diff --git a/.binder/environment.yml b/.binder/environment.yml deleted file mode 100644 index 8ed0559..0000000 --- a/.binder/environment.yml +++ /dev/null @@ -1,15 +0,0 @@ -name: geoid-toolkit -channels: - - conda-forge -dependencies: - - python>=3.6 - - notebook - - cartopy - - gdal - - h5py - - lxml - - matplotlib - - netCDF4 - - numpy - - pyproj - - python-dateutil diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index aaa92f8..ddb396b 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -21,12 +21,11 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel twine + pip install build setuptools wheel twine - name: Build and publish env: TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | - python setup.py sdist bdist_wheel + python -m build twine upload dist/* - diff --git a/.github/workflows/python-request.yml b/.github/workflows/python-request.yml index 30d357c..f476ebe 100644 --- a/.github/workflows/python-request.yml +++ b/.github/workflows/python-request.yml @@ -14,34 +14,21 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: [3.11] env: OS: ${{ matrix.os }} - PYTHON: ${{ matrix.python-version }} defaults: run: shell: bash -l {0} steps: - uses: actions/checkout@v4 - - name: Set up mamba ${{ matrix.python-version }} - uses: mamba-org/setup-micromamba@v1 with: - micromamba-version: 'latest' - environment-file: .binder/environment.yml - init-shell: bash - environment-name: geoid-toolkit - cache-environment: true - post-cleanup: 'all' - create-args: >- - python=${{ matrix.python-version }} - flake8 - pytest - pytest-cov - cython + lfs: true + - name: Set up pixi environment + uses: prefix-dev/setup-pixi@v0.9.1 - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + pixi run lint # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + pixi run lint "--exit-zero --max-complexity=10 --max-line-length=127" diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..dd2dac5 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,123 @@ +# Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +- Offensive comments related to gender, gender identity and expression, sexual orientation, + disability, mental illness, physical appearance, body size, race, or religion +- Deliberate misgendering or use of "dead" or rejected names +- The use of sexualized language or imagery, and sexual attention or + advances of any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Incitement or threats of violence towards any individual, + including encouraging a person to commit suicide or to engage in self-harm +- Publishing others' private information, such as a physical or email + address, without their explicit permission +- Advocating for, or encouraging, any of the above behavior +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior can be +reported to the organizational leaders responsible for enforcement. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This code of conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/) +[Code of Conduct](https://www.contributor-covenant.org/version/2/1/code_of_conduct.html) and +the [Geek Feminism](http://geekfeminism.wikia.com) +[Community Anti-Harassment Policy](http://geekfeminism.wikia.com/wiki/Community_anti-harassment/Policy). + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +We have adapted these documents for our own use under the terms of the +[Creative Commons Attribution License](https://creativecommons.org/licenses/by/4.0/). diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 0000000..2ba184e --- /dev/null +++ b/CONTRIBUTORS.md @@ -0,0 +1 @@ +- [Tyler Sutterley (University of Washington)](http://psc.apl.uw.edu/people/investigators/tyler-sutterley/) diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst deleted file mode 100644 index 2f20db9..0000000 --- a/CONTRIBUTORS.rst +++ /dev/null @@ -1 +0,0 @@ -- `Tyler Sutterley (University of Washington) `_ diff --git a/MANIFEST.in b/MANIFEST.in index a42d6d3..b3e5b60 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -4,5 +4,3 @@ prune doc* prune notebooks* exclude *.cfg exclude *.yml -include requirements.txt -include version.txt diff --git a/README.rst b/README.rst index 71ffca0..8382bb0 100644 --- a/README.rst +++ b/README.rst @@ -91,7 +91,7 @@ Download Disclaimer ########## -This project contains work and contributions from the `scientific community <./CONTRIBUTORS.rst>`_. +This project contains work and contributions from the `scientific community <./CONTRIBUTORS.md>`_. This program is not sponsored or maintained by the Universities Space Research Association (USRA), the Center for Space Research at the University of Texas (UTCSR), the Jet Propulsion Laboratory (JPL), the German Research Centre for Geosciences (GeoForschungsZentrum, GFZ) or NASA. diff --git a/doc/environment.yml b/doc/environment.yml deleted file mode 100755 index 0d596fa..0000000 --- a/doc/environment.yml +++ /dev/null @@ -1,23 +0,0 @@ -name: geoid-docs -channels: - - conda-forge -dependencies: - - docutils - - fontconfig - - freetype - - future - - graphviz - - lxml - - markupsafe==2.0.1 - - numpy - - numpydoc - - pip - - python>=3.6 - - python-dateutil - - pyyaml - - sphinx - - sphinx-argparse>=0.4 - - sphinxcontrib-bibtex - - sphinx_rtd_theme - - pip: - - .. diff --git a/doc/source/_assets/logo.png b/doc/source/_assets/logo.png new file mode 100644 index 0000000..a6c6e07 Binary files /dev/null and b/doc/source/_assets/logo.png differ diff --git a/doc/source/_static/style.css b/doc/source/_static/style.css index 0011c7f..86ce2c8 100644 --- a/doc/source/_static/style.css +++ b/doc/source/_static/style.css @@ -1,3 +1,18 @@ +/* color adjustments to fit logo theme */ +.wy-menu > .caption > span.caption-text { + color: #eb7858; +} +.wy-nav-top { + background-color: #eb7858; + color: #ffffff; +} +.wy-side-nav-search { + background-color: #eb7858; +} +.wy-side-nav-search input[type="text"] { + border-color: #2f0f3e; +} + /* fix for position of equation numbers * https://github.com/rtfd/sphinx_rtd_theme/issues/301 */ @@ -14,3 +29,17 @@ visibility: visible; margin-right: -0.7em; } + +/* fix for property line spacing +* https://github.com/rtfd/sphinx_rtd_theme/issues/1301 +*/ +.property { + display: block !important; + padding-right: 8px; + max-width: 100%; +} + +/* caption positions for tables and figures */ +.docutils caption { + caption-side: bottom; +} diff --git a/doc/source/conf.py b/doc/source/conf.py index cd9ff22..4e9180e 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -37,14 +37,24 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + "matplotlib.sphinxext.plot_directive", + "myst_nb", "numpydoc", 'sphinxcontrib.bibtex', "sphinx.ext.autodoc", "sphinx.ext.graphviz", "sphinx.ext.viewcode", + "sphinx_design", "sphinxarg.ext" ] +# use myst for notebooks +source_suffix = { + ".rst": "restructuredtext", + ".ipynb": "myst-nb", +} +nb_execution_mode = "off" + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -63,6 +73,9 @@ pygments_style = 'native' bibtex_bibfiles = ['_assets/geoid-refs.bib'] bibtex_default_style = 'plain' +plot_html_show_formats = False +numfig = True +numfig_secnum_depth = 1 # -- Options for HTML output ------------------------------------------------- @@ -76,11 +89,14 @@ # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' -html_theme_options = {} +html_theme_options = { + "logo_only": True, +} # 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_logo = "_assets/logo.png" html_static_path = ['_static'] repository_url = f"https://github.com/tsutterley/geoid-toolkit" html_context = { diff --git a/doc/source/getting_started/Code-of-Conduct.rst b/doc/source/getting_started/Code-of-Conduct.rst new file mode 100644 index 0000000..eea72ab --- /dev/null +++ b/doc/source/getting_started/Code-of-Conduct.rst @@ -0,0 +1,2 @@ +.. include:: ../../../CODE_OF_CONDUCT.md + :parser: commonmark \ No newline at end of file diff --git a/doc/source/getting_started/Contributing.rst b/doc/source/getting_started/Contributing.rst index 12639fa..aeb9795 100644 --- a/doc/source/getting_started/Contributing.rst +++ b/doc/source/getting_started/Contributing.rst @@ -2,9 +2,16 @@ Contribution Guidelines ======================= -We welcome and invite contributions from anyone at any career stage and with any amount of coding experience towards the development of ``geoid-toolkit``. -We appreciate any and all contributions made to the project. -You will be recognized for your work by being listed as one of the `project contributors <./Citations.html#contributors>`_. +``geoid-toolkit`` is an open source project. +We welcome any help in maintaining and developing the software and documentation. +Anyone at *any career stage and with any level of coding experience* can contribute towards the development of ``geoid-toolkit``. +Please read our `code of conduct <./Code-of-Conduct.html>`_ before contributing to ``geoid-toolkit`` development. +You will be recognized for your work by being listed as one of the `project contributors <../project/Contributors.html>`_. + +.. note:: + + If you have found a problem in ``geoid-toolkit``, or you would like to suggest an improvement or modification, + please submit a `GitHub issue `_ and we will get back to you. Ways to Contribute ------------------ @@ -29,10 +36,10 @@ If not, *please* submit a new issue so that we are made aware of the problem. Please provide as much detail as possible when writing the description of your bug report. Providing information and examples will help us resolve issues faster. -Contributing Code or Examples ------------------------------ +Contributing Code +----------------- We follow a standard Forking Workflow for code changes and additions. -Submitted code goes through the pull request process for `continuous integration (CI) testing <./Contributing.html#continuous-integration>`_ and comments. +Submitted code goes through the pull request process for `continuous integration (CI) testing <../project/Testing.html#continuous-integration>`_ and comments. General Guidelines ^^^^^^^^^^^^^^^^^^ @@ -51,7 +58,7 @@ Steps to Contribute 2) Either by cloning to your local system or working in `GitHub Codespaces `_, create a work environment to make your changes. 3) Add your fork as the ``origin`` remote and the original project repository as the ``upstream`` remote. While this step isn't a necessary, it allows you to keep your fork up to date in the future. 4) Create a new branch to do your work. -5) Make your changes on the new branch and add yourself to the list of project `contributors `_. +5) Make your changes on the new branch and add yourself to the list of project `contributors `_. 6) Push your work to GitHub under your fork of the project. 7) Submit a `Pull Request `_ from your forked branch to the project repository. @@ -60,20 +67,10 @@ Adding Examples Examples may be in the form of executable scripts or interactive `Jupyter Notebooks <../user_guide/Examples.html>`_. Fully working (but unrendered) examples should be submitted with the same steps as above. -Continuous Integration -^^^^^^^^^^^^^^^^^^^^^^ -We use `GitHub Actions `_ continuous integration (CI) services to build and test the project on Linux (Ubuntu) and Mac Operating Systems. -The configuration files for this service are in `.github/workflows `_. -The workflows rely on the `requirements.txt `_ file to install the required dependencies. - -The GitHub Actions jobs include: - -* Running `flake8 `_ to check the code for style and compilation errors - Semantic Commit Messages ^^^^^^^^^^^^^^^^^^^^^^^^ -Commit messages should follow the `Conventional Commits `_ specification: +Please follow the `Conventional Commits `_ specification for your commit messages to help organize the pull requests: .. code-block:: bash @@ -88,5 +85,5 @@ where ```` is one of the following: - ``docs``: changing the documentation - ``style``: changing the line order or adding comments - ``refactor``: changing the names of variables or programs -- ``ci``: changing the `continuous integration <./Contributing.html#continuous-integration>`_ configuration files or scripts -- ``test``: adding or updating `continuous integration tests <./Contributing.html#continuous-integration>`_ +- ``ci``: changing the `continuous integration <../project/Testing.html#continuous-integration>`_ configuration files or scripts +- ``test``: adding or updating `continuous integration tests <../project/Testing.html#continuous-integration>`_ diff --git a/doc/source/getting_started/Install.rst b/doc/source/getting_started/Install.rst index 29462ef..b9c10c2 100644 --- a/doc/source/getting_started/Install.rst +++ b/doc/source/getting_started/Install.rst @@ -19,6 +19,9 @@ The simplest installation for most users will likely be using ``conda`` or ``mam conda update geoid-toolkit +Development Install +################### + To use the development repository, please fork ``geoid-toolkit`` into your own account and then clone onto your system: .. code-block:: bash @@ -31,8 +34,43 @@ To use the development repository, please fork ``geoid-toolkit`` into your own a python3 -m pip install --user . +To include all optional dependencies: + +.. code-block:: bash + + python3 -m pip install --user .[all] + The development version of ``geoid-toolkit`` can also be installed directly from GitHub using ``pip``: .. code-block:: bash python3 -m pip install --user git+https://github.com/tsutterley/geoid-toolkit.git + +Package Management with ``pixi`` +################################ + +Alternatively ``pixi`` can be used to create a `streamlined environment `_ after cloning the repository: + +.. code-block:: bash + + pixi install + +``pixi`` maintains isolated environments for each project, allowing for different versions of +``geoid-toolkit`` and its dependencies to be used without conflict. The ``pixi.lock`` file within the +repository defines the required packages and versions for the environment. + +``pixi`` can also create shells for running programs within the environment: + +.. code-block:: bash + + pixi shell + +To see the available tasks within the ``geoid-toolkit`` workspace: + +.. code-block:: bash + + pixi task list + +.. note:: + + ``pixi`` is under active development and may change in future releases diff --git a/doc/source/index.rst b/doc/source/index.rst index 047f22c..318e1d1 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -1,18 +1,68 @@ -============= -geoid-toolkit -============= +=========================== +geoid-toolkit Documentation +=========================== -Python tools for obtaining and working with static gravity field coefficients -and calculating geoid heights +Welcome to the documentation for ``geoid-toolkit``, a set of Python tools +for obtaining and working with static gravity field coefficients +and calculating geoid heights. + +Introduction +------------ + +.. grid:: 2 2 2 2 + :padding: 0 + + .. grid-item-card:: Installation + :text-align: center + :link: ./getting_started/Install.html + + :material-outlined:`download;5em` + + .. grid-item-card:: Examples + :text-align: center + :link: ./user_guide/Examples.html + + :material-outlined:`apps;5em` + +Contribute +---------- + +.. grid:: 2 2 4 4 + :padding: 0 + + .. grid-item-card:: Guidelines + :text-align: center + :link: ./getting_started/Contributing.html + + :material-outlined:`groups;5em` + + .. grid-item-card:: Code of Conduct + :text-align: center + :link: ./getting_started/Code-of-Conduct.html + + :material-outlined:`gavel;5em` + + .. grid-item-card:: Issues + :text-align: center + :link: https://github.com/tsutterley/geoid-toolkit/issues + + :material-outlined:`bug_report;5em` + + .. grid-item-card:: Citation Information + :text-align: center + :link: ./project/Citations.html + + :material-outlined:`alternate_email;5em` .. toctree:: :maxdepth: 2 + :hidden: :caption: Getting Started getting_started/Install.rst getting_started/Contributing.rst + getting_started/Code-of-Conduct.rst getting_started/Resources.rst - getting_started/Citations.rst .. toctree:: :maxdepth: 1 @@ -55,9 +105,19 @@ and calculating geoid heights api_reference/read_EGM2008_geoid_grids.rst api_reference/read_ICGEM_geoid_grids.rst +.. toctree:: + :maxdepth: 1 + :hidden: + :caption: Project Details + + project/Contributors.rst + project/Licenses.rst + project/Testing.rst + project/Citations.rst + .. toctree:: :maxdepth: 1 :hidden: :caption: Bibliography - getting_started/Bibliography.rst + project/Bibliography.rst diff --git a/notebooks/Calculate-Geoidal-Undulation.ipynb b/doc/source/notebooks/Calculate-Geoidal-Undulation.ipynb similarity index 85% rename from notebooks/Calculate-Geoidal-Undulation.ipynb rename to doc/source/notebooks/Calculate-Geoidal-Undulation.ipynb index 95c6c27..0a7850f 100644 --- a/notebooks/Calculate-Geoidal-Undulation.ipynb +++ b/doc/source/notebooks/Calculate-Geoidal-Undulation.ipynb @@ -4,24 +4,29 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Computes and plots geoid undulations from a gravity model\n", + "Calculate Geoidal Undulation\n", + "============================ \n", + "\n", + "This ({nb-download}`notebook `) computes and plots geoid undulations from a gravity model\n", + "\n", + "## Python Dependencies\n", "\n", - "#### PYTHON DEPENDENCIES: \n", "- [numpy: Scientific Computing Tools For Python](https://numpy.org) \n", "- [matplotlib: Python 2D plotting library](http://matplotlib.org/) \n", "- [cartopy: Python package designed for geospatial data processing](https://scitools.org.uk/cartopy) \n", "- [lxml: processing XML and HTML in Python](https://pypi.python.org/pypi/lxml) \n", "\n", - "#### PROGRAM DEPENDENCIES: \n", - "- utilities.py: download and management utilities for syncing files\n", - "- geoid_undulation.py: geoidal undulation at a given latitude and longitude \n", - "- read_ICGEM_harmonics.py: reads the coefficients for a given gravity model file \n", - "- calculate_tidal_offset.py: calculates the C20 offset for a tidal system \n", - "- real_potential.py: real potential at a latitude and height for gravity model \n", - "- norm_potential.py: normal potential of an ellipsoid at a latitude and height \n", - "- norm_gravity.py: normal gravity of an ellipsoid at a latitude and height \n", - "- ref_ellipsoid.py: Computes parameters for a reference ellipsoid \n", - "- gauss_weights.py: Computes Gaussian weights as a function of degree " + "## Program Dependencies\n", + "\n", + "- `utilities.py`: download and management utilities for syncing files\n", + "- `geoid_undulation.py`: geoidal undulation at a given latitude and longitude \n", + "- `read_ICGEM_harmonics.py`: reads the coefficients for a given gravity model file \n", + "- `calculate_tidal_offset.py`: calculates the C20 offset for a tidal system \n", + "- `real_potential.py`: real potential at a latitude and height for gravity model \n", + "- `norm_potential.py`: normal potential of an ellipsoid at a latitude and height \n", + "- `norm_gravity.py`: normal gravity of an ellipsoid at a latitude and height \n", + "- `ref_ellipsoid.py`: Computes parameters for a reference ellipsoid \n", + "- `gauss_weights.py`: Computes Gaussian weights as a function of degree " ] }, { @@ -51,7 +56,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#### Choose gravity model" + "### Choose gravity model" ] }, { @@ -75,7 +80,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#### Read gravity model coefficients" + "### Read gravity model coefficients" ] }, { @@ -107,7 +112,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#### Calculate map of geoid height" + "### Calculate map of geoid height" ] }, { @@ -138,7 +143,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#### Create output plot" + "### Create output plot" ] }, { diff --git a/doc/source/getting_started/Bibliography.rst b/doc/source/project/Bibliography.rst similarity index 100% rename from doc/source/getting_started/Bibliography.rst rename to doc/source/project/Bibliography.rst diff --git a/doc/source/getting_started/Citations.rst b/doc/source/project/Citations.rst similarity index 55% rename from doc/source/getting_started/Citations.rst rename to doc/source/project/Citations.rst index 02cc80b..8428b50 100644 --- a/doc/source/getting_started/Citations.rst +++ b/doc/source/project/Citations.rst @@ -4,42 +4,23 @@ Citation Information References ########## + The programs included in this software have contributed most recently to the following work: - T. C. Sutterley, T. Markus, T. A. Neumann, M. van den Broeke, J. M. van Wessem, - and S. R. M. Ligtenberg, "Antarctic ice shelf thickness change from multimission - lidar mapping", *The Cryosphere*, 13(7), 1801-1817, (2020). - `doi: 10.5194/tc-13-1801-2019 `_ - T. C. Sutterley and I. Velicogna, "Improved estimates of geocenter variability from time-variable gravity and ocean model outputs", *Remote Sensing*, 11(18), 2108, (2019). `doi: 10.3390/rs11182108 `_ -If you have used ``geoid-toolkit`` in your work, please consider citing our library: +.. admonition:: Please consider citing our library T. C. Sutterley, et al., "geoid-toolkit: Python tools for obtaining and working with static gravity field coefficients for calculating geoid heights", (2019). `doi: 10.5281/zenodo.5768711 `_ -Contributors -############ - -.. include:: ../../../CONTRIBUTORS.rst - -Development -########### -This is an open source project. We welcome any help in maintaining and developing the software and documentation. -Anyone at any career stage and with any level of coding experience can contribute. -Please see the `Contribution Guidelines <./Contributing.html>`_ for more information. - -Problem Reports -############### -If you have found a problem in these programs, or you would like to suggest an improvement or modification, -please submit a `GitHub issue `_ and we will get back to you. - Dependencies ############ + This software is also dependent on other commonly used Python packages: - `cartopy: Python package designed for geospatial data processing `_ @@ -54,5 +35,21 @@ This software is also dependent on other commonly used Python packages: Disclaimer ########## -This program is not sponsored or maintained by the Universities Space Research Association (USRA), the Center for Space Research at the University of Texas (UTCSR), the Jet Propulsion Laboratory (JPL), the German Research Centre for Geosciences (GeoForschungsZentrum, GFZ) or NASA. -It is provided here for your convenience but *with no guarantees whatsoever*. \ No newline at end of file + +This work is currently supported by the NASA GRACE-FO Science Team (Grant Number 80NSSC24K1153). +This program is not sponsored or maintained by the Universities Space Research Association (USRA), +the Center for Space Research at the University of Texas (UTCSR), +the Jet Propulsion Laboratory (JPL), +the German Research Centre for Geosciences (GeoForschungsZentrum, GFZ) or NASA. + +.. caution:: + This software is provided here for your convenience but *with no guarantees whatsoever*. + +This product includes software developed at: + +- University of California, Irvine, Department of Earth System Science +- Jet Propulsion Laboratory, California Institute of Technology +- National Aeronautics and Space Administration, Goddard Space Flight Center +- University of Washington, Applied Physics Laboratory, Polar Science Center + +.. |euml| unicode:: U+00EB .. LATIN SMALL LETTER E WITH DIAERESIS diff --git a/doc/source/project/Contributors.rst b/doc/source/project/Contributors.rst new file mode 100644 index 0000000..4dab9c9 --- /dev/null +++ b/doc/source/project/Contributors.rst @@ -0,0 +1,6 @@ +============ +Contributors +============ + +.. include:: ../../../CONTRIBUTORS.md + :parser: commonmark \ No newline at end of file diff --git a/doc/source/project/Licenses.rst b/doc/source/project/Licenses.rst new file mode 100644 index 0000000..654daf3 --- /dev/null +++ b/doc/source/project/Licenses.rst @@ -0,0 +1,15 @@ +======== +Licenses +======== + +MIT License +=========== + +The source code of ``geoid-toolkit`` is licensed under a MIT license: + +.. include:: ../../../LICENSE + +Other Licenses +============== + +The content of ``geoid-toolkit`` including documentation and notebooks is licensed under a `Creative Commons Attribution 4.0 Attribution license `_ (CC BY 4.0). diff --git a/doc/source/project/Testing.rst b/doc/source/project/Testing.rst new file mode 100644 index 0000000..cb783d1 --- /dev/null +++ b/doc/source/project/Testing.rst @@ -0,0 +1,66 @@ +======= +Testing +======= + +``geoid-toolkit`` uses the ``pytest`` framework to run tests and verify outputs. +Running the test suite requires a `dev installation <../getting_started/Install.html>`_ of the ``geoid-toolkit`` package to include all of the optional dependencies. + +.. code-block:: bash + + python -m pip install --editable '.[dev]' + +Running the Test Suite +^^^^^^^^^^^^^^^^^^^^^^ + +Using the ``pytest`` command: + +.. code-block:: bash + + pytest --directory test/ + +Using ``pixi``: + +.. code-block:: bash + + pixi run test "--directory " + +The test suite is run in verbose mode as a default. + +Coverage Reports +^^^^^^^^^^^^^^^^ + +Coverage reports can be generated using the ``pytest-cov`` plugin (which is installed with the dev installation). + +.. code-block:: bash + + pytest --cov geoid_toolkit --cov-report=term + +.. code-block:: bash + + pixi run test "--cov ../geoid_toolkit --cov-report=term" + +Parallelization +^^^^^^^^^^^^^^^ + +As a default, the ``pytest`` suite is run in parallel using the ``pytest-xdist`` plugin (which is also installed with the dev installation). +To run in series and disable parallelization, set the number of processes to 0: + +.. code-block:: bash + + pytest -n 0 + +.. code-block:: bash + + pixi run test "-n 0"_ + +Continuous Integration +^^^^^^^^^^^^^^^^^^^^^^ +We use `GitHub Actions `_ continuous integration (CI) services to build and test the project on Linux (``ubuntu-latest``), Mac (``macos-latest``) and Windows (``windows-latest``) Operating Systems. +The configuration files for this service are in the `GitHub workflows `_ directory. +The workflows use ``pixi`` to install the required dependencies and build the custom environment. + +The GitHub Actions jobs include: + +* Running `flake8 `_ to check the code for style and compilation errors +* Running the test suite on multiple combinations of OS and Python version +* Uploading source and wheel distributions to `PyPI `_ (on releases) diff --git a/doc/source/user_guide/Examples.rst b/doc/source/user_guide/Examples.rst index e669bcc..4d743ee 100755 --- a/doc/source/user_guide/Examples.rst +++ b/doc/source/user_guide/Examples.rst @@ -4,13 +4,18 @@ Examples ======== -Jupyter Notebooks providing demonstrations of the ``geoid-toolkit`` functionality: +.. important:: + Running the example notebooks requires a `full installation <../getting_started/Install.html>`_ to include all of the optional dependencies. -- Creating Spatial Maps |github spatial| |nbviewer spatial| - Creates a spatial map of geoidal undulations on a global Equirectangular projection using coefficients from a gravity field model +.. toctree:: + :maxdepth: 1 + :hidden: -.. |github spatial| image:: https://img.shields.io/badge/GitHub-view-6f42c1?style=flat&logo=Github - :target: https://github.com/tsutterley/geoid-toolkit/blob/main/notebooks/Calculate-Geoidal-Undulation.ipynb + ../notebooks/Calculate-Geoidal-Undulation -.. |nbviewer spatial| image:: https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg - :target: https://nbviewer.jupyter.org/github/tsutterley/geoid-toolkit/blob/main/notebooks/Calculate-Geoidal-Undulation.ipynb +.. grid:: 1 2 4 4 + + .. grid-item-card:: Calculate Geoidal Undulation + :text-align: center + :link: ../notebooks/Calculate-Geoidal-Undulation.html + :link-alt: Calculates geoidal undulations from a gravity field model diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..bff2263 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,11497 @@ +version: 6 +environments: + all: + channels: + - 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Alpha", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Physics", +] + +[project.urls] +Homepage = "https://geoid-toolkit.readthedocs.io" +Documentation = "https://geoid-toolkit.readthedocs.io" +Repository = "https://github.com/tsutterley/geoid-toolkit" +Issues = "https://github.com/tsutterley/geoid-toolkit/issues" + +[project.optional-dependencies] +all = ["cartopy", "gdal", "h5py", "jupyterlab", "matplotlib", "netCDF4", "notebook", "pyproj"] +doc = ["docutils", "graphviz", "myst-nb", "numpydoc", "sphinx", "sphinx-argparse>=0.4", "sphinxcontrib-bibtex", "sphinx-design", "sphinx_rtd_theme"] +dev = ["flake8", "pytest>=4.6", "pytest-cov", "pytest-xdist"] + +[tool.setuptools.packages.find] +exclude = ["test*", "run*"] + +[tool.pytest.ini_options] +minversion = "6.0" +norecursedirs = ".git" +addopts = "-n auto --verbose --capture=no" +python_files = [ + "test*.py" +] +testpaths = [ + "test" +] + +[tool.coverage.run] +branch = true +source = [ + "geoid-toolkit", + "test", +] +omit = [ + "setup.py", + "conf.py", + "scripts/*", +] + +[tool.coverage.report] +show_missing = true +precision = 2 + +[tool.ruff] +line-length = 80 +indent-width = 4 + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.ruff.format] +quote-style = "single" +indent-style = "space" +docstring-code-format = false + +[tool.pixi.workspace] +name = "geoid-toolkit" +authors = ["geoid-toolkit contributors"] +channels = ["conda-forge"] +platforms = ["osx-arm64", "linux-64", "win-64"] + +[tool.pixi.pypi-dependencies] +geoid-toolkit = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "default" } +all = { features = ["all"], solve-group = "default" } +dev = { features = ["all", "dev", "doc"], solve-group = "default" } +doc = { features = ["all", "doc"], solve-group = "default" } + +[tool.pixi.tasks.start] +cmd = "jupyter lab" +cwd = "doc/source/notebooks" +description = "Start JupyterLab in the notebooks directory" + +[tool.pixi.tasks.export-env] +args = [ { "arg" = "flags", "default" = "" } ] +cmd = "pixi workspace export conda-environment {{ flags }} > environment.yml" +description = "Export workspace to a conda environment file" + +[tool.pixi.feature.doc.tasks.docs] +args = [ { "arg" = "flags", "default" = "" } ] +cmd = "make html {{ flags }}" +cwd = "doc" +description = "Create HTML documentation with sphinx" + +[tool.pixi.feature.dev.tasks.lint] +args = [ { "arg" = "flags", "default" = "--select=E9,F63,F7,F82 --show-source" }, { "arg" = "test", "default" = "." } ] +cmd = "flake8 {{ test }} --count {{ flags }} --statistics --extend-exclude 'build/,run/,*.ipynb_checkpoints/,.pixi/'" +description = "Run flake8 to check for compilation errors" + +[tool.pixi.dependencies] +lxml = "*" +numpy = "*" +python-dateutil = "*" + +[tool.pixi.feature.all.dependencies] +cartopy = "*" +gdal = "*" +h5py = "*" +jupyterlab = "*" +matplotlib-base = "*" +netCDF4 = "*" +notebook = "*" +pyproj = "*" + +[tool.pixi.feature.dev.dependencies] +flake8 = "*" +pytest = "*" +pytest-cov = "*" +pytest-xdist = "*" + +[tool.pixi.feature.doc.dependencies] +docutils = "*" +graphviz = "*" +markupsafe = "*" +myst-nb = "*" +numpydoc = "*" +sphinx = "*" +sphinx-argparse = "*" +sphinxcontrib-bibtex = "*" +sphinx-design = "*" +sphinx_rtd_theme = "*" diff --git a/readthedocs.yml b/readthedocs.yml index be3de2c..3c1ae0f 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -7,17 +7,21 @@ version: 2 # Configuration for the documentation build process build: - os: "ubuntu-22.04" + os: "ubuntu-lts-latest" tools: - python: "mambaforge-22.9" + python: "3.13" + jobs: + create_environment: + - asdf plugin add pixi + - asdf install pixi latest + - asdf global pixi latest + install: + - pixi install -e doc + build: + html: + - pixi run -e doc sphinx-build -T -b html doc/source $READTHEDOCS_OUTPUT/html -# Build documentation in the docs/ directory with Sphinx +# Build documentation with Sphinx sphinx: + builder: html configuration: doc/source/conf.py - -# Optionally build your docs in additional formats such as PDF and ePub -formats: [] - -# Optionally set the version of conda and environment required to build your docs -conda: - environment: doc/environment.yml diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index dd6b82b..0000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,5 +0,0 @@ -flake8 -pytest>=4.6 -pytest-cov -numpy -cython diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 605f05b..0000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -lxml -numpy -python-dateutil diff --git a/setup.py b/setup.py index 6a94606..9e497c8 100644 --- a/setup.py +++ b/setup.py @@ -1,98 +1,10 @@ import os -import sys -import logging -import subprocess -from setuptools import setup, find_packages - -logging.basicConfig(stream=sys.stderr, level=logging.INFO) -log = logging.getLogger() - -# package description and keywords -description = 'Reads gravity model coefficients and calculates geoid heights' -keywords = 'static gravity field, geoid height, physical geodesy' -# get long_description from README.rst -with open("README.rst", mode='r', encoding='utf8') as fh: - long_description = fh.read() -long_description_content_type = "text/x-rst" - -# install requirements and dependencies -on_rtd = os.environ.get('READTHEDOCS') == 'True' -if on_rtd: - install_requires = [] -else: - # get install requirements - with open('requirements.txt', mode='r', encoding='utf8') as fh: - install_requires = [line.split().pop(0) for line in fh.read().splitlines()] - -# get version -with open('version.txt', mode='r', encoding='utf8') as fh: - version = fh.read() +from setuptools import setup # list of all scripts to be included with package scripts=[os.path.join('scripts',f) for f in os.listdir('scripts') if f.endswith('.py')] -# run cmd from the command line -def check_output(cmd): - return subprocess.check_output(cmd).decode('utf') - -# check if GDAL is installed -gdal_output = [None] * 4 -try: - for i, flag in enumerate(("--cflags", "--libs", "--datadir", "--version")): - gdal_output[i] = check_output(['gdal-config', flag]).strip() -except Exception as exc: - log.warning('Failed to get options via gdal-config') -else: - log.info(f"GDAL version from via gdal-config: {gdal_output[3]}") -# if setting GDAL version from via gdal-config -if gdal_output[3] and ('gdal' in install_requires): - # add version information to gdal in install_requires - gdal_index = install_requires.index('gdal') - install_requires[gdal_index] = f'gdal=={gdal_output[3]}' -elif any(install_requires) and ('gdal' in install_requires): - # gdal version not found - gdal_index = install_requires.index('gdal') - install_requires.pop(gdal_index) - -# check if HDF5 is installed -hdf5_output = [None] * 2 -try: - for i, cmd in enumerate((["h5cc","-showconfig"], ["h5dump","--version"])): - hdf5_output[i] = check_output(cmd).strip() - # parse HDF5 version from h5dump - hdf5_version = hdf5_output[1].split().pop(2) -except Exception as exc: - log.warning('Failed to get HDF5 options') -else: - log.info(f"HDF5 version from via h5dump: {hdf5_version}") -# if the HDF5 version not found -if not any(hdf5_output) and ('h5py' in install_requires): - hdf5_index = install_requires.index('h5py') - install_requires.pop(hdf5_index) - setup( name='geoid-toolkit', - version=version, - description=description, - long_description=long_description, - long_description_content_type=long_description_content_type, - url='https://github.com/tsutterley/geoid-toolkit', - author='Tyler Sutterley', - author_email='tsutterl@uw.edu', - license='MIT', - classifiers=[ - 'Development Status :: 3 - Alpha', - 'Intended Audience :: Science/Research', - 'Topic :: Scientific/Engineering :: Physics', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.6', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - ], - keywords=keywords, - packages=find_packages(), - install_requires=install_requires, scripts=scripts, - include_package_data=True, ) diff --git a/version.txt b/version.txt deleted file mode 100644 index 45a1b3f..0000000 --- a/version.txt +++ /dev/null @@ -1 +0,0 @@ -1.1.2