chore(deps): update dependency pytest-cov to v4

Reviewed-on: #28

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 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.
 
+### [0.8.8](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.7...0.8.8) (2023-04-09)
+
+
+### Features
+
+* adds fast calc that allows for variable temp ([36454d5](https://gitea.deepak.science:2222/physics/pdme/commit/36454d5044d93b6b178e016b84dd59a5ebaf15e2))
+
 ### [0.8.7](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.6...0.8.7) (2022-09-17)
 
 

README.md

@@ -5,7 +5,7 @@
 [![Jenkins](https://img.shields.io/jenkins/build?jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fpdme%2Fjob%2Fmaster&style=flat-square)](https://jenkins.deepak.science/job/gitea-physics/job/pdme/job/master/)
 ![Jenkins tests](https://img.shields.io/jenkins/tests?compact_message&jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fpdme%2Fjob%2Fmaster%2F&style=flat-square)
 ![Jenkins Coverage](https://img.shields.io/jenkins/coverage/cobertura?jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fpdme%2Fjob%2Fmaster%2F&style=flat-square)
-![Maintenance](https://img.shields.io/maintenance/yes/2022?style=flat-square)
+![Maintenance](https://img.shields.io/maintenance/yes/2023?style=flat-square)
 
 This repo has library code for evaluating dipole models.
 

pdme/util/fast_v_calc.py

@@ -69,6 +69,47 @@ def fast_vs_for_dipoleses(
 	return numpy.einsum("...j->...", ases * bses)
 
 
+def fast_vs_for_asymmetric_dipoleses(
+	dot_inputs: numpy.ndarray, dipoleses: numpy.ndarray, temp: numpy.ndarray
+) -> numpy.ndarray:
+	"""
+	No error correction here baby.
+	Expects dot_inputs to be numpy array of [rx, ry, rz, f] entries, so a n by 4 where n is number of measurement points.
+
+	Dipoleses are expected to be array of arrays of arrays:
+	list of sets of dipoles which are part of a single arrangement to be added together.
+	Within each dipole, the expected format is [px, py, pz, sx, sy, sz, e1, e2, w]
+	The passed in w is expected to be half the actual. This is bad, but here for historical reasons to be changed later.
+	"""
+	raw_ps = dipoleses[:, :, 0:3]
+	ss = dipoleses[:, :, 3:6]
+	e1s = dipoleses[:, :, 6]
+	e2s = dipoleses[:, :, 7]
+	raw_ws = dipoleses[:, :, 8]
+
+	rs = dot_inputs[:, 0:3]
+	fs = dot_inputs[:, 3]
+
+	diffses = rs[:, None] - ss[:, None, :]
+
+	w1s = numpy.exp(-e1s / temp) * raw_ws
+	w2s = numpy.exp(-e2s / temp) * raw_ws
+
+	mag_prefactor = 4 * ((w1s * w2s) / ((w1s + w2s) ** 2))
+	ws = w1s + w2s
+
+	# some annoying broadcast thing here?
+	ps = (raw_ps.T * mag_prefactor.T).T
+
+	norms = numpy.linalg.norm(diffses, axis=3) ** 3
+
+	ases = (numpy.einsum("abcd,acd->abc", diffses, ps) / norms) ** 2
+
+	bses = (1 / numpy.pi) * (ws[:, None, :] / (fs[:, None] ** 2 + ws[:, None, :] ** 2))
+
+	return numpy.einsum("...j->...", ases * bses)
+
+
 def between(a: numpy.ndarray, low: numpy.ndarray, high: numpy.ndarray) -> numpy.ndarray:
 	"""
 	Intended specifically for the case where a is a list of arrays, and each array must be between the single array low and high, but without error checking.

poetry.lock

@@ -93,7 +93,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "coverage"
-version = "6.4.4"
+version = "7.2.3"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -316,8 +316,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-testing = ["pytest-benchmark", "pytest"]
+dev = ["pre-commit", "tox"]
-dev = ["tox", "pre-commit"]
+testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
@@ -430,14 +430,19 @@ testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtuale
 
 [[package]]
 name = "scipy"
-version = "1.8.0"
+version = "1.10.0"
-description = "SciPy: Scientific Library for Python"
+description = "Fundamental algorithms for scientific computing in Python"
 category = "main"
 optional = false
-python-versions = ">=3.8,<3.11"
+python-versions = "<3.12,>=3.8"
 
 [package.dependencies]
-numpy = ">=1.17.3,<1.25.0"
+numpy = ">=1.19.5,<1.27.0"
+
+[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"
@@ -461,7 +466,7 @@ executing = "*"
 pure-eval = "*"
 
 [package.extras]
-tests = ["cython", "littleutils", "pygments", "typeguard", "pytest"]
+tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
 
 [[package]]
 name = "toml"
@@ -509,7 +514,7 @@ python-versions = "*"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8,<3.10"
-content-hash = "64f2993cf53f0eb309ca4ce27a20a9b4afdd3c6674b43e0e61349e06eabb7f2a"
+content-hash = "6be63839fba38d5e4fe8a6e32d7a748a74d5984180261233a0c5ae06c8c42005"
 
 [metadata.files]
 appnope = []

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pdme"
-version = "0.8.7"
+version = "0.8.8"
 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 = "~1.8"
+scipy = "~1.10"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"

tests/util/test_fast_v_calc.py

@@ -107,3 +107,28 @@ def test_between():
 	expected = numpy.array([False, False, True])
 
 	numpy.testing.assert_array_equal(actual, expected, err_msg="Between calc wrong")
+
+
+def test_fast_v_calc_asymmetric_multidipoles_but_symmetric():
+	# expected format is [px, py, pz, sx, sy, sz, e1, e2, w]
+	d1 = [1, 2, 3, 4, 5, 6, 1, 1, 7 / 2]
+	d2 = [2, 5, 3, 4, -5, -6, 2, 2, 2 / 2]
+
+	dipoles = numpy.array([[d1, d2]])
+
+	dot_inputs = numpy.array([[-1, -1, -1, 11], [2, 3, 1, 5.5]])
+	# expected_ij is for dot i, dipole j
+	expected_11 = 0.00001421963287022476
+	expected_12 = 0.00001107180225755457
+	expected_21 = 0.000345021108583681380388722
+	expected_22 = 0.0000377061050587914705139781
+
+	expected = numpy.array([[expected_11 + expected_12, expected_21 + expected_22]])
+
+	numpy.testing.assert_allclose(
+		pdme.util.fast_v_calc.fast_vs_for_asymmetric_dipoleses(
+			dot_inputs, dipoles, 1e10
+		),
+		expected,
+		err_msg="Voltages at dot aren't as expected for multidipole calc.",
+	)