feat: adds temp aware guy using new pdme temp-flexible feature for bundling temp models
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@ -3,6 +3,7 @@ from deepdog.meta import __version__
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from deepdog.bayes_run import BayesRun
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from deepdog.bayes_run_simulpairs import BayesRunSimulPairs
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from deepdog.real_spectrum_run import RealSpectrumRun
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from deepdog.temp_aware_real_spectrum_run import TempAwareRealSpectrumRun
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def get_version():
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@ -14,6 +15,7 @@ __all__ = [
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"BayesRun",
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"BayesRunSimulPairs",
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"RealSpectrumRun",
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"TempAwareRealSpectrumRun",
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]
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227
deepdog/temp_aware_real_spectrum_run.py
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227
deepdog/temp_aware_real_spectrum_run.py
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@ -0,0 +1,227 @@
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import pdme.inputs
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import pdme.model
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import pdme.measurement
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import pdme.measurement.input_types
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import pdme.measurement.oscillating_dipole
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import pdme.util.fast_v_calc
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import pdme.util.fast_nonlocal_spectrum
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from typing import Sequence, Tuple, List, Dict, Union, Mapping
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import datetime
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import csv
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import multiprocessing
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import logging
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import numpy
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# TODO: remove hardcode
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CHUNKSIZE = 50
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_logger = logging.getLogger(__name__)
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def get_a_result_fast_filter(input) -> int:
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# (
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# model,
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# self.dot_inputs_array_dict,
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# low_high_dict,
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# self.monte_carlo_count,
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# seed,
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# )
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model, dot_inputs_dict, low_high_dict, monte_carlo_count, seed = input
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rng = numpy.random.default_rng(seed)
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# 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.
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sample_dipoles = model.get_monte_carlo_dipole_inputs(
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monte_carlo_count, None, rng_to_use=rng
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)
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current_sample = sample_dipoles
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for temp in dot_inputs_dict.keys():
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dot_inputs = dot_inputs_dict[temp]
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lows, highs = low_high_dict[temp]
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_logger.info(f"current sample length: {len(current_sample)}")
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_logger.info(f"workng on temp {temp}")
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for di, low, high in zip(dot_inputs, lows, highs):
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if len(current_sample) < 1:
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break
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vals = pdme.util.fast_v_calc.fast_vs_for_asymmetric_dipoleses(
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numpy.array([di]), current_sample, temp
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)
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current_sample = current_sample[
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numpy.all((vals > low) & (vals < high), axis=1)
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]
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return len(current_sample)
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class TempAwareRealSpectrumRun:
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"""
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A bayes run given some real data, with potentially variable temperature.
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Parameters
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----------
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measurements_dict : Dict[float, Sequence[pdme.measurement.DotRangeMeasurement]]
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The dot inputs for this bayes run, in a dictionary indexed by temperatures
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models_with_names : models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
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The models to evaluate.
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actual_model : pdme.model.DipoleModel
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The model which is actually correct.
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filename_slug : str
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The filename slug to include.
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run_count: int
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The number of runs to do.
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"""
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def __init__(
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self,
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measurements_dict: Mapping[
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float, Sequence[pdme.measurement.DotRangeMeasurement]
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],
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models_with_names: Sequence[Tuple[str, pdme.model.DipoleModel]],
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filename_slug: str,
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monte_carlo_count: int = 10000,
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monte_carlo_cycles: int = 10,
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target_success: int = 100,
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max_monte_carlo_cycles_steps: int = 10,
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chunksize: int = CHUNKSIZE,
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initial_seed: int = 12345,
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) -> None:
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self.measurements_dict = measurements_dict
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self.dot_inputs_dict = {
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k: [(measure.r, measure.f) for measure in measurements]
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for k, measurements in measurements_dict.items()
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}
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self.dot_inputs_array_dict = {
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k: pdme.measurement.input_types.dot_inputs_to_array(dot_inputs)
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for k, dot_inputs in self.dot_inputs_dict.items()
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}
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self.models = [model for (_, model) in models_with_names]
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self.model_names = [name for (name, _) in models_with_names]
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self.model_count = len(self.models)
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self.monte_carlo_count = monte_carlo_count
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self.monte_carlo_cycles = monte_carlo_cycles
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self.target_success = target_success
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self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
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self.csv_fields = []
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self.compensate_zeros = True
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self.chunksize = chunksize
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for name in self.model_names:
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self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
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# for now initialise priors as uniform.
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self.probabilities = [1 / self.model_count] * self.model_count
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timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
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ff_string = "fast_filter"
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self.filename = f"{timestamp}-{filename_slug}.realdata.{ff_string}.bayesrun.csv"
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self.initial_seed = initial_seed
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def go(self) -> None:
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with open(self.filename, "a", newline="") as outfile:
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writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
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writer.writeheader()
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low_high_dict = {}
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for temp, measurements in self.measurements_dict.items():
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(
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lows,
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highs,
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) = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(
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measurements
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)
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low_high_dict[temp] = (lows, highs)
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# define a new seed sequence for each run
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seed_sequence = numpy.random.SeedSequence(self.initial_seed)
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results = []
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_logger.debug("Going to iterate over models now")
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for model_count, (model, model_name) in enumerate(
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zip(self.models, self.model_names)
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):
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_logger.debug(f"Doing model #{model_count}: {model_name}")
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core_count = multiprocessing.cpu_count() - 1 or 1
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with multiprocessing.Pool(core_count) as pool:
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cycle_count = 0
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cycle_success = 0
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cycles = 0
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while (cycles < self.max_monte_carlo_cycles_steps) and (
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cycle_success <= self.target_success
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):
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_logger.debug(f"Starting cycle {cycles}")
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cycles += 1
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current_success = 0
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cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
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# generate a seed from the sequence for each core.
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# note this needs to be inside the loop for monte carlo cycle steps!
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# that way we get more stuff.
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seeds = seed_sequence.spawn(self.monte_carlo_cycles)
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result_func = get_a_result_fast_filter
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current_success = sum(
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pool.imap_unordered(
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result_func,
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[
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(
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model,
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self.dot_inputs_array_dict,
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low_high_dict,
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self.monte_carlo_count,
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seed,
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)
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for seed in seeds
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],
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self.chunksize,
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)
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)
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cycle_success += current_success
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_logger.debug(f"current running successes: {cycle_success}")
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results.append((cycle_count, cycle_success))
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_logger.debug("Done, constructing output now")
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row: Dict[str, Union[int, float, str]] = {}
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successes: List[float] = []
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counts: List[int] = []
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for model_index, (name, (count, result)) in enumerate(
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zip(self.model_names, results)
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):
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row[f"{name}_success"] = result
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row[f"{name}_count"] = count
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successes.append(max(result, 0.5))
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counts.append(count)
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success_weight = sum(
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[
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(succ / count) * prob
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for succ, count, prob in zip(successes, counts, self.probabilities)
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]
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)
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new_probabilities = [
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(succ / count) * old_prob / success_weight
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for succ, count, old_prob in zip(successes, counts, self.probabilities)
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]
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self.probabilities = new_probabilities
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for name, probability in zip(self.model_names, self.probabilities):
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row[f"{name}_prob"] = probability
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_logger.info(row)
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with open(self.filename, "a", newline="") as outfile:
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writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
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writer.writerow(row)
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414
poetry.lock
generated
414
poetry.lock
generated
@ -1,39 +1,17 @@
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[[package]]
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name = "atomicwrites"
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version = "1.4.0"
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description = "Atomic file writes."
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category = "dev"
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optional = false
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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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[[package]]
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name = "attrs"
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version = "21.4.0"
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description = "Classes Without Boilerplate"
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category = "dev"
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optional = false
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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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[package.extras]
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dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
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docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
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tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
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tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
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[[package]]
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name = "black"
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version = "22.3.0"
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version = "22.12.0"
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description = "The uncompromising code formatter."
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category = "dev"
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optional = false
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python-versions = ">=3.6.2"
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python-versions = ">=3.7"
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[package.dependencies]
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click = ">=8.0.0"
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mypy-extensions = ">=0.4.3"
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pathspec = ">=0.9.0"
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platformdirs = ">=2"
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tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
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tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
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typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
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[package.extras]
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@ -44,7 +22,7 @@ uvloop = ["uvloop (>=0.15.2)"]
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[[package]]
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name = "bleach"
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version = "5.0.0"
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version = "6.0.0"
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description = "An easy safelist-based HTML-sanitizing tool."
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category = "dev"
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optional = false
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@ -55,12 +33,11 @@ six = ">=1.9.0"
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webencodings = "*"
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[package.extras]
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css = ["tinycss2 (>=1.1.0)"]
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dev = ["pip-tools (==6.5.1)", "pytest (==7.1.1)", "flake8 (==4.0.1)", "tox (==3.24.5)", "sphinx (==4.3.2)", "twine (==4.0.0)", "wheel (==0.37.1)", "hashin (==0.17.0)", "black (==22.3.0)", "mypy (==0.942)"]
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css = ["tinycss2 (>=1.1.0,<1.2)"]
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[[package]]
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name = "certifi"
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version = "2022.5.18.1"
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version = "2022.12.7"
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description = "Python package for providing Mozilla's CA Bundle."
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category = "dev"
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optional = false
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@ -68,7 +45,7 @@ python-versions = ">=3.6"
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[[package]]
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name = "cffi"
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version = "1.15.0"
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version = "1.15.1"
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description = "Foreign Function Interface for Python calling C code."
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category = "dev"
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optional = false
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@ -79,14 +56,11 @@ pycparser = "*"
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[[package]]
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name = "charset-normalizer"
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version = "2.0.12"
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version = "3.1.0"
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description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
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category = "dev"
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optional = false
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python-versions = ">=3.5.0"
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[package.extras]
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unicode_backport = ["unicodedata2"]
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python-versions = ">=3.7.0"
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[[package]]
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name = "click"
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@ -112,15 +86,15 @@ click = "*"
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[[package]]
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name = "colorama"
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version = "0.4.4"
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version = "0.4.6"
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description = "Cross-platform colored terminal text."
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category = "dev"
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optional = false
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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
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[[package]]
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name = "coverage"
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version = "6.4.2"
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version = "7.2.3"
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description = "Code coverage measurement for Python"
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category = "dev"
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optional = false
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@ -134,7 +108,7 @@ toml = ["tomli"]
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[[package]]
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name = "cryptography"
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version = "37.0.2"
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version = "40.0.1"
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description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
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category = "dev"
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optional = false
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@ -144,31 +118,41 @@ python-versions = ">=3.6"
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cffi = ">=1.12"
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[package.extras]
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docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
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docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
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docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
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pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
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sdist = ["setuptools_rust (>=0.11.4)"]
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pep8test = ["black", "ruff", "mypy", "check-manifest"]
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sdist = ["setuptools-rust (>=0.11.4)"]
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ssh = ["bcrypt (>=3.1.5)"]
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test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
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test = ["pytest (>=6.2.0)", "pytest-shard (>=0.1.2)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601"]
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test-randomorder = ["pytest-randomly"]
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tox = ["tox"]
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[[package]]
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||||
name = "docutils"
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||||
version = "0.18.1"
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||||
version = "0.19"
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||||
description = "Docutils -- Python Documentation Utilities"
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category = "dev"
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optional = false
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||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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python-versions = ">=3.7"
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[[package]]
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name = "dotty-dict"
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version = "1.3.0"
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version = "1.3.1"
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||||
description = "Dictionary wrapper for quick access to deeply nested keys."
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category = "dev"
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optional = false
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python-versions = "*"
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python-versions = ">=3.5,<4.0"
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[package.dependencies]
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setuptools_scm = "*"
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[[package]]
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||||
name = "exceptiongroup"
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||||
version = "1.1.1"
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||||
description = "Backport of PEP 654 (exception groups)"
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category = "dev"
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optional = false
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python-versions = ">=3.7"
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[package.extras]
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||||
test = ["pytest (>=6)"]
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[[package]]
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||||
name = "flake8"
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||||
@ -185,19 +169,19 @@ pyflakes = ">=2.4.0,<2.5.0"
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[[package]]
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||||
name = "gitdb"
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||||
version = "4.0.9"
|
||||
version = "4.0.10"
|
||||
description = "Git Object Database"
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||||
category = "dev"
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||||
optional = false
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||||
python-versions = ">=3.6"
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python-versions = ">=3.7"
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[package.dependencies]
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smmap = ">=3.0.1,<6"
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[[package]]
|
||||
name = "gitpython"
|
||||
version = "3.1.27"
|
||||
description = "GitPython is a python library used to interact with Git repositories"
|
||||
version = "3.1.31"
|
||||
description = "GitPython is a Python library used to interact with Git repositories"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
@ -207,7 +191,7 @@ gitdb = ">=4.0.1,<5"
|
||||
|
||||
[[package]]
|
||||
name = "idna"
|
||||
version = "3.3"
|
||||
version = "3.4"
|
||||
description = "Internationalized Domain Names in Applications (IDNA)"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -215,7 +199,7 @@ python-versions = ">=3.5"
|
||||
|
||||
[[package]]
|
||||
name = "importlib-metadata"
|
||||
version = "4.11.4"
|
||||
version = "6.2.1"
|
||||
description = "Read metadata from Python packages"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -225,26 +209,56 @@ python-versions = ">=3.7"
|
||||
zipp = ">=0.5"
|
||||
|
||||
[package.extras]
|
||||
docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
|
||||
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)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
|
||||
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 = "5.12.0"
|
||||
description = "Read resources from Python packages"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[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)"]
|
||||
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"
|
||||
version = "1.1.1"
|
||||
description = "iniconfig: brain-dead simple config-ini parsing"
|
||||
version = "2.0.0"
|
||||
description = "brain-dead simple config-ini parsing"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "invoke"
|
||||
version = "1.7.1"
|
||||
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]
|
||||
more-itertools = "*"
|
||||
|
||||
[package.extras]
|
||||
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 = "jeepney"
|
||||
version = "0.8.0"
|
||||
@ -259,21 +273,24 @@ trio = ["trio", "async-generator"]
|
||||
|
||||
[[package]]
|
||||
name = "keyring"
|
||||
version = "23.6.0"
|
||||
version = "23.13.1"
|
||||
description = "Store and access your passwords safely."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[package.dependencies]
|
||||
importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
|
||||
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 = "<0.1.0 || >0.1.0,<0.1.1 || >0.1.1", markers = "sys_platform == \"win32\""}
|
||||
pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
|
||||
SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
|
||||
|
||||
[package.extras]
|
||||
docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
|
||||
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)"]
|
||||
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"
|
||||
@ -283,6 +300,14 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "more-itertools"
|
||||
version = "9.1.0"
|
||||
description = "More routines for operating on iterables, beyond itertools"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "mypy"
|
||||
version = "0.971"
|
||||
@ -303,11 +328,11 @@ reports = ["lxml"]
|
||||
|
||||
[[package]]
|
||||
name = "mypy-extensions"
|
||||
version = "0.4.3"
|
||||
description = "Experimental type system extensions for programs checked with the mypy typechecker."
|
||||
version = "1.0.0"
|
||||
description = "Type system extensions for programs checked with the mypy type checker."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[[package]]
|
||||
name = "numpy"
|
||||
@ -319,26 +344,23 @@ python-versions = ">=3.8"
|
||||
|
||||
[[package]]
|
||||
name = "packaging"
|
||||
version = "21.3"
|
||||
version = "23.0"
|
||||
description = "Core utilities for Python packages"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.dependencies]
|
||||
pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "pathspec"
|
||||
version = "0.9.0"
|
||||
version = "0.11.1"
|
||||
description = "Utility library for gitignore style pattern matching of file paths."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "pdme"
|
||||
version = "0.8.6"
|
||||
version = "0.8.8"
|
||||
description = "Python dipole model evaluator"
|
||||
category = "main"
|
||||
optional = false
|
||||
@ -346,30 +368,30 @@ python-versions = ">=3.8,<3.10"
|
||||
|
||||
[package.dependencies]
|
||||
numpy = ">=1.22.3,<2.0.0"
|
||||
scipy = ">=1.8,<1.9"
|
||||
scipy = ">=1.10,<1.11"
|
||||
|
||||
[[package]]
|
||||
name = "pkginfo"
|
||||
version = "1.8.3"
|
||||
description = "Query metadatdata from sdists / bdists / installed packages."
|
||||
version = "1.9.6"
|
||||
description = "Query metadata from sdists / bdists / installed packages."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.extras]
|
||||
testing = ["nose", "coverage"]
|
||||
testing = ["pytest", "pytest-cov"]
|
||||
|
||||
[[package]]
|
||||
name = "platformdirs"
|
||||
version = "2.5.2"
|
||||
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
|
||||
version = "3.2.0"
|
||||
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"
|
||||
|
||||
[package.extras]
|
||||
docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
|
||||
test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
|
||||
docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)", "sphinx (>=6.1.3)"]
|
||||
test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2.2)"]
|
||||
|
||||
[[package]]
|
||||
name = "pluggy"
|
||||
@ -383,14 +405,6 @@ python-versions = ">=3.6"
|
||||
dev = ["pre-commit", "tox"]
|
||||
testing = ["pytest", "pytest-benchmark"]
|
||||
|
||||
[[package]]
|
||||
name = "py"
|
||||
version = "1.11.0"
|
||||
description = "library with cross-python path, ini-parsing, io, code, log facilities"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
|
||||
|
||||
[[package]]
|
||||
name = "pycodestyle"
|
||||
version = "2.8.0"
|
||||
@ -417,43 +431,33 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[[package]]
|
||||
name = "pygments"
|
||||
version = "2.12.0"
|
||||
version = "2.14.0"
|
||||
description = "Pygments is a syntax highlighting package written in Python."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[[package]]
|
||||
name = "pyparsing"
|
||||
version = "3.0.9"
|
||||
description = "pyparsing module - Classes and methods to define and execute parsing grammars"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6.8"
|
||||
|
||||
[package.extras]
|
||||
diagrams = ["railroad-diagrams", "jinja2"]
|
||||
plugins = ["importlib-metadata"]
|
||||
|
||||
[[package]]
|
||||
name = "pytest"
|
||||
version = "7.1.2"
|
||||
version = "7.3.0"
|
||||
description = "pytest: simple powerful testing with Python"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[package.dependencies]
|
||||
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
|
||||
attrs = ">=19.2.0"
|
||||
colorama = {version = "*", markers = "sys_platform == \"win32\""}
|
||||
exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
|
||||
iniconfig = "*"
|
||||
packaging = "*"
|
||||
pluggy = ">=0.12,<2.0"
|
||||
py = ">=1.8.2"
|
||||
tomli = ">=1.0.0"
|
||||
tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
|
||||
|
||||
[package.extras]
|
||||
testing = ["argcomplete", "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", "xmlschema"]
|
||||
|
||||
[[package]]
|
||||
name = "pytest-cov"
|
||||
@ -472,7 +476,7 @@ testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtuale
|
||||
|
||||
[[package]]
|
||||
name = "python-gitlab"
|
||||
version = "3.5.0"
|
||||
version = "3.13.0"
|
||||
description = "Interact with GitLab API"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -480,7 +484,7 @@ python-versions = ">=3.7.0"
|
||||
|
||||
[package.dependencies]
|
||||
requests = ">=2.25.0"
|
||||
requests-toolbelt = ">=0.9.1"
|
||||
requests-toolbelt = ">=0.10.1"
|
||||
|
||||
[package.extras]
|
||||
autocompletion = ["argcomplete (>=1.10.0,<3)"]
|
||||
@ -488,7 +492,7 @@ yaml = ["PyYaml (>=5.2)"]
|
||||
|
||||
[[package]]
|
||||
name = "python-semantic-release"
|
||||
version = "7.29.1"
|
||||
version = "7.33.2"
|
||||
description = "Automatic Semantic Versioning for Python projects"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -500,17 +504,18 @@ 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 = ">=0.10.0,<0.11.0"
|
||||
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 (>=5,<6)", "pytest-xdist (>=1,<2)", "pytest-mock (>=2,<3)", "responses (==0.13.3)", "mock (==1.3.0)"]
|
||||
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"
|
||||
@ -522,7 +527,7 @@ python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "readme-renderer"
|
||||
version = "35.0"
|
||||
version = "37.3"
|
||||
description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -538,7 +543,7 @@ md = ["cmarkgfm (>=0.8.0)"]
|
||||
|
||||
[[package]]
|
||||
name = "requests"
|
||||
version = "2.28.0"
|
||||
version = "2.28.2"
|
||||
description = "Python HTTP for Humans."
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -546,21 +551,21 @@ python-versions = ">=3.7, <4"
|
||||
|
||||
[package.dependencies]
|
||||
certifi = ">=2017.4.17"
|
||||
charset-normalizer = ">=2.0.0,<2.1.0"
|
||||
charset-normalizer = ">=2,<4"
|
||||
idna = ">=2.5,<4"
|
||||
urllib3 = ">=1.21.1,<1.27"
|
||||
|
||||
[package.extras]
|
||||
socks = ["PySocks (>=1.5.6,!=1.5.7)"]
|
||||
use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
|
||||
use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
|
||||
|
||||
[[package]]
|
||||
name = "requests-toolbelt"
|
||||
version = "0.9.1"
|
||||
version = "0.10.1"
|
||||
description = "A utility belt for advanced users of python-requests"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[package.dependencies]
|
||||
requests = ">=2.0.1,<3.0.0"
|
||||
@ -578,18 +583,23 @@ idna2008 = ["idna"]
|
||||
|
||||
[[package]]
|
||||
name = "scipy"
|
||||
version = "1.8.0"
|
||||
description = "SciPy: Scientific Library for Python"
|
||||
version = "1.10.0"
|
||||
description = "Fundamental algorithms for scientific computing in Python"
|
||||
category = "main"
|
||||
optional = false
|
||||
python-versions = ">=3.8,<3.11"
|
||||
python-versions = "<3.12,>=3.8"
|
||||
|
||||
[package.dependencies]
|
||||
numpy = ">=1.17.3,<1.25.0"
|
||||
numpy = ">=1.19.5,<1.27.0"
|
||||
|
||||
[package.extras]
|
||||
test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"]
|
||||
doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc"]
|
||||
dev = ["mypy", "typing-extensions", "pycodestyle", "flake8", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"]
|
||||
|
||||
[[package]]
|
||||
name = "secretstorage"
|
||||
version = "3.3.2"
|
||||
version = "3.3.3"
|
||||
description = "Python bindings to FreeDesktop.org Secret Service API"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -607,22 +617,6 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[[package]]
|
||||
name = "setuptools-scm"
|
||||
version = "6.4.2"
|
||||
description = "the blessed package to manage your versions by scm tags"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.dependencies]
|
||||
packaging = ">=20.0"
|
||||
tomli = ">=1.0.0"
|
||||
|
||||
[package.extras]
|
||||
test = ["pytest (>=6.2)", "virtualenv (>20)"]
|
||||
toml = ["setuptools (>=42)"]
|
||||
|
||||
[[package]]
|
||||
name = "six"
|
||||
version = "1.16.0"
|
||||
@ -649,19 +643,19 @@ python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "tomlkit"
|
||||
version = "0.10.2"
|
||||
version = "0.11.7"
|
||||
description = "Style preserving TOML library"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6,<4.0"
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "tqdm"
|
||||
version = "4.64.0"
|
||||
version = "4.65.0"
|
||||
description = "Fast, Extensible Progress Meter"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
|
||||
python-versions = ">=3.7"
|
||||
|
||||
[package.dependencies]
|
||||
colorama = {version = "*", markers = "platform_system == \"Windows\""}
|
||||
@ -694,7 +688,7 @@ urllib3 = ">=1.26.0"
|
||||
|
||||
[[package]]
|
||||
name = "typing-extensions"
|
||||
version = "4.2.0"
|
||||
version = "4.5.0"
|
||||
description = "Backported and Experimental Type Hints for Python 3.7+"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -702,15 +696,15 @@ python-versions = ">=3.7"
|
||||
|
||||
[[package]]
|
||||
name = "urllib3"
|
||||
version = "1.26.9"
|
||||
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|
||||
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|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
|
||||
|
||||
[package.extras]
|
||||
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|
||||
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||||
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|
||||
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
|
||||
|
||||
[[package]]
|
||||
@ -723,81 +717,149 @@ python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "zipp"
|
||||
version = "3.8.0"
|
||||
version = "3.15.0"
|
||||
description = "Backport of pathlib-compatible object wrapper for zip files"
|
||||
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|
||||
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|
||||
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|
||||
|
||||
[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)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
|
||||
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|
||||
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"]
|
||||
|
||||
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|
||||
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||||
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||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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{file = "numpy-1.22.3-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c34ea7e9d13a70bf2ab64a2532fe149a9aced424cd05a2c4ba662fd989e3e45f"},
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|
||||
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|
||||
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|
||||
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|
||||
pdme = []
|
||||
pkginfo = []
|
||||
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|
||||
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|
||||
py = []
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
{file = "pytest-cov-3.0.0.tar.gz", hash = "sha256:e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470"},
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||||
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|
||||
python-gitlab = []
|
||||
python-semantic-release = []
|
||||
pywin32-ctypes = []
|
||||
pywin32-ctypes = [
|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
rfc3986 = [
|
||||
{file = "rfc3986-2.0.0-py2.py3-none-any.whl", hash = "sha256:50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd"},
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||||
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|
||||
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|
||||
secretstorage = []
|
||||
semver = []
|
||||
setuptools-scm = []
|
||||
six = []
|
||||
smmap = []
|
||||
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|
||||
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|
||||
{file = "semver-2.13.0-py2.py3-none-any.whl", hash = "sha256:ced8b23dceb22134307c1b8abfa523da14198793d9787ac838e70e29e77458d4"},
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||||
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||||
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|
||||
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|
||||
{file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
|
||||
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||||
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|
||||
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|
||||
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||||
{file = "smmap-5.0.0.tar.gz", hash = "sha256:c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936"},
|
||||
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|
||||
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|
||||
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
|
||||
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
|
||||
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|
||||
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|
||||
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|
||||
twine = []
|
||||
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|
||||
{file = "twine-3.8.0-py3-none-any.whl", hash = "sha256:d0550fca9dc19f3d5e8eadfce0c227294df0a2a951251a4385797c8a6198b7c8"},
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
zipp = []
|
||||
|
||||
@ -8,7 +8,7 @@ authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
|
||||
python = "^3.8,<3.10"
|
||||
pdme = "^0.8.6"
|
||||
numpy = "1.22.3"
|
||||
scipy = "1.8.0"
|
||||
scipy = "1.10"
|
||||
|
||||
[tool.poetry.dev-dependencies]
|
||||
pytest = ">=6"
|
||||
|
||||
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Reference in New Issue
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