chore(release): 0.7.7

CHANGELOG.md

@@ -2,6 +2,34 @@
 
 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.
 
+### [0.7.7](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.6...0.7.7) (2024-02-29)
+
+
+### Bug Fixes
+
+* fixes phase calculation issue with setting input array ([48e41cb](https://gitea.deepak.science:2222/physics/deepdog/commit/48e41cbd2c58d4c4d2747822d618d7d55257643d))
+
+### [0.7.6](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.5...0.7.6) (2024-02-28)
+
+
+### Features
+
+* adds ability to use phase measurements only for correlations ([bb72e90](https://gitea.deepak.science:2222/physics/deepdog/commit/bb72e903d14704a3783daf2dbc1797b90880aa85))
+
+
+### Bug Fixes
+
+* fixes typeerror vs indexerror on bare float as cost in subset simulation ([65e1948](https://gitea.deepak.science:2222/physics/deepdog/commit/65e19488359d7f5656660da7da8f32ed474989c3))
+
+### [0.7.5](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.4...0.7.5) (2023-12-09)
+
+
+### Features
+
+* adds direct monte carlo package ([1741807](https://gitea.deepak.science:2222/physics/deepdog/commit/1741807be43d08fb51bc94518dd3b67585c04c20))
+* adds longchain logging if logging last generation ([b4e5f53](https://gitea.deepak.science:2222/physics/deepdog/commit/b4e5f5372682fc64c3734a96c4a899e018f127ce))
+* allows disabling timestamp in subset simulation bayes results ([9a4548d](https://gitea.deepak.science:2222/physics/deepdog/commit/9a4548def45a01f1f518135d4237c3dc09dcc342))
+
 ### [0.7.4](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.3...0.7.4) (2023-07-27)
 
 

deepdog/bayes_run_with_ss.py

@@ -73,6 +73,7 @@ class BayesRunWithSubspaceSimulation:
 		ss_dump_last_generation=False,
 		ss_initial_costs_chunk_size=100,
 		write_output_to_bayesruncsv=True,
+		use_timestamp_for_output=True,
 	) -> None:
 		self.dot_inputs = pdme.inputs.inputs_with_frequency_range(
 			dot_positions, frequency_range
@@ -110,8 +111,11 @@ class BayesRunWithSubspaceSimulation:
 
 		self.probabilities = [1 / self.model_count] * self.model_count
 
-		timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+		if use_timestamp_for_output:
-		self.filename = f"{timestamp}-{filename_slug}.bayesrunwithss.csv"
+			timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
+			self.filename = f"{timestamp}-{filename_slug}.bayesrunwithss.csv"
+		else:
+			self.filename = f"{filename_slug}.bayesrunwithss.csv"
 		self.max_frequency = max_frequency
 
 		if end_threshold is not None:

deepdog/direct_monte_carlo/__init__.py

@@ -0,0 +1,6 @@
+from deepdog.direct_monte_carlo.direct_mc import (
+	DirectMonteCarloRun,
+	DirectMonteCarloConfig,
+)
+
+__all__ = ["DirectMonteCarloRun", "DirectMonteCarloConfig"]

deepdog/direct_monte_carlo/direct_mc.py

@@ -0,0 +1,157 @@
+import pdme.model
+import pdme.measurement
+import pdme.measurement.input_types
+import pdme.subspace_simulation
+from typing import Tuple, Sequence
+from dataclasses import dataclass
+import logging
+import numpy
+import numpy.random
+import pdme.util.fast_v_calc
+
+_logger = logging.getLogger(__name__)
+
+
+@dataclass
+class DirectMonteCarloResult:
+	successes: int
+	monte_carlo_count: int
+	likelihood: float
+
+
+@dataclass
+class DirectMonteCarloConfig:
+	monte_carlo_count_per_cycle: int = 10000
+	monte_carlo_cycles: int = 10
+	target_success: int = 100
+	max_monte_carlo_cycles_steps: int = 10
+	monte_carlo_seed: int = 1234
+	write_successes_to_file: bool = False
+	tag: str = ""
+
+
+class DirectMonteCarloRun:
+	"""
+	A single model Direct Monte Carlo run, currently implemented only using single threading.
+	An encapsulation of the steps needed for a Bayes run.
+
+	Parameters
+	----------
+	model_name_pair : Sequence[Tuple(str, pdme.model.DipoleModel)]
+	The model to evaluate, with name.
+
+	measurements: Sequence[pdme.measurement.DotRangeMeasurement]
+	The measurements as dot ranges to use as the bounds for the Monte Carlo calculation.
+
+	monte_carlo_count_per_cycle: int
+	The number of Monte Carlo iterations to use in a single cycle calculation.
+
+	monte_carlo_cycles: int
+	The number of cycles to use in each step.
+	Increasing monte_carlo_count_per_cycle increases memory usage (and runtime), while this increases runtime, allowing
+	control over memory use.
+
+	target_success: int
+	The number of successes to target before exiting early.
+	Should likely be ~100 but can go higher to.
+
+	max_monte_carlo_cycles_steps: int
+	The number of steps to use. Each step consists of monte_carlo_cycles cycles, each of which has monte_carlo_count_per_cycle iterations.
+
+	monte_carlo_seed: int
+	The seed to use for the RNG.
+	"""
+
+	def __init__(
+		self,
+		model_name_pair: Tuple[str, pdme.model.DipoleModel],
+		measurements: Sequence[pdme.measurement.DotRangeMeasurement],
+		config: DirectMonteCarloConfig,
+	):
+		self.model_name, self.model = model_name_pair
+
+		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
+		)
+
+		self.config = config
+		(
+			self.lows,
+			self.highs,
+		) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+			self.measurements
+		)
+
+	def _single_run(self, seed) -> numpy.ndarray:
+		rng = numpy.random.default_rng(seed)
+
+		sample_dipoles = self.model.get_monte_carlo_dipole_inputs(
+			self.config.monte_carlo_count_per_cycle, -1, rng
+		)
+
+		current_sample = sample_dipoles
+		for di, low, high in zip(self.dot_inputs_array, self.lows, self.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 current_sample
+
+	def execute(self) -> DirectMonteCarloResult:
+		step_count = 0
+		total_success = 0
+		total_count = 0
+
+		count_per_step = (
+			self.config.monte_carlo_count_per_cycle * self.config.monte_carlo_cycles
+		)
+		seed_sequence = numpy.random.SeedSequence(self.config.monte_carlo_seed)
+		while (step_count < self.config.max_monte_carlo_cycles_steps) and (
+			total_success < self.config.target_success
+		):
+			_logger.debug(f"Executing step {step_count}")
+			for cycle_i, seed in enumerate(
+				seed_sequence.spawn(self.config.monte_carlo_cycles)
+			):
+				cycle_success_configs = self._single_run(seed)
+				cycle_success_count = len(cycle_success_configs)
+				if cycle_success_count > 0:
+					_logger.debug(
+						f"For cycle {cycle_i} received {cycle_success_count} successes"
+					)
+					_logger.debug(cycle_success_configs)
+					if self.config.write_successes_to_file:
+						sorted_by_freq = numpy.array(
+							[
+								pdme.subspace_simulation.sort_array_of_dipoles_by_frequency(
+									dipole_config
+								)
+								for dipole_config in cycle_success_configs
+							]
+						)
+						dipole_count = numpy.array(cycle_success_configs).shape[1]
+						for n in range(dipole_count):
+							numpy.savetxt(
+								f"{self.config.tag}_{step_count}_{cycle_i}_dipole_{n}.csv",
+								sorted_by_freq[:, n],
+								delimiter=",",
+							)
+				total_success += cycle_success_count
+			_logger.debug(f"At end of step {step_count} have {total_success} successes")
+			step_count += 1
+			total_count += count_per_step
+
+		return DirectMonteCarloResult(
+			successes=total_success,
+			monte_carlo_count=total_count,
+			likelihood=total_success / total_count,
+		)

deepdog/real_spectrum_run.py

@@ -66,6 +66,42 @@ def get_a_result_fast_filter_pairs(input) -> int:
 	return len(current_sample)
 
 
+def get_a_result_fast_filter_pair_phase_only(input) -> int:
+	(
+		model,
+		pair_inputs,
+		pair_phase_lows,
+		pair_phase_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 pi, plow, phigh in zip(pair_inputs, pair_phase_lows, pair_phase_highs):
+		if len(current_sample) < 1:
+			break
+		vals = pdme.util.fast_nonlocal_spectrum.signarg(
+			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
 
@@ -108,6 +144,11 @@ class RealSpectrumRun:
 
 	run_count: int
 	The number of runs to do.
+
+	If pair_measurements is not None, uses pair measurement method (and single measurements too).
+	If pair_phase_measurements is not None, ignores measurements and uses phase measurements _only_
+	This is lazy design on my part.
+
 	"""
 
 	def __init__(
@@ -125,6 +166,9 @@ class RealSpectrumRun:
 		pair_measurements: Optional[
 			Sequence[pdme.measurement.DotPairRangeMeasurement]
 		] = None,
+		pair_phase_measurements: Optional[
+			Sequence[pdme.measurement.DotPairRangeMeasurement]
+		] = None,
 	) -> None:
 		self.measurements = measurements
 		self.dot_inputs = [(measure.r, measure.f) for measure in self.measurements]
@@ -136,6 +180,21 @@ class RealSpectrumRun:
 		if pair_measurements is not None:
 			self.pair_measurements = pair_measurements
 			self.use_pair_measurements = True
+			self.use_pair_phase_measurements = False
+
+			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
+				)
+			)
+		elif pair_phase_measurements is not None:
+			self.use_pair_measurements = False
+			self.use_pair_phase_measurements = True
+			self.pair_phase_measurements = pair_phase_measurements
 			self.dot_pair_inputs = [
 				(measure.r1, measure.r2, measure.f)
 				for measure in self.pair_measurements
@@ -147,6 +206,7 @@ class RealSpectrumRun:
 			)
 		else:
 			self.use_pair_measurements = False
+			self.use_pair_phase_measurements = False
 
 		self.models = [model for (_, model) in models_with_names]
 		self.model_names = [name for (name, _) in models_with_names]
@@ -198,6 +258,16 @@ class RealSpectrumRun:
 				self.pair_measurements
 			)
 
+		pair_phase_lows = None
+		pair_phase_highs = None
+		if self.use_pair_phase_measurements:
+			(
+				pair_phase_lows,
+				pair_phase_highs,
+			) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
+				self.pair_phase_measurements
+			)
+
 		# define a new seed sequence for each run
 		seed_sequence = numpy.random.SeedSequence(self.initial_seed)
 
@@ -249,6 +319,24 @@ class RealSpectrumRun:
 								self.chunksize,
 							)
 						)
+					elif self.use_pair_phase_measurements:
+						current_success = sum(
+							pool.imap_unordered(
+								get_a_result_fast_filter_pairs,
+								[
+									(
+										model,
+										self.dot_pair_inputs_array,
+										pair_phase_lows,
+										pair_phase_highs,
+										self.monte_carlo_count,
+										seed,
+									)
+									for seed in seeds
+								],
+								self.chunksize,
+							)
+						)
 					else:
 
 						current_success = sum(

deepdog/subset_simulation/subset_simulation_impl.py

@@ -101,11 +101,17 @@ class SubsetSimulation:
 		# _logger.debug(sample_dipoles.shape)
 
 		raw_costs = []
-		_logger.debug(f"Using iterated cost function thing with chunk size {self.initial_cost_chunk_size}")
+		_logger.debug(
+			f"Using iterated cost function thing with chunk size {self.initial_cost_chunk_size}"
+		)
 
 		for x in range(0, len(sample_dipoles), self.initial_cost_chunk_size):
 			_logger.debug(f"doing chunk {x}")
-			raw_costs.extend(self.cost_function_to_use(sample_dipoles[x: x + self.initial_cost_chunk_size]))
+			raw_costs.extend(
+				self.cost_function_to_use(
+					sample_dipoles[x : x + self.initial_cost_chunk_size]
+				)
+			)
 		costs = numpy.array(raw_costs)
 
 		_logger.debug(f"costs: {costs}")
@@ -143,6 +149,37 @@ class SubsetSimulation:
 						delimiter=",",
 					)
 
+				next_seeds_as_array = numpy.array([s for _, s in next_seeds])
+				stdevs = self.get_stdevs_from_arrays(next_seeds_as_array)
+				_logger.info(f"got stdevs: {stdevs.stdevs}")
+				all_long_chains = []
+				for seed_index, (c, s) in enumerate(
+					next_seeds[:: len(next_seeds) // 20]
+				):
+					# chain = mcmc(s, threshold_cost, n_s, model, dot_inputs_array, actual_measurement_array, mcmc_rng, curr_cost=c, stdevs=stdevs)
+					# until new version gotta do
+					_logger.debug(f"\t{seed_index}: doing long chain on the next seed")
+
+					long_chain = self.model.get_mcmc_chain(
+						s,
+						self.cost_function_to_use,
+						1000,
+						threshold_cost,
+						stdevs,
+						initial_cost=c,
+						rng_arg=mcmc_rng,
+					)
+					for _, chained in long_chain:
+						all_long_chains.append(chained)
+				all_long_chains_array = numpy.array(all_long_chains)
+				for n in range(self.model.n):
+					_logger.info(f"{all_long_chains_array[:, n].shape}")
+					numpy.savetxt(
+						f"long_chain_generation_{self.n_c}_{self.n_s}_{i}_dipole_{n}.csv",
+						all_long_chains_array[:, n],
+						delimiter=",",
+					)
+
 			if self.keep_probs_list:
 				for cost_index, cost_chain in enumerate(all_chains[: -self.n_c]):
 					probs_list.append(
@@ -178,7 +215,7 @@ class SubsetSimulation:
 				for cost, chained in chain:
 					try:
 						filtered_cost = cost[0]
-					except IndexError:
+					except (IndexError, TypeError):
 						filtered_cost = cost
 					all_chains.append((filtered_cost, chained))
 			_logger.debug("finished mcmc")

poetry.lock

@@ -20,24 +20,9 @@ d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
-[[package]]
-name = "bleach"
-version = "6.0.0"
-description = "An easy safelist-based HTML-sanitizing tool."
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-six = ">=1.9.0"
-webencodings = "*"
-
-[package.extras]
-css = ["tinycss2 (>=1.1.0,<1.2)"]
-
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
@@ -45,18 +30,18 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "cffi"
-version = "1.15.1"
+version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 
 [package.dependencies]
 pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.1.0"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "dev"
 optional = false
@@ -64,7 +49,7 @@ python-versions = ">=3.7.0"
 
 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
@@ -92,21 +77,13 @@ category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 
-[[package]]
-name = "colored"
-version = "1.4.4"
-description = "Simple library for color and formatting to terminal"
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "coverage"
-version = "7.2.7"
+version = "7.4.3"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
@@ -116,28 +93,28 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
-version = "40.0.1"
+version = "42.0.5"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-cffi = ">=1.12"
+cffi = {version = ">=1.12", markers = "platform_python_implementation != \"PyPy\""}
 
 [package.extras]
 docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
-docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
+docstest = ["pyenchant (>=1.6.11)", "readme-renderer", "sphinxcontrib-spelling (>=4.0.1)"]
-pep8test = ["black", "ruff", "mypy", "check-manifest"]
+nox = ["nox"]
-sdist = ["setuptools-rust (>=0.11.4)"]
+pep8test = ["ruff", "mypy", "check-sdist", "click"]
+sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["pytest (>=6.2.0)", "pytest-shard (>=0.1.2)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601"]
+test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist", "pretend", "certifi"]
 test-randomorder = ["pytest-randomly"]
-tox = ["tox"]
 
 [[package]]
 name = "docutils"
-version = "0.19"
+version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
 category = "dev"
 optional = false
@@ -153,7 +130,7 @@ python-versions = ">=3.5,<4.0"
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
@@ -177,7 +154,7 @@ pyflakes = ">=2.4.0,<2.5.0"
 
 [[package]]
 name = "gitdb"
-version = "4.0.10"
+version = "4.0.11"
 description = "Git Object Database"
 category = "dev"
 optional = false
@@ -188,7 +165,7 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.31"
+version = "3.1.42"
 description = "GitPython is a Python library used to interact with Git repositories"
 category = "dev"
 optional = false
@@ -197,9 +174,12 @@ python-versions = ">=3.7"
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
+[package.extras]
+test = ["black", "coverage", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "mock"]
+
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 category = "dev"
 optional = false
@@ -207,34 +187,34 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "importlib-metadata"
-version = "6.2.1"
+version = "7.0.1"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.12.0"
+version = "6.1.2"
 description = "Read resources from Python packages"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)", "pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -246,26 +226,26 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "invoke"
-version = "1.7.3"
+version = "2.2.0"
 description = "Pythonic task execution"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "jaraco.classes"
-version = "3.2.3"
+version = "3.3.1"
 description = "Utility functions for Python class constructs"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 more-itertools = "*"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff (>=0.2.1)", "pytest-mypy"]
 
 [[package]]
 name = "jeepney"
@@ -281,11 +261,11 @@ trio = ["trio", "async-generator"]
 
 [[package]]
 name = "keyring"
-version = "23.13.1"
+version = "24.3.1"
 description = "Store and access your passwords safely."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.11.4", markers = "python_version < \"3.12\""}
@@ -296,9 +276,9 @@ pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
 SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
-completion = ["shtab"]
+completion = ["shtab (>=1.1.0)"]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff (>=0.2.1)", "pytest-mypy"]
 
 [[package]]
 name = "mccabe"
@@ -310,11 +290,11 @@ python-versions = "*"
 
 [[package]]
 name = "more-itertools"
-version = "9.1.0"
+version = "10.2.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [[package]]
 name = "mypy"
@@ -342,6 +322,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "nh3"
+version = "0.2.15"
+description = "Python bindings to the ammonia HTML sanitization library."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "numpy"
 version = "1.22.3"
@@ -352,7 +340,7 @@ python-versions = ">=3.8"
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.2"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
@@ -360,15 +348,15 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "pathspec"
-version = "0.11.1"
+version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [[package]]
 name = "pdme"
-version = "0.9.1"
+version = "0.9.3"
 description = "Python dipole model evaluator"
 category = "main"
 optional = false
@@ -391,23 +379,23 @@ testing = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "platformdirs"
-version = "3.2.0"
+version = "4.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)", "sphinx (>=6.1.3)"]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.25.2)", "sphinx (>=7.2.6)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest (>=7.4.3)"]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 
 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -439,33 +427,34 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.14.0"
+version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pytest"
-version = "7.3.0"
+version = "8.0.2"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
+pluggy = ">=1.3.0,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -484,7 +473,7 @@ testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtuale
 
 [[package]]
 name = "python-gitlab"
-version = "3.13.0"
+version = "3.15.0"
 description = "Interact with GitLab API"
 category = "dev"
 optional = false
@@ -500,7 +489,7 @@ yaml = ["PyYaml (>=5.2)"]
 
 [[package]]
 name = "python-semantic-release"
-version = "7.33.2"
+version = "7.34.6"
 description = "Automatic Semantic Versioning for Python projects"
 category = "dev"
 optional = false
@@ -511,7 +500,7 @@ click = ">=7,<9"
 click-log = ">=0.3,<1"
 dotty-dict = ">=1.3.0,<2"
 gitpython = ">=3.0.8,<4"
-invoke = ">=1.4.1,<2"
+invoke = ">=1.4.1,<3"
 packaging = "*"
 python-gitlab = ">=2,<4"
 requests = ">=2.25,<3"
@@ -521,29 +510,29 @@ twine = ">=3,<4"
 
 [package.extras]
 dev = ["tox", "isort", "black"]
-docs = ["Sphinx (==1.3.6)", "Jinja2 (==3.0.3)"]
+docs = ["Sphinx (==1.8.6)", "Jinja2 (==3.0.3)"]
 mypy = ["mypy", "types-requests"]
 test = ["coverage (>=5,<6)", "pytest (>=7,<8)", "pytest-xdist (>=1,<2)", "pytest-mock (>=2,<3)", "responses (==0.13.3)", "mock (==1.3.0)"]
 
 [[package]]
 name = "pywin32-ctypes"
-version = "0.2.0"
+version = "0.2.2"
-description = ""
+description = "A (partial) reimplementation of pywin32 using ctypes/cffi"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "readme-renderer"
-version = "37.3"
+version = "43.0"
-description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
+description = "readme_renderer is a library for rendering readme descriptions for Warehouse"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.dependencies]
-bleach = ">=2.1.0"
 docutils = ">=0.13.1"
+nh3 = ">=0.2.14"
 Pygments = ">=2.5.1"
 
 [package.extras]
@@ -551,17 +540,17 @@ md = ["cmarkgfm (>=0.8.0)"]
 
 [[package]]
 name = "requests"
-version = "2.28.2"
+version = "2.31.0"
 description = "Python HTTP for Humans."
 category = "dev"
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
 
 [package.dependencies]
 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
@@ -569,7 +558,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-toolbelt"
-version = "0.10.1"
+version = "1.0.0"
 description = "A utility belt for advanced users of python-requests"
 category = "dev"
 optional = false
@@ -625,33 +614,24 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
-[[package]]
-name = "six"
-version = "1.16.0"
-description = "Python 2 and 3 compatibility utilities"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-
 [[package]]
 name = "smmap"
-version = "5.0.0"
+version = "5.0.1"
 description = "A pure Python implementation of a sliding window memory map manager"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "syrupy"
-version = "4.0.8"
+version = "4.6.1"
 description = "Pytest Snapshot Test Utility"
 category = "dev"
 optional = false
 python-versions = ">=3.8.1,<4"
 
 [package.dependencies]
-colored = ">=1.3.92,<2.0.0"
+pytest = ">=7.0.0,<9.0.0"
-pytest = ">=7.0.0,<8.0.0"
 
 [[package]]
 name = "tomli"
@@ -663,7 +643,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "tomlkit"
-version = "0.11.7"
+version = "0.12.4"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
@@ -671,7 +651,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "tqdm"
-version = "4.65.0"
+version = "4.66.2"
 description = "Fast, Extensible Progress Meter"
 category = "dev"
 optional = false
@@ -681,7 +661,7 @@ python-versions = ">=3.7"
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -708,60 +688,51 @@ urllib3 = ">=1.26.0"
 
 [[package]]
 name = "typing-extensions"
-version = "4.5.0"
+version = "4.10.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "2.2.1"
 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.*, !=3.5.*"
+python-versions = ">=3.8"
 
 [package.extras]
-brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
+h2 = ["h2 (>=4,<5)"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-
+zstd = ["zstandard (>=0.18.0)"]
-[[package]]
-name = "webencodings"
-version = "0.5.1"
-description = "Character encoding aliases for legacy web content"
-category = "dev"
-optional = false
-python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.8.1,<3.10"
-content-hash = "e1531b1493bac50ffe5e8f9a46a64d9b66198f7021f6d643c72f21cb53dc77ec"
+content-hash = "b7f33da5b5a2af6bcb2a4c95cf391d04a76047d4f7e5c105b7cc38c73563fa51"
 
 [metadata.files]
 black = []
-bleach = []
 certifi = []
 cffi = []
 charset-normalizer = []
 click = []
 click-log = []
 colorama = []
-colored = []
 coverage = []
 cryptography = []
 docutils = []
@@ -782,6 +753,7 @@ mccabe = []
 more-itertools = []
 mypy = []
 mypy-extensions = []
+nh3 = []
 numpy = []
 packaging = []
 pathspec = []
@@ -805,7 +777,6 @@ rfc3986 = []
 scipy = []
 secretstorage = []
 semver = []
-six = []
 smmap = []
 syrupy = []
 tomli = []
@@ -814,5 +785,4 @@ tqdm = []
 twine = []
 typing-extensions = []
 urllib3 = []
-webencodings = []
 zipp = []

pyproject.toml

@@ -1,12 +1,12 @@
 [tool.poetry]
 name = "deepdog"
-version = "0.7.4"
+version = "0.7.7"
 description = ""
 authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.10"
-pdme = "^0.9.1"
+pdme = "^0.9.3"
 numpy = "1.22.3"
 scipy = "1.10"
 

tests/test_bayes_run_with_ss.py

@@ -151,7 +151,7 @@ def test_bayesss_with_tighter_cost(snapshot):
 		ss_default_upper_w_log_step=4,
 		ss_dump_last_generation=False,
 		write_output_to_bayesruncsv=False,
-		ss_initial_costs_chunk_size=1
+		ss_initial_costs_chunk_size=1,
 	)
 	result = square_run.go()