Adds sphinx docs which suck

.flake8

@@ -1,2 +1,3 @@
 [flake8]
-ignore = W191
+ignore = W191, E501
+max-line-length = 120

.gitignore

@@ -45,6 +45,7 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+pytest.xml
 *.cover
 *.py,cover
 .hypothesis/
@@ -69,7 +70,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
 
 # PyBuilder
 .pybuilder/

Jenkinsfile

@@ -0,0 +1,73 @@
+pipeline {
+	agent {
+	  kubernetes {
+		label 'pathfinder'  // all your pods will be named with this prefix, followed by a unique id
+		idleMinutes 5  // how long the pod will live after no jobs have run on it
+		yamlFile 'jenkins/ci-agent-pod.yaml'  // path to the pod definition relative to the root of our project
+		defaultContainer 'python'  // define a default container if more than a few stages use it, will default to jnlp container
+	  }
+	}
+
+	options {
+		parallelsAlwaysFailFast()
+	}
+
+	environment {
+		POETRY_HOME="/opt/poetry"
+		POETRY_VERSION="1.1.4"
+	}
+
+	stages {
+		stage('Build') {
+			steps {
+				echo 'Building...'
+				sh 'python --version'
+				sh 'curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python'
+				sh '${POETRY_HOME}/bin/poetry --version'
+				sh '${POETRY_HOME}/bin/poetry install'
+			}
+		}
+		stage('Test') {
+			parallel{
+				stage('pytest') {
+					steps {
+						sh '${POETRY_HOME}/bin/poetry run pytest'
+					}
+				}
+				stage('lint') {
+					steps {
+						sh '${POETRY_HOME}/bin/poetry run flake8'
+					}
+				}
+				stage('mypy') {
+					steps {
+						sh '${POETRY_HOME}/bin/poetry run mypy pathfinder'
+					}
+				}
+			}
+		}
+
+	}
+	post {
+		always {
+			echo 'This will always run'
+			junit 'pytest.xml'
+			cobertura coberturaReportFile: 'coverage.xml'
+			mail (bcc: '',
+				body: "Project: ${env.JOB_NAME} <br>Build Number: ${env.BUILD_NUMBER} <br> Build URL: ${env.BUILD_URL}", cc: '', charset: 'UTF-8', from: 'jenkins@jenkins.deepak.science', mimeType: 'text/html', replyTo: 'dmallubhotla+jenkins@gmail.com', subject: "${env.JOB_NAME} #${env.BUILD_NUMBER}: Build ${currentBuild.currentResult}", to: "dmallubhotla+ci@gmail.com")
+		}
+		success {
+			echo 'This will run only if successful'
+		}
+		failure {
+			echo 'This will run only if failed'
+		}
+		unstable {
+			echo 'This will run only if the run was marked as unstable'
+		}
+		changed {
+			echo 'This will run only if the state of the Pipeline has changed'
+			echo 'For example, if the Pipeline was previously failing but is now successful'
+		}
+	}
+}

do.sh

@@ -16,6 +16,10 @@ test() {
    poetry run pytest
 }
 
+htmlcov() {
+	poetry run pytest --cov-report=html
+}
+
 all() {
    build && test
 }

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,55 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pathfinder'
+copyright = '2021, Deepak Mallubhotla'
+author = 'Deepak Mallubhotla'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+	'sphinx.ext.autodoc',
+	'sphinx.ext.coverage',
+	'sphinx.ext.napoleon'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,15 @@
+Welcome to pathfinder's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,7 @@
+pathfinder
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   pathfinder

docs/source/pathfinder.model.rst

@@ -0,0 +1,37 @@
+pathfinder.model package
+========================
+
+Submodules
+----------
+
+pathfinder.model.dot module
+---------------------------
+
+.. automodule:: pathfinder.model.dot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pathfinder.model.model module
+-----------------------------
+
+.. automodule:: pathfinder.model.model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pathfinder.model.staticdipole module
+------------------------------------
+
+.. automodule:: pathfinder.model.staticdipole
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pathfinder.model
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pathfinder.rst

@@ -0,0 +1,29 @@
+pathfinder package
+==================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pathfinder.model
+
+Submodules
+----------
+
+pathfinder.meta module
+----------------------
+
+.. automodule:: pathfinder.meta
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pathfinder
+   :members:
+   :undoc-members:
+   :show-inheritance:

jenkins/ci-agent-pod.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: Pod
+spec:
+  containers:  # list of containers that you want present for your build, you can define a default container in the Jenkinsfile
+    - name: python
+      image: python:3.8
+      command: ["tail", "-f", "/dev/null"]  # this or any command that is bascially a noop is required, this is so that you don't overwrite the entrypoint of the base container
+      imagePullPolicy: Always # use cache or pull image for agent
+      resources:  # limits the resources your build contaienr
+        requests:
+          memory: "2Gi"
+          cpu: "500m"
+        limits:
+          memory: "2Gi"

pathfinder/model/__init__.py

@@ -0,0 +1,5 @@
+from pathfinder.model.dot import DotMeasurement
+from pathfinder.model.model import DotDipoleModel
+from pathfinder.model.staticdipole import StaticDipole
+
+__all__ = ['DotMeasurement', 'DotDipoleModel', 'StaticDipole']

pathfinder/model/dot.py

@@ -0,0 +1,73 @@
+from dataclasses import dataclass
+import numpy
+import numpy.typing
+
+from pathfinder.model.staticdipole import StaticDipole
+
+
+@dataclass
+class DotMeasurement():
+	'''
+	Representation of a dot measuring static dipoles.
+
+	Parameters
+	----------
+	v : float
+		The voltage measured at the dot.
+	r : numpy.ndarray
+		The position of the dot.
+	'''
+	v: float
+	r: numpy.ndarray
+
+	def __post_init__(self) -> None:
+		self.r = numpy.array(self.r)
+
+	def v_for_point(self, pt: numpy.ndarray) -> float:
+		'''
+		Returns the voltage for a static dipole represented as a phase space point.
+
+		Parameters
+		----------
+		pt: A length 6 numpy array representing a dipole, as (px, py, pz, sx, sy, sz).
+
+		Returns
+		----------
+		float
+			The voltage from that dipole at the point.
+		'''
+		p = pt[0:3]  # hardcoded here because chances
+		s = pt[3:6]  # are we'll only ever work in 3d.
+
+		dipole = StaticDipole(p, s)
+
+		return dipole.v_at_position(self.r)
+
+	def cost(self, pts: numpy.ndarray) -> float:
+		# 6 because dipole in 3d has 6 degrees of freedom.
+		pt_length = 6
+		# creates numpy.ndarrays in groups of pt_length.
+		# Will throw problems for irregular points, but that's okay for now.
+		chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
+		return sum(self.v_for_point(pt) for pt in chunked_pts) - self.v
+
+	def jac_pt(self, pt: numpy.ndarray) -> numpy.ndarray:
+		p = pt[0:3]  # hardcoded here because chances
+		s = pt[3:6]  # are we'll only ever work in 3d.
+
+		diff = self.r - s
+
+		p_divs = diff / (numpy.linalg.norm(diff)**3)
+
+		r_divs = -p / (numpy.linalg.norm(diff)**3) + 3 * p.dot(diff) * diff / (numpy.linalg.norm(diff)**5)
+
+		return numpy.append(p_divs, r_divs)
+
+	def jac(self, pts: numpy.ndarray) -> numpy.ndarray:
+		# 6 because dipole in 3d has 6 degrees of freedom.
+		pt_length = 6
+		# creates numpy.ndarrays in groups of pt_length.
+		# Will throw problems for irregular points, but that's okay for now.
+		chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
+
+		return numpy.append([], [self.jac_pt(pt) for pt in chunked_pts])

pathfinder/model/model.py

@@ -0,0 +1,37 @@
+from typing import Callable, Sequence
+import numpy
+
+from pathfinder.model.dot import DotMeasurement
+
+
+class DotDipoleModel():
+	'''
+	Model of n static dipoles with a collection of voltage measurements
+	at dots at different positions.
+
+	Parameters
+	----------
+	dots : Sequence[Dot]
+		A collection of dots representing a series of measured voltages.
+	n: int
+		The number of dipoles to assume.
+	'''
+	def __init__(self, dots: Sequence[DotMeasurement], n: int) -> None:
+		self.dots = dots
+		self.m = len(dots)
+		self.n = n
+
+	def __repr__(self) -> str:
+		return f'DotDipoleModel({repr(list(self.dots))}, {self.n})'
+
+	def costs(self) -> Callable[[numpy.ndarray], numpy.ndarray]:
+		def costs_to_return(pt: numpy.ndarray) -> numpy.ndarray:
+			return numpy.array([dot.cost(pt) for dot in self.dots])
+
+		return costs_to_return
+
+	def jac(self) -> Callable[[numpy.ndarray], numpy.ndarray]:
+		def jac_to_return(pts: numpy.ndarray) -> numpy.ndarray:
+			return numpy.array([dot.jac(pts) for dot in self.dots])
+
+		return jac_to_return

pathfinder/model/staticdipole.py

@@ -0,0 +1,31 @@
+from dataclasses import dataclass
+import numpy
+import numpy.typing
+
+
+@dataclass
+class StaticDipole():
+	'''
+	Representation of a static dipoles, either known or guessed.
+
+	Parameters
+	----------
+	p : numpy.ndarray
+		The static dipole moment.
+	s : numpy.ndarray
+		The position of the dipole.
+	'''
+	p: numpy.ndarray
+	s: numpy.ndarray
+
+	def __post_init__(self) -> None:
+		'''
+			Coerce the inputs into numpy arrays.
+		'''
+		self.p = numpy.array(self.p)
+		self.s = numpy.array(self.s)
+
+	def v_at_position(self, r: numpy.typing.ArrayLike) -> float:
+
+		diff = r - self.s
+		return self.p.dot(diff) / (numpy.linalg.norm(diff)**3)

poetry.lock

@@ -1,107 +1,172 @@
 [[package]]
+name = "alabaster"
+version = "0.7.12"
+description = "A configurable sidebar-enabled Sphinx theme"
 category = "dev"
-description = "Atomic file writes."
+optional = false
-marker = "sys_platform == \"win32\""
+python-versions = "*"
+
+[[package]]
 name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.0"
 
 [[package]]
-category = "dev"
-description = "Classes Without Boilerplate"
 name = "attrs"
+version = "21.2.0"
+description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "21.2.0"
 
 [package.extras]
-dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
 
 [[package]]
+name = "babel"
+version = "2.9.1"
+description = "Internationalization utilities"
 category = "dev"
-description = "Cross-platform colored terminal text."
+optional = false
-marker = "sys_platform == \"win32\""
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.dependencies]
+pytz = ">=2015.7"
+
+[[package]]
+name = "certifi"
+version = "2021.5.30"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "charset-normalizer"
+version = "2.0.4"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "dev"
+optional = false
+python-versions = ">=3.5.0"
+
+[package.extras]
+unicode_backport = ["unicodedata2"]
+
+[[package]]
 name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "0.4.4"
 
 [[package]]
-category = "dev"
-description = "Code coverage measurement for Python"
 name = "coverage"
+version = "5.5"
+description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
-version = "5.5"
 
 [package.extras]
 toml = ["toml"]
 
 [[package]]
+name = "docutils"
+version = "0.17.1"
+description = "Docutils -- Python Documentation Utilities"
 category = "dev"
-description = "the modular source code checker: pep8 pyflakes and co"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
 name = "flake8"
+version = "3.9.2"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "3.9.2"
 
 [package.dependencies]
 mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
 
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
-
 [[package]]
+name = "idna"
+version = "3.2"
+description = "Internationalized Domain Names in Applications (IDNA)"
 category = "dev"
-description = "Read metadata from Python packages"
-marker = "python_version < \"3.8\""
-name = "importlib-metadata"
-optional = false
-python-versions = ">=3.6"
-version = "4.6.1"
-
-[package.dependencies]
-zipp = ">=0.5"
-
-[package.dependencies.typing-extensions]
-python = "<3.8"
-version = ">=3.6.4"
-
-[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
-
-[[package]]
-category = "dev"
-description = "iniconfig: brain-dead simple config-ini parsing"
-name = "iniconfig"
-optional = false
-python-versions = "*"
-version = "1.1.1"
-
-[[package]]
-category = "dev"
-description = "McCabe checker, plugin for flake8"
-name = "mccabe"
-optional = false
-python-versions = "*"
-version = "0.6.1"
-
-[[package]]
-category = "dev"
-description = "Optional static typing for Python"
-name = "mypy"
 optional = false
 python-versions = ">=3.5"
+
+[[package]]
+name = "imagesize"
+version = "1.2.0"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "iniconfig"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "jinja2"
+version = "3.0.1"
+description = "A very fast and expressive template engine."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
+[[package]]
+name = "markupsafe"
+version = "2.0.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "more-itertools"
+version = "8.8.0"
+description = "More routines for operating on iterables, beyond itertools"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "mypy"
 version = "0.790"
+description = "Optional static typing for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
 
 [package.dependencies]
 mypy-extensions = ">=0.4.3,<0.5.0"
@@ -112,104 +177,111 @@ typing-extensions = ">=3.7.4"
 dmypy = ["psutil (>=4.0)"]
 
 [[package]]
-category = "dev"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
 name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.4.3"
 
 [[package]]
-category = "dev"
+name = "numpy"
-description = "Core utilities for Python packages"
+version = "1.21.1"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
 name = "packaging"
+version = "21.0"
+description = "Core utilities for Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
-version = "21.0"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
 name = "pluggy"
+version = "0.13.1"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.1"
-
-[package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
-category = "dev"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
 name = "py"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "1.10.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
-category = "dev"
-description = "Python style guide checker"
 name = "pycodestyle"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "2.7.0"
-
+description = "Python style guide checker"
-[[package]]
 category = "dev"
-description = "passive checker of Python programs"
-name = "pyflakes"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.3.1"
 
 [[package]]
+name = "pyflakes"
+version = "2.3.1"
+description = "passive checker of Python programs"
 category = "dev"
-description = "Python parsing module"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "pygments"
+version = "2.10.0"
+description = "Pygments is a syntax highlighting package written in Python."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
 name = "pyparsing"
+version = "2.4.7"
+description = "Python parsing module"
+category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "2.4.7"
 
 [[package]]
-category = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "6.2.4"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
-version = "6.2.4"
 
 [package.dependencies]
-atomicwrites = ">=1.0"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=19.2.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<1.0.0a1"
 py = ">=1.8.2"
 toml = "*"
 
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
-
 [package.extras]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-category = "dev"
-description = "Pytest plugin for measuring coverage."
 name = "pytest-cov"
+version = "2.12.1"
+description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.12.1"
 
 [package.dependencies]
 coverage = ">=5.2.1"
@@ -220,47 +292,199 @@ toml = "*"
 testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
 
 [[package]]
+name = "pytz"
+version = "2021.1"
+description = "World timezone definitions, modern and historical"
 category = "dev"
-description = "Python Library for Tom's Obvious, Minimal Language"
-name = "toml"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "0.10.2"
-
-[[package]]
-category = "dev"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
-name = "typed-ast"
 optional = false
 python-versions = "*"
-version = "1.4.3"
 
 [[package]]
+name = "requests"
+version = "2.26.0"
+description = "Python HTTP for Humans."
 category = "dev"
-description = "Backported and Experimental Type Hints for Python 3.5+"
-name = "typing-extensions"
 optional = false
-python-versions = "*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
-version = "3.10.0.0"
 
-[[package]]
+[package.dependencies]
-category = "dev"
+certifi = ">=2017.4.17"
-description = "Backport of pathlib-compatible object wrapper for zip files"
+charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
-marker = "python_version < \"3.8\""
+idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
-name = "zipp"
+urllib3 = ">=1.21.1,<1.27"
-optional = false
-python-versions = ">=3.6"
-version = "3.5.0"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
+
+[[package]]
+name = "scipy"
+version = "1.5.4"
+description = "SciPy: Scientific Library for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+numpy = ">=1.14.5"
+
+[[package]]
+name = "snowballstemmer"
+version = "2.1.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "sphinx"
+version = "4.1.2"
+description = "Python documentation generator"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+alabaster = ">=0.7,<0.8"
+babel = ">=1.3"
+colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.14,<0.18"
+imagesize = "*"
+Jinja2 = ">=2.3"
+packaging = "*"
+Pygments = ">=2.0"
+requests = ">=2.5.0"
+snowballstemmer = ">=1.1"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.5"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.900)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"]
+test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.2"
+description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.2"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.0"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest", "html5lib"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+test = ["pytest", "flake8", "mypy"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.3"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.5"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+
+[[package]]
+name = "typed-ast"
+version = "1.4.3"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "typing-extensions"
+version = "3.10.0.0"
+description = "Backported and Experimental Type Hints for Python 3.5+"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "urllib3"
+version = "1.26.6"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
+
+[package.extras]
+brotli = ["brotlipy (>=0.6.0)"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
+socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [metadata]
-content-hash = "b3de1ca8a251edc8dae2c93e878deb3131846055ac2a6d6b34e43ea20a8f1ea2"
+lock-version = "1.1"
-python-versions = "^3.7"
+python-versions = "^3.8,<3.10"
+content-hash = "c24b9a131366246119b2d28776b98d7430e983e25389ad6691928b6e78ab0673"
 
 [metadata.files]
+alabaster = [
+    {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
+    {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
+]
 atomicwrites = [
     {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
@@ -269,6 +493,18 @@ attrs = [
     {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
     {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
 ]
+babel = [
+    {file = "Babel-2.9.1-py2.py3-none-any.whl", hash = "sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9"},
+    {file = "Babel-2.9.1.tar.gz", hash = "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"},
+]
+certifi = [
+    {file = "certifi-2021.5.30-py2.py3-none-any.whl", hash = "sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8"},
+    {file = "certifi-2021.5.30.tar.gz", hash = "sha256:2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee"},
+]
+charset-normalizer = [
+    {file = "charset-normalizer-2.0.4.tar.gz", hash = "sha256:f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3"},
+    {file = "charset_normalizer-2.0.4-py3-none-any.whl", hash = "sha256:0c8911edd15d19223366a194a513099a302055a962bca2cec0f54b8b63175d8b"},
+]
 colorama = [
     {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
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@@ -327,22 +563,94 @@ coverage = [
     {file = "coverage-5.5-pp37-none-any.whl", hash = "sha256:2a3859cb82dcbda1cfd3e6f71c27081d18aa251d20a17d87d26d4cd216fb0af4"},
     {file = "coverage-5.5.tar.gz", hash = "sha256:ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c"},
 ]
+docutils = [
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+    {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
+]
 flake8 = [
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 ]
-importlib-metadata = [
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+    {file = "idna-3.2.tar.gz", hash = "sha256:467fbad99067910785144ce333826c71fb0e63a425657295239737f7ecd125f3"},
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+    {file = "scipy-1.5.4.tar.gz", hash = "sha256:4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b"},
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+    {file = "snowballstemmer-2.1.0.tar.gz", hash = "sha256:e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914"},
+]
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+    {file = "Sphinx-4.1.2-py3-none-any.whl", hash = "sha256:46d52c6cee13fec44744b8c01ed692c18a640f6910a725cbb938bc36e8d64544"},
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+]
+sphinxcontrib-applehelp = [
+    {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
+    {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
+]
+sphinxcontrib-devhelp = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
+sphinxcontrib-htmlhelp = [
+    {file = "sphinxcontrib-htmlhelp-2.0.0.tar.gz", hash = "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"},
+    {file = "sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl", hash = "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07"},
+]
+sphinxcontrib-jsmath = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+sphinxcontrib-qthelp = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
+sphinxcontrib-serializinghtml = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
 toml = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
@@ -436,7 +845,7 @@ typing-extensions = [
     {file = "typing_extensions-3.10.0.0-py3-none-any.whl", hash = "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"},
     {file = "typing_extensions-3.10.0.0.tar.gz", hash = "sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342"},
 ]
-zipp = [
+urllib3 = [
-    {file = "zipp-3.5.0-py3-none-any.whl", hash = "sha256:957cfda87797e389580cb8b9e3870841ca991e2125350677b2ca83a0e99390a3"},
+    {file = "urllib3-1.26.6-py2.py3-none-any.whl", hash = "sha256:39fb8672126159acb139a7718dd10806104dec1e2f0f6c88aab05d17df10c8d4"},
-    {file = "zipp-3.5.0.tar.gz", hash = "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4"},
+    {file = "urllib3-1.26.6.tar.gz", hash = "sha256:f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f"},
 ]

pyproject.toml

@@ -5,14 +5,26 @@ description = ""
 authors = ["Deepak <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
-python = "^3.7"
+python = "^3.8,<3.10"
+numpy = "^1.21.1"
+scipy = "~1.5"
+more-itertools = "^8.8.0"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"
 flake8 = "^3.8.4"
 pytest-cov = "^2.10.1"
 mypy = "^0.790"
+Sphinx = "^4.1.2"
 
 [build-system]
 requires = ["poetry>=0.12"]
 build-backend = "poetry.masonry.api"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--junitxml pytest.xml --cov pathfinder --cov-report=xml:coverage.xml --cov-fail-under=90"
+junit_family = "xunit1"
+
+[tool.mypy]
+plugins = "numpy.typing.mypy_plugin"

scripts/patch.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+set -Eeuo pipefail
+
+if [ -z "$(git status --porcelain)" ]; then 
+	# Working directory clean
+	branch_name=$(git symbolic-ref -q HEAD)
+	branch_name=${branch_name##refs/heads/}
+	branch_name=${branch_name:-HEAD}
+	
+	poetry version patch
+	version=`sed 's/version = "\([0-9]*.[0-9]*.[0-9]*\)"/\1/p' -n <pyproject.toml`
+	read -p "Create commit for version $version? " -n 1 -r
+	echo    # (optional) move to a new line
+	if [[ $REPLY =~ ^[Yy]$ ]]
+	then
+		# do dangerous stuff
+		echo "Creating a new patch"
+		git add pyproject.toml
+		git commit -m "Created version $version"
+		git tag -a "$version" -m "patch.sh created version $version"
+		git push --tags
+	else
+		echo "Surrendering, clean up by reverting pyproject.toml..."
+		exit 2
+	fi
+else 
+	echo "Can't create patch version, working tree unclean..."
+	exit 1
+fi

tests/model/test_dot.py

@@ -0,0 +1,45 @@
+import numpy
+import numpy.testing
+
+import pathfinder.model as model
+
+
+def test_dot():
+	dot = model.DotMeasurement(0.235, (1, 2, 3))
+	assert dot.v == 0.235
+	numpy.testing.assert_array_equal(dot.r, (1, 2, 3), "These arrays should have been equal!")
+
+
+def test_dot_v_from_dipole():
+	# for a dot located at (1, 2, 3)
+	dot = model.DotMeasurement(50, (1, 2, 3))
+
+	# and dipole located at (4, 7, 11) with p=(8, 9, 10)
+	pt = numpy.array((8, 9, 10, 4, 7, 11))
+
+	# V should be -0.153584
+	target = -0.1535844174880402
+	cost = -50.1535844174880402
+
+	numpy.testing.assert_allclose(dot.v_for_point(pt), target, err_msg="v from dipole at a dot was incorrect!")
+	numpy.testing.assert_allclose(dot.cost(pt), cost, err_msg="cost from dipole at a dot was incorrect!")
+
+
+def test_dot_jac():
+	# for a dot located at (1, 2, 3)
+	dot = model.DotMeasurement(50, (1, 2, 3))
+
+	# and dipole located at (4, 7, 11) with p=(8, 9, 10)
+	pt = numpy.array((8, 9, 10, 4, 7, 11))
+
+	target_jac_pt = [-0.003092303707812889, -0.005153839513021483, -0.00824614322083437, 0.0058585481811285, 0.01423090787983279, 0.02730483137919137]
+
+	# assume a second dipole at (12, 13, -5), with p = (-1, -2, -3)
+	second_target = [-0.002054993939616119, -0.002054993939616119, 0.001494541046993541, 5.494636202182148e-6, 0.0001923122670763748, 0.0006923241614749492]
+	pt2 = numpy.array((-1, -2, -3, 12, 13, -5))
+	jac_row_target = target_jac_pt + second_target
+	pts = numpy.append(pt, pt2)
+
+	assert len(dot.jac_pt(pt)) == 6
+	numpy.testing.assert_allclose(dot.jac_pt(pt), target_jac_pt, err_msg="Jac pt doesn't match Mathematica result.")
+	numpy.testing.assert_allclose(dot.jac(pts), jac_row_target, err_msg="whole row should match")

tests/model/test_model.py

@@ -0,0 +1,107 @@
+import numpy
+import pathfinder.model as model
+import scipy.optimize
+import pytest
+
+
+def test_dotdipolemodel_repr():
+	mod = model.DotDipoleModel((), 1)
+	assert repr(mod) == "DotDipoleModel([], 1)"
+
+
+def test_dotdipolemodel_m():
+	mod = model.DotDipoleModel([model.DotMeasurement(1, (0, 0, 0)), model.DotMeasurement(2, (0, 0, 0))], 1)
+	assert mod.m == 2
+
+
+def print_result(msg, result):
+	print(msg)
+	print(f"\tResult: {result.x}")
+	print(f"\tSuccess: {result.success}. {result.message}")
+	try:
+		print(f"\tFunc evals: {result.nfev}")
+	except AttributeError:
+		pass
+	try:
+		print(f"\tJacb evals: {result.njev}")
+	except AttributeError:
+		pass
+
+
+@pytest.mark.skip(reason="old")
+def test_dot_dipole_model_jac():
+	v1 = -0.05547767706400186526225414
+	v2 = -0.06018573388098888319642888
+	v3 = -0.06364032191901859480476888
+	v4 = -0.06488383879243851188402150
+	v5 = -0.06297148063759813929659130
+	v6 = -0.05735489606460216
+	v7 = -0.07237320672886623
+	v8 = -0.1082531754730548
+
+	c1 = model.DotMeasurement(v1, [0, 0, 1])
+	c2 = model.DotMeasurement(v2, [0, 0, 2])
+	c3 = model.DotMeasurement(v3, [0, 0, 3])
+	c4 = model.DotMeasurement(v4, [0, 0, 4])
+	c5 = model.DotMeasurement(v5, [0, 0, 5])
+	c6 = model.DotMeasurement(v6, [0, 0, 6])
+	c7 = model.DotMeasurement(v7, [1, 1, 7])
+	c8 = model.DotMeasurement(v8, [1, 2, 3])
+
+	mod = model.DotDipoleModel([c1, c2, c3, c4, c5, c6], 1)
+	res = scipy.optimize.least_squares(mod.costs(), numpy.array([1, 2, 3, 4, 5, 6]), jac=mod.jac(), ftol=1e-12)
+	print_result("6 dots, least sq", res)
+	mod2 = model.DotDipoleModel([c1, c2, c3, c4, c5, c6, c7, c8], 1)
+	res2 = scipy.optimize.least_squares(mod2.costs(), numpy.array([0, 0, 0, 0, 0, 0]), jac=mod2.jac(), ftol=1e-12, gtol=3e-16)
+	print_result("7 dots, least squares", res2)
+	print(mod2.costs()(res2.x))
+	print(mod2.costs()(numpy.array([1, 3, 5, 5, 6, 7])))
+
+
+@pytest.mark.skip(reason="bad test")
+def test_dot_2dipoles_model_jac():
+	dots_12andone = [
+		model.DotMeasurement(-0.1978319326584865, [-4, -1, 0]),
+		model.DotMeasurement(-0.1273171638293727, [-4, -5, 0]),
+		model.DotMeasurement(-0.05545025617224288, [-4, -9, 0]),
+		model.DotMeasurement(-0.4960209997369774, [-1, -1, 0]),
+		model.DotMeasurement(-0.1763373289754278, [-1, -5, 0]),
+		model.DotMeasurement(-0.04946346672578462, [-1, -9, 0]),
+		model.DotMeasurement(-0.5633156098386561, [1, -1, 0]),
+		model.DotMeasurement(-0.113765134433174, [1, -5, 0]),
+		model.DotMeasurement(-0.0294893572499722, [1, -9, 0]),
+		model.DotMeasurement(0.7794941616360612, [4, -1, 0]),
+		model.DotMeasurement(0.1110683086477768, [4, -5, 0]),
+		model.DotMeasurement(0.01183272220840589, [4, -9, 0]),
+		model.DotMeasurement(-0.1096485462119833, [1, 1, 1]),
+		model.DotMeasurement(-0.3925851888077783, [1, 1, -1])
+	]
+	# dots = [
+	# 	model.Dot(-0.1978319326584865, [-4, -1, 0]),
+	# 	model.Dot(-0.1273171638293727, [-4, -5, 0]),
+	# 	model.Dot(-0.05545025617224288, [-4, -9, 0]),
+	# 	model.Dot(-0.4960209997369774, [-1, -1, 0]),
+	# 	model.Dot(-0.1763373289754278, [-1, -5, 0]),
+	# 	model.Dot(-0.04946346672578462, [-1, -9, 0]),
+	# 	model.Dot(-0.5633156098386561, [1, -1, 0]),
+	# 	model.Dot(-0.113765134433174, [1, -5, 0]),
+	# 	model.Dot(-0.0294893572499722, [1, -9, 0]),
+	# 	model.Dot(0.7794941616360612, [4, -1, 0]),
+	# 	model.Dot(0.1110683086477768, [4, -5, 0]),
+	# 	model.Dot(0.01183272220840589, [4, -9, 0]),
+	# 	model.Dot(-0.0261092728062841, [-4, -13, 0]),
+	# 	model.Dot(-0.02035559593904894, [-1, -13, 0]),
+	# 	model.Dot(-0.01296894715810522, [1, -13, 0]),
+	# 	model.Dot(0.0003306001626435171, [4, -13, 0]),
+	# 	model.Dot(0.2612817068810759, [7, -1, 0]),
+	# 	model.Dot(0.1203841445911355, [7, -5, 0]),
+	# 	model.Dot(0.03425933872931543, [7, -9, 0]),
+	# 	model.Dot(0.01068547688208644, [7, -13, 0]),
+	# ]
+
+	mod = model.DotDipoleModel(dots_12andone, 2)
+	res = scipy.optimize.least_squares(mod.costs(), numpy.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]), jac=mod.jac(), ftol=1e-12)
+	print_result("6 dots, least sq", res)
+	print(mod.costs()(res.x))
+	for val in res.x:
+		print(val)