chore(deps): update dependency python-semantic-release to v8

Reviewed-on: #32

CHANGELOG.md

@@ -2,6 +2,25 @@
 
 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.
 
+### [0.7.2](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.1...0.7.2) (2023-07-24)
+
+
+### Features
+
+* clamps results now ([9bb8fc5](https://gitea.deepak.science:2222/physics/deepdog/commit/9bb8fc50fe1bd1a285a333c5a396bfb6ac3176cf))
+
+
+### Bug Fixes
+
+* fixes clamping format etc. ([a170a3c](https://gitea.deepak.science:2222/physics/deepdog/commit/a170a3ce01adcec356e5aaab9abcc0ec4accd64b))
+
+### [0.7.1](https://gitea.deepak.science:2222/physics/deepdog/compare/0.7.0...0.7.1) (2023-07-24)
+
+
+### Features
+
+* adds subset simulation stuff ([33cab9a](https://gitea.deepak.science:2222/physics/deepdog/commit/33cab9ab4179cec13ae9e591a8ffc32df4dda989))
+
 ## [0.7.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.6.7...0.7.0) (2023-05-01)
 
 

deepdog/__init__.py

@@ -4,6 +4,7 @@ from deepdog.bayes_run import BayesRun
 from deepdog.bayes_run_simulpairs import BayesRunSimulPairs
 from deepdog.real_spectrum_run import RealSpectrumRun
 from deepdog.temp_aware_real_spectrum_run import TempAwareRealSpectrumRun
+from deepdog.bayes_run_with_ss import BayesRunWithSubspaceSimulation
 
 
 def get_version():
@@ -16,6 +17,7 @@ __all__ = [
 	"BayesRunSimulPairs",
 	"RealSpectrumRun",
 	"TempAwareRealSpectrumRun",
+	"BayesRunWithSubspaceSimulation",
 ]
 
 

deepdog/bayes_run_with_ss.py

@@ -0,0 +1,232 @@
+import deepdog.subset_simulation
+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, Optional
+import datetime
+import csv
+import logging
+import numpy
+import numpy.typing
+
+
+# TODO: remove hardcode
+CHUNKSIZE = 50
+
+# TODO: It's garbage to have this here duplicated from pdme.
+DotInput = Tuple[numpy.typing.ArrayLike, float]
+
+
+CLAMPING_FACTOR = 10
+
+_logger = logging.getLogger(__name__)
+
+
+class BayesRunWithSubspaceSimulation:
+	"""
+	A single 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 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,
+		max_frequency: float = 20,
+		end_threshold: float = None,
+		run_count=100,
+		chunksize: int = CHUNKSIZE,
+		ss_n_c: int = 500,
+		ss_n_s: int = 100,
+		ss_m_max: int = 15,
+		ss_target_cost: Optional[float] = None,
+		ss_level_0_seed: int = 200,
+		ss_mcmc_seed: int = 20,
+		ss_use_adaptive_steps=True,
+		ss_default_phi_step=0.01,
+		ss_default_theta_step=0.01,
+		ss_default_r_step=0.01,
+		ss_default_w_log_step=0.01,
+		ss_default_upper_w_log_step=4,
+	) -> 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_with_names = models_with_names
+		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.n: int
+		try:
+			self.n = self.actual_model.n  # type: ignore
+		except AttributeError:
+			self.n = 1
+
+		self.model_count = len(self.models)
+
+		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}_likelihood", 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}.bayesrunwithss.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}"
+				)
+
+		self.ss_n_c = ss_n_c
+		self.ss_n_s = ss_n_s
+		self.ss_m_max = ss_m_max
+		self.ss_target_cost = ss_target_cost
+		self.ss_level_0_seed = ss_level_0_seed
+		self.ss_mcmc_seed = ss_mcmc_seed
+		self.ss_use_adaptive_steps = ss_use_adaptive_steps
+		self.ss_default_phi_step = ss_default_phi_step
+		self.ss_default_theta_step = ss_default_theta_step
+		self.ss_default_r_step = ss_default_r_step
+		self.ss_default_w_log_step = ss_default_w_log_step
+		self.ss_default_upper_w_log_step = ss_default_upper_w_log_step
+
+		self.run_count = run_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()
+
+		for run in range(1, self.run_count + 1):
+
+			# Generate the actual dipoles
+			actual_dipoles = self.actual_model.get_dipoles(self.max_frequency)
+
+			measurements = actual_dipoles.get_dot_measurements(self.dot_inputs)
+
+			_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
+
+			# define a new seed sequence for each run
+
+			results = []
+			_logger.debug("Going to iterate over models now")
+			for model_count, model in enumerate(self.models_with_names):
+				_logger.debug(f"Doing model #{model_count}, {model[0]}")
+				subset_run = deepdog.subset_simulation.SubsetSimulation(
+					model,
+					self.dot_inputs,
+					measurements,
+					self.ss_n_c,
+					self.ss_n_s,
+					self.ss_m_max,
+					self.ss_target_cost,
+					self.ss_level_0_seed,
+					self.ss_mcmc_seed,
+					self.ss_use_adaptive_steps,
+					self.ss_default_phi_step,
+					self.ss_default_theta_step,
+					self.ss_default_r_step,
+					self.ss_default_w_log_step,
+					self.ss_default_upper_w_log_step,
+				)
+				results.append(subset_run.execute())
+
+			_logger.debug("Done, constructing output now")
+			row = {
+				"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[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
+
+			likelihoods: List[float] = []
+
+			for (name, result) in zip(self.model_names, results):
+				if result.over_target_likelihood is None:
+					clamped_likelihood = result.probs_list[-1][0] / CLAMPING_FACTOR
+					_logger.warning(f"got a none result, clamping to {clamped_likelihood}")
+				else:
+					clamped_likelihood = result.over_target_likelihood
+				likelihoods.append(clamped_likelihood)
+				row[f"{name}_likelihood"] = clamped_likelihood
+
+			success_weight = sum(
+				[
+					likelihood * prob
+					for likelihood, prob in zip(likelihoods, self.probabilities)
+				]
+			)
+			new_probabilities = [
+				likelihood * old_prob / success_weight
+				for likelihood, old_prob in zip(likelihoods, 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/subset_simulation/__init__.py

@@ -0,0 +1,3 @@
+from deepdog.subset_simulation.subset_simulation_impl import SubsetSimulation
+
+__all__ = ["SubsetSimulation"]

deepdog/subset_simulation/subset_simulation_impl.py

@@ -0,0 +1,309 @@
+import logging
+import numpy
+import pdme.measurement
+import pdme.measurement.input_types
+import pdme.subspace_simulation
+from typing import Sequence, Tuple, Optional
+
+from dataclasses import dataclass
+
+_logger = logging.getLogger(__name__)
+
+
+@dataclass
+class SubsetSimulationResult:
+	probs_list: Sequence[Tuple]
+	over_target_cost: Optional[float]
+	over_target_likelihood: Optional[float]
+	under_target_cost: Optional[float]
+	under_target_likelihood: Optional[float]
+
+
+class SubsetSimulation:
+	def __init__(
+		self,
+		model_name_pair,
+		dot_inputs,
+		actual_measurements: Sequence[pdme.measurement.DotMeasurement],
+		n_c: int,
+		n_s: int,
+		m_max: int,
+		target_cost: Optional[float] = None,
+		level_0_seed: int = 200,
+		mcmc_seed: int = 20,
+		use_adaptive_steps=True,
+		default_phi_step=0.01,
+		default_theta_step=0.01,
+		default_r_step=0.01,
+		default_w_log_step=0.01,
+		default_upper_w_log_step=4,
+	):
+		name, model = model_name_pair
+		self.model_name = name
+		self.model = model
+		_logger.info(f"got model {self.model_name}")
+
+		self.dot_inputs_array = pdme.measurement.input_types.dot_inputs_to_array(
+			dot_inputs
+		)
+		# _logger.debug(f"actual measurements: {actual_measurements}")
+		self.actual_measurement_array = numpy.array([m.v for m in actual_measurements])
+
+		def cost_function_to_use(dipoles_to_test):
+			return pdme.subspace_simulation.proportional_costs_vs_actual_measurement(
+				self.dot_inputs_array, self.actual_measurement_array, dipoles_to_test
+			)
+
+		self.cost_function_to_use = cost_function_to_use
+
+		self.n_c = n_c
+		self.n_s = n_s
+		self.m_max = m_max
+
+		self.level_0_seed = level_0_seed
+		self.mcmc_seed = mcmc_seed
+
+		self.use_adaptive_steps = use_adaptive_steps
+		self.default_phi_step = default_phi_step
+		self.default_theta_step = default_theta_step
+		self.default_r_step = default_r_step
+		self.default_w_log_step = default_w_log_step
+		self.default_upper_w_log_step = default_upper_w_log_step
+
+		_logger.info("using params:")
+		_logger.info(f"\tn_c: {self.n_c}")
+		_logger.info(f"\tn_s: {self.n_s}")
+		_logger.info(f"\tm: {self.m_max}")
+		_logger.info("let's do level 0...")
+
+		self.target_cost = target_cost
+		_logger.info(f"will stop at target cost {target_cost}")
+
+	def execute(self) -> SubsetSimulationResult:
+
+		probs_list = []
+
+		sample_dipoles = self.model.get_monte_carlo_dipole_inputs(
+			self.n_c * self.n_s,
+			-1,
+			rng_to_use=numpy.random.default_rng(self.level_0_seed),
+		)
+		# _logger.debug(sample_dipoles)
+		# _logger.debug(sample_dipoles.shape)
+		costs = self.cost_function_to_use(sample_dipoles)
+
+		_logger.debug(f"costs: {costs}")
+		sorted_indexes = costs.argsort()[::-1]
+
+		_logger.debug(costs[sorted_indexes])
+		_logger.debug(sample_dipoles[sorted_indexes])
+
+		sorted_costs = costs[sorted_indexes]
+		sorted_dipoles = sample_dipoles[sorted_indexes]
+
+		threshold_cost = sorted_costs[-self.n_c]
+
+		all_dipoles = numpy.array(
+			[
+				pdme.subspace_simulation.sort_array_of_dipoles_by_frequency(samp)
+				for samp in sorted_dipoles
+			]
+		)
+		all_chains = list(zip(sorted_costs, all_dipoles))
+
+		mcmc_rng = numpy.random.default_rng(self.mcmc_seed)
+
+		for i in range(self.m_max):
+			next_seeds = all_chains[-self.n_c:]
+
+			for cost_index, cost_chain in enumerate(all_chains[: -self.n_c]):
+				probs_list.append(
+					(
+						((self.n_c * self.n_s - cost_index) / (self.n_c * self.n_s))
+						/ (self.n_s ** (i)),
+						cost_chain[0],
+						i + 1,
+					)
+				)
+
+			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_chains = []
+			for c, s in next_seeds:
+				# 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
+				chain = self.model.get_mcmc_chain(
+					s,
+					self.cost_function_to_use,
+					self.n_s,
+					threshold_cost,
+					stdevs,
+					initial_cost=c,
+					rng_arg=mcmc_rng,
+				)
+				for cost, chained in chain:
+					try:
+						filtered_cost = cost[0]
+					except IndexError:
+						filtered_cost = cost
+					all_chains.append((filtered_cost, chained))
+
+			# _logger.debug(all_chains)
+
+			all_chains.sort(key=lambda c: c[0], reverse=True)
+
+			threshold_cost = all_chains[-self.n_c][0]
+			_logger.info(
+				f"current threshold cost: {threshold_cost}, at P = (1 / {self.n_s})^{i + 1}"
+			)
+			if (self.target_cost is not None) and (threshold_cost < self.target_cost):
+				_logger.info(
+					f"got a threshold cost {threshold_cost}, less than {self.target_cost}. will leave early"
+				)
+
+				cost_list = [c[0] for c in all_chains]
+				over_index = reverse_bisect_right(cost_list, self.target_cost)
+
+				shorter_probs_list = []
+				for cost_index, cost_chain in enumerate(all_chains):
+					probs_list.append(
+						(
+							((self.n_c * self.n_s - cost_index) / (self.n_c * self.n_s))
+							/ (self.n_s ** (i)),
+							cost_chain[0],
+							i + 1,
+						)
+					)
+					shorter_probs_list.append(
+						(
+							cost_chain[0],
+							((self.n_c * self.n_s - cost_index) / (self.n_c * self.n_s))
+							/ (self.n_s ** (i)),
+						)
+					)
+				# _logger.info(shorter_probs_list)
+				result = SubsetSimulationResult(
+					probs_list=probs_list,
+					over_target_cost=shorter_probs_list[over_index - 1][0],
+					over_target_likelihood=shorter_probs_list[over_index - 1][1],
+					under_target_cost=shorter_probs_list[over_index][0],
+					under_target_likelihood=shorter_probs_list[over_index][1],
+				)
+				return result
+
+			# _logger.debug([c[0] for c in all_chains[-n_c:]])
+			_logger.info(f"doing level {i + 1}")
+
+		for cost_index, cost_chain in enumerate(all_chains):
+			probs_list.append(
+				(
+					((self.n_c * self.n_s - cost_index) / (self.n_c * self.n_s))
+					/ (self.n_s ** (self.m_max)),
+					cost_chain[0],
+					self.m_max + 1,
+				)
+			)
+		threshold_cost = all_chains[-self.n_c][0]
+		_logger.info(
+			f"final threshold cost: {threshold_cost}, at P = (1 / {self.n_s})^{self.m_max + 1}"
+		)
+		for a in all_chains[-10:]:
+			_logger.info(a)
+		# for prob, prob_cost in probs_list:
+		# 	_logger.info(f"\t{prob}: {prob_cost}")
+		probs_list.sort(key=lambda c: c[0], reverse=True)
+		result = SubsetSimulationResult(
+			probs_list=probs_list,
+			over_target_cost=None,
+			over_target_likelihood=None,
+			under_target_cost=None,
+			under_target_likelihood=None,
+		)
+		return result
+
+	def get_stdevs_from_arrays(
+		self, array
+	) -> pdme.subspace_simulation.MCMCStandardDeviation:
+		# stdevs = get_stdevs_from_arrays(next_seeds_as_array, model)
+		if self.use_adaptive_steps:
+
+			stdev_array = []
+			count = array.shape[1]
+			for dipole_index in range(count):
+				selected = array[:, dipole_index]
+				pxs = selected[:, 0]
+				pys = selected[:, 1]
+				pzs = selected[:, 2]
+				thetas = numpy.arccos(pzs / self.model.pfixed)
+				phis = numpy.arctan2(pys, pxs)
+
+				rstdevs = numpy.maximum(
+					numpy.std(selected, axis=0)[3:6],
+					self.default_r_step / (self.n_s * 10),
+				)
+				frequency_stdevs = numpy.minimum(
+					numpy.maximum(
+						numpy.std(numpy.log(selected[:, -1])),
+						self.default_w_log_step / (self.n_s * 10),
+					),
+					self.default_upper_w_log_step,
+				)
+				stdev_array.append(
+					pdme.subspace_simulation.DipoleStandardDeviation(
+						p_theta_step=max(
+							numpy.std(thetas), self.default_theta_step / (self.n_s * 10)
+						),
+						p_phi_step=max(
+							numpy.std(phis), self.default_phi_step / (self.n_s * 10)
+						),
+						rx_step=rstdevs[0],
+						ry_step=rstdevs[1],
+						rz_step=rstdevs[2],
+						w_log_step=frequency_stdevs,
+					)
+				)
+		else:
+			default_stdev = pdme.subspace_simulation.DipoleStandardDeviation(
+				self.default_phi_step,
+				self.default_theta_step,
+				self.default_r_step,
+				self.default_r_step,
+				self.default_r_step,
+				self.default_w_log_step,
+			)
+			stdev_array = [default_stdev]
+		stdevs = pdme.subspace_simulation.MCMCStandardDeviation(stdev_array)
+		return stdevs
+
+
+def reverse_bisect_right(a, x, lo=0, hi=None):
+	"""Return the index where to insert item x in list a, assuming a is sorted in descending order.
+
+	The return value i is such that all e in a[:i] have e >= x, and all e in
+	a[i:] have e < x.  So if x already appears in the list, a.insert(x) will
+	insert just after the rightmost x already there.
+
+	Optional args lo (default 0) and hi (default len(a)) bound the
+	slice of a to be searched.
+
+	Essentially, the function returns number of elements in a which are >= than x.
+	>>> a = [8, 6, 5, 4, 2]
+	>>> reverse_bisect_right(a, 5)
+	3
+	>>> a[:reverse_bisect_right(a, 5)]
+	[8, 6, 5]
+	"""
+	if lo < 0:
+		raise ValueError("lo must be non-negative")
+	if hi is None:
+		hi = len(a)
+	while lo < hi:
+		mid = (lo + hi) // 2
+		if x > a[mid]:
+			hi = mid
+		else:
+			lo = mid + 1
+	return lo

poetry.lock

@@ -20,6 +20,21 @@ 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"
@@ -28,6 +43,17 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "cffi"
+version = "1.15.1"
+description = "Foreign Function Interface for Python calling C code."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+pycparser = "*"
+
 [[package]]
 name = "charset-normalizer"
 version = "3.1.0"
@@ -47,6 +73,17 @@ python-versions = ">=3.7"
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
+[[package]]
+name = "click-log"
+version = "0.4.0"
+description = "Logging integration for Click"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+click = "*"
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -69,6 +106,35 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "cryptography"
+version = "40.0.1"
+description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cffi = ">=1.12"
+
+[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)"]
+pep8test = ["black", "ruff", "mypy", "check-manifest"]
+sdist = ["setuptools-rust (>=0.11.4)"]
+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-randomorder = ["pytest-randomly"]
+tox = ["tox"]
+
+[[package]]
+name = "docutils"
+version = "0.19"
+description = "Docutils -- Python Documentation Utilities"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "dotty-dict"
 version = "1.3.1"
@@ -131,9 +197,25 @@ category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "importlib-metadata"
+version = "6.2.1"
+description = "Read metadata from Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[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)"]
+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)"]
+
 [[package]]
 name = "importlib-resources"
-version = "5.7.0"
+version = "5.12.0"
 description = "Read resources from Python packages"
 category = "dev"
 optional = false
@@ -143,8 +225,8 @@ python-versions = ">=3.7"
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "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"]
 
 [[package]]
 name = "iniconfig"
@@ -155,48 +237,61 @@ optional = false
 python-versions = ">=3.7"
 
 [[package]]
-name = "jinja2"
-version = "3.1.2"
-description = "A very fast and expressive template engine."
+name = "invoke"
+version = "1.7.3"
+description = "Pythonic task execution"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "jaraco.classes"
+version = "3.2.3"
+description = "Utility functions for Python class constructs"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-MarkupSafe = ">=2.0"
+more-itertools = "*"
 
 [package.extras]
-i18n = ["Babel (>=2.7)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "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)"]
 
 [[package]]
-name = "markdown-it-py"
-version = "3.0.0"
-description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "dev"
-optional = false
-python-versions = ">=3.8"
-
-[package.dependencies]
-mdurl = ">=0.1,<1.0"
-
-[package.extras]
-benchmarking = ["psutil", "pytest", "pytest-benchmark"]
-code_style = ["pre-commit (>=3.0,<4.0)"]
-compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
-linkify = ["linkify-it-py (>=1,<3)"]
-plugins = ["mdit-py-plugins"]
-profiling = ["gprof2dot"]
-rtd = ["mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-book-theme", "jupyter-sphinx"]
-testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
-
-[[package]]
-name = "markupsafe"
-version = "2.1.3"
-description = "Safely add untrusted strings to HTML/XML markup."
+name = "jeepney"
+version = "0.8.0"
+description = "Low-level, pure Python DBus protocol wrapper."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
+[package.extras]
+test = ["pytest", "pytest-trio", "pytest-asyncio (>=0.17)", "testpath", "trio", "async-timeout"]
+trio = ["trio", "async-generator"]
+
+[[package]]
+name = "keyring"
+version = "23.13.1"
+description = "Store and access your passwords safely."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+importlib-metadata = {version = ">=4.11.4", markers = "python_version < \"3.12\""}
+importlib-resources = {version = "*", markers = "python_version < \"3.9\""}
+"jaraco.classes" = "*"
+jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""}
+pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
+SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
+
+[package.extras]
+completion = ["shtab"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "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"]
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -206,9 +301,9 @@ optional = false
 python-versions = "*"
 
 [[package]]
-name = "mdurl"
-version = "0.1.2"
-description = "Markdown URL utilities"
+name = "more-itertools"
+version = "9.1.0"
+description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
@@ -265,16 +360,27 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "pdme"
-version = "0.8.8"
+version = "0.9.1"
 description = "Python dipole model evaluator"
 category = "main"
 optional = false
-python-versions = ">=3.8,<3.10"
+python-versions = ">=3.8.1,<3.10"
 
 [package.dependencies]
 numpy = ">=1.22.3,<2.0.0"
 scipy = ">=1.10,<1.11"
 
+[[package]]
+name = "pkginfo"
+version = "1.9.6"
+description = "Query metadata from sdists / bdists / installed packages."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+testing = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "platformdirs"
 version = "3.2.0"
@@ -308,19 +414,12 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
-name = "pydantic"
-version = "1.10.11"
-description = "Data validation and settings management using python type hints"
+name = "pycparser"
+version = "2.21"
+description = "C parser in Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-typing-extensions = ">=4.2.0"
-
-[package.extras]
-dotenv = ["python-dotenv (>=0.10.4)"]
-email = ["email-validator (>=1.0.3)"]
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pyflakes"
@@ -393,30 +492,54 @@ yaml = ["PyYaml (>=5.2)"]
 
 [[package]]
 name = "python-semantic-release"
-version = "8.0.0"
+version = "7.33.2"
 description = "Automatic Semantic Versioning for Python projects"
 category = "dev"
 optional = false
+python-versions = "*"
+
+[package.dependencies]
+click = ">=7,<9"
+click-log = ">=0.3,<1"
+dotty-dict = ">=1.3.0,<2"
+gitpython = ">=3.0.8,<4"
+invoke = ">=1.4.1,<2"
+packaging = "*"
+python-gitlab = ">=2,<4"
+requests = ">=2.25,<3"
+semver = ">=2.10,<3"
+tomlkit = ">=0.10,<1.0"
+twine = ">=3,<4"
+
+[package.extras]
+dev = ["tox", "isort", "black"]
+docs = ["Sphinx (==1.3.6)", "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"
+description = ""
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "readme-renderer"
+version = "37.3"
+description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
+category = "dev"
+optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-click = ">=7,<9"
-dotty-dict = ">=1.3.0,<2"
-gitpython = ">=3.0.8,<4"
-importlib-resources = "5.7"
-jinja2 = ">=3.1.2,<4"
-pydantic = ">=1.10.2,<2"
-python-gitlab = ">=2,<4"
-requests = ">=2.25,<3"
-rich = ">=12.5.1"
-shellingham = ">=1.5.0.post1"
-tomlkit = ">=0.10,<1.0"
+bleach = ">=2.1.0"
+docutils = ">=0.13.1"
+Pygments = ">=2.5.1"
 
 [package.extras]
-dev = ["tox", "isort", "black"]
-docs = ["Sphinx (<=6.0.0)", "sphinxcontrib-apidoc (==0.3.0)", "sphinx-autobuild (==2021.03.14)", "furo (>=2023.3.27)"]
-mypy = ["mypy", "types-requests", "types-click"]
-test = ["coverage[toml] (>=6,<7)", "pytest (>=7,<8)", "pytest-xdist (>=2,<3)", "pytest-mock (>=3,<4)", "pytest-lazy-fixture (>=0.6.3,<0.7.0)", "pytest-cov (>=4,<5)", "responses (==0.21.0)", "requests-mock (>=1.10.0,<2)", "types-pytest-lazy-fixture (>=0.6.3.3)"]
+md = ["cmarkgfm (>=0.8.0)"]
 
 [[package]]
 name = "requests"
@@ -448,20 +571,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 requests = ">=2.0.1,<3.0.0"
 
 [[package]]
-name = "rich"
-version = "13.4.2"
-description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+name = "rfc3986"
+version = "2.0.0"
+description = "Validating URI References per RFC 3986"
 category = "dev"
 optional = false
-python-versions = ">=3.7.0"
-
-[package.dependencies]
-markdown-it-py = ">=2.2.0"
-pygments = ">=2.13.0,<3.0.0"
-typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""}
+python-versions = ">=3.7"
 
 [package.extras]
-jupyter = ["ipywidgets (>=7.5.1,<9)"]
+idna2008 = ["idna"]
 
 [[package]]
 name = "scipy"
@@ -480,12 +598,32 @@ doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.
 dev = ["mypy", "typing-extensions", "pycodestyle", "flake8", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"]
 
 [[package]]
-name = "shellingham"
-version = "1.5.1"
-description = "Tool to Detect Surrounding Shell"
+name = "secretstorage"
+version = "3.3.3"
+description = "Python bindings to FreeDesktop.org Secret Service API"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
+
+[package.dependencies]
+cryptography = ">=2.0"
+jeepney = ">=0.6"
+
+[[package]]
+name = "semver"
+version = "2.13.0"
+description = "Python helper for Semantic Versioning (http://semver.org/)"
+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"
@@ -511,6 +649,43 @@ category = "dev"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "tqdm"
+version = "4.65.0"
+description = "Fast, Extensible Progress Meter"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
+telegram = ["requests"]
+
+[[package]]
+name = "twine"
+version = "3.8.0"
+description = "Collection of utilities for publishing packages on PyPI"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = ">=0.4.3"
+importlib-metadata = ">=3.6"
+keyring = ">=15.1"
+pkginfo = ">=1.8.1"
+readme-renderer = ">=21.0"
+requests = ">=2.20"
+requests-toolbelt = ">=0.8.0,<0.9.0 || >0.9.0"
+rfc3986 = ">=1.4.0"
+tqdm = ">=4.14"
+urllib3 = ">=1.26.0"
+
 [[package]]
 name = "typing-extensions"
 version = "4.5.0"
@@ -532,6 +707,14 @@ brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
 secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
+[[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"
@@ -546,53 +729,68 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-co
 
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.8,<3.10"
-content-hash = "bb6b00922b534cf7a7f4b7df39d0b6f6c04742ba80089fb6a9f49ff6f8f8156e"
+python-versions = ">=3.8.1,<3.10"
+content-hash = "0161af7edf18c16819f1ce083ab491c17c9809f2770219725131451b1a16a970"
 
 [metadata.files]
 black = []
+bleach = []
 certifi = []
+cffi = []
 charset-normalizer = []
 click = []
+click-log = []
 colorama = []
 coverage = []
+cryptography = []
+docutils = []
 dotty-dict = []
 exceptiongroup = []
 flake8 = []
 gitdb = []
 gitpython = []
 idna = []
+importlib-metadata = []
 importlib-resources = []
 iniconfig = []
-jinja2 = []
-markdown-it-py = []
-markupsafe = []
+invoke = []
+"jaraco.classes" = []
+jeepney = []
+keyring = []
 mccabe = []
-mdurl = []
+more-itertools = []
 mypy = []
 mypy-extensions = []
 numpy = []
 packaging = []
 pathspec = []
 pdme = []
+pkginfo = []
 platformdirs = []
 pluggy = []
 pycodestyle = []
-pydantic = []
+pycparser = []
 pyflakes = []
 pygments = []
 pytest = []
 pytest-cov = []
 python-gitlab = []
 python-semantic-release = []
+pywin32-ctypes = []
+readme-renderer = []
 requests = []
 requests-toolbelt = []
-rich = []
+rfc3986 = []
 scipy = []
-shellingham = []
+secretstorage = []
+semver = []
+six = []
 smmap = []
 tomli = []
 tomlkit = []
+tqdm = []
+twine = []
 typing-extensions = []
 urllib3 = []
+webencodings = []
 zipp = []

pyproject.toml

@@ -1,12 +1,12 @@
 [tool.poetry]
 name = "deepdog"
-version = "0.7.0"
+version = "0.7.2"
 description = ""
 authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
-python = "^3.8,<3.10"
-pdme = "^0.8.6"
+python = ">=3.8.1,<3.10"
+pdme = "^0.9.1"
 numpy = "1.22.3"
 scipy = "1.10"