refactor: use pyproject.toml for builds

.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/*
-

.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"

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/).

CONTRIBUTORS.md

@@ -0,0 +1 @@
+- [Tyler Sutterley (University of Washington)](http://psc.apl.uw.edu/people/investigators/tyler-sutterley/)

MANIFEST.in

@@ -4,5 +4,3 @@ prune doc*
 prune notebooks*
 exclude *.cfg
 exclude *.yml
-include requirements.txt
-include version.txt

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.

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;
+}

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 = {

doc/source/getting_started/Code-of-Conduct.rst

@@ -0,0 +1,2 @@
+.. include:: ../../../CODE_OF_CONDUCT.md
+    :parser: commonmark