Migrate to pyproject.toml and deprecate local meta.yaml (#771)

* Update requirements.txt

* update requirements.txt

* pyproject.toml

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add pyprpoject.toml

* update pyproject.toml

* revert changes in test dir

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* revert changes in benchmarks

* update conf.py

* update pyproject.toml

* update install docs

* update install docs

* update instal guide

* update instal guide

* update instal guide

* update instalation.rst

* add back setup.py for compatibility

* update optional dependencies

* Create MANIFEST.in

* add ruff to dev dependencies

* use matplotlib instead of matplotlib-base

* Remove .txt from LICENSE

* Update MANIFEST.in

Co-authored-by: Anissa Zacharias <anissaz@ucar.edu>

* update pyproject.toml

* remove references to meta.yaml

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Anissa Zacharias <anissaz@ucar.edu>

.github/ISSUE_TEMPLATE/release_request.md

@@ -11,7 +11,6 @@ Date of intended release:
 ## Release progress checklist
 
 - [ ] CI tests are passing
-- [ ] update version number in `meta.yaml`
 - [ ] a new tag and release has been made on GitHub
 - [ ] feedstock PR has been merged
 - [ ] release on pypi action has been triggered and run successfully

.pre-commit-config.yaml

@@ -10,14 +10,13 @@ repos:
     hooks:
     - id: check-yaml               # Checks the syntax of .yaml files.
       args: [--allow-multiple-documents]
-      exclude: 'meta.yaml'    # Exclude this because it gives an error for '%' in Line 1 and couldn't fix yet
     - id: end-of-file-fixer        # Makes sure files end with a newline.
     - id: trailing-whitespace      # Checks for any tabs or spaces after the last non-whitespace character on the line.
     - id: check-docstring-first    # Checks that code comes after the docstrings.
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.5
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff

MANIFEST.in

@@ -0,0 +1,18 @@
+include LICENSE
+include README.md
+
+recursive-include uxarray *.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+exclude .gitignore
+exclude .pre-commit-config.yaml
+exclude .readthedocs.yml
+
+include *.md
+include *.toml
+include *.txt
+prune test*
+prune ci*
+prune .github*
+prune docs*
+prune benchmarks*

docs/conf.py

@@ -121,21 +121,6 @@ def __getattr__(cls, name):
 copyright = "{}, Uxarray".format(current_year)
 author = "UXARRAY"
 
-
-# The version info for the project being documented
-def read_version():
-    for line in open("../meta.yaml").readlines():
-        index = line.find("set version")
-        if index > -1:
-            return line[index + 15 :].replace('" %}', "").strip()
-
-
-# The short X.Y version.
-version = read_version()
-
-# The full version, including alpha/beta/rc tags.
-release = read_version()
-
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 # This is also used if you do content translation via gettext catalogs.

docs/installation.rst

@@ -32,6 +32,31 @@ An alternative to Conda is using pip::
 
     pip install uxarray
 
+This installs the minimum set of required dependencies, which includes the following:
+
+.. literalinclude:: ../pyproject.toml
+   :language: toml
+   :start-after: minimal dependencies start
+   :end-before: minimal dependencies end
+
+
+UXarray also maintains other dependency sets for different subsets of functionality::
+
+    $ python -m pip install "uxarray[math]"       # Install optional dependencies for accurate math utlities
+    $ python -m pip install "uxarray[dev]"        # Install optional dependencies for development
+    $ python -m pip install "uxarray[complete]"   # Install all optional dependencies
+
+The above commands should install most of the optional dependencies. However,
+some packages which are either not listed on PyPI or require extra
+installation steps are excluded. To know which dependencies would be
+installed, take a look at the ``[project.optional-dependencies]`` section in
+``pyproject.toml``:
+
+.. literalinclude:: ../pyproject.toml
+   :language: toml
+   :start-at: [project.optional-dependencies]
+   :end-before: [project.urls]
+
 Installing UXarray from source (Github)
 ---------------------------------------
 

pyproject.toml

@@ -0,0 +1,74 @@
+[project]
+classifiers=[
+  "Operating System :: OS Independent",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  'Operating System :: Microsoft :: Windows',
+  'Operating System :: Unix',
+  'Operating System :: MacOS',
+  "Topic :: Scientific/Engineering",
+]
+
+dynamic = ["version"]
+keywords = ["unstructured grids"]
+description = "Xarray-styled package for reading and directly operating on unstructured grid datasets following UGRID conventions"
+license = {file = "LICENSE"}
+name = "uxarray"
+readme = "README.md"
+requires-python = ">=3.9"
+
+# minimal dependencies start
+dependencies = [
+  "antimeridian",
+  "cartopy",
+  "cartopy",
+  "dask[dataframe]",
+  "datashader",
+  "geoviews",
+  "holoviews",
+  "matplotlib",
+  "matplotlib-inline",
+  "netcdf4",
+  "numba",
+  "numpy",
+  "pandas<2.1.0",
+  "pyarrow",
+  "requests",
+  "scikit-learn",
+  "scipy",
+  "shapely",
+  "spatialpandas",
+  "xarray",
+]
+# minimal dependencies end
+
+[project.optional-dependencies]
+complete = ["uxarray[math, dev]"]
+math = ['gmpy2', 'pyfma']
+dev = ['pathlib', 'pre_commit', 'pytest', 'pytest-cov', 'ruff']
+
+[project.urls]
+Documentation = "uxarray.readthedocs.io/"
+Source = "https://github.com/UXARRAY/uxarray"
+Tracker = "https://github.com/UXARRAY/uxarray/issues"
+
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools>=60",
+  "setuptools-scm>=8",
+]
+
+[tool.setuptools.packages]
+find = {}
+
+[tool.setuptools_scm]
+fallback_version = "9999"
+
+[tool.ruff]
+extend-exclude = ["test","benchmarks"]

setup.py

@@ -1,50 +1,3 @@
-#''' setup.py is needed, but only to make namespaces happen
+from setuptools import setup
 
-from setuptools import find_packages, setup
-
-with open("README.md") as f:
-    long_description = f.read()
-
-with open("requirements.txt") as f:
-    requirements = f.read().strip().split("\n")
-
-
-#''' moved into function, can now be used other places
-def version():
-    for line in open("meta.yaml").readlines():
-        index = line.find("set version")
-        if index > -1:
-            return line[index + 15 :].replace('" %}', "").strip()
-
-
-setup(
-    name="uxarray",
-    version=version(),
-    maintainer="UXARRAY",
-    maintainer_email="",
-    python_requires=">=3.9",
-    install_requires=requirements,
-    description="""Unstructured grid model reading and recognizing with xarray.""",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    classifiers=[
-        "Operating System :: OS Independent",
-        "Intended Audience :: Science/Research",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Topic :: Scientific/Engineering",
-    ],
-    include_package_data=True,
-    packages=find_packages(exclude=["docs", "test", "docs.*", "test.*"]),
-    # namespace_packages=['UXARRAY'],
-    url="https://github.com/UXARRAY/uxarray",
-    project_urls={
-        # 'Documentation': 'https://uxarray.readthedocs.io',
-        "Source": "https://github.com/UXARRAY/uxarray",
-        "Tracker": "https://github.com/UXARRAY/uxarray/issues",
-    },
-    zip_safe=False,
-)
+setup(use_scm_version={"fallback_version": "9999"})

uxarray/grid/grid.py

@@ -1,4 +1,5 @@
 """uxarray.core.grid module."""
+
 import xarray as xr
 import numpy as np