Merge pull request #258 from ajhynes7/use_poetry

Use poetry and `pyproject.toml`

.github/workflows/main.yml

@@ -17,8 +17,11 @@ jobs:
               with:
                   python-version: ${{ matrix.python-version }}
 
+            - name: Install Poetry
+              uses: snok/install-poetry@v1.1.2
+
             - name: Install tox
-              run: pip install -r requirements/tox.txt
+              run: pip install tox==3.23.0
 
             - name: Run tox
               run: tox
@@ -29,3 +32,9 @@ jobs:
                   fail_ci_if_error: true
                   verbose: true
                   gcov_prefix: ${{ env.GITHUB_WORKSPACE }}
+
+            - name: Build and publish to PyPI
+              if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+              uses: JRubics/poetry-publish@v1
+              with:
+                  pypi_token: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -11,5 +11,6 @@ docs/source/api_reference/*/
 docs/source/computations/*/
 docs/source/gallery/
 htmlcov/
+poetry.lock
 
 !.github/

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
           - id: check-merge-conflict
           - id: check-yaml
           - id: end-of-file-fixer
-          - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/asottile/reorder_python_imports
       rev: v2.4.0
@@ -20,6 +19,11 @@ repos:
       hooks:
           - id: black
             args: [-S, -l 120]
+    - repo: https://github.com/asottile/add-trailing-comma
+      rev: v2.1.0
+      hooks:
+          - id: add-trailing-comma
+            args: [--py36-plus]
     - repo: https://gitlab.com/pycqa/flake8
       rev: 3.8.4
       hooks:

docs/source/conf.py

@@ -63,7 +63,7 @@
             '../../examples/intersection',
             '../../examples/fitting',
             '../../examples/triangle',
-        ]
+        ],
     ),
 }
 

examples/fitting/plot_line_2d.py

@@ -20,7 +20,7 @@
         [6, 5],
         [5, 6],
         [7, 8],
-    ]
+    ],
 )
 
 line_fit = Line.best_fit(points)

examples/fitting/plot_line_3d.py

@@ -20,7 +20,7 @@
         [6, 5, 5],
         [6, 6, 5],
         [7, 6, 7],
-    ]
+    ],
 )
 
 line_fit = Line.best_fit(points)

mypy.ini

@@ -0,0 +1,2 @@
+[mypy]
+mypy_path = stubs

pyproject.toml

@@ -0,0 +1,65 @@
+[tool.poetry]
+
+name = "scikit-spatial"
+version = "5.2.0"
+description = "Spatial objects and computations based on NumPy arrays."
+license = "BSD"
+
+authors = ["Andrew Hynes <andrewjhynes@gmail.com>"]
+
+readme = "README.rst"
+
+repository = "https://github.com/ajhynes7/scikit-spatial"
+documentation = "https://scikit-spatial.readthedocs.io"
+
+keywords = ["NumPy", "matplotlib", "visualization", "spatial", "linear algebra"]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering",
+]
+
+packages = [{ include = "skspatial", from = "src" }]
+
+
+[tool.poetry.dependencies]
+python = "^3.7"
+
+numpy = "^1.20"
+matplotlib = "^3"
+
+# Pre-commit
+pre-commit = { version = "2.11.1", optional = true }
+
+# Types
+mypy = { version = "0.812", optional = true }
+
+# Testing
+pytest = { version = "6.2.2", optional = true }
+pytest-cov = { version = "2.11.1", optional = true }
+hypothesis = { version = "6.8.1", optional = true }
+
+# Docs
+Sphinx = { version = "3.5.2", optional = true }
+numpydoc = { version = "1.1.0", optional = true }
+sphinx-bootstrap-theme = { version = "0.7.1", optional = true }
+sphinx-gallery = { version = "0.8.2", optional = true }
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+
+[tool.poetry.extras]
+pre_commit = ["pre-commit"]
+types = ["mypy"]
+base_test = ["pytest", "pytest-cov"]
+property = ["hypothesis"]
+docs = ["Sphinx", "numpydoc", "sphinx-bootstrap-theme", "sphinx-gallery"]

src/skspatial/measurement.py

@@ -49,7 +49,10 @@ def area_triangle(point_a: array_like, point_b: array_like, point_c: array_like)
 
 
 def volume_tetrahedron(
-    point_a: array_like, point_b: array_like, point_c: array_like, point_d: array_like
+    point_a: array_like,
+    point_b: array_like,
+    point_c: array_like,
+    point_d: array_like,
 ) -> np.float64:
     """
     Return the volume of a tetrahedron defined by four points.

src/skspatial/objects/plane.py

@@ -590,6 +590,13 @@ def best_fit(cls, points: array_like, tol: float | None = None, **kwargs) -> Pla
         ValueError
             If the points are collinear or are not 3D.
 
+        References
+        ----------
+        Using SVD for some fitting problems
+        Inge Söderkvist
+        Algorithm 3.1
+        https://www.ltu.se/cms_fs/1.51590!/svd-fitting.pdf
+
         Examples
         --------
         >>> from skspatial.objects import Plane
@@ -627,12 +634,14 @@ def best_fit(cls, points: array_like, tol: float | None = None, **kwargs) -> Pla
         points_centered, centroid = points.mean_center(return_centroid=True)
 
         u, _, _ = np.linalg.svd(points_centered.T, **kwargs)
-        normal = Vector(u[:, -1])
+        normal = Vector(u[:, 2])
 
         return cls(centroid, normal)
 
     def to_mesh(
-        self, lims_x: array_like = (-1, 1), lims_y: array_like = (-1, 1)
+        self,
+        lims_x: array_like = (-1, 1),
+        lims_y: array_like = (-1, 1),
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         """
         Return coordinate matrices for the 3D surface of the plane.

src/skspatial/objects/sphere.py

@@ -33,7 +33,7 @@ class Sphere(_BaseSphere, _ToPointsMixin):
     Attributes
     ----------
     point : (3,) Point
-        Center of the circle.
+        Center of the sphere.
     radius : {int, float}
         Radius of the sphere.
     dimension : int

tests/unit/objects/test_line_plane.py

@@ -7,7 +7,8 @@
 
 @pytest.mark.parametrize("class_spatial", [Line, Plane])
 @pytest.mark.parametrize(
-    ("point", "vector"), [([0, 0], [0, 0]), ([1, 1], [0, 0]), ([1, 1, 1], [0, 0, 0]), ([4, 5, 2, 3], [0, 0, 0, 0])]
+    ("point", "vector"),
+    [([0, 0], [0, 0]), ([1, 1], [0, 0]), ([1, 1, 1], [0, 0, 0]), ([4, 5, 2, 3], [0, 0, 0, 0])],
 )
 def test_zero_vector_failure(class_spatial, point, vector):
 

tests/unit/objects/test_plane.py

@@ -263,15 +263,25 @@ def test_sum_squares_plane(plane, points, error_expected):
         (
             [
                 [0, 0, 0],
-                [0, 0, 1],
-                [0, 1, 0],
-                [0, 1, 1],
                 [1, 0, 0],
-                [1, 0, 1],
+                [2, 0, 0],
+                [0, 1, 0],
                 [1, 1, 0],
+                [2, 1, 0],
+                [0, 2, 0],
+                [1, 2, 0],
+                [2, 2, 0],
+                [0, 0, 1],
+                [1, 0, 1],
+                [2, 0, 1],
+                [0, 1, 1],
                 [1, 1, 1],
+                [2, 1, 1],
+                [0, 2, 1],
+                [1, 2, 1],
+                [2, 2, 1],
             ],
-            Plane([0.5, 0.5, 0.5], [0, 1, 0]),
+            Plane([1, 1, 0.5], [0, 0, 1]),
         ),
     ],
 )