chore(deps): update dependency scipy to ~1.9

CHANGELOG.md

@@ -2,19 +2,6 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
-### [0.8.7](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.6...0.8.7) (2022-09-17)
-
-
-### Features
-
-* adds xy model for convenience to pdme ([e894c89](https://gitea.deepak.science:2222/physics/pdme/commit/e894c897029c05a1d4754e7930ae9ba2be7a1cfd))
-* moves xy model up to model package ([2a1ae3b](https://gitea.deepak.science:2222/physics/pdme/commit/2a1ae3b1a7f7e10469b7fd2930fee0b338f0c03f))
-
-
-### Bug Fixes
-
-* Correctly generates monte carlo version of xy model dipoles ([5acf0ac](https://gitea.deepak.science:2222/physics/pdme/commit/5acf0ac347382705674bb596440d27cba3730bac))
-
 ### [0.8.6](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.5...0.8.6) (2022-06-13)
 
 

pdme/model/__init__.py

@@ -11,10 +11,6 @@ from pdme.model.log_spaced_random_choice_model import (
 	LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel,
 )
 
-from pdme.model.log_spaced_random_choice_xy_model import (
-	LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel,
-)
-
 from pdme.model.log_spaced_random_choice_fixed_orientation_model import (
 	LogSpacedRandomCountMultipleDipoleFixedMagnitudeFixedOrientationModel,
 )
@@ -25,6 +21,5 @@ __all__ = [
 	"MultipleDipoleFixedMagnitudeModel",
 	"RandomCountMultipleDipoleFixedMagnitudeModel",
 	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel",
-	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel",
 	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeFixedOrientationModel",
 ]

pdme/model/log_spaced_random_choice_xy_model.py

@@ -1,125 +0,0 @@
-import numpy
-import numpy.random
-from pdme.model.model import DipoleModel
-from pdme.measurement import (
-	OscillatingDipole,
-	OscillatingDipoleArrangement,
-)
-
-
-class LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(DipoleModel):
-	"""
-	Model of multiple oscillating dipoles with a fixed magnitude, but free rotation in XY plane. Spaced logarithmically.
-
-	Parameters
-	----------
-
-	wexp_min: log-10 lower bound for dipole frequency
-	wexp_min: log-10 upper bound for dipole frequency
-
-	pfixed : float
-	The fixed dipole magnitude.
-
-	n_max : int
-	The maximum number of dipoles.
-
-	prob_occupancy : float
-	The probability of dipole occupancy
-	"""
-
-	def __init__(
-		self,
-		xmin: float,
-		xmax: float,
-		ymin: float,
-		ymax: float,
-		zmin: float,
-		zmax: float,
-		wexp_min: float,
-		wexp_max: float,
-		pfixed: float,
-		n_max: int,
-		prob_occupancy: float,
-	) -> None:
-		self.xmin = xmin
-		self.xmax = xmax
-		self.ymin = ymin
-		self.ymax = ymax
-		self.zmin = zmin
-		self.zmax = zmax
-		self.wexp_min = wexp_min
-		self.wexp_max = wexp_max
-		self.pfixed = pfixed
-		self.rng = numpy.random.default_rng()
-		self.n_max = n_max
-		if prob_occupancy >= 1 or prob_occupancy <= 0:
-			raise ValueError(
-				f"The probability of a dipole site occupancy must be between 0 and 1, got {prob_occupancy}"
-			)
-		self.prob_occupancy = prob_occupancy
-
-	def __repr__(self) -> str:
-		return f"LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel({self.xmin}, {self.xmax}, {self.ymin}, {self.ymax}, {self.zmin}, {self.zmax}, {self.wexp_min}, {self.wexp_max}, {self.pfixed}, {self.n_max}, {self.prob_occupancy})"
-
-	def get_dipoles(
-		self, max_frequency: float, rng_to_use: numpy.random.Generator = None
-	) -> OscillatingDipoleArrangement:
-		rng: numpy.random.Generator
-		if rng_to_use is None:
-			rng = self.rng
-		else:
-			rng = rng_to_use
-
-		dipoles = []
-
-		n = rng.binomial(self.n_max, self.prob_occupancy)
-
-		for i in range(n):
-			phi = rng.uniform(0, 2 * numpy.pi)
-			px = self.pfixed * numpy.cos(phi)
-			py = self.pfixed * numpy.sin(phi)
-			pz = 0
-			s_pts = numpy.array(
-				(
-					rng.uniform(self.xmin, self.xmax),
-					rng.uniform(self.ymin, self.ymax),
-					rng.uniform(self.zmin, self.zmax),
-				)
-			)
-			frequency = 10 ** rng.uniform(self.wexp_min, self.wexp_max)
-
-			dipoles.append(
-				OscillatingDipole(numpy.array([px, py, pz]), s_pts, frequency)
-			)
-		return OscillatingDipoleArrangement(dipoles)
-
-	def get_monte_carlo_dipole_inputs(
-		self,
-		monte_carlo_n: int,
-		_: float,
-		rng_to_use: numpy.random.Generator = None,
-	) -> numpy.ndarray:
-
-		rng: numpy.random.Generator
-		if rng_to_use is None:
-			rng = self.rng
-		else:
-			rng = rng_to_use
-
-		shape = (monte_carlo_n, self.n_max)
-		phi = 2 * numpy.pi * rng.random(shape)
-
-		p_mask = rng.binomial(1, self.prob_occupancy, shape)
-		p_magnitude = self.pfixed * p_mask
-
-		px = p_magnitude * numpy.cos(phi)
-		py = p_magnitude * numpy.sin(phi)
-		pz = p_magnitude * 0
-
-		sx = rng.uniform(self.xmin, self.xmax, shape)
-		sy = rng.uniform(self.ymin, self.ymax, shape)
-		sz = rng.uniform(self.zmin, self.zmax, shape)
-
-		w = 10 ** rng.uniform(self.wexp_min, self.wexp_max, shape)
-
-		return numpy.stack([px, py, pz, sx, sy, sz, w], axis=-1)

poetry.lock

@@ -93,7 +93,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "coverage"
-version = "7.0.3"
+version = "6.4.2"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -316,8 +316,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-dev = ["pre-commit", "tox"]
+testing = ["pytest-benchmark", "pytest"]
-testing = ["pytest", "pytest-benchmark"]
+dev = ["tox", "pre-commit"]
 
 [[package]]
 name = "prompt-toolkit"
@@ -426,23 +426,18 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
 
 [[package]]
 name = "scipy"
-version = "1.10.0"
+version = "1.9.0"
-description = "Fundamental algorithms for scientific computing in Python"
+description = "SciPy: Scientific Library for Python"
 category = "main"
 optional = false
-python-versions = "<3.12,>=3.8"
+python-versions = ">=3.8,<3.12"
 
 [package.dependencies]
-numpy = ">=1.19.5,<1.27.0"
+numpy = ">=1.18.5,<1.25.0"
-
-[package.extras]
-test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"]
-doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc"]
-dev = ["mypy", "typing-extensions", "pycodestyle", "flake8", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"]
 
 [[package]]
 name = "six"
@@ -466,7 +461,7 @@ executing = "*"
 pure-eval = "*"
 
 [package.extras]
-tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
+tests = ["cython", "littleutils", "pygments", "typeguard", "pytest"]
 
 [[package]]
 name = "toml"
@@ -514,7 +509,7 @@ python-versions = "*"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8,<3.10"
-content-hash = "f5614947eb2f77e9cd8bd9dc026a924f4cb7394c3fef9cb175ab5afbe201ca73"
+content-hash = "ba562365abd9c6b04b231a9f307c8ae109fdb50b99e793a28a33b1438374bfbb"
 
 [metadata.files]
 appnope = []

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pdme"
-version = "0.8.7"
+version = "0.8.6"
 description = "Python dipole model evaluator"
 authors = ["Deepak <dmallubhotla+github@gmail.com>"]
 license = "GPL-3.0-only"
@@ -9,7 +9,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.8,<3.10"
 numpy = "^1.22.3"
-scipy = "~1.10"
+scipy = "~1.9"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"

tests/model/test_log_spaced_random_count_multiple_dipole_fixed_magnitude_xy_model.py

@@ -1,206 +0,0 @@
-from pdme.model import LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel
-import numpy
-import logging
-import pytest
-
-
-_logger = logging.getLogger(__name__)
-
-
-def test_random_count_multiple_dipole_xy_wrong_probability():
-	with pytest.raises(ValueError):
-		LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-			-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 2
-		)
-
-
-def test_repr_random_count_multiple_dipole_fixed_mag_xy():
-	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-		-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 0.5
-	)
-	assert (
-		repr(model)
-		== "LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 0.5)"
-	), "Repr should be what I want."
-
-
-def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_multiple_xy():
-
-	p_fixed = 10
-	dipole_count = 5
-
-	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-		-10, 10, -5, 5, 2, 3, 0, 5, p_fixed, dipole_count, 0.5
-	)
-
-	dipole_arrangement = model.get_dipoles(20, numpy.random.default_rng(1234))
-	dipoles = dipole_arrangement.dipoles
-
-	assert (
-		len(dipoles) == dipole_count
-	), "Should have had multiple dipole based on count generated."
-
-
-def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_invariant_xy():
-
-	x_min = -10
-	x_max = 10
-	y_min = -5
-	y_max = 5
-	z_min = 2
-	z_max = 3
-	p_fixed = 10
-	max_frequency = 5
-
-	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-		x_min, x_max, y_min, y_max, z_min, z_max, 0, max_frequency, p_fixed, 1, 0.5
-	)
-	model.rng = numpy.random.default_rng(1234)
-
-	dipole_arrangement = model.get_dipoles(5)
-	dipoles = dipole_arrangement.dipoles
-
-	assert len(dipoles) == 1, "Should have only had one dipole generated."
-	for i in range(10):
-		dipole_arrangement = model.get_dipoles(max_frequency)
-		dipoles = dipole_arrangement.dipoles
-
-		assert len(dipoles) in (
-			0,
-			1,
-		), "Should have either zero or one dipole generated."
-
-		if len(dipoles) > 0:
-			min_s = numpy.array([x_min, y_min, z_min])
-			max_s = numpy.array([x_max, y_max, z_max])
-
-			numpy.testing.assert_equal(
-				numpy.logical_and(min_s < dipoles[0].s, max_s > dipoles[0].s),
-				True,
-				f"Dipole location [{dipoles[0].s}] should have been between min [{min_s}] and max [{max_s}] bounds.",
-			)
-			assert (
-				dipoles[0].w < 10 ** max_frequency and dipoles[0].w > 10**0
-			), "Dipole frequency should have been between 0 and max."
-
-			numpy.testing.assert_allclose(
-				numpy.linalg.norm(dipoles[0].p),
-				p_fixed,
-				err_msg="Should have had the expected dipole moment magnitude.",
-			)
-
-			_logger.warning(dipoles[0].p)
-			numpy.testing.assert_allclose(
-				dipoles[0].p[2],
-				0,
-				err_msg="Should have had zero z magnitude.",
-			)
-
-
-def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_invariant_monte_carlo_xy():
-
-	x_min = -10
-	x_max = 10
-	y_min = -5
-	y_max = 5
-	z_min = 2
-	z_max = 3
-	p_fixed = 10
-	max_frequency = 5
-	monte_carlo_n = 20
-
-	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-		x_min, x_max, y_min, y_max, z_min, z_max, 0, max_frequency, p_fixed, 1, 0.5
-	)
-	model.rng = numpy.random.default_rng(1234)
-
-	dipole_arrangement = model.get_dipoles(5)
-	dipoles = dipole_arrangement.dipoles
-
-	assert len(dipoles) == 1, "Should have only had one dipole generated."
-	for i in range(10):
-		dipoles = model.get_monte_carlo_dipole_inputs(monte_carlo_n, max_frequency)
-
-		min_s = numpy.array([x_min, y_min, z_min])
-		max_s = numpy.array([x_max, y_max, z_max])
-
-		_logger.warning(dipoles)
-		_logger.warning(dipoles[:, 0, 0:3])
-		_logger.warning(dipoles[:, 0, 3:6])
-		_logger.warning(dipoles[:, 0, 6])
-
-		ps = dipoles[:, 0, 0:3]
-		ss = dipoles[:, 0, 3:6]
-		ws = dipoles[:, 0, 6]
-
-		numpy.testing.assert_equal(
-			numpy.logical_and(min_s < ss, max_s > ss).all(),
-			True,
-			f"Dipole location [{ss}] should have been between min [{min_s}] and max [{max_s}] bounds.",
-		)
-		assert (ws < 10**max_frequency).all() and (
-			ws > 10**0
-		).all(), "Dipole frequency should have been between 0 and max."
-
-		norms = numpy.linalg.norm(ps, axis=1)
-		filtered_norms = norms[norms > 0]
-		numpy.testing.assert_allclose(
-			filtered_norms,
-			p_fixed,
-			err_msg="Should have had the expected dipole moment magnitude.",
-		)
-
-		numpy.testing.assert_allclose(
-			ps[:, 2],
-			0,
-			err_msg="Should have had zero z magnitude.",
-		)
-
-
-def test_random_count_multiple_dipole_shape():
-
-	x_min = -10
-	x_max = 10
-	y_min = -5
-	y_max = 5
-	z_min = 2
-	z_max = 3
-	p_fixed = 10
-	max_frequency = 5
-	num_dipoles = 13
-	monte_carlo_n = 11
-
-	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
-		x_min,
-		x_max,
-		y_min,
-		y_max,
-		z_min,
-		z_max,
-		0,
-		max_frequency,
-		p_fixed,
-		num_dipoles,
-		0.5,
-	)
-	model.rng = numpy.random.default_rng(1234)
-
-	actual_shape = model.get_monte_carlo_dipole_inputs(
-		monte_carlo_n, max_frequency
-	).shape
-
-	numpy.testing.assert_equal(
-		actual_shape,
-		(monte_carlo_n, num_dipoles, 7),
-		err_msg="shape was wrong for monte carlo outputs",
-	)
-
-	actual_shape = model.get_monte_carlo_dipole_inputs(
-		monte_carlo_n, max_frequency, rng_to_use=numpy.random.default_rng(1515)
-	).shape
-
-	numpy.testing.assert_equal(
-		actual_shape,
-		(monte_carlo_n, num_dipoles, 7),
-		err_msg="shape was wrong for monte carlo outputs",
-	)