake](https://cmake.org/)\n", - " - a compatible C compiler\n", - " - a compatible C++ compiler\n", - "\n", - " You can find more information about which compilers can be used with cmake from the [cmake documentation page](https://cmake.org/documentation/).\n", - "\n", - "2. In addition, Tcplotter requires Python >= 3.10 with the following Python libraries:\n", - "\n", - " - `numpy`\n", - " - `matplotlib-base`\n", - " - `scipy`\n", - "\n", - "3. Once the required Python libraries have been installed, you can download the Tcplotter code from GitHub by visiting the [Tcplotter GitHub page](https://github.com/HUGG/tcplotter), clicking on the **Code** button on the upper right side of the page, and selecting **Download ZIP**. After the download completes, you can extract the files using your preferred software.\n", - "\n", - "4. At this point, you will need to compile the software for calculating the thermochronometer ages using cmake. You can find instructions about how to do this on the [Tccore package GitHub page](https://github.com/HUGG/Tc_core/).\n", + "```bash\n", + "pip install git+https://github.com/HUGG/tcplotter.git\n", + "```\n", "\n", - "5. You can now do a local install of Tcplotter using `pip` by navigating to the bast `tcplotter` directory in a terminal and running the following:\n", + "Tcplotter requires Python >= 3.10. All required Python libraries (`matplotlib`, `numpy`, `scipy` and `tcages`) are installed automatically.\n", "\n", - " ```bash\n", - " pip install -e .\n", - " ```\n", + "If you would like to modify the code, you can instead clone the repository and do an editable install:\n", "\n", - " This will install Tcplotter locally for your use.\n", + "```bash\n", + "git clone https://github.com/HUGG/tcplotter.git\n", + "cd tcplotter\n", + "pip install -e .\n", + "```\n", "\n", "### Testing the installation\n", "\n", - "At this point you should have a working Tcplotter installation. You can test it by running on of the Tcplotter command-line programs. For example, you could run the following in a terminal where Tcplotter is installed:\n", + "At this point you should have a working Tcplotter installation. You can test it by running one of the Tcplotter command-line programs. For example, you could run the following in a terminal where Tcplotter is installed:\n", "\n", "```bash\n", "eu-vs-radius\n", "```\n", "\n", - "This should produce a contour plot of cooling ages and closure temperatures for a range of effective uranium and grain radius values.\n", - "\n" + "This should produce a contour plot of cooling ages and closure temperatures for a range of effective uranium and grain radius values." ] }, { diff --git a/docs/requirements.txt b/docs/requirements.txt index 65bb9d6..d666fcd 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,14 +1,8 @@ -numpydoc -sphinx-book-theme -nbsphinx +sphinx-book-theme==1.2.0 ipython -jupyter-book myst-parser myst-nb -sphinx_copybutton sphinx -sphinx-thebe -sphinx-togglebutton matplotlib numpy scipy diff --git a/environment.yml b/environment.yml index 7c11640..af0a78a 100644 --- a/environment.yml +++ b/environment.yml @@ -2,10 +2,11 @@ name: tcplotter-binder channels: - conda-forge dependencies: + - ipywidgets - matplotlib >= 3.8 - numpy - scipy - python >= 3.10 - pip - pip: - - tcplotter \ No newline at end of file + - tcplotter>=0.5 diff --git a/notebooks/tcplotter.ipynb b/notebooks/tcplotter.ipynb index 7ce6fbf..c89a581 100644 --- a/notebooks/tcplotter.ipynb +++ b/notebooks/tcplotter.ipynb @@ -409,7 +409,7 @@ " use_widget=True,\n", " cooling_rate=1.0,\n", " plot_type=3,\n", - " age_data_file=\"sample_data.csv\",\n", + " age_data_file=\"../data/sample_data.csv\",\n", " calc_misfit=True,\n", ")" ] diff --git a/postBuild b/postBuild deleted file mode 100644 index cca166c..0000000 --- a/postBuild +++ /dev/null @@ -1,8 +0,0 @@ -# Compile codes for (U-Th)/He and FT age prediction -git clone https://github.com/HUGG/Tc_core.git -cd Tc_core/src/ketch_aft -make && make install -cd .. -cd RDAAM_He -make && make install -cd ../../.. diff --git a/pyproject.toml b/pyproject.toml index 0ac0285..d6285fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "tcplotter" -version = "0.4.0" +version = "0.5.0.dev1" authors = [ {name = "Dave Whipp", email = "david.whipp@helsinki.fi"}, ] @@ -29,8 +29,8 @@ classifiers = [ "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Programming Language :: Python :: 3.14", + "Programming Language :: Python :: 3.15", "Programming Language :: Python :: 3 :: Only", - "Operating System :: OS Independent", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Physics", ] @@ -38,8 +38,13 @@ dependencies = [ "matplotlib", "numpy", "scipy", + "tcages>=0.3", ] +[project.optional-dependencies] +lint = ["ruff"] +tests = ["pytest"] + [project.urls] homepage = "https://tcplotter.readthedocs.io/" repository = "https://github.com/HUGG/tcplotter" @@ -50,3 +55,17 @@ time-vs-temp = "tcplotter.time_vs_temp:main" eu-vs-radius = "tcplotter.eu_vs_radius:main" rate-vs-radius-eu = "tcplotter.rate_vs_radius_eu:main" rate-vs-age-tc = "tcplotter.rate_vs_age_tc:main" + +[tool.pytest.ini_options] +testpaths = ["tests"] + +[tool.ruff] +line-length = 88 +target-version = "py310" + +[tool.ruff.lint] +# Pyflakes (F) and a subset of pycodestyle (E) errors, as used for Tc1D +select = ["E4", "E7", "E9", "F"] + +[tool.ruff.format] +quote-style = "double" diff --git a/src/tcplotter/__init__.py b/src/tcplotter/__init__.py index 390bc90..1310f4e 100644 --- a/src/tcplotter/__init__.py +++ b/src/tcplotter/__init__.py @@ -2,3 +2,13 @@ from .tcplotter import eu_vs_radius from .tcplotter import rate_vs_radius_eu from .tcplotter import rate_vs_age_tc + +__all__ = ["time_vs_temp", "eu_vs_radius", "rate_vs_radius_eu", "rate_vs_age_tc"] + +from importlib.metadata import PackageNotFoundError, version + +try: + __version__ = version("tcplotter") +except PackageNotFoundError: + # Package is not installed (e.g. running from a source checkout) + __version__ = "dev" diff --git a/src/tcplotter/rate_vs_age_tc.py b/src/tcplotter/rate_vs_age_tc.py index 6eb04b5..8a21a32 100755 --- a/src/tcplotter/rate_vs_age_tc.py +++ b/src/tcplotter/rate_vs_age_tc.py @@ -223,7 +223,7 @@ def main(): parser.add_argument( "--no-clean-up-files", dest="no_clean_up_files", - help="Do not delete temporary files", + help="Deprecated and has no effect (no temporary files are created)", action="store_true", default=False, ) diff --git a/src/tcplotter/tcplotter.py b/src/tcplotter/tcplotter.py index 15e5406..36ab911 100644 --- a/src/tcplotter/tcplotter.py +++ b/src/tcplotter/tcplotter.py @@ -4,8 +4,8 @@ import numpy as np from pathlib import Path from scipy.interpolate import interp1d, RegularGridInterpolator -import shutil -import subprocess +import tcages +import warnings # Define function for calculating effective uranium concentration @@ -14,20 +14,6 @@ def calc_eu(uranium, thorium): return uranium + 0.238 * thorium -def check_execs() -> None: - """Checks whether all required executables exist.""" - - # Check that executables are in $PATH - for executable in ("RDAAM_He", "ketch_aft"): - exec_path = shutil.which(executable) - if exec_path is None: - raise FileNotFoundError( - f"{executable} executable not found. See instructions at https://github.com/HUGG/Tc_core to fix this." - ) - - return None - - def create_output_directory(wd, dir=""): """Creates a new directory in working directory.""" newdir = wd / dir @@ -66,7 +52,7 @@ def read_age_data(file, ap_x, ap_y, zr_x, zr_y): f"Warning: eU concentration for {data[i][0].lower()} age on line {i + 1} not within modelled range." ) print( - f" This age will be excluded from plotting and the misfit calculation." + " This age will be excluded from plotting and the misfit calculation." ) # Check if value is not within radius range elif not (min(ap_y) <= float(data[i][4]) <= max(ap_y)): @@ -74,7 +60,7 @@ def read_age_data(file, ap_x, ap_y, zr_x, zr_y): f"Warning: Grain radius for {data[i][0].lower()} age on line {i + 1} not within modelled range." ) print( - f" This age will be excluded from plotting and the misfit calculation." + " This age will be excluded from plotting and the misfit calculation." ) else: ahe_age.append(float(data[i][1])) @@ -90,7 +76,7 @@ def read_age_data(file, ap_x, ap_y, zr_x, zr_y): f"Warning: eU concentration for {data[i][0].lower()} age {i + 1} not within modelled range." ) print( - f" This age will be excluded from plotting and the misfit calculation." + " This age will be excluded from plotting and the misfit calculation." ) # Check if value is not within radius range elif not (min(zr_y) <= float(data[i][4]) <= max(zr_y)): @@ -98,7 +84,7 @@ def read_age_data(file, ap_x, ap_y, zr_x, zr_y): f"Warning: Grain radius for {data[i][0].lower()} age {i + 1} not within modelled range." ) print( - f" This age will be excluded from plotting and the misfit calculation." + " This age will be excluded from plotting and the misfit calculation." ) else: zhe_age.append(float(data[i][1])) @@ -118,7 +104,7 @@ def read_age_data(file, ap_x, ap_y, zr_x, zr_y): print( f"Warning: {data[i][0].lower()} age on line {i + 1} missing radius value." ) - print(f" Age will not be plotted.") + print(" Age will not be plotted.") # Create new lists with data file values n_ahe = len(ahe_age) n_zhe = len(zhe_age) @@ -151,7 +137,6 @@ def calculate_misfit(age_data, age_list, param_x, param_y): std_dev.append(age_data[1][i]) # Calculate misfit misfit = chi_squared(measured_ages, predicted_ages, std_dev) - n_ages = len(measured_ages) return misfit[0] @@ -454,9 +439,6 @@ def eu_vs_radius( ) use_widget = False - # Define location of RDAAM executable - rdaam_path = shutil.which("RDAAM_He") - # Define working directory wd = Path.cwd() @@ -500,9 +482,6 @@ def eu_vs_radius( else: raise ValueError("Bad value for plot_type. Should be 1, 2, or 3.") - # Define time-temperature history filename - tt_filename = "simple_time_temp.txt" - # Set plot style plt.style.use(plot_style) @@ -563,11 +542,6 @@ def eu_vs_radius( input_tt_path = wd / input_tt_file time_hist, temp_hist = read_tt_history(input_tt_path) - # Write cooling history points to file - with open(tt_filename, "w") as f: - for i in range(len(time_hist)): - f.write(f"{time_hist[i]:.4f},{temp_hist[i]:.1f}\n") - # Echo total model run time and cooling rate if verbose and cooling_hist_type == 1: print( @@ -612,52 +586,35 @@ def eu_vs_radius( zr_y_list.append(zr_radius) # Calculate (U-Th)/He ages - command = ( - rdaam_path - + " " - + tt_filename - + " " - + str(ap_radius) - + " " - + str(ap_uranium) - + " " - + str(ap_thorium) - + " " - + str(zr_radius) - + " " - + str(zr_uranium) - + " " - + str(zr_thorium) - ) - p = subprocess.Popen( - command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT + he_ages = tcages.he_ages( + time_hist, + temp_hist, + ap_rad=ap_radius, + ap_u=ap_uranium, + ap_th=ap_thorium, + zr_rad=zr_radius, + zr_u=zr_uranium, + zr_th=zr_thorium, ) - - # Parse output for ages - stdout = p.stdout.readlines() - corr_ahe_age = stdout[0].split()[7].decode("UTF-8") - corr_zhe_age = stdout[1].split()[7].decode("UTF-8") + corr_ahe_age = he_ages.ahe_corr + corr_zhe_age = he_ages.zhe_corr # Find closure temperatures from cooling ages and thermal history tc_interp = interp1d(time_hist, temp_hist) - ahe_tc = tc_interp(float(corr_ahe_age)) - zhe_tc = tc_interp(float(corr_zhe_age)) + ahe_tc = tc_interp(corr_ahe_age) + zhe_tc = tc_interp(corr_zhe_age) # Add closure temperatures, ages to lists ahe_tc_list.append(ahe_tc) - ahe_age_list.append(float(corr_ahe_age)) + ahe_age_list.append(corr_ahe_age) zhe_tc_list.append(zhe_tc) - zhe_age_list.append(float(corr_zhe_age)) + zhe_age_list.append(corr_zhe_age) if verbose: print( - f"AHe: {float(corr_ahe_age):.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {float(corr_zhe_age):.2f} Ma (Tc: {zhe_tc:.1f}°C)" + f"AHe: {corr_ahe_age:.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {corr_zhe_age:.2f} Ma (Tc: {zhe_tc:.1f}°C)" ) - # Clean up Tt file - tt_file = Path(wd, tt_filename) - tt_file.unlink() - # Calculate age misfits if age data file is used and option is selected if calc_misfit: if (num_ahe_age_data > 0) or (num_zhe_age_data > 0): @@ -675,9 +632,9 @@ def eu_vs_radius( ) else: print( - f"Warning: Misfit calculation requested, but no AHe or ZHe ages found in data file." + "Warning: Misfit calculation requested, but no AHe or ZHe ages found in data file." ) - print(f" Misfit will not be calculated.") + print(" Misfit will not be calculated.") # Apatite eU versus radius if plot_type == 1: @@ -690,7 +647,7 @@ def eu_vs_radius( age_max = max(ahe_age_list) # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_age = ax[0].tricontour( + ax[0].tricontour( ap_x_list, ap_y_list, ahe_age_list, @@ -702,7 +659,7 @@ def eu_vs_radius( linewidths=2.0, ) # Create age contour fill - ap_contourf_age = ax[0].tricontourf( + ax[0].tricontourf( ap_x_list, ap_y_list, ahe_age_list, @@ -753,7 +710,7 @@ def eu_vs_radius( # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc = ax[1].tricontour( + ax[1].tricontour( ap_x_list, ap_y_list, ahe_tc_list, @@ -803,7 +760,7 @@ def eu_vs_radius( age_max = max(zhe_age_list) # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_age = ax[0].tricontour( + ax[0].tricontour( zr_x_list, zr_y_list, zhe_age_list, @@ -815,7 +772,7 @@ def eu_vs_radius( linewidths=2.0, ) # Create age contour fill - zr_contourf_age = ax[0].tricontourf( + ax[0].tricontourf( zr_x_list, zr_y_list, zhe_age_list, @@ -866,7 +823,7 @@ def eu_vs_radius( # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc = ax[1].tricontour( + ax[1].tricontour( zr_x_list, zr_y_list, zhe_tc_list, @@ -916,7 +873,7 @@ def eu_vs_radius( age_max = max(ahe_age_list) # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_age = ax[0][0].tricontour( + ax[0][0].tricontour( ap_x_list, ap_y_list, ahe_age_list, @@ -928,7 +885,7 @@ def eu_vs_radius( linewidths=2.0, ) # Create age contour fill - ap_contourf_age = ax[0][0].tricontourf( + ax[0][0].tricontourf( ap_x_list, ap_y_list, ahe_age_list, @@ -979,7 +936,7 @@ def eu_vs_radius( # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc = ax[0][1].tricontour( + ax[0][1].tricontour( ap_x_list, ap_y_list, ahe_tc_list, @@ -1027,7 +984,7 @@ def eu_vs_radius( age_max = max(zhe_age_list) # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_age = ax[1][0].tricontour( + ax[1][0].tricontour( zr_x_list, zr_y_list, zhe_age_list, @@ -1039,7 +996,7 @@ def eu_vs_radius( linewidths=2.0, ) # Create age contour fill - zr_contourf_age = ax[1][0].tricontourf( + ax[1][0].tricontourf( zr_x_list, zr_y_list, zhe_age_list, @@ -1090,7 +1047,7 @@ def eu_vs_radius( # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc = ax[1][1].tricontour( + ax[1][1].tricontour( zr_x_list, zr_y_list, zhe_tc_list, @@ -1380,9 +1337,6 @@ def rate_vs_radius_eu( ) use_widget = False - # Define location of RDAAM executable - rdaam_path = shutil.which("RDAAM_He") - # Define working directory wd = Path.cwd() @@ -1403,7 +1357,7 @@ def rate_vs_radius_eu( # Calculate effective uranium ap_eu = calc_eu(ap_u, ap_thorium) - zr_eu = calc_eu(zr_u, zr_thorium) + calc_eu(zr_u, zr_thorium) # Total number of models total_models = len(ap_u) * len(rates) + len(ap_rad) * len(rates) @@ -1418,9 +1372,6 @@ def rate_vs_radius_eu( else: raise ValueError("Bad value for parameter plot_type. Must be 1, 2, or 3.") - # Define time-temperature history filename - tt_filename = "simple_time_temp.txt" - # Set plot style plt.style.use(plot_style) @@ -1433,12 +1384,8 @@ def rate_vs_radius_eu( # Set plot loop variables ap_x1 = rates ap_y1 = ap_rad - zr_x1 = rates - zr_y1 = zr_rad ap_x2 = rates ap_y2 = ap_eu - zr_x2 = rates - zr_y2 = zr_eu # Create lists for storing closure temperatures, ages ahe_tc_list1 = [] @@ -1492,11 +1439,10 @@ def rate_vs_radius_eu( ap_y_list1.append(ap_radius) zr_y_list1.append(zr_radius) - # Write synthetic cooling history points to file + # Define synthetic cooling history start_time = temp_max / rate - with open(tt_filename, "w") as f: - f.write("0.0,0.0\n") - f.write("{0:.4f},{1:.1f}".format(start_time, temp_max)) + time_hist = [0.0, start_time] + temp_hist = [0.0, temp_max] # Screen output if verbose: @@ -1505,36 +1451,23 @@ def rate_vs_radius_eu( ) # Calculate (U-Th)/He ages - command = ( - rdaam_path - + " " - + tt_filename - + " " - + str(ap_radius) - + " " - + str(ap_uranium) - + " " - + str(ap_thorium) - + " " - + str(zr_radius) - + " " - + str(zr_uranium) - + " " - + str(zr_thorium) - ) - p = subprocess.Popen( - command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT + he_ages = tcages.he_ages( + time_hist, + temp_hist, + ap_rad=ap_radius, + ap_u=ap_uranium, + ap_th=ap_thorium, + zr_rad=zr_radius, + zr_u=zr_uranium, + zr_th=zr_thorium, ) - - # Parse output for ages - stdout = p.stdout.readlines() - corr_ahe_age = stdout[0].split()[7].decode("UTF-8") - corr_zhe_age = stdout[1].split()[7].decode("UTF-8") + corr_ahe_age = he_ages.ahe_corr + corr_zhe_age = he_ages.zhe_corr # Find closure temperatures from cooling ages and thermal history - tc_interp = interp1d([0.0, start_time], [0.0, temp_max]) - ahe_tc = tc_interp(float(corr_ahe_age)) - zhe_tc = tc_interp(float(corr_zhe_age)) + tc_interp = interp1d(time_hist, temp_hist) + ahe_tc = tc_interp(corr_ahe_age) + zhe_tc = tc_interp(corr_zhe_age) # Add closure temperatures to lists ahe_tc_list1.append(ahe_tc) @@ -1542,7 +1475,7 @@ def rate_vs_radius_eu( if verbose: print( - f"AHe: {float(corr_ahe_age):.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {float(corr_zhe_age):.2f} Ma (Tc: {zhe_tc:.1f}°C)" + f"AHe: {corr_ahe_age:.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {corr_zhe_age:.2f} Ma (Tc: {zhe_tc:.1f}°C)" ) # Loop over plotables - loop 2: rate versus eU @@ -1569,11 +1502,10 @@ def rate_vs_radius_eu( ap_y_list2.append(ap_uranium) zr_y_list2.append(zr_uranium) - # Write synthetic cooling history points to file + # Define synthetic cooling history start_time = temp_max / rate - with open(tt_filename, "w") as f: - f.write("0.0,0.0\n") - f.write("{0:.4f},{1:.1f}".format(start_time, temp_max)) + time_hist = [0.0, start_time] + temp_hist = [0.0, temp_max] # Screen output if verbose: @@ -1582,36 +1514,23 @@ def rate_vs_radius_eu( ) # Calculate (U-Th)/He ages - command = ( - rdaam_path - + " " - + tt_filename - + " " - + str(ap_radius) - + " " - + str(ap_uranium) - + " " - + str(ap_thorium) - + " " - + str(zr_radius) - + " " - + str(zr_uranium) - + " " - + str(zr_thorium) + he_ages = tcages.he_ages( + time_hist, + temp_hist, + ap_rad=ap_radius, + ap_u=ap_uranium, + ap_th=ap_thorium, + zr_rad=zr_radius, + zr_u=zr_uranium, + zr_th=zr_thorium, ) - p = subprocess.Popen( - command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT - ) - - # Parse output for ages - stdout = p.stdout.readlines() - corr_ahe_age = stdout[0].split()[7].decode("UTF-8") - corr_zhe_age = stdout[1].split()[7].decode("UTF-8") + corr_ahe_age = he_ages.ahe_corr + corr_zhe_age = he_ages.zhe_corr # Find closure temperatures from cooling ages and thermal history - tc_interp = interp1d([0.0, start_time], [0.0, temp_max]) - ahe_tc = tc_interp(float(corr_ahe_age)) - zhe_tc = tc_interp(float(corr_zhe_age)) + tc_interp = interp1d(time_hist, temp_hist) + ahe_tc = tc_interp(corr_ahe_age) + zhe_tc = tc_interp(corr_zhe_age) # Add closure temperatures to lists ahe_tc_list2.append(ahe_tc) @@ -1619,19 +1538,15 @@ def rate_vs_radius_eu( if verbose: print( - f"AHe: {float(corr_ahe_age):.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {float(corr_zhe_age):.2f} Ma (Tc: {zhe_tc:.1f}°C)" + f"AHe: {corr_ahe_age:.2f} Ma (Tc: {ahe_tc:.1f}°C); ZHe: {corr_zhe_age:.2f} Ma (Tc: {zhe_tc:.1f}°C)" ) - # Clean up temporary tt file - tt_file = Path(wd, tt_filename) - tt_file.unlink() - # Plot only values for apatite (U-Th)/He if plot_type == 1: # --- Apatite cooling rate versus radius --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc1 = ax[0].tricontour( + ax[0].tricontour( ap_x_list1, ap_y_list1, ahe_tc_list1, @@ -1641,7 +1556,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - ap_contourf_tc1 = ax[0].tricontourf( + ax[0].tricontourf( ap_x_list1, ap_y_list1, ahe_tc_list1, @@ -1666,7 +1581,7 @@ def rate_vs_radius_eu( # --- Apatite cooling rate versus eU plot --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc2 = ax[1].tricontour( + ax[1].tricontour( ap_x_list2, ap_y_list2, ahe_tc_list2, @@ -1676,7 +1591,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - ap_contourf_tc2 = ax[1].tricontourf( + ax[1].tricontourf( ap_x_list2, ap_y_list2, ahe_tc_list2, @@ -1703,7 +1618,7 @@ def rate_vs_radius_eu( # --- Zircon cooling rate versus radius --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc1 = ax[0].tricontour( + ax[0].tricontour( zr_x_list1, zr_y_list1, zhe_tc_list1, @@ -1713,7 +1628,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - zr_contourf_tc1 = ax[0].tricontourf( + ax[0].tricontourf( zr_x_list1, zr_y_list1, zhe_tc_list1, @@ -1738,7 +1653,7 @@ def rate_vs_radius_eu( # --- Zircon cooling rate versus eU plot --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc2 = ax[1].tricontour( + ax[1].tricontour( zr_x_list2, zr_y_list2, zhe_tc_list2, @@ -1748,7 +1663,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - zr_contourf_tc2 = ax[1].tricontourf( + ax[1].tricontourf( zr_x_list2, zr_y_list2, zhe_tc_list2, @@ -1775,7 +1690,7 @@ def rate_vs_radius_eu( # --- Apatite cooling rate versus radius --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc1 = ax[0][0].tricontour( + ax[0][0].tricontour( ap_x_list1, ap_y_list1, ahe_tc_list1, @@ -1785,7 +1700,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - ap_contourf_tc1 = ax[0][0].tricontourf( + ax[0][0].tricontourf( ap_x_list1, ap_y_list1, ahe_tc_list1, @@ -1810,7 +1725,7 @@ def rate_vs_radius_eu( # --- Apatite cooling rate versus eU plot --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - ap_contour_tc2 = ax[0][1].tricontour( + ax[0][1].tricontour( ap_x_list2, ap_y_list2, ahe_tc_list2, @@ -1820,7 +1735,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - ap_contourf_tc2 = ax[0][1].tricontourf( + ax[0][1].tricontourf( ap_x_list2, ap_y_list2, ahe_tc_list2, @@ -1845,7 +1760,7 @@ def rate_vs_radius_eu( # --- Zircon cooling rate versus radius plot --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc1 = ax[1][0].tricontour( + ax[1][0].tricontour( zr_x_list1, zr_y_list1, zhe_tc_list1, @@ -1855,7 +1770,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - zr_contourf_tc1 = ax[1][0].tricontourf( + ax[1][0].tricontourf( zr_x_list1, zr_y_list1, zhe_tc_list1, @@ -1880,7 +1795,7 @@ def rate_vs_radius_eu( # --- Zircon cooling rate versus eU plot --- # Create colored contour lines to fill gaps between filled contours in pdf files if save_plot and plot_file_format == "pdf": - zr_contour_tc2 = ax[1][1].tricontour( + ax[1][1].tricontour( zr_x_list2, zr_y_list2, zhe_tc_list2, @@ -1890,7 +1805,7 @@ def rate_vs_radius_eu( linewidths=2.0, ) # Create closure temperature contour fill - zr_contourf_tc2 = ax[1][1].tricontourf( + ax[1][1].tricontourf( zr_x_list2, zr_y_list2, zhe_tc_list2, @@ -2100,7 +2015,7 @@ def rate_vs_age_tc( display_plot : bool, default=True Flag for whether to display the plot. clean_up_files : bool, default=True - Flag for whether to delete temporary output files after the code has run. + Deprecated and has no effect. Temporary files are no longer created. verbose : bool, default=False Enable/disable verbose output. use_widget : bool, default=False @@ -2131,11 +2046,13 @@ def rate_vs_age_tc( ) use_widget = False - # Define location of RDAAM executable - rdaam_path = shutil.which("RDAAM_He") - - # Define location of ketch_aft executable - ketch_path = shutil.which("ketch_aft") + # Warn about use of deprecated clean_up_files parameter + if not clean_up_files: + warnings.warn( + "clean_up_files is deprecated and has no effect, as temporary files are no longer created. It will be removed in a future version.", + DeprecationWarning, + stacklevel=2, + ) # Define working directory wd = Path.cwd() @@ -2168,9 +2085,6 @@ def rate_vs_age_tc( f"High eU (ap={ap_u_list[2]:.1f}, zr={zr_u_list[2]:.1f} ppm)", ] - # Define time-temperature history filename - tt_filename = "simple_time_temp.txt" - # Calculate total number of models that will be run total_models = len(ap_u_list) * len(rates) @@ -2231,66 +2145,45 @@ def rate_vs_age_tc( # Define thermal history start_time = temp_max / rate - with open(tt_filename, "w") as f: - f.write("0.0,0.0\n") - f.write("{0:.4f},{1:.1f}".format(start_time, temp_max)) + time_hist = [0.0, start_time] + temp_hist = [0.0, temp_max] # Calculate He ages - command = ( - rdaam_path - + " " - + tt_filename - + " " - + str(ap_rad) - + " " - + str(ap_uranium) - + " " - + str(ap_thorium) - + " " - + str(zr_rad) - + " " - + str(zr_uranium) - + " " - + str(zr_thorium) - ) - p = subprocess.Popen( - command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT + he_ages = tcages.he_ages( + time_hist, + temp_hist, + ap_rad=ap_rad, + ap_u=ap_uranium, + ap_th=ap_thorium, + zr_rad=zr_rad, + zr_u=zr_uranium, + zr_th=zr_thorium, ) - - # Parse output for ages - stdout = p.stdout.readlines() - corr_ahe_age = stdout[0].split()[7].decode("UTF-8") - corr_zhe_age = stdout[1].split()[7].decode("UTF-8") + corr_ahe_age = he_ages.ahe_corr + corr_zhe_age = he_ages.zhe_corr # Calculate AFT age - command = ketch_path + " " + tt_filename - p = subprocess.Popen( - command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT - ) - - # Parse output for AFT age - stdout = p.stdout.readlines() - aft_age = stdout[0].split()[4][:-1].decode("UTF-8") + aft_age = tcages.aft_age(time_hist, temp_hist).age # Use predicted ages to get closure temperature - tc_interp = interp1d([0.0, start_time], [0.0, temp_max]) - ahe_tc = tc_interp(float(corr_ahe_age)) - aft_tc = tc_interp(float(aft_age)) - zhe_tc = tc_interp(float(corr_zhe_age)) + tc_interp = interp1d(time_hist, temp_hist) + ahe_tc = tc_interp(corr_ahe_age) + aft_tc = tc_interp(aft_age) + zhe_tc = tc_interp(corr_zhe_age) # Add current iteration values to plotable lists rate_list.append(rate) ahe_tc_list.append(ahe_tc) aft_tc_list.append(aft_tc) zhe_tc_list.append(zhe_tc) - ahe_age_list.append(float(corr_ahe_age)) - aft_age_list.append(float(aft_age)) - zhe_age_list.append(float(corr_zhe_age)) + ahe_age_list.append(corr_ahe_age) + aft_age_list.append(aft_age) + zhe_age_list.append(corr_zhe_age) # Echo ages for this iteration if verbose: print( - f"AHe: {float(corr_ahe_age):.2f} Ma (Tc: {ahe_tc:.1f}°C); AFT: {float(aft_age):.2f} Ma (Tc: {aft_tc:.1f}°C); ZHe: {float(corr_zhe_age):.2f} Ma (Tc: {zhe_tc:.1f}°C) -- total time: {start_time:.1f} Myr" + f"AHe: {corr_ahe_age:.2f} Ma (Tc: {ahe_tc:.1f}°C); AFT: {aft_age:.2f} Ma (Tc: {aft_tc:.1f}°C); ZHe: {corr_zhe_age:.2f} Ma (Tc: {zhe_tc:.1f}°C) -- total time: {start_time:.1f} Myr" ) # Assign uncertainties if plotting ages @@ -2447,14 +2340,6 @@ def rate_vs_age_tc( else: ax[i].legend() - # Delete temporary tt file - if clean_up_files: - tt_file = Path(wd, tt_filename) - tt_file.unlink() - ft_path = Path(wd, "ft_length.csv") - if ft_path.exists(): - ft_path.unlink() - # Use tight layout plt.tight_layout() diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..fd209f7 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,15 @@ +import matplotlib + +# Use a non-interactive backend so tests run without a display +matplotlib.use("Agg") + +import matplotlib.pyplot as plt # noqa: E402 +import pytest # noqa: E402 + + +@pytest.fixture(autouse=True) +def run_in_tmp_path(tmp_path, monkeypatch): + """Run each test in an empty temporary directory and close figures afterwards.""" + monkeypatch.chdir(tmp_path) + yield tmp_path + plt.close("all") diff --git a/tests/test_tcplotter.py b/tests/test_tcplotter.py new file mode 100644 index 0000000..a695ca0 --- /dev/null +++ b/tests/test_tcplotter.py @@ -0,0 +1,123 @@ +import re +from pathlib import Path + +import pytest + +import tcplotter +from tcplotter.tcplotter import calc_eu + +DATA_DIR = Path(__file__).resolve().parents[1] / "data" + +# Ages from rate_vs_age_tc(num_points=5, plot_type=3, verbose=True), as calculated +# by the RDAAM_He and ketch_aft executables used by tcplotter 0.4.0 (2 decimals). +# Rows: low, intermediate and high eU; each row is (AHe, AFT, ZHe) for 5 cooling rates. +REFERENCE_AGES = [ + (317.15, 716.28, 1313.11), + (67.92, 149.78, 209.10), + (15.59, 30.87, 33.97), + (3.45, 6.27, 5.50), + (0.74, 1.26, 0.92), + (595.03, 716.28, 1468.25), + (91.93, 149.78, 279.64), + (15.97, 30.87, 47.12), + (3.45, 6.27, 7.80), + (0.74, 1.26, 1.27), + (763.16, 716.28, 0.00), + (128.91, 149.78, 140.03), + (20.69, 30.87, 58.31), + (3.55, 6.27, 10.37), + (0.74, 1.26, 1.74), +] + + +def test_calc_eu(): + assert calc_eu(10.0, 40.0) == pytest.approx(19.52) + + +def test_rate_vs_age_tc_matches_reference(capsys): + """Predicted ages match those from the original age prediction executables.""" + tcplotter.rate_vs_age_tc( + num_points=5, plot_type=3, display_plot=False, verbose=True + ) + out = capsys.readouterr().out + ages = re.findall(r"AHe: ([\d.]+) Ma.*AFT: ([\d.]+) Ma.*ZHe: ([\d.]+) Ma", out) + assert len(ages) == len(REFERENCE_AGES) + for predicted, expected in zip(ages, REFERENCE_AGES): + assert [float(a) for a in predicted] == pytest.approx(expected, abs=0.011) + + +def test_time_vs_temp(): + tcplotter.time_vs_temp(display_plot=False) + + +@pytest.mark.parametrize("plot_type", [1, 2, 3]) +def test_eu_vs_radius_plot_types(plot_type): + tcplotter.eu_vs_radius(num_points=3, plot_type=plot_type, display_plot=False) + + +def test_eu_vs_radius_custom_history(): + tcplotter.eu_vs_radius( + num_points=3, + cooling_hist_type=2, + time_hist=[0.0, 10.0, 30.0], + temp_hist=[0.0, 80.0, 200.0], + display_plot=False, + tt_plot=True, + ) + + +def test_eu_vs_radius_history_from_file(tmp_path): + tt_file = tmp_path / "tt.csv" + tt_file.write_text( + "Time (Ma),Temperature (C)\n0.0,10.0\n5.0,60.0\n20.0,90.0\n40.0,250.0\n" + ) + tcplotter.eu_vs_radius( + num_points=3, cooling_hist_type=3, input_tt_file="tt.csv", display_plot=False + ) + + +def test_eu_vs_radius_misfit(capsys): + tcplotter.eu_vs_radius( + num_points=3, + age_data_file=str(DATA_DIR / "sample_data.csv"), + calc_misfit=True, + display_plot=False, + ) + assert "Total misfit" in capsys.readouterr().out + + +@pytest.mark.parametrize("plot_type", [1, 2, 3]) +def test_rate_vs_radius_eu(plot_type): + tcplotter.rate_vs_radius_eu(num_points=3, plot_type=plot_type, display_plot=False) + + +@pytest.mark.parametrize("plot_type", [1, 2, 3]) +def test_rate_vs_age_tc_plot_types(plot_type): + tcplotter.rate_vs_age_tc(num_points=3, plot_type=plot_type, display_plot=False) + + +def test_no_temporary_files_left(tmp_path): + tcplotter.eu_vs_radius(num_points=3, display_plot=False) + tcplotter.rate_vs_radius_eu(num_points=3, display_plot=False) + tcplotter.rate_vs_age_tc(num_points=3, display_plot=False) + assert list(tmp_path.iterdir()) == [] + + +def test_save_plot(tmp_path): + tcplotter.rate_vs_age_tc( + num_points=3, + display_plot=False, + save_plot=True, + plot_file_format="png", + plot_dpi=50, + ) + assert len(list((tmp_path / "png").glob("*.png"))) == 1 + + +def test_clean_up_files_is_deprecated(): + with pytest.warns(DeprecationWarning, match="clean_up_files"): + tcplotter.rate_vs_age_tc(num_points=3, display_plot=False, clean_up_files=False) + + +def test_version(): + assert tcplotter.__version__ not in ("", "dev")