From 9eab7818a9e3a67cfca922667fb758fd54c0217b Mon Sep 17 00:00:00 2001
From: "P. L. Lim" <2090236+pllim@users.noreply.github.com>
Date: Wed, 11 Oct 2023 20:25:01 -0400
Subject: [PATCH] Bump minversions, update CI (#240)

* Bump minversions, update CI

* Lots of clean-up
---
 .github/workflows/spherical_geometry.yml      |  61 +++--
 CHANGES.rst                                   |  10 +-
 MANIFEST.in                                   |   5 +-
 .../tests/coveragerc => coveragerc            |   0
 licenses/LICENSE.rst                          |   2 +-
 pyproject.toml                                |   2 +-
 setup.cfg                                     |  19 +-
 setup.py                                      |   9 +-
 spherical_geometry/__init__.py                |   8 +-
 spherical_geometry/graph.py                   |   4 +-
 spherical_geometry/great_circle_arc.py        |   3 -
 spherical_geometry/polygon.py                 |   1 -
 spherical_geometry/tests/setup_package.py     |   3 -
 spherical_geometry/tests/test_basic.py        |   2 -
 spherical_geometry/tests/test_intersection.py |   5 +-
 spherical_geometry/tests/test_union.py        |   5 +-
 spherical_geometry/utils/__init__.py          |   4 -
 spherical_geometry/utils/compat/__init__.py   |   4 -
 spherical_geometry/utils/compat/weakref.py    |  19 --
 spherical_geometry/utils/compat/weakrefset.py | 213 ------------------
 spherical_geometry/vector.py                  |   2 -
 21 files changed, 76 insertions(+), 305 deletions(-)
 rename spherical_geometry/tests/coveragerc => coveragerc (100%)
 delete mode 100755 spherical_geometry/tests/setup_package.py
 delete mode 100755 spherical_geometry/utils/__init__.py
 delete mode 100644 spherical_geometry/utils/compat/__init__.py
 delete mode 100644 spherical_geometry/utils/compat/weakref.py
 delete mode 100644 spherical_geometry/utils/compat/weakrefset.py

diff --git a/.github/workflows/spherical_geometry.yml b/.github/workflows/spherical_geometry.yml
index a9c7ffc..debd505 100644
--- a/.github/workflows/spherical_geometry.yml
+++ b/.github/workflows/spherical_geometry.yml
@@ -1,7 +1,5 @@
 name: Spherical Geometry CI
 
-# Change 'on' section and add code coverage.
-
 on:
   push:
     branches:
@@ -9,23 +7,30 @@ on:
     tags:
       - "*"
   pull_request:
-    branches:
   schedule:
     # Run every Monday at 6am UTC
     - cron: '0 6 * * 1'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
   build:
     name: Python Testing ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -35,6 +40,28 @@ jobs:
         python -m pip install -e .[test]
     - name: Test with pytest
       run: |
+        pip freeze
+        pytest
+
+  devdeps:
+    name: Python Testing with dev versions of dependencies
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --pre --upgrade --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
+        python -m pip install --pre --upgrade --extra-index-url https://pypi.anaconda.org/astropy/simple astropy
+        python -m pip install -e .[test]
+    - name: Test with pytest
+      run: |
+        pip freeze
         pytest
 
   doc_build:
@@ -42,11 +69,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         sudo apt-get install graphviz texlive-latex-extra dvipng
@@ -54,6 +81,7 @@ jobs:
         python -m pip install -e .[docs]
     - name: Build documents with sphinx
       run: |
+        pip freeze
         sphinx-build docs build/docs
 
   code_coverage:
@@ -61,20 +89,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install -e .[test]
     - name: Test with pytest and code coverage
       run: |
+        pip freeze
         pytest --cov-report=xml --cov=. --cov-config=setup.cfg
     - name: Upload coverage to codecoverage
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml
 
@@ -83,11 +112,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.11'
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
diff --git a/CHANGES.rst b/CHANGES.rst
index fac152a..6c047aa 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -4,8 +4,8 @@
 Release Notes
 =============
 
-1.2.24 (unreleased)
-===================
+1.3 (unreleased)
+================
 
 - Add documentation to ``polygon.py`` for the ``SphericalPolygon``
   method ``multi_union`` has exponential time behavior and cannot
@@ -18,6 +18,12 @@ Release Notes
   https://github.com/spacetelescope/spherical_geometry/issues/232
   is resolved. [#233]
 
+- Removed unused ``spherical_geometry.utils`` module. [#239]
+
+- Minimum supported version for Python is now 3.9. [#239]
+
+- Minimum supported version for NumPy is now 1.20. [#239]
+
 
 1.2.23 (10-October-2022)
 ========================
diff --git a/MANIFEST.in b/MANIFEST.in
index 5c119e6..524eba4 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -2,12 +2,11 @@ include README.rst
 include CHANGES.rst
 
 include setup.cfg
+include pyproject.toml
 
-recursive-include *.pyx *.c *.pxd
+recursive-include *.c
 recursive-include docs *
 recursive-include licenses *
-recursive-include cextern *
-recursive-include scripts *
 
 prune build
 prune docs/_build
diff --git a/spherical_geometry/tests/coveragerc b/coveragerc
similarity index 100%
rename from spherical_geometry/tests/coveragerc
rename to coveragerc
diff --git a/licenses/LICENSE.rst b/licenses/LICENSE.rst
index 7edcf72..021d379 100644
--- a/licenses/LICENSE.rst
+++ b/licenses/LICENSE.rst
@@ -1,4 +1,4 @@
-Copyright (C) 2011,2014 Association of Universities for Research in
+Copyright (C) 2011-2023 Association of Universities for Research in
 Astronomy (AURA)
 
 Redistribution and use in source and binary forms, with or without
diff --git a/pyproject.toml b/pyproject.toml
index 07ba7aa..5939726 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools>=38.2.5", "setuptools_scm", "wheel", "oldest-supported-numpy"]
+requires = ["setuptools>=38.2.5", "setuptools_scm", "numpy>=1.25,<2"]
diff --git a/setup.cfg b/setup.cfg
index d6543d3..8d570af 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,16 +1,12 @@
-[build_sphinx]
-source-dir = docs
-build-dir = docs/_build
-all_files = 1
-
-[upload_docs]
-upload-dir = docs/_build/html
-show-response = 1
-
-[tools:pytest]
-minversion = 4.2
+[tool:pytest]
+minversion = 6
 junit_family = xunit2
 norecursedirs = .git build docs/_build
+xfail_strict = true
+filterwarnings =
+    error
+    ignore:numpy\.ndarray size changed:RuntimeWarning
+    ignore:numpy\.ufunc size changed:RuntimeWarning
 
 [metadata]
 package_name = spherical_geometry
@@ -32,4 +28,3 @@ omit =
     spherical_geometry/tests/*
     # And list again for running against installed versions
     */spherical_geometry/tests/*
-
diff --git a/setup.py b/setup.py
index df5e1e2..f98fb9c 100644
--- a/setup.py
+++ b/setup.py
@@ -68,10 +68,7 @@ def qd_config(arg):
     exit(1)
 
 # Get some values from the setup.cfg
-try:
-    from ConfigParser import ConfigParser
-except ImportError:
-    from configparser import ConfigParser
+from configparser import ConfigParser
 conf = ConfigParser()
 conf.read(['setup.cfg'])
 metadata = dict(conf.items('metadata'))
@@ -134,9 +131,9 @@ def qd_config(arg):
     description=DESCRIPTION,
     install_requires=[
         'astropy>=5.0.4',
-        'numpy>=1.18',
+        'numpy>=1.20',
     ],
-    python_requiers='>=3.8',
+    python_requiers='>=3.9',
     extras_require={
         'test': [
             'pytest',
diff --git a/spherical_geometry/__init__.py b/spherical_geometry/__init__.py
index 873e2c3..5a8b56b 100755
--- a/spherical_geometry/__init__.py
+++ b/spherical_geometry/__init__.py
@@ -1,6 +1,4 @@
-from pkg_resources import get_distribution, DistributionNotFound
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
-    # package is not installed
-    __version__ = 'unknown'
+    from .version import version as __version__
+except ImportError:
+    __version__ = ''
diff --git a/spherical_geometry/graph.py b/spherical_geometry/graph.py
index 0be7e00..d5111be 100644
--- a/spherical_geometry/graph.py
+++ b/spherical_geometry/graph.py
@@ -6,16 +6,14 @@
 This contains the code that does the actual unioning of regions.
 """
 # TODO: Weak references for memory management problems?
-from __future__ import absolute_import, division, unicode_literals, print_function
 
 # STDLIB
-import itertools
+import weakref
 
 # THIRD-PARTY
 import numpy as np
 
 # LOCAL
-from .utils.compat import weakref
 from . import great_circle_arc as gca
 from . import vector
 from .polygon import (SingleSphericalPolygon, SphericalPolygon,
diff --git a/spherical_geometry/great_circle_arc.py b/spherical_geometry/great_circle_arc.py
index 9a57c76..39c9361 100644
--- a/spherical_geometry/great_circle_arc.py
+++ b/spherical_geometry/great_circle_arc.py
@@ -11,9 +11,6 @@
 section of those circles between two points on the unit sphere.
 """
 
-from __future__ import with_statement, division, absolute_import, unicode_literals
-
-import math
 from .vector import two_d
 
 # THIRD-PARTY
diff --git a/spherical_geometry/polygon.py b/spherical_geometry/polygon.py
index 12ae9eb..4dfd246 100644
--- a/spherical_geometry/polygon.py
+++ b/spherical_geometry/polygon.py
@@ -6,7 +6,6 @@
 The `spherical_geometry.polygon` module defines the `SphericalPolygon` class for
 managing polygons on the unit sphere.
 """
-from __future__ import division, print_function, unicode_literals, absolute_import
 
 # STDLIB
 from copy import copy, deepcopy
diff --git a/spherical_geometry/tests/setup_package.py b/spherical_geometry/tests/setup_package.py
deleted file mode 100755
index a7670e4..0000000
--- a/spherical_geometry/tests/setup_package.py
+++ /dev/null
@@ -1,3 +0,0 @@
-def get_package_data():
-    return {
-        _ASTROPY_PACKAGE_NAME_ + '.tests': ['coveragerc', 'data/*']}
diff --git a/spherical_geometry/tests/test_basic.py b/spherical_geometry/tests/test_basic.py
index c7a95a5..6eb99bf 100644
--- a/spherical_geometry/tests/test_basic.py
+++ b/spherical_geometry/tests/test_basic.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import
-
 import os
 import os.path
 import math
diff --git a/spherical_geometry/tests/test_intersection.py b/spherical_geometry/tests/test_intersection.py
index 3331474..40cd8c4 100644
--- a/spherical_geometry/tests/test_intersection.py
+++ b/spherical_geometry/tests/test_intersection.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, absolute_import
-
 # STDLIB
 import codecs
 import functools
@@ -8,10 +6,10 @@
 import os
 import random
 import sys
-import pytest
 
 # THIRD-PARTY
 import numpy as np
+import pytest
 from numpy.testing import assert_array_almost_equal
 
 # LOCAL
@@ -121,6 +119,7 @@ def test3():
     return [poly1, poly3]
 
 
+@pytest.mark.filterwarnings("ignore:CPERROR.*")
 def test4():
     from astropy.io import fits
     from astropy import wcs as pywcs
diff --git a/spherical_geometry/tests/test_union.py b/spherical_geometry/tests/test_union.py
index 1c5dea1..2868f32 100644
--- a/spherical_geometry/tests/test_union.py
+++ b/spherical_geometry/tests/test_union.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, absolute_import
-
 # STDLIB
 import codecs
 import functools
@@ -11,6 +9,7 @@
 
 # THIRD-PARTY
 import numpy as np
+import pytest
 from numpy.testing import assert_array_almost_equal
 
 # LOCAL
@@ -113,6 +112,7 @@ def test2():
     return [poly1, poly2, poly3, poly4, poly5, poly6]
 
 
+@pytest.mark.filterwarnings("ignore:CPERROR.*")
 def test5():
     from astropy.io import fits
     from astropy import wcs as pywcs
@@ -139,6 +139,7 @@ def test6():
     null_union = chipA1.union(chipA2)
 
 
+@pytest.mark.filterwarnings("ignore:CPERROR.*")
 @union_test(0, 90)
 def test7():
     from astropy.io import fits
diff --git a/spherical_geometry/utils/__init__.py b/spherical_geometry/utils/__init__.py
deleted file mode 100755
index c750873..0000000
--- a/spherical_geometry/utils/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
-
-# This sub-module is destined for common non-package specific utility
-# functions that will ultimately be merged into `astropy.utils`
diff --git a/spherical_geometry/utils/compat/__init__.py b/spherical_geometry/utils/compat/__init__.py
deleted file mode 100644
index 6c2ccc0..0000000
--- a/spherical_geometry/utils/compat/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
-
-# This sub-module contains packages added for compatability with
-# versions of Python other than 2.7
diff --git a/spherical_geometry/utils/compat/weakref.py b/spherical_geometry/utils/compat/weakref.py
deleted file mode 100644
index 8688472..0000000
--- a/spherical_geometry/utils/compat/weakref.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
-"""
-A replacement wrapper around the weakref module that adds WeakSet for
-versions of python that are missing it.
-
-Instead of importing weakref, other modules should use this as follows::
-
-    from .utils.compat import weakref
-
-"""
-from __future__ import absolute_import
-
-import weakref
-
-# python2.7 and later provide a WeakSet class
-if not hasattr(weakref, 'WeakSet'):
-    from .weakrefset import WeakSet
-
-from weakref import *
diff --git a/spherical_geometry/utils/compat/weakrefset.py b/spherical_geometry/utils/compat/weakrefset.py
deleted file mode 100644
index 072c453..0000000
--- a/spherical_geometry/utils/compat/weakrefset.py
+++ /dev/null
@@ -1,213 +0,0 @@
-from __future__ import with_statement
-
-from _weakref import ref
-
-__all__ = ['WeakSet']
-
-__version__ = '1.0.0'
-
-
-
-class _IterationGuard(object):
-    # This context manager registers itself in the current iterators of the
-    # weak container, such as to delay all removals until the context manager
-    # exits.
-    # This technique should be relatively thread-safe (since sets are).
-
-    def __init__(self, weakcontainer):
-        # Don't create cycles
-        self.weakcontainer = ref(weakcontainer)
-
-    def __enter__(self):
-        w = self.weakcontainer()
-        if w is not None:
-            w._iterating.add(self)
-        return self
-
-    def __exit__(self, e, t, b):
-        w = self.weakcontainer()
-        if w is not None:
-            s = w._iterating
-            s.remove(self)
-            if not s:
-                w._commit_removals()
-
-
-class WeakSet(object):
-    def __init__(self, data=None):
-        self.data = set()
-        def _remove(item, selfref=ref(self)):
-            self = selfref()
-            if self is not None:
-                if self._iterating:
-                    self._pending_removals.append(item)
-                else:
-                    self.data.discard(item)
-        self._remove = _remove
-        # A list of keys to be removed
-        self._pending_removals = []
-        self._iterating = set()
-        if data is not None:
-            self.update(data)
-
-    def _commit_removals(self):
-        l = self._pending_removals
-        discard = self.data.discard
-        while l:
-            discard(l.pop())
-
-    def __iter__(self):
-        with _IterationGuard(self):
-            for itemref in self.data:
-                item = itemref()
-                if item is not None:
-                    yield item
-
-    def __len__(self):
-        return sum(x() is not None for x in self.data)
-
-    def __contains__(self, item):
-        return ref(item) in self.data
-
-    def __reduce__(self):
-        return (self.__class__, (list(self),),
-                getattr(self, '__dict__', None))
-
-    __hash__ = None
-
-    def add(self, item):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.add(ref(item, self._remove))
-
-    def clear(self):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.clear()
-
-    def copy(self):
-        return self.__class__(self)
-
-    def pop(self):
-        if self._pending_removals:
-            self._commit_removals()
-        while True:
-            try:
-                itemref = self.data.pop()
-            except KeyError:
-                raise KeyError('pop from empty WeakSet')
-            item = itemref()
-            if item is not None:
-                return item
-
-    def remove(self, item):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.remove(ref(item))
-
-    def discard(self, item):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.discard(ref(item))
-
-    def update(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        if isinstance(other, self.__class__):
-            self.data.update(other.data)
-        else:
-            for element in other:
-                self.add(element)
-
-    def __ior__(self, other):
-        self.update(other)
-        return self
-
-    # Helper functions for simple delegating methods.
-    def _apply(self, other, method):
-        if not isinstance(other, self.__class__):
-            other = self.__class__(other)
-        newdata = method(other.data)
-        newset = self.__class__()
-        newset.data = newdata
-        return newset
-
-    def difference(self, other):
-        return self._apply(other, self.data.difference)
-    __sub__ = difference
-
-    def difference_update(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        if self is other:
-            self.data.clear()
-        else:
-            self.data.difference_update(ref(item) for item in other)
-    def __isub__(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        if self is other:
-            self.data.clear()
-        else:
-            self.data.difference_update(ref(item) for item in other)
-        return self
-
-    def intersection(self, other):
-        return self._apply(other, self.data.intersection)
-    __and__ = intersection
-
-    def intersection_update(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.intersection_update(ref(item) for item in other)
-    def __iand__(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        self.data.intersection_update(ref(item) for item in other)
-        return self
-
-    def issubset(self, other):
-        return self.data.issubset(ref(item) for item in other)
-    __lt__ = issubset
-
-    def __le__(self, other):
-        return self.data <= set(ref(item) for item in other)
-
-    def issuperset(self, other):
-        return self.data.issuperset(ref(item) for item in other)
-    __gt__ = issuperset
-
-    def __ge__(self, other):
-        return self.data >= set(ref(item) for item in other)
-
-    def __eq__(self, other):
-        if not isinstance(other, self.__class__):
-            return NotImplemented
-        return self.data == set(ref(item) for item in other)
-
-    def symmetric_difference(self, other):
-        return self._apply(other, self.data.symmetric_difference)
-    __xor__ = symmetric_difference
-
-    def symmetric_difference_update(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        if self is other:
-            self.data.clear()
-        else:
-            self.data.symmetric_difference_update(ref(item) for item in other)
-    def __ixor__(self, other):
-        if self._pending_removals:
-            self._commit_removals()
-        if self is other:
-            self.data.clear()
-        else:
-            self.data.symmetric_difference_update(ref(item) for item in other)
-        return self
-
-    def union(self, other):
-        return self._apply(other, self.data.union)
-    __or__ = union
-
-    def isdisjoint(self, other):
-        return len(self.intersection(other)) == 0
diff --git a/spherical_geometry/vector.py b/spherical_geometry/vector.py
index 87c42c7..1b7a07d 100644
--- a/spherical_geometry/vector.py
+++ b/spherical_geometry/vector.py
@@ -7,8 +7,6 @@
 vectors and converting them to and from other representations.
 """
 
-from __future__ import unicode_literals
-
 # THIRD-PARTY
 import numpy as np