chore(release): 0.7.0

Reviewed-on: #30

.gitignore

@@ -114,6 +114,10 @@ ENV/
 env.bak/
 venv.bak/
 
+# direnv
+.envrc
+.direnv
+
 # Spyder project settings
 .spyderproject
 .spyproject

CHANGELOG.md

@@ -2,6 +2,150 @@
 
 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.
 
+## [0.7.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.7...0.7.0) (2023-05-01)
+
+
+### ⚠ BREAKING CHANGES
+
+* removes fastfilter parameter because it should never be needed
+
+### Features
+
+* adds pair capability to real spectrum run hopefully ([a089951](https://gitea.deepak.science:2222/physics/deepdog/commit/a089951bbefcd8a0b2efeb49b7a8090412cbb23d))
+* removes fastfilter parameter because it should never be needed ([a015daf](https://gitea.deepak.science:2222/physics/deepdog/commit/a015daf5ff6fa5f6155c8d7e02981b588840a5b0))
+
+### [0.6.7](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.6...0.6.7) (2023-04-14)
+
+
+### Features
+
+* adds option to cap core count for real spectrum run ([bf15f4a](https://gitea.deepak.science:2222/physics/deepdog/commit/bf15f4a7b7f59504983624e7d512ed7474372032))
+* adds option to cap core count for temp aware run ([12903b2](https://gitea.deepak.science:2222/physics/deepdog/commit/12903b2540cefb040174d230bc0d04719a6dc1b7))
+
+
+### Bug Fixes
+
+* avoids redefinition of core count in loop ([1cf4454](https://gitea.deepak.science:2222/physics/deepdog/commit/1cf44541531541088198bd4599d467df3e1acbcf))
+
+### [0.6.6](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.5...0.6.6) (2023-04-09)
+
+
+### Bug Fixes
+
+* removes bad logging in multiprocessing function ([8fd1b75](https://gitea.deepak.science:2222/physics/deepdog/commit/8fd1b75e1378301210bfa8f14dd09174bbd21414))
+
+### [0.6.5](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.4...0.6.5) (2023-04-09)
+
+
+### Features
+
+* adds temp aware guy using new pdme temp-flexible feature for bundling temp models ([de1ec3e](https://gitea.deepak.science:2222/physics/deepdog/commit/de1ec3e70062d418e0d4c89716905cc9313d2e26))
+
+### [0.6.4](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.3...0.6.4) (2022-08-13)
+
+
+### Features
+
+* Prints model names while running ([7ea1d71](https://gitea.deepak.science:2222/physics/deepdog/commit/7ea1d715f67e81c9fa841c5a62f1cc700ff7363d))
+
+### [0.6.3](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.2...0.6.3) (2022-06-12)
+
+
+### Features
+
+* adds fast filter variant ([2c5c122](https://gitea.deepak.science:2222/physics/deepdog/commit/2c5c1228209e51d17253f07470e2f1e6dc6872d7))
+* adds tester for fast filter real spectrum ([0a1a277](https://gitea.deepak.science:2222/physics/deepdog/commit/0a1a27759b0d4ab01da214b76ab14bf2b1fe00e3))
+
+### [0.6.2](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.1...0.6.2) (2022-05-26)
+
+
+### Features
+
+* adds better import api for real data run ([d7e0f13](https://gitea.deepak.science:2222/physics/deepdog/commit/d7e0f13ca55197b24cb534c80f321ee76b9c4a40))
+
+### [0.6.1](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.0...0.6.1) (2022-05-22)
+
+
+### Features
+
+* adds new runner for real spectra ([bd56f24](https://gitea.deepak.science:2222/physics/deepdog/commit/bd56f247748babb2ee1f2a1182d25aa968bff5a5))
+
+## [0.6.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.5.0...0.6.0) (2022-05-22)
+
+
+### ⚠ BREAKING CHANGES
+
+* bayes run now handles multidipoles with changes to output file format etc.
+* logs multiple dipoles better maybe
+* switches over to pdme new stuff, uses models and scraps discretisations entirely
+* removes alt_bayes bayes distinction, which was superfluous when only alt worked
+
+### Features
+
+* adds pdme 0.7.0 for multiprocessing ([874d876](https://gitea.deepak.science:2222/physics/deepdog/commit/874d876c9d774433b034d47c4cc0cdac41e6f2c7))
+* bayes run now handles multidipoles with changes to output file format etc. ([5d0a7a4](https://gitea.deepak.science:2222/physics/deepdog/commit/5d0a7a4be09c58f8f8f859384f01d7912a98b8b9))
+* logs multiple dipoles better maybe ([ae8977b](https://gitea.deepak.science:2222/physics/deepdog/commit/ae8977bb1e4d6cd71e88ea0876da8f4318e030b6))
+* removes alt_bayes bayes distinction, which was superfluous when only alt worked ([101569d](https://gitea.deepak.science:2222/physics/deepdog/commit/101569d749e4f3f1842886aa2fd3321b8132278b))
+* switches over to pdme new stuff, uses models and scraps discretisations entirely ([6e29f7a](https://gitea.deepak.science:2222/physics/deepdog/commit/6e29f7a702b578c266a42bba23ac973d155ada10))
+* Uses multidipole for bayes run, with more verbose output ([df89776](https://gitea.deepak.science:2222/physics/deepdog/commit/df8977655de977fd3c4f7383dd9571e551eb1382))
+
+
+### Bug Fixes
+
+* another bug fix for csv generation ([b7da3d6](https://gitea.deepak.science:2222/physics/deepdog/commit/b7da3d61cc5c128cba1d2fcb3770b71b7f6fc4b8))
+* fixes crash when dipole count is smaller than expected max during file write ([b5e0ecb](https://gitea.deepak.science:2222/physics/deepdog/commit/b5e0ecb52886b32d9055302eacfabb69338026b4))
+* fixes format string in csv output for headers ([9afa209](https://gitea.deepak.science:2222/physics/deepdog/commit/9afa209864cdb9255988778e987fe05952848fd4))
+* fixes random issue ([eec926a](https://gitea.deepak.science:2222/physics/deepdog/commit/eec926aaac654f78942b4c6b612e4d1cdcbf81dc))
+* moves logging successes to after they've actually happened ([0caad05](https://gitea.deepak.science:2222/physics/deepdog/commit/0caad05e3cc6a9adba8bf937c3d2f944e1b096a3))
+* now doesn't double randomise frequency ([23b202b](https://gitea.deepak.science:2222/physics/deepdog/commit/23b202beb81cb89f7f20b691e83116fa53764902))
+* whoops deleted word multiprocessing ([31070b5](https://gitea.deepak.science:2222/physics/deepdog/commit/31070b5342c265d930b4c51402f42a3ee2415066))
+
+## [0.5.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.4.0...0.5.0) (2022-04-30)
+
+
+### ⚠ BREAKING CHANGES
+
+* simulpairs now uses different rng calculator
+
+### Features
+
+* adds simulpairs run ([e9277c3](https://gitea.deepak.science:2222/physics/deepdog/commit/e9277c3da777359feb352c0b19f3bb029248ba2f))
+* has better parallelisation ([edf0ba6](https://gitea.deepak.science:2222/physics/deepdog/commit/edf0ba6532c0588fce32341709cdb70e384b83f4))
+* simulpairs now uses different rng calculator ([50dbc48](https://gitea.deepak.science:2222/physics/deepdog/commit/50dbc4835e60bace9e9b4ba37415f073a3c9e479))
+
+
+### Bug Fixes
+
+* better parallelisation hopefully ([42829c0](https://gitea.deepak.science:2222/physics/deepdog/commit/42829c0327e080e18be2fb75e746f6ac0d7c2f6d))
+* Makes altbayessimulpairs available in package ([492a5e6](https://gitea.deepak.science:2222/physics/deepdog/commit/492a5e6681c85f95840e28cfd5d4ce4ca1d54eba))
+* stronger names ([0954429](https://gitea.deepak.science:2222/physics/deepdog/commit/0954429e2d015a105ff16dfbb9e7a352bf53e5e9))
+* Uses correct filename arg for passed in rng ([349341b](https://gitea.deepak.science:2222/physics/deepdog/commit/349341b405375a43b933f1fd7db4ee9fc501def3))
+* uses correct filename for pairs guy ([4c06b39](https://gitea.deepak.science:2222/physics/deepdog/commit/4c06b3912c811c93c310b1d9e4c153f2014c4f8b))
+
+## [0.4.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.5...0.4.0) (2022-04-10)
+
+
+### ⚠ BREAKING CHANGES
+
+* Adds pair calculations, with changing api format
+
+### Features
+
+* Adds dynamic cycle count increases to help reach minimum success count ([ec7b4ca](https://gitea.deepak.science:2222/physics/deepdog/commit/ec7b4cac393c15e94c513215c4f1ba32be2ae87a))
+* Adds pair calculations, with changing api format ([6463b13](https://gitea.deepak.science:2222/physics/deepdog/commit/6463b135ef2d212b565864b5ac1b655e014d2194))
+
+
+### Bug Fixes
+
+* uses bigfix from pdme for negatives ([c1c711f](https://gitea.deepak.science:2222/physics/deepdog/commit/c1c711f47b574d3a9b8a24dbcbdd7f50b9be8ea9))
+
+### [0.3.5](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.4...0.3.5) (2022-03-07)
+
+
+### Features
+
+* makes chunksize configurable ([88d9613](https://gitea.deepak.science:2222/physics/deepdog/commit/88d961313c1db0d49fd96939aa725a8706fa0412))
+
 ### [0.3.4](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.3...0.3.4) (2022-03-06)
 
 

Jenkinsfile

@@ -4,7 +4,7 @@ pipeline {
 		label 'deepdog'  // 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
+		defaultContainer 'poetry'  // define a default container if more than a few stages use it, will default to jnlp container
 	  }
 	}
 
@@ -12,36 +12,30 @@ pipeline {
 		parallelsAlwaysFailFast()
 	}
 
-	environment {
-		POETRY_HOME="/opt/poetry"
-		POETRY_VERSION="1.1.12"
-	}
-
 	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 --version'
-				sh '${POETRY_HOME}/bin/poetry --version'
+				sh 'poetry install'
-				sh '${POETRY_HOME}/bin/poetry install'
 			}
 		}
 		stage('Test') {
 			parallel{
 				stage('pytest') {
 					steps {
-						sh '${POETRY_HOME}/bin/poetry run pytest'
+						sh 'poetry run pytest'
 					}
 				}
 				stage('lint') {
 					steps {
-						sh '${POETRY_HOME}/bin/poetry run flake8 deepdog tests'
+						sh 'poetry run flake8 deepdog tests'
 					}
 				}
 				stage('mypy') {
 					steps {
-						sh '${POETRY_HOME}/bin/poetry run mypy deepdog'
+						sh 'poetry run mypy deepdog'
 					}
 				}
 			}
@@ -57,7 +51,7 @@ pipeline {
 			}
 			steps {
 				echo 'Deploying...'
-				sh '${POETRY_HOME}/bin/poetry publish -u ${PYPI_USR} -p ${PYPI_PSW} --build'
+				sh 'poetry publish -u ${PYPI_USR} -p ${PYPI_PSW} --build'
 			}
 		}
 

README.md

@@ -5,7 +5,7 @@
 [![Jenkins](https://img.shields.io/jenkins/build?jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fdeepdog%2Fjob%2Fmaster&style=flat-square)](https://jenkins.deepak.science/job/gitea-physics/job/deepdog/job/master/)
 ![Jenkins tests](https://img.shields.io/jenkins/tests?compact_message&jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fdeepdog%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%2Fdeepdog%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)
 
 The DiPole DiaGnostic tool.
 

deepdog/__init__.py

@@ -1,15 +1,22 @@
 import logging
 from deepdog.meta import __version__
 from deepdog.bayes_run import BayesRun
-from deepdog.alt_bayes_run import AltBayesRun
+from deepdog.bayes_run_simulpairs import BayesRunSimulPairs
-from deepdog.diagnostic import Diagnostic
+from deepdog.real_spectrum_run import RealSpectrumRun
+from deepdog.temp_aware_real_spectrum_run import TempAwareRealSpectrumRun
 
 
 def get_version():
 	return __version__
 
 
-__all__ = ["get_version", "BayesRun", "AltBayesRun", "Diagnostic"]
+__all__ = [
+	"get_version",
+	"BayesRun",
+	"BayesRunSimulPairs",
+	"RealSpectrumRun",
+	"TempAwareRealSpectrumRun",
+]
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

deepdog/alt_bayes_run.py

@@ -1,133 +0,0 @@
-import pdme.model
-import pdme.measurement.oscillating_dipole
-import pdme.util.fast_v_calc
-from typing import Sequence, Tuple, List
-import datetime
-import csv
-import multiprocessing
-import logging
-import numpy
-
-
-# TODO: remove hardcode
-CHUNKSIZE = 20
-
-# TODO: It's garbage to have this here duplicated from pdme.
-DotInput = Tuple[numpy.typing.ArrayLike, float]
-
-
-_logger = logging.getLogger(__name__)
-
-
-def get_a_result(input) -> int:
-	discretisation, dot_inputs, lows, highs, monte_carlo_count, max_frequency = input
-	sample_dipoles = discretisation.get_model().get_n_single_dipoles(monte_carlo_count, max_frequency)
-	vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
-	return numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs))
-
-
-class AltBayesRun():
-	'''
-	A single Bayes run for a given set of dots.
-
-	Parameters
-	----------
-	dot_inputs : Sequence[DotInput]
-		The dot inputs for this bayes run.
-	discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
-		The models to evaluate.
-	actual_model_discretisation : pdme.model.Discretisation
-		The discretisation for the model which is actually correct.
-	filename_slug : str
-		The filename slug to include.
-	run_count: int
-		The number of runs to do.
-	'''
-	def __init__(self, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int, low_error: float = 0.9, high_error: float = 1.1, monte_carlo_count: int = 10000, monte_carlo_cycles: int = 10, max_frequency: float = 20, end_threshold: float = None) -> None:
-		self.dot_inputs = dot_inputs
-		self.dot_inputs_array = pdme.measurement.oscillating_dipole.dot_inputs_to_array(dot_inputs)
-		self.discretisations = [disc for (_, disc) in discretisations_with_names]
-		self.model_names = [name for (name, _) in discretisations_with_names]
-		self.actual_model = actual_model
-		self.model_count = len(self.discretisations)
-		self.monte_carlo_count = monte_carlo_count
-		self.monte_carlo_cycles = monte_carlo_cycles
-		self.run_count = run_count
-		self.low_error = low_error
-		self.high_error = high_error
-		self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"]
-		self.compensate_zeros = True
-		for name in self.model_names:
-			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
-
-		self.probabilities = [1 / self.model_count] * self.model_count
-
-		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
-		self.filename = f"{timestamp}-{filename_slug}.altbayes.csv"
-		self.max_frequency = max_frequency
-
-		if end_threshold is not None:
-			if 0 < end_threshold < 1:
-				self.end_threshold: float = end_threshold
-				self.use_end_threshold = True
-				_logger.info(f"Will abort early, at {self.end_threshold}.")
-			else:
-				raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
-
-	def go(self) -> None:
-		with open(self.filename, "a", newline="") as outfile:
-			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
-			writer.writeheader()
-
-		for run in range(1, self.run_count + 1):
-
-			rng = numpy.random.default_rng()
-			frequency = rng.uniform(1, self.max_frequency)
-
-			# Generate the actual dipoles
-			actual_dipoles = self.actual_model.get_dipoles(frequency)
-
-			dots = actual_dipoles.get_percent_range_dot_measurements(self.dot_inputs, self.low_error, self.high_error)
-			lows, highs = pdme.measurement.oscillating_dipole.dot_range_measurements_low_high_arrays(dots)
-			_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
-
-			results = []
-			_logger.debug("Going to iterate over discretisations now")
-			for disc_count, discretisation in enumerate(self.discretisations):
-				_logger.debug(f"Doing discretisation #{disc_count}")
-				with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
-					results.append(sum(
-						pool.imap_unordered(get_a_result, [(discretisation, self.dot_inputs_array, lows, highs, self.monte_carlo_count, self.max_frequency)] * self.monte_carlo_cycles, CHUNKSIZE)
-					))
-
-			_logger.debug("Done, constructing output now")
-			row = {
-				"dipole_moment": actual_dipoles.dipoles[0].p,
-				"dipole_location": actual_dipoles.dipoles[0].s,
-				"dipole_frequency": actual_dipoles.dipoles[0].w
-			}
-			successes: List[float] = []
-			counts: List[int] = []
-			for model_index, (name, result) in enumerate(zip(self.model_names, results)):
-
-				row[f"{name}_success"] = result
-				row[f"{name}_count"] = self.monte_carlo_count * self.monte_carlo_cycles
-				successes.append(max(result, 0.5))
-				counts.append(self.monte_carlo_count * self.monte_carlo_cycles)
-
-			success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
-			new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
-			self.probabilities = new_probabilities
-			for name, probability in zip(self.model_names, self.probabilities):
-				row[f"{name}_prob"] = probability
-			_logger.info(row)
-
-			with open(self.filename, "a", newline="") as outfile:
-				writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
-				writer.writerow(row)
-
-			if self.use_end_threshold:
-				max_prob = max(self.probabilities)
-				if max_prob > self.end_threshold:
-					_logger.info(f"Aborting early, because {max_prob} is greater than {self.end_threshold}")
-					break

deepdog/bayes_run.py

@@ -1,17 +1,19 @@
+import pdme.inputs
 import pdme.model
+import pdme.measurement.input_types
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+import pdme.util.fast_nonlocal_spectrum
 from typing import Sequence, Tuple, List
 import datetime
-import itertools
 import csv
+import multiprocessing
 import logging
 import numpy
-import scipy.optimize
-import multiprocessing
 
 
 # TODO: remove hardcode
-COST_THRESHOLD = 1e-10
+CHUNKSIZE = 50
-
 
 # TODO: It's garbage to have this here duplicated from pdme.
 DotInput = Tuple[numpy.typing.ArrayLike, float]
@@ -20,43 +22,126 @@ DotInput = Tuple[numpy.typing.ArrayLike, float]
 _logger = logging.getLogger(__name__)
 
 
-def get_a_result(discretisation, dots, index) -> Tuple[Tuple[int, ...], scipy.optimize.OptimizeResult]:
+def get_a_result(input) -> int:
-	return (index, discretisation.solve_for_index(dots, index))
+	model, dot_inputs, lows, highs, monte_carlo_count, max_frequency, seed = input
+
+	rng = numpy.random.default_rng(seed)
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, max_frequency, rng_to_use=rng
+	)
+	vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(dot_inputs, sample_dipoles)
+	return numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs))
 
 
-class BayesRun():
+def get_a_result_using_pairs(input) -> int:
-	'''
+	(
+		model,
+		dot_inputs,
+		pair_inputs,
+		local_lows,
+		local_highs,
+		nonlocal_lows,
+		nonlocal_highs,
+		monte_carlo_count,
+		max_frequency,
+	) = input
+	sample_dipoles = model.get_n_single_dipoles(monte_carlo_count, max_frequency)
+	local_vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
+	local_matches = pdme.util.fast_v_calc.between(local_vals, local_lows, local_highs)
+	nonlocal_vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal(
+		pair_inputs, sample_dipoles
+	)
+	nonlocal_matches = pdme.util.fast_v_calc.between(
+		nonlocal_vals, nonlocal_lows, nonlocal_highs
+	)
+	combined_matches = numpy.logical_and(local_matches, nonlocal_matches)
+	return numpy.count_nonzero(combined_matches)
+
+
+class BayesRun:
+	"""
 	A single Bayes run for a given set of dots.
 
 	Parameters
 	----------
 	dot_inputs : Sequence[DotInput]
-		The dot inputs for this bayes run.
+	The dot inputs for this bayes run.
-	discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
+
-		The models to evaluate.
+	models_with_names : Sequence[Tuple(str, pdme.model.DipoleModel)]
-	actual_model_discretisation : pdme.model.Discretisation
+	The models to evaluate.
-		The discretisation for the model which is actually correct.
+
+	actual_model : pdme.model.DipoleModel
+	The model which is actually correct.
+
 	filename_slug : str
-		The filename slug to include.
+	The filename slug to include.
+
 	run_count: int
-		The number of runs to do.
+	The number of runs to do.
-	'''
+	"""
-	def __init__(self, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int, max_frequency: float = None, end_threshold: float = None) -> None:
+
-		self.dot_inputs = dot_inputs
+	def __init__(
-		self.discretisations = [disc for (_, disc) in discretisations_with_names]
+		self,
-		self.model_names = [name for (name, _) in discretisations_with_names]
+		dot_positions: Sequence[numpy.typing.ArrayLike],
+		frequency_range: Sequence[float],
+		models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+		actual_model: pdme.model.DipoleModel,
+		filename_slug: str,
+		run_count: int = 100,
+		low_error: float = 0.9,
+		high_error: float = 1.1,
+		monte_carlo_count: int = 10000,
+		monte_carlo_cycles: int = 10,
+		target_success: int = 100,
+		max_monte_carlo_cycles_steps: int = 10,
+		max_frequency: float = 20,
+		end_threshold: float = None,
+		chunksize: int = CHUNKSIZE,
+	) -> None:
+		self.dot_inputs = pdme.inputs.inputs_with_frequency_range(
+			dot_positions, frequency_range
+		)
+		self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
+			self.dot_inputs
+		)
+
+		self.models = [model for (_, model) in models_with_names]
+		self.model_names = [name for (name, _) in models_with_names]
 		self.actual_model = actual_model
-		self.model_count = len(self.discretisations)
+
+		self.n: int
+		try:
+			self.n = self.actual_model.n  # type: ignore
+		except AttributeError:
+			self.n = 1
+
+		self.model_count = len(self.models)
+		self.monte_carlo_count = monte_carlo_count
+		self.monte_carlo_cycles = monte_carlo_cycles
+		self.target_success = target_success
+		self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
 		self.run_count = run_count
-		self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"]
+		self.low_error = low_error
+		self.high_error = high_error
+
+		self.csv_fields = []
+		for i in range(self.n):
+			self.csv_fields.extend(
+				[
+					f"dipole_moment_{i+1}",
+					f"dipole_location_{i+1}",
+					f"dipole_frequency_{i+1}",
+				]
+			)
 		self.compensate_zeros = True
+		self.chunksize = chunksize
 		for name in self.model_names:
 			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
 
 		self.probabilities = [1 / self.model_count] * self.model_count
 
 		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
-		self.filename = f"{timestamp}-{filename_slug}.csv"
+		self.filename = f"{timestamp}-{filename_slug}.bayesrun.csv"
 		self.max_frequency = max_frequency
 
 		if end_threshold is not None:
@@ -65,7 +150,9 @@ class BayesRun():
 				self.use_end_threshold = True
 				_logger.info(f"Will abort early, at {self.end_threshold}.")
 			else:
-				raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
+				raise ValueError(
+					f"end_threshold should be between 0 and 1, but is actually {end_threshold}"
+				)
 
 	def go(self) -> None:
 		with open(self.filename, "a", newline="") as outfile:
@@ -73,56 +160,122 @@ class BayesRun():
 			writer.writeheader()
 
 		for run in range(1, self.run_count + 1):
-			frequency: float = run
-			if self.max_frequency is not None and self.max_frequency > 1:
-				rng = numpy.random.default_rng()
-				frequency = rng.uniform(1, self.max_frequency)
-			dipoles = self.actual_model.get_dipoles(frequency)
 
-			dots = dipoles.get_dot_measurements(self.dot_inputs)
+			# Generate the actual dipoles
-			_logger.info(f"Going to work on dipole at {dipoles.dipoles}")
+			actual_dipoles = self.actual_model.get_dipoles(self.max_frequency)
+
+			dots = actual_dipoles.get_percent_range_dot_measurements(
+				self.dot_inputs, self.low_error, self.high_error
+			)
+			(
+				lows,
+				highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				dots
+			)
+
+			_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
+
+			# define a new seed sequence for each run
+			seed_sequence = numpy.random.SeedSequence(run)
 
 			results = []
-			_logger.debug("Going to iterate over discretisations now")
+			_logger.debug("Going to iterate over models now")
-			for disc_count, discretisation in enumerate(self.discretisations):
+			for model_count, model in enumerate(self.models):
-				_logger.debug(f"Doing discretisation #{disc_count}")
+				_logger.debug(f"Doing model #{model_count}")
-				with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
+				core_count = multiprocessing.cpu_count() - 1 or 1
-					results.append(pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(dots), discretisation.all_indices())))
+				with multiprocessing.Pool(core_count) as pool:
+					cycle_count = 0
+					cycle_success = 0
+					cycles = 0
+					while (cycles < self.max_monte_carlo_cycles_steps) and (
+						cycle_success <= self.target_success
+					):
+						_logger.debug(f"Starting cycle {cycles}")
+						cycles += 1
+						current_success = 0
+						cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
+
+						# generate a seed from the sequence for each core.
+						# note this needs to be inside the loop for monte carlo cycle steps!
+						# that way we get more stuff.
+						seeds = seed_sequence.spawn(self.monte_carlo_cycles)
+
+						current_success = sum(
+							pool.imap_unordered(
+								get_a_result,
+								[
+									(
+										model,
+										self.dot_inputs_array,
+										lows,
+										highs,
+										self.monte_carlo_count,
+										self.max_frequency,
+										seed,
+									)
+									for seed in seeds
+								],
+								self.chunksize,
+							)
+						)
+
+						cycle_success += current_success
+						_logger.debug(f"current running successes: {cycle_success}")
+					results.append((cycle_count, cycle_success))
 
 			_logger.debug("Done, constructing output now")
 			row = {
-				"dipole_moment": dipoles.dipoles[0].p,
+				"dipole_moment_1": actual_dipoles.dipoles[0].p,
-				"dipole_location": dipoles.dipoles[0].s,
+				"dipole_location_1": actual_dipoles.dipoles[0].s,
-				"dipole_frequency": dipoles.dipoles[0].w
+				"dipole_frequency_1": actual_dipoles.dipoles[0].w,
 			}
+			for i in range(1, self.n):
+				try:
+					current_dipoles = actual_dipoles.dipoles[i]
+					row[f"dipole_moment_{i+1}"] = current_dipoles.p
+					row[f"dipole_location_{i+1}"] = current_dipoles.s
+					row[f"dipole_frequency_{i+1}"] = current_dipoles.w
+				except IndexError:
+					_logger.info(f"Not writing anymore, saw end after {i}")
+					break
+
 			successes: List[float] = []
 			counts: List[int] = []
-			for model_index, (name, result) in enumerate(zip(self.model_names, results)):
+			for model_index, (name, (count, result)) in enumerate(
-				count = 0
+				zip(self.model_names, results)
-				success = 0
+			):
-				for idx, val in result:
-					count += 1
-					if val.success and val.cost <= COST_THRESHOLD:
-						success += 1
 
-				row[f"{name}_success"] = success
+				row[f"{name}_success"] = result
 				row[f"{name}_count"] = count
-				successes.append(max(success, 0.5))
+				successes.append(max(result, 0.5))
 				counts.append(count)
 
-			success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
+			success_weight = sum(
-			new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
+				[
+					(succ / count) * prob
+					for succ, count, prob in zip(successes, counts, self.probabilities)
+				]
+			)
+			new_probabilities = [
+				(succ / count) * old_prob / success_weight
+				for succ, count, old_prob in zip(successes, counts, self.probabilities)
+			]
 			self.probabilities = new_probabilities
 			for name, probability in zip(self.model_names, self.probabilities):
 				row[f"{name}_prob"] = probability
 			_logger.info(row)
 
 			with open(self.filename, "a", newline="") as outfile:
-				writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+				writer = csv.DictWriter(
+					outfile, fieldnames=self.csv_fields, dialect="unix"
+				)
 				writer.writerow(row)
 
 			if self.use_end_threshold:
 				max_prob = max(self.probabilities)
 				if max_prob > self.end_threshold:
-					_logger.info(f"Aborting early, because {max_prob} is greater than {self.end_threshold}")
+					_logger.info(
+						f"Aborting early, because {max_prob} is greater than {self.end_threshold}"
+					)
 					break

deepdog/bayes_run_simulpairs.py

@@ -0,0 +1,382 @@
+import pdme.inputs
+import pdme.model
+import pdme.measurement.input_types
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+import pdme.util.fast_nonlocal_spectrum
+from typing import Sequence, Tuple, List
+import datetime
+import csv
+import multiprocessing
+import logging
+import numpy
+import numpy.random
+
+
+# TODO: remove hardcode
+CHUNKSIZE = 50
+
+# TODO: It's garbage to have this here duplicated from pdme.
+DotInput = Tuple[numpy.typing.ArrayLike, float]
+
+
+_logger = logging.getLogger(__name__)
+
+
+def get_a_simul_result_using_pairs(input) -> numpy.ndarray:
+	(
+		model,
+		dot_inputs,
+		pair_inputs,
+		local_lows,
+		local_highs,
+		nonlocal_lows,
+		nonlocal_highs,
+		monte_carlo_count,
+		monte_carlo_cycles,
+		max_frequency,
+		seed,
+	) = input
+
+	rng = numpy.random.default_rng(seed)
+	local_total = 0
+	combined_total = 0
+
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, max_frequency, rng_to_use=rng
+	)
+	local_vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(dot_inputs, sample_dipoles)
+	local_matches = pdme.util.fast_v_calc.between(local_vals, local_lows, local_highs)
+	nonlocal_vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal_dipoleses(
+		pair_inputs, sample_dipoles
+	)
+	nonlocal_matches = pdme.util.fast_v_calc.between(
+		nonlocal_vals, nonlocal_lows, nonlocal_highs
+	)
+	combined_matches = numpy.logical_and(local_matches, nonlocal_matches)
+
+	local_total += numpy.count_nonzero(local_matches)
+	combined_total += numpy.count_nonzero(combined_matches)
+	return numpy.array([local_total, combined_total])
+
+
+class BayesRunSimulPairs:
+	"""
+	A dual pairs-nonpairs Bayes run for a given set of dots.
+
+	Parameters
+	----------
+	dot_inputs : Sequence[DotInput]
+	The dot inputs for this bayes run.
+
+	models_with_names : Sequence[Tuple(str, pdme.model.DipoleModel)]
+	The models to evaluate.
+
+	actual_model : pdme.model.DipoleModel
+	The modoel for the model which is actually correct.
+
+	filename_slug : str
+	The filename slug to include.
+
+	run_count: int
+	The number of runs to do.
+	"""
+
+	def __init__(
+		self,
+		dot_positions: Sequence[numpy.typing.ArrayLike],
+		frequency_range: Sequence[float],
+		models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+		actual_model: pdme.model.DipoleModel,
+		filename_slug: str,
+		run_count: int = 100,
+		low_error: float = 0.9,
+		high_error: float = 1.1,
+		pairs_high_error=None,
+		pairs_low_error=None,
+		monte_carlo_count: int = 10000,
+		monte_carlo_cycles: int = 10,
+		target_success: int = 100,
+		max_monte_carlo_cycles_steps: int = 10,
+		max_frequency: float = 20,
+		end_threshold: float = None,
+		chunksize: int = CHUNKSIZE,
+	) -> None:
+		self.dot_inputs = pdme.inputs.inputs_with_frequency_range(
+			dot_positions, frequency_range
+		)
+		self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
+			self.dot_inputs
+		)
+
+		self.dot_pair_inputs = pdme.inputs.input_pairs_with_frequency_range(
+			dot_positions, frequency_range
+		)
+		self.dot_pair_inputs_array = (
+			pdme.measurement.input_types.dot_pair_inputs_to_array(self.dot_pair_inputs)
+		)
+
+		self.models = [mod for (_, mod) in models_with_names]
+		self.model_names = [name for (name, _) in models_with_names]
+		self.actual_model = actual_model
+
+		self.n: int
+		try:
+			self.n = self.actual_model.n  # type: ignore
+		except AttributeError:
+			self.n = 1
+
+		self.model_count = len(self.models)
+		self.monte_carlo_count = monte_carlo_count
+		self.monte_carlo_cycles = monte_carlo_cycles
+		self.target_success = target_success
+		self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
+		self.run_count = run_count
+		self.low_error = low_error
+		self.high_error = high_error
+		if pairs_low_error is None:
+			self.pairs_low_error = self.low_error
+		else:
+			self.pairs_low_error = pairs_low_error
+		if pairs_high_error is None:
+			self.pairs_high_error = self.high_error
+		else:
+			self.pairs_high_error = pairs_high_error
+
+		self.csv_fields = []
+		for i in range(self.n):
+			self.csv_fields.extend(
+				[
+					f"dipole_moment_{i+1}",
+					f"dipole_location_{i+1}",
+					f"dipole_frequency_{i+1}",
+				]
+			)
+		self.compensate_zeros = True
+		self.chunksize = chunksize
+		for name in self.model_names:
+			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
+
+		self.probabilities_no_pairs = [1 / self.model_count] * self.model_count
+		self.probabilities_pairs = [1 / self.model_count] * self.model_count
+
+		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+		self.filename_pairs = f"{timestamp}-{filename_slug}.simulpairs.yespairs.csv"
+		self.filename_no_pairs = f"{timestamp}-{filename_slug}.simulpairs.noopairs.csv"
+
+		self.max_frequency = max_frequency
+
+		if end_threshold is not None:
+			if 0 < end_threshold < 1:
+				self.end_threshold: float = end_threshold
+				self.use_end_threshold = True
+				_logger.info(f"Will abort early, at {self.end_threshold}.")
+			else:
+				raise ValueError(
+					f"end_threshold should be between 0 and 1, but is actually {end_threshold}"
+				)
+
+	def go(self) -> None:
+		with open(self.filename_pairs, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+		with open(self.filename_no_pairs, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+
+		for run in range(1, self.run_count + 1):
+
+			# Generate the actual dipoles
+			actual_dipoles = self.actual_model.get_dipoles(self.max_frequency)
+
+			dots = actual_dipoles.get_percent_range_dot_measurements(
+				self.dot_inputs, self.low_error, self.high_error
+			)
+			(
+				lows,
+				highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				dots
+			)
+
+			pair_lows, pair_highs = (None, None)
+			pair_measurements = actual_dipoles.get_percent_range_dot_pair_measurements(
+				self.dot_pair_inputs, self.pairs_low_error, self.pairs_high_error
+			)
+			(
+				pair_lows,
+				pair_highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				pair_measurements
+			)
+
+			_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
+
+			# define a new seed sequence for each run
+			seed_sequence = numpy.random.SeedSequence(run)
+
+			results_pairs = []
+			results_no_pairs = []
+			_logger.debug("Going to iterate over models now")
+			for model_count, model in enumerate(self.models):
+				_logger.debug(f"Doing model #{model_count}")
+
+				core_count = multiprocessing.cpu_count() - 1 or 1
+				with multiprocessing.Pool(core_count) as pool:
+					cycle_count = 0
+					cycle_success_pairs = 0
+					cycle_success_no_pairs = 0
+					cycles = 0
+					while (cycles < self.max_monte_carlo_cycles_steps) and (
+						min(cycle_success_pairs, cycle_success_no_pairs)
+						<= self.target_success
+					):
+						_logger.debug(f"Starting cycle {cycles}")
+
+						cycles += 1
+						current_success_pairs = 0
+						current_success_no_pairs = 0
+						cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
+
+						# generate a seed from the sequence for each core.
+						# note this needs to be inside the loop for monte carlo cycle steps!
+						# that way we get more stuff.
+
+						seeds = seed_sequence.spawn(self.monte_carlo_cycles)
+						_logger.debug(f"Creating {self.monte_carlo_cycles} seeds")
+						current_success_both = numpy.array(
+							sum(
+								pool.imap_unordered(
+									get_a_simul_result_using_pairs,
+									[
+										(
+											model,
+											self.dot_inputs_array,
+											self.dot_pair_inputs_array,
+											lows,
+											highs,
+											pair_lows,
+											pair_highs,
+											self.monte_carlo_count,
+											self.monte_carlo_cycles,
+											self.max_frequency,
+											seed,
+										)
+										for seed in seeds
+									],
+									self.chunksize,
+								)
+							)
+						)
+						current_success_no_pairs = current_success_both[0]
+						current_success_pairs = current_success_both[1]
+
+						cycle_success_no_pairs += current_success_no_pairs
+						cycle_success_pairs += current_success_pairs
+						_logger.debug(
+							f"(pair, no_pair) successes are {(cycle_success_pairs, cycle_success_no_pairs)}"
+						)
+					results_pairs.append((cycle_count, cycle_success_pairs))
+					results_no_pairs.append((cycle_count, cycle_success_no_pairs))
+
+			_logger.debug("Done, constructing output now")
+			row_pairs = {
+				"dipole_moment_1": actual_dipoles.dipoles[0].p,
+				"dipole_location_1": actual_dipoles.dipoles[0].s,
+				"dipole_frequency_1": actual_dipoles.dipoles[0].w,
+			}
+			row_no_pairs = {
+				"dipole_moment_1": actual_dipoles.dipoles[0].p,
+				"dipole_location_1": actual_dipoles.dipoles[0].s,
+				"dipole_frequency_1": actual_dipoles.dipoles[0].w,
+			}
+			for i in range(1, self.n):
+				try:
+					current_dipoles = actual_dipoles.dipoles[i]
+					row_pairs[f"dipole_moment_{i+1}"] = current_dipoles.p
+					row_pairs[f"dipole_location_{i+1}"] = current_dipoles.s
+					row_pairs[f"dipole_frequency_{i+1}"] = current_dipoles.w
+					row_no_pairs[f"dipole_moment_{i+1}"] = current_dipoles.p
+					row_no_pairs[f"dipole_location_{i+1}"] = current_dipoles.s
+					row_no_pairs[f"dipole_frequency_{i+1}"] = current_dipoles.w
+				except IndexError:
+					_logger.info(f"Not writing anymore, saw end after {i}")
+					break
+
+			successes_pairs: List[float] = []
+			successes_no_pairs: List[float] = []
+			counts: List[int] = []
+			for model_index, (
+				name,
+				(count_pair, result_pair),
+				(count_no_pair, result_no_pair),
+			) in enumerate(zip(self.model_names, results_pairs, results_no_pairs)):
+
+				row_pairs[f"{name}_success"] = result_pair
+				row_pairs[f"{name}_count"] = count_pair
+				successes_pairs.append(max(result_pair, 0.5))
+
+				row_no_pairs[f"{name}_success"] = result_no_pair
+				row_no_pairs[f"{name}_count"] = count_no_pair
+				successes_no_pairs.append(max(result_no_pair, 0.5))
+
+				counts.append(count_pair)
+
+			success_weight_pair = sum(
+				[
+					(succ / count) * prob
+					for succ, count, prob in zip(
+						successes_pairs, counts, self.probabilities_pairs
+					)
+				]
+			)
+			success_weight_no_pair = sum(
+				[
+					(succ / count) * prob
+					for succ, count, prob in zip(
+						successes_no_pairs, counts, self.probabilities_no_pairs
+					)
+				]
+			)
+			new_probabilities_pair = [
+				(succ / count) * old_prob / success_weight_pair
+				for succ, count, old_prob in zip(
+					successes_pairs, counts, self.probabilities_pairs
+				)
+			]
+			new_probabilities_no_pair = [
+				(succ / count) * old_prob / success_weight_no_pair
+				for succ, count, old_prob in zip(
+					successes_no_pairs, counts, self.probabilities_no_pairs
+				)
+			]
+			self.probabilities_pairs = new_probabilities_pair
+			self.probabilities_no_pairs = new_probabilities_no_pair
+			for name, probability_pair, probability_no_pair in zip(
+				self.model_names, self.probabilities_pairs, self.probabilities_no_pairs
+			):
+				row_pairs[f"{name}_prob"] = probability_pair
+				row_no_pairs[f"{name}_prob"] = probability_no_pair
+			_logger.debug(row_pairs)
+			_logger.debug(row_no_pairs)
+
+			with open(self.filename_pairs, "a", newline="") as outfile:
+				writer = csv.DictWriter(
+					outfile, fieldnames=self.csv_fields, dialect="unix"
+				)
+				writer.writerow(row_pairs)
+			with open(self.filename_no_pairs, "a", newline="") as outfile:
+				writer = csv.DictWriter(
+					outfile, fieldnames=self.csv_fields, dialect="unix"
+				)
+				writer.writerow(row_no_pairs)
+
+			if self.use_end_threshold:
+				max_prob = min(
+					max(self.probabilities_pairs), max(self.probabilities_no_pairs)
+				)
+				if max_prob > self.end_threshold:
+					_logger.info(
+						f"Aborting early, because {max_prob} is greater than {self.end_threshold}"
+					)
+					break

deepdog/diagnostic.py

@@ -1,99 +0,0 @@
-from pdme.measurement import OscillatingDipole, OscillatingDipoleArrangement
-import pdme
-from deepdog.bayes_run import DotInput
-import datetime
-import numpy
-from dataclasses import dataclass
-import logging
-from typing import Sequence, Tuple
-import csv
-import itertools
-import multiprocessing
-
-_logger = logging.getLogger(__name__)
-
-
-def get_a_result(discretisation, dots, index):
-	return (index, discretisation.solve_for_index(dots, index))
-
-
-@dataclass
-class SingleDipoleDiagnostic():
-	model: str
-	index: Tuple
-	bounds: Tuple
-	actual_dipole: OscillatingDipole
-	result_dipole: OscillatingDipole
-	success: bool
-
-	def __post_init__(self) -> None:
-		self.p_actual_x = self.actual_dipole.p[0]
-		self.p_actual_y = self.actual_dipole.p[1]
-		self.p_actual_z = self.actual_dipole.p[2]
-		self.s_actual_x = self.actual_dipole.s[0]
-		self.s_actual_y = self.actual_dipole.s[1]
-		self.s_actual_z = self.actual_dipole.s[2]
-		self.p_result_x = self.result_dipole.p[0]
-		self.p_result_y = self.result_dipole.p[1]
-		self.p_result_z = self.result_dipole.p[2]
-		self.s_result_x = self.result_dipole.s[0]
-		self.s_result_y = self.result_dipole.s[1]
-		self.s_result_z = self.result_dipole.s[2]
-		self.w_actual = self.actual_dipole.w
-		self.w_result = self.result_dipole.w
-
-
-class Diagnostic():
-	'''
-	Represents a diagnostic for a single dipole moment given a set of discretisations.
-
-	Parameters
-	----------
-	dot_inputs : Sequence[DotInput]
-		The dot inputs for this diagnostic.
-	discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
-		The models to evaluate.
-	actual_model_discretisation : pdme.model.Discretisation
-		The discretisation for the model which is actually correct.
-	filename_slug : str
-		The filename slug to include.
-	run_count: int
-		The number of runs to do.
-	'''
-	def __init__(self, actual_dipole_moment: numpy.ndarray, actual_dipole_position: numpy.ndarray, actual_dipole_frequency: float, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], filename_slug: str) -> None:
-		self.dipoles = OscillatingDipoleArrangement([OscillatingDipole(actual_dipole_moment, actual_dipole_position, actual_dipole_frequency)])
-		self.dots = self.dipoles.get_dot_measurements(dot_inputs)
-
-		self.discretisations_with_names = discretisations_with_names
-		self.model_count = len(self.discretisations_with_names)
-
-		self.csv_fields = ["model", "index", "bounds", "p_actual_x", "p_actual_y", "p_actual_z", "s_actual_x", "s_actual_y", "s_actual_z", "w_actual", "success", "p_result_x", "p_result_y", "p_result_z", "s_result_x", "s_result_y", "s_result_z", "w_result"]
-
-		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
-		self.filename = f"{timestamp}-{filename_slug}.diag.csv"
-
-	def go(self):
-		with open(self.filename, "a", newline="") as outfile:
-			# csv fields
-			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix')
-			writer.writeheader()
-
-		for (name, discretisation) in self.discretisations_with_names:
-			_logger.info(f"Working on discretisation {name}")
-
-			results = []
-			with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
-				results = pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(self.dots), discretisation.all_indices()))
-
-			with open(self.filename, "a", newline='') as outfile:
-				writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix', extrasaction="ignore")
-
-				for idx, result in results:
-
-					bounds = discretisation.bounds(idx)
-
-					actual_success = result.success and result.cost <= 1e-10
-					diag_row = SingleDipoleDiagnostic(name, idx, bounds, self.dipoles.dipoles[0], discretisation.model.solution_as_dipoles(result.normalised_x)[0], actual_success)
-					row = vars(diag_row)
-					_logger.debug(f"Writing result {row}")
-					writer.writerow(row)

deepdog/meta.py

@@ -1,3 +1,3 @@
 from importlib.metadata import version
 
-__version__ = version('deepdog')
+__version__ = version("deepdog")

deepdog/real_spectrum_run.py

@@ -0,0 +1,307 @@
+import pdme.inputs
+import pdme.model
+import pdme.measurement
+import pdme.measurement.input_types
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+import pdme.util.fast_nonlocal_spectrum
+from typing import Sequence, Tuple, List, Dict, Union, Optional
+import datetime
+import csv
+import multiprocessing
+import logging
+import numpy
+
+
+# TODO: remove hardcode
+CHUNKSIZE = 50
+
+
+_logger = logging.getLogger(__name__)
+
+
+def get_a_result_fast_filter_pairs(input) -> int:
+	(
+		model,
+		dot_inputs,
+		lows,
+		highs,
+		pair_inputs,
+		pair_lows,
+		pair_highs,
+		monte_carlo_count,
+		seed,
+	) = input
+
+	rng = numpy.random.default_rng(seed)
+	# TODO: A long term refactor is to pull the frequency stuff out from here. The None stands for max_frequency, which is unneeded in the actually useful models.
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, None, rng_to_use=rng
+	)
+
+	current_sample = sample_dipoles
+	for di, low, high in zip(dot_inputs, lows, highs):
+
+		if len(current_sample) < 1:
+			break
+		vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(
+			numpy.array([di]), current_sample
+		)
+
+		current_sample = current_sample[numpy.all((vals > low) & (vals < high), axis=1)]
+
+	for pi, plow, phigh in zip(pair_inputs, pair_lows, pair_highs):
+		if len(current_sample) < 1:
+			break
+		vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal_dipoleses(
+			numpy.array([pi]), current_sample
+		)
+
+		current_sample = current_sample[
+			numpy.all(
+				((vals > plow) & (vals < phigh)) | ((vals < plow) & (vals > phigh)),
+				axis=1,
+			)
+		]
+	return len(current_sample)
+
+
+def get_a_result_fast_filter(input) -> int:
+	model, dot_inputs, lows, highs, monte_carlo_count, seed = input
+
+	rng = numpy.random.default_rng(seed)
+	# TODO: A long term refactor is to pull the frequency stuff out from here. The None stands for max_frequency, which is unneeded in the actually useful models.
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, None, rng_to_use=rng
+	)
+
+	current_sample = sample_dipoles
+	for di, low, high in zip(dot_inputs, lows, highs):
+
+		if len(current_sample) < 1:
+			break
+		vals = pdme.util.fast_v_calc.fast_vs_for_dipoleses(
+			numpy.array([di]), current_sample
+		)
+
+		current_sample = current_sample[numpy.all((vals > low) & (vals < high), axis=1)]
+	return len(current_sample)
+
+
+class RealSpectrumRun:
+	"""
+	A bayes run given some real data.
+
+	Parameters
+	----------
+	measurements : Sequence[pdme.measurement.DotRangeMeasurement]
+	The dot inputs for this bayes run.
+
+	models_with_names : Sequence[Tuple(str, pdme.model.DipoleModel)]
+	The models to evaluate.
+
+	actual_model : pdme.model.DipoleModel
+	The model which is actually correct.
+
+	filename_slug : str
+	The filename slug to include.
+
+	run_count: int
+	The number of runs to do.
+	"""
+
+	def __init__(
+		self,
+		measurements: Sequence[pdme.measurement.DotRangeMeasurement],
+		models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+		filename_slug: str,
+		monte_carlo_count: int = 10000,
+		monte_carlo_cycles: int = 10,
+		target_success: int = 100,
+		max_monte_carlo_cycles_steps: int = 10,
+		chunksize: int = CHUNKSIZE,
+		initial_seed: int = 12345,
+		cap_core_count: int = 0,
+		pair_measurements: Optional[
+			Sequence[pdme.measurement.DotPairRangeMeasurement]
+		] = None,
+	) -> None:
+		self.measurements = measurements
+		self.dot_inputs = [(measure.r, measure.f) for measure in self.measurements]
+
+		self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
+			self.dot_inputs
+		)
+
+		if pair_measurements is not None:
+			self.pair_measurements = pair_measurements
+			self.use_pair_measurements = True
+			self.dot_pair_inputs = [
+				(measure.r1, measure.r2, measure.f)
+				for measure in self.pair_measurements
+			]
+			self.dot_pair_inputs_array = (
+				pdme.measurement.input_types.dot_pair_inputs_to_array(
+					self.dot_pair_inputs
+				)
+			)
+		else:
+			self.use_pair_measurements = False
+
+		self.models = [model for (_, model) in models_with_names]
+		self.model_names = [name for (name, _) in models_with_names]
+		self.model_count = len(self.models)
+
+		self.monte_carlo_count = monte_carlo_count
+		self.monte_carlo_cycles = monte_carlo_cycles
+		self.target_success = target_success
+		self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
+
+		self.csv_fields = []
+
+		self.compensate_zeros = True
+		self.chunksize = chunksize
+		for name in self.model_names:
+			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
+
+		# for now initialise priors as uniform.
+		self.probabilities = [1 / self.model_count] * self.model_count
+
+		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+
+		ff_string = "fast_filter"
+
+		self.filename = f"{timestamp}-{filename_slug}.realdata.{ff_string}.bayesrun.csv"
+		self.initial_seed = initial_seed
+
+		self.cap_core_count = cap_core_count
+
+	def go(self) -> None:
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+
+		(
+			lows,
+			highs,
+		) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+			self.measurements
+		)
+
+		pair_lows = None
+		pair_highs = None
+		if self.use_pair_measurements:
+			(
+				pair_lows,
+				pair_highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				self.pair_measurements
+			)
+
+		# define a new seed sequence for each run
+		seed_sequence = numpy.random.SeedSequence(self.initial_seed)
+
+		results = []
+		_logger.debug("Going to iterate over models now")
+		core_count = multiprocessing.cpu_count() - 1 or 1
+		if (self.cap_core_count >= 1) and (self.cap_core_count < core_count):
+			core_count = self.cap_core_count
+		_logger.info(f"Using {core_count} cores")
+		for model_count, (model, model_name) in enumerate(
+			zip(self.models, self.model_names)
+		):
+			_logger.debug(f"Doing model #{model_count}: {model_name}")
+			with multiprocessing.Pool(core_count) as pool:
+				cycle_count = 0
+				cycle_success = 0
+				cycles = 0
+				while (cycles < self.max_monte_carlo_cycles_steps) and (
+					cycle_success <= self.target_success
+				):
+					_logger.debug(f"Starting cycle {cycles}")
+					cycles += 1
+					current_success = 0
+					cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
+
+					# generate a seed from the sequence for each core.
+					# note this needs to be inside the loop for monte carlo cycle steps!
+					# that way we get more stuff.
+					seeds = seed_sequence.spawn(self.monte_carlo_cycles)
+
+					if self.use_pair_measurements:
+						current_success = sum(
+							pool.imap_unordered(
+								get_a_result_fast_filter_pairs,
+								[
+									(
+										model,
+										self.dot_inputs_array,
+										lows,
+										highs,
+										self.dot_pair_inputs_array,
+										pair_lows,
+										pair_highs,
+										self.monte_carlo_count,
+										seed,
+									)
+									for seed in seeds
+								],
+								self.chunksize,
+							)
+						)
+					else:
+
+						current_success = sum(
+							pool.imap_unordered(
+								get_a_result_fast_filter,
+								[
+									(
+										model,
+										self.dot_inputs_array,
+										lows,
+										highs,
+										self.monte_carlo_count,
+										seed,
+									)
+									for seed in seeds
+								],
+								self.chunksize,
+							)
+						)
+
+					cycle_success += current_success
+					_logger.debug(f"current running successes: {cycle_success}")
+				results.append((cycle_count, cycle_success))
+
+		_logger.debug("Done, constructing output now")
+		row: Dict[str, Union[int, float, str]] = {}
+
+		successes: List[float] = []
+		counts: List[int] = []
+		for model_index, (name, (count, result)) in enumerate(
+			zip(self.model_names, results)
+		):
+
+			row[f"{name}_success"] = result
+			row[f"{name}_count"] = count
+			successes.append(max(result, 0.5))
+			counts.append(count)
+
+		success_weight = sum(
+			[
+				(succ / count) * prob
+				for succ, count, prob in zip(successes, counts, self.probabilities)
+			]
+		)
+		new_probabilities = [
+			(succ / count) * old_prob / success_weight
+			for succ, count, old_prob in zip(successes, counts, self.probabilities)
+		]
+		self.probabilities = new_probabilities
+		for name, probability in zip(self.model_names, self.probabilities):
+			row[f"{name}_prob"] = probability
+		_logger.info(row)
+
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writerow(row)

deepdog/temp_aware_real_spectrum_run.py

@@ -0,0 +1,231 @@
+import pdme.inputs
+import pdme.model
+import pdme.measurement
+import pdme.measurement.input_types
+import pdme.measurement.oscillating_dipole
+import pdme.util.fast_v_calc
+import pdme.util.fast_nonlocal_spectrum
+from typing import Sequence, Tuple, List, Dict, Union, Mapping
+import datetime
+import csv
+import multiprocessing
+import logging
+import numpy
+
+
+# TODO: remove hardcode
+CHUNKSIZE = 50
+
+
+_logger = logging.getLogger(__name__)
+
+
+def get_a_result_fast_filter(input) -> int:
+	# 								(
+	# 	model,
+	# 	self.dot_inputs_array_dict,
+	# 	low_high_dict,
+	# 	self.monte_carlo_count,
+	# 	seed,
+	# )
+	model, dot_inputs_dict, low_high_dict, monte_carlo_count, seed = input
+
+	rng = numpy.random.default_rng(seed)
+	# TODO: A long term refactor is to pull the frequency stuff out from here. The None stands for max_frequency, which is unneeded in the actually useful models.
+	sample_dipoles = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_count, None, rng_to_use=rng
+	)
+
+	current_sample = sample_dipoles
+	for temp in dot_inputs_dict.keys():
+		dot_inputs = dot_inputs_dict[temp]
+		lows, highs = low_high_dict[temp]
+		for di, low, high in zip(dot_inputs, lows, highs):
+
+			if len(current_sample) < 1:
+				break
+			vals = pdme.util.fast_v_calc.fast_vs_for_asymmetric_dipoleses(
+				numpy.array([di]), current_sample, temp
+			)
+
+			current_sample = current_sample[
+				numpy.all((vals > low) & (vals < high), axis=1)
+			]
+	return len(current_sample)
+
+
+class TempAwareRealSpectrumRun:
+	"""
+	A bayes run given some real data, with potentially variable temperature.
+
+	Parameters
+	----------
+	measurements_dict : Dict[float, Sequence[pdme.measurement.DotRangeMeasurement]]
+	The dot inputs for this bayes run, in a dictionary indexed by temperatures
+
+	models_with_names : models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+
+	The models to evaluate.
+
+	actual_model : pdme.model.DipoleModel
+	The model which is actually correct.
+
+	filename_slug : str
+	The filename slug to include.
+
+	run_count: int
+	The number of runs to do.
+	"""
+
+	def __init__(
+		self,
+		measurements_dict: Mapping[
+			float, Sequence[pdme.measurement.DotRangeMeasurement]
+		],
+		models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
+		filename_slug: str,
+		monte_carlo_count: int = 10000,
+		monte_carlo_cycles: int = 10,
+		target_success: int = 100,
+		max_monte_carlo_cycles_steps: int = 10,
+		chunksize: int = CHUNKSIZE,
+		initial_seed: int = 12345,
+		cap_core_count: int = 0,
+	) -> None:
+		self.measurements_dict = measurements_dict
+		self.dot_inputs_dict = {
+			k: [(measure.r, measure.f) for measure in measurements]
+			for k, measurements in measurements_dict.items()
+		}
+
+		self.dot_inputs_array_dict = {
+			k: pdme.measurement.input_types.dot_inputs_to_array(dot_inputs)
+			for k, dot_inputs in self.dot_inputs_dict.items()
+		}
+
+		self.models = [model for (_, model) in models_with_names]
+		self.model_names = [name for (name, _) in models_with_names]
+		self.model_count = len(self.models)
+
+		self.monte_carlo_count = monte_carlo_count
+		self.monte_carlo_cycles = monte_carlo_cycles
+		self.target_success = target_success
+		self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
+
+		self.csv_fields = []
+
+		self.compensate_zeros = True
+		self.chunksize = chunksize
+		for name in self.model_names:
+			self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
+
+		# for now initialise priors as uniform.
+		self.probabilities = [1 / self.model_count] * self.model_count
+
+		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+		ff_string = "fast_filter"
+		self.filename = f"{timestamp}-{filename_slug}.realdata.{ff_string}.bayesrun.csv"
+		self.initial_seed = initial_seed
+
+		self.cap_core_count = cap_core_count
+
+	def go(self) -> None:
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writeheader()
+
+		low_high_dict = {}
+		for temp, measurements in self.measurements_dict.items():
+			(
+				lows,
+				highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				measurements
+			)
+			low_high_dict[temp] = (lows, highs)
+
+		# define a new seed sequence for each run
+		seed_sequence = numpy.random.SeedSequence(self.initial_seed)
+
+		results = []
+		_logger.debug("Going to iterate over models now")
+		core_count = multiprocessing.cpu_count() - 1 or 1
+		if (self.cap_core_count >= 1) and (self.cap_core_count < core_count):
+			core_count = self.cap_core_count
+		_logger.info(f"Using {core_count} cores")
+		for model_count, (model, model_name) in enumerate(
+			zip(self.models, self.model_names)
+		):
+			_logger.debug(f"Doing model #{model_count}: {model_name}")
+			with multiprocessing.Pool(core_count) as pool:
+				cycle_count = 0
+				cycle_success = 0
+				cycles = 0
+				while (cycles < self.max_monte_carlo_cycles_steps) and (
+					cycle_success <= self.target_success
+				):
+					_logger.debug(f"Starting cycle {cycles}")
+					cycles += 1
+					current_success = 0
+					cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
+
+					# generate a seed from the sequence for each core.
+					# note this needs to be inside the loop for monte carlo cycle steps!
+					# that way we get more stuff.
+					seeds = seed_sequence.spawn(self.monte_carlo_cycles)
+
+					result_func = get_a_result_fast_filter
+
+					current_success = sum(
+						pool.imap_unordered(
+							result_func,
+							[
+								(
+									model,
+									self.dot_inputs_array_dict,
+									low_high_dict,
+									self.monte_carlo_count,
+									seed,
+								)
+								for seed in seeds
+							],
+							self.chunksize,
+						)
+					)
+
+					cycle_success += current_success
+					_logger.debug(f"current running successes: {cycle_success}")
+				results.append((cycle_count, cycle_success))
+
+		_logger.debug("Done, constructing output now")
+		row: Dict[str, Union[int, float, str]] = {}
+
+		successes: List[float] = []
+		counts: List[int] = []
+		for model_index, (name, (count, result)) in enumerate(
+			zip(self.model_names, results)
+		):
+
+			row[f"{name}_success"] = result
+			row[f"{name}_count"] = count
+			successes.append(max(result, 0.5))
+			counts.append(count)
+
+		success_weight = sum(
+			[
+				(succ / count) * prob
+				for succ, count, prob in zip(successes, counts, self.probabilities)
+			]
+		)
+		new_probabilities = [
+			(succ / count) * old_prob / success_weight
+			for succ, count, old_prob in zip(successes, counts, self.probabilities)
+		]
+		self.probabilities = new_probabilities
+		for name, probability in zip(self.model_names, self.probabilities):
+			row[f"{name}_prob"] = probability
+		_logger.info(row)
+
+		with open(self.filename, "a", newline="") as outfile:
+			writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
+			writer.writerow(row)

do.sh

@@ -16,6 +16,11 @@ test() {
    poetry run pytest
 }
 
+fmt() {
+	poetry run black .
+	find . -type f -name "*.py" -exec sed -i -e 's/    /\t/g' {} \;
+}
+
 release() {
    ./scripts/release.sh
 }

flake.lock

@@ -0,0 +1,95 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1648297722,
+        "narHash": "sha256-W+qlPsiZd8F3XkzXOzAoR+mpFqzm3ekQkJNa+PIh1BQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "0f8662f1319ad6abf89b3380dd2722369fc51ade",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "0f8662f1319ad6abf89b3380dd2722369fc51ade",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "locked": {
+        "lastModified": 1653893745,
+        "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1655087213,
+        "narHash": "sha256-4R5oQ+OwGAAcXWYrxC4gFMTUSstGxaN8kN7e8hkum/8=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "37b6b161e536fddca54424cf80662bce735bdd1e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "37b6b161e536fddca54424cf80662bce735bdd1e",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1655046959,
+        "narHash": "sha256-gxqHZKq1ReLDe6ZMJSbmSZlLY95DsVq5o6jQihhzvmw=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "07bf3d25ce1da3bee6703657e6a787a4c6cdcea9",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "poetry2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs_2"
+      },
+      "locked": {
+        "lastModified": 1654921554,
+        "narHash": "sha256-hkfMdQAHSwLWlg0sBVvgrQdIiBP45U1/ktmFpY4g2Mo=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "7b71679fa7df00e1678fc3f1d1d4f5f372341b63",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "7b71679fa7df00e1678fc3f1d1d4f5f372341b63",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "poetry2nix": "poetry2nix"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,63 @@
+{
+  description = "Application packaged using poetry2nix";
+
+  inputs.flake-utils.url = "github:numtide/flake-utils?rev=0f8662f1319ad6abf89b3380dd2722369fc51ade";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs?rev=37b6b161e536fddca54424cf80662bce735bdd1e";
+  inputs.poetry2nix.url = "github:nix-community/poetry2nix?rev=7b71679fa7df00e1678fc3f1d1d4f5f372341b63";
+
+  outputs = { self, nixpkgs, flake-utils, poetry2nix }:
+    {
+      # Nixpkgs overlay providing the application
+      overlay = nixpkgs.lib.composeManyExtensions [
+        poetry2nix.overlay
+        (final: prev: {
+          # The application
+          deepdog = prev.poetry2nix.mkPoetryApplication {
+            overrides = final.poetry2nix.overrides.withDefaults (self: super: {
+              # …
+              # workaround https://github.com/nix-community/poetry2nix/issues/568
+              pdme = super.pdme.overridePythonAttrs (old: {
+                buildInputs = old.buildInputs or [ ] ++ [ final.python39.pkgs.poetry-core ];
+              });
+            });
+            projectDir = ./.;
+          };
+          deepdogEnv = prev.poetry2nix.mkPoetryEnv {
+            overrides = final.poetry2nix.overrides.withDefaults (self: super: {
+              # …
+              # workaround https://github.com/nix-community/poetry2nix/issues/568
+              pdme = super.pdme.overridePythonAttrs (old: {
+                buildInputs = old.buildInputs or [ ] ++ [ final.python39.pkgs.poetry-core ];
+              });
+            });
+            projectDir = ./.;
+          };
+        })
+      ];
+    } // (flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs {
+          inherit system;
+          overlays = [ self.overlay ];
+        };
+      in
+      {
+        apps = {
+          deepdog = pkgs.deepdog;
+        };
+
+        defaultApp = pkgs.deepdog;
+        devShell = pkgs.mkShell {
+          buildInputs = [
+            pkgs.poetry
+            pkgs.deepdogEnv
+            pkgs.deepdog
+          ];
+          shellHook = ''
+            export DO_NIX_CUSTOM=1
+          '';
+          packages = [ pkgs.nodejs-16_x ];
+        };
+
+      }));
+}

jenkins/ci-agent-pod.yaml

@@ -1,9 +1,11 @@
 apiVersion: v1
 kind: Pod
 spec:
+  imagePullSecrets:
+    - name: regcreds
   containers:  # list of containers that you want present for your build, you can define a default container in the Jenkinsfile
-    - name: python
+    - name: poetry
-      image: python:3.8
+      image: ghcr.io/dmallubhotla/poetry-image:1
       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

pyproject.toml

@@ -1,19 +1,22 @@
 [tool.poetry]
 name = "deepdog"
-version = "0.3.4"
+version = "0.7.0"
 description = ""
 authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = "^3.8,<3.10"
-pdme = "^0.5.4"
+pdme = "^0.8.6"
+numpy = "1.22.3"
+scipy = "1.10"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"
 flake8 = "^4.0.1"
 pytest-cov = "^3.0.0"
-mypy = "^0.931"
+mypy = "^0.971"
 python-semantic-release = "^7.24.0"
+black = "^22.3.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]