Merge pull request #46 from lsst/tickets/DM-35347

DM-35347: Switch to pyproject.toml

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Reformat code with isort/black
+4b97dad9311110ee7a3d30332af50242053bd543

.github/pull_request_template.md

@@ -0,0 +1,4 @@
+## Checklist
+
+- [ ] ran Jenkins
+- [ ] added a release note for user-visible changes to `doc/changes`

.github/workflows/build.yaml

@@ -11,6 +11,10 @@ on:
 jobs:
   build_and_test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+
     steps:
       - uses: actions/checkout@v3
         with:
@@ -20,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: ${{ matrix.python-version }}
           cache: "pip"
           cache-dependency-path: "setup.cfg"
 
@@ -47,8 +51,6 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: 3.8
-          cache: "pip"
-          cache-dependency-path: "setup.cfg"
 
       - name: Install dependencies
         run: |
@@ -78,25 +80,21 @@ jobs:
 
     steps:
       # uncomment when building aarch64
-      #- name: Set up QEMU
-      #  uses: docker/setup-qemu-action@v2
-      #  if: runner.os == 'Linux'
-      #  with:
-      #    platforms: arm64
+      # - name: Set up QEMU
+      #   uses: docker/setup-qemu-action@v2
+      #   if: runner.os == 'Linux'
+      #   with:
+      #     platforms: arm64
 
       - uses: actions/checkout@v3
         with:
           # Need to clone everything to embed the versiona
           fetch-depth: 0
-          cache: "pip"
-          cache-dependency-path: "setup.cfg"
 
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
           python-version: 3.8
-          cache: "pip"
-          cache-dependency-path: "setup.cfg"
 
       - name: Install dependencies
         run: |

.github/workflows/docstyle.yaml

@@ -0,0 +1,13 @@
+name: Run docstyle
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/docstyle.yaml@main
+    with:
+      args: "python/lsst/sphgeom/"

.github/workflows/formatting.yaml

@@ -0,0 +1,11 @@
+name: Check Python formatting
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/formatting.yaml@main

.github/workflows/yamllint.yaml

@@ -0,0 +1,11 @@
+name: Lint YAML Files
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/yamllint.yaml@main

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-yaml
+        args:
+          - "--unsafe"
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8

.yamllint.yaml

@@ -0,0 +1,16 @@
+extends: default
+
+rules:
+  document-start: {present: false}
+  line-length:
+    max: 132
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+    ignore: |
+      /.github/workflows/lint.yaml
+  truthy:
+    # "on" as a key in workflows confuses things
+    ignore: |
+      /.github/workflows/
+  indentation:
+    indent-sequences: consistent

pyproject.toml

@@ -1,12 +1,81 @@
 [build-system]
-build-backend = "setuptools.build_meta"
 requires = [
-    "setuptools >= 46.6.0",
+    "setuptools",
+    "lsst-versions >= 1.3.0",
     "wheel",
     "pybind11 >= 2.5.0",
     "numpy >= 1.18",
-    "lsst-versions",
 ]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "lsst-sphgeom"
+description = "A spherical geometry library."
+license = {text = "GPLv3+ License"}
+readme = "README.md"
+authors = [
+    {name="Rubin Observatory Data Management", email="dm-admin@lists.lsst.org"},
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Astronomy",
+]
+keywords = ["lsst"]
+dependencies = [
+   "numpy >=1.18",
+   "healpy"
+]
+dynamic = ["version"]
+
+[project.urls]
+"Homepage" = "https://github.com/lsst/sphgeom"
+
+[project.optional-dependencies]
+test = [
+    "pytest >= 3.2",
+    "flake8 >= 3.7.5",
+    "pytest-flake8 >= 1.0.4",
+]
+yaml = ["pyyaml >= 5.1"]
+
+[tool.setuptools.packages.find]
+where = ["python"]
+
+[tool.setuptools]
+zip-safe = false
+license-files = ["LICENSE"]
+
+[tool.setuptools.dynamic]
+version = { attr = "lsst_versions.get_lsst_version" }
+
+[tool.black]
+line-length = 110
+target-version = ["py38"]
+
+[tool.isort]
+profile = "black"
+line_length = 110
 
 [tool.lsst_versions]
 write_to = "python/lsst/sphgeom/version.py"
+
+[tool.pytest.ini_options]
+addopts = "--flake8"
+flake8-ignore = ["E133", "E226", "E228", "N802", "N803", "N806", "N812", "N815", "N816", "W503"]
+
+[tool.pydocstyle]
+convention = "numpy"
+# Our coding style does not require docstrings for magic methods (D105)
+# Our docstyle documents __init__ at the class level (D107)
+# We allow methods to inherit docstrings and this is not compatible with D102.
+# Docstring at the very first line is not required
+# D200, D205 and D400 all complain if the first sentence of the docstring does
+# not fit on one line.
+add-ignore = ["D107", "D105", "D102", "D100", "D200", "D205", "D400"]

python/lsst/__init__.py

@@ -1,2 +1,3 @@
 import pkgutil
+
 __path__ = pkgutil.extend_path(__path__, __name__)

python/lsst/sphgeom/__init__.py

@@ -23,11 +23,11 @@
 """lsst.sphgeom
 """
 
+from ._healpixPixelization import *
 from ._sphgeom import *
 from ._sphgeom import Pixelization
-from .version import *
 from ._yaml import *
 from .pixelization_abc import *
-from ._healpixPixelization import *
+from .version import *
 
 PixelizationABC.register(Pixelization)

python/lsst/sphgeom/_healpixPixelization.py

@@ -22,8 +22,7 @@
 
 import numpy as np
 
-from ._sphgeom import RangeSet, Region, UnitVector3d
-from ._sphgeom import Box, Circle, ConvexPolygon, Ellipse
+from ._sphgeom import Box, Circle, ConvexPolygon, Ellipse, RangeSet, Region, UnitVector3d
 from .pixelization_abc import PixelizationABC
 
 
@@ -35,6 +34,7 @@ class HealpixPixelization(PixelizationABC):
     level : `int`
         Pixelization level.  HEALPix nside = 2**level
     """
+
     MAX_LEVEL = 17
 
     def __init__(self, level: int):
@@ -50,7 +50,7 @@ def __init__(self, level: int):
 
         # Values used to do pixel/region intersections
         self._bit_shift = 8
-        self._nside_highres = self._nside*(2**(self._bit_shift//2))
+        self._nside_highres = self._nside * (2 ** (self._bit_shift // 2))
 
     @property
     def nside(self):
@@ -74,6 +74,7 @@ def pixel(self, i) -> Region:
 
     def index(self, v: UnitVector3d) -> int:
         import healpy as hp
+
         return hp.vec2pix(self._nside, v.x(), v.y(), v.z(), nest=True)
 
     def toString(self, i: int) -> str:
@@ -89,9 +90,7 @@ def envelope(self, region: Region, maxRanges: int = 0):
 
         # Dilate the high resolution pixels by one to ensure that the full
         # region is completely covered at high resolution.
-        neighbors = hp.get_all_neighbours(self._nside_highres,
-                                          pixels_highres,
-                                          nest=True)
+        neighbors = hp.get_all_neighbours(self._nside_highres, pixels_highres, nest=True)
         # Shift back to the original resolution and uniquify
         pixels = np.unique(np.right_shift(neighbors, self._bit_shift))
 
@@ -112,10 +111,10 @@ def interior(self, region: Region, maxRanges: int = 0):
         # the center index points to x, y, z.
         corners = hp.boundaries(self._nside, pixels, step=1, nest=True)
 
-        corners_int = region.contains(corners[:, 0, :].ravel(),
-                                      corners[:, 1, :].ravel(),
-                                      corners[:, 2, :].ravel()).reshape((len(pixels), 4))
-        interior = (np.sum(corners_int, axis=1) == 4)
+        corners_int = region.contains(
+            corners[:, 0, :].ravel(), corners[:, 1, :].ravel(), corners[:, 2, :].ravel()
+        ).reshape((len(pixels), 4))
+        interior = np.sum(corners_int, axis=1) == 4
         pixels = pixels[interior]
 
         return RangeSet(pixels)
@@ -152,26 +151,21 @@ def _interior_pixels_from_region(self, nside: int, region: Region):
         if _circle is not None:
             center = _circle.getCenter()
             vec = np.array([center.x(), center.y(), center.z()]).T
-            pixels = hp.query_disc(nside,
-                                   vec,
-                                   _circle.getOpeningAngle().asRadians(),
-                                   inclusive=False,
-                                   nest=True)
+            pixels = hp.query_disc(
+                nside, vec, _circle.getOpeningAngle().asRadians(), inclusive=False, nest=True
+            )
         else:
             vertices = np.array([[v.x(), v.y(), v.z()] for v in _poly.getVertices()])
-            pixels = hp.query_polygon(nside,
-                                      vertices,
-                                      inclusive=False,
-                                      nest=True)
+            pixels = hp.query_polygon(nside, vertices, inclusive=False, nest=True)
 
         return pixels
 
     def __eq__(self, other):
         if isinstance(other, HealpixPixelization):
-            return (self._level == other._level)
+            return self._level == other._level
 
     def __repr__(self):
         return f"HealpixPixelization({self._level})"
 
     def __reduce__(self):
-        return (self.__class__, (self._level, ))
+        return (self.__class__, (self._level,))