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0.1.5 ... 0.4.0

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f168666045 chore(release): 0.4.0
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2022-04-10 10:21:47 -05:00
604916a829 Merge pull request 'pairs' (#5) from pairs into master
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Reviewed-on: #5
2022-04-10 15:20:05 +00:00
941313a14c style: whitespace fixes
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2022-04-10 10:05:15 -05:00
cb64c0b7b6 Merge branch 'master' into pairs 2022-04-10 10:03:47 -05:00
ec7b4cac39 feat: Adds dynamic cycle count increases to help reach minimum success count
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2022-03-28 15:46:40 -05:00
31e6cfaf51 lint: lint fixes
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2022-03-28 12:28:24 -05:00
c1c711f47b fix: uses bigfix from pdme for negatives
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2022-03-28 10:52:28 -05:00
6463b135ef feat!: Adds pair calculations, with changing api format
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2022-03-27 19:01:14 -05:00
a283cbd670 Merge pull request 'chore(deps): update dependency mypy to ^0.942' (#3) from renovate/mypy-0.x into master
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2022-03-25 13:15:07 +00:00
0b45172ca0 chore(deps): update dependency mypy to ^0.942
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2022-03-25 01:30:47 +00:00
b6383d0a47 Merge pull request 'chore(deps): update dependency mypy to ^0.941' (#2) from renovate/mypy-0.x into master
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2022-03-19 00:54:39 +00:00
450d8e0ec9 chore(deps): update dependency mypy to ^0.941
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2022-03-15 01:30:59 +00:00
f81904a898 chore(release): 0.3.5
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2022-03-06 18:42:26 -06:00
88d961313c feat: makes chunksize configurable
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2022-03-06 18:42:05 -06:00
fa82caa752 chore(release): 0.3.4
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2022-03-06 17:31:47 -06:00
0784cd53d7 feat: Changes chunksize for multiprocessing
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2022-03-06 17:31:17 -06:00
fb4b012491 chore(release): 0.3.3
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2022-03-06 17:23:15 -06:00
8617e4d274 fix: Fixes count to use cycles as well
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2022-03-06 17:22:52 -06:00
fe2af1644e chore(release): 0.3.2
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2022-03-06 17:18:42 -06:00
e6d8d33c27 feat: Adds monte carlo cycles to trade off space and cpu 2022-03-06 17:18:24 -06:00
e00dc95f02 docs: readme badges
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2022-03-06 16:48:49 -06:00
527be26fb2 chore(release): 0.3.1
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2022-03-06 16:45:45 -06:00
456c81bca5 Merge branch 'master' of ssh://gitea.deepak.science:2222/physics/deepdog 2022-03-06 16:45:16 -06:00
7284dbeb34 feat: Adds alt bayes solver with monte carlo sampler 2022-03-06 16:45:09 -06:00
d078004773 feat: Updates to pdme version for faster bayes resolution 2022-03-06 15:53:49 -06:00
0441cde421 chore: adds release to do.sh 2022-03-06 15:51:32 -06:00
a9e91779bc chore: adds standard-version release stuff 2022-03-06 15:50:39 -06:00
751bc66704 Merge pull request 'Configure Renovate' (#1) from renovate/configure into master
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2022-02-23 19:44:38 +00:00
413ff16acc chore(deps): add renovate.json 2022-02-23 19:42:04 +00:00
5118173f09 chore: Adds semantic release to dev dependencies
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2022-02-14 10:00:59 -06:00
semantic-release
6dfc26104a 0.3.0
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2022-02-14 09:57:42 -06:00
3a6be738b1 feat: Actually uses probabilities to update bayes
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2022-02-14 09:51:02 -06:00
bd240900b4 fix: Actually logs end threshold 2022-02-14 09:50:08 -06:00
0e1fbec043 fix: Fixes bug with end_threshold and better error logging 2022-02-14 09:44:04 -06:00
3d3b1a83f6 feat: Adds end threshold for early abort 2022-02-14 09:27:40 -06:00
63cecba824 Created version 0.2.4
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2022-02-06 19:50:07 -06:00
344998835d fix: Fixes linting 2022-02-06 19:49:02 -06:00
838aeb0cf3 Created version 0.2.3
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2022-02-06 19:46:10 -06:00
e715d329fd fix: diagnostic adds frequencies 2022-02-06 19:46:05 -06:00
521b49f14c Created version 0.2.2
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2022-02-06 19:37:15 -06:00
6d65e8dec5 fix: ignores extra fields in dictwriter 2022-02-06 19:36:59 -06:00
36354c2f2c Adds patch
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2022-02-06 19:29:17 -06:00
3534593557 fix: Take first element of solution list 2022-02-06 19:28:54 -06:00
6ada52f82c Minor version bump
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2022-02-06 19:03:24 -06:00
34e124b18f feat: Adds better diagnostic of full dipole info 2022-02-06 19:03:04 -06:00
14 changed files with 1161 additions and 158 deletions

10
.versionrc Normal file
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{
"bumpFiles": [
{
"filename": "pyproject.toml",
"updater": "scripts/standard-version/pyproject-updater.js"
}
],
"sign": true,
"tag-prefix": ""
}

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CHANGELOG.md Normal file
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# Changelog
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.
## [0.4.0](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.5...0.4.0) (2022-04-10)
### ⚠ BREAKING CHANGES
* Adds pair calculations, with changing api format
### Features
* Adds dynamic cycle count increases to help reach minimum success count ([ec7b4ca](https://gitea.deepak.science:2222/physics/deepdog/commit/ec7b4cac393c15e94c513215c4f1ba32be2ae87a))
* Adds pair calculations, with changing api format ([6463b13](https://gitea.deepak.science:2222/physics/deepdog/commit/6463b135ef2d212b565864b5ac1b655e014d2194))
### Bug Fixes
* uses bigfix from pdme for negatives ([c1c711f](https://gitea.deepak.science:2222/physics/deepdog/commit/c1c711f47b574d3a9b8a24dbcbdd7f50b9be8ea9))
### [0.3.5](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.4...0.3.5) (2022-03-07)
### Features
* makes chunksize configurable ([88d9613](https://gitea.deepak.science:2222/physics/deepdog/commit/88d961313c1db0d49fd96939aa725a8706fa0412))
### [0.3.4](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.3...0.3.4) (2022-03-06)
### Features
* Changes chunksize for multiprocessing ([0784cd5](https://gitea.deepak.science:2222/physics/deepdog/commit/0784cd53d79e00684506604f094b5d820b3994d4))
### [0.3.3](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.2...0.3.3) (2022-03-06)
### Bug Fixes
* Fixes count to use cycles as well ([8617e4d](https://gitea.deepak.science:2222/physics/deepdog/commit/8617e4d2742b112cc824068150682ce3b2cdd879))
### [0.3.2](https://gitea.deepak.science:2222/physics/deepdog/compare/0.3.1...0.3.2) (2022-03-06)
### Features
* Adds monte carlo cycles to trade off space and cpu ([e6d8d33](https://gitea.deepak.science:2222/physics/deepdog/commit/e6d8d33c27e7922581e91c10de4f5faff2a51f8b))
### [0.3.1](https://gitea.deepak.science:2222/physics/deepdog/compare/v0.3.0...v0.3.1) (2022-03-06)
### Features
* Adds alt bayes solver with monte carlo sampler ([7284dbe](https://gitea.deepak.science:2222/physics/deepdog/commit/7284dbeb34ef46189d81fb719252dfa74b8e9fa8))
* Updates to pdme version for faster bayes resolution ([d078004](https://gitea.deepak.science:2222/physics/deepdog/commit/d078004773d9d9dccd0a9a52ca96aa57690f9b7e))

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@@ -1,3 +1,18 @@
# deepdog # deepdog
The dipole diagnostic tool. [![Conventional Commits](https://img.shields.io/badge/Conventional%20Commits-1.0.0-green.svg?style=flat-square)](https://conventionalcommits.org)
[![PyPI](https://img.shields.io/pypi/v/deepdog?style=flat-square)](https://pypi.org/project/deepdog/)
[![Jenkins](https://img.shields.io/jenkins/build?jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fdeepdog%2Fjob%2Fmaster&style=flat-square)](https://jenkins.deepak.science/job/gitea-physics/job/deepdog/job/master/)
![Jenkins tests](https://img.shields.io/jenkins/tests?compact_message&jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fdeepdog%2Fjob%2Fmaster%2F&style=flat-square)
![Jenkins Coverage](https://img.shields.io/jenkins/coverage/cobertura?jobUrl=https%3A%2F%2Fjenkins.deepak.science%2Fjob%2Fgitea-physics%2Fjob%2Fdeepdog%2Fjob%2Fmaster%2F&style=flat-square)
![Maintenance](https://img.shields.io/maintenance/yes/2022?style=flat-square)
The DiPole DiaGnostic tool.
## Getting started
`poetry install` to start locally
Commit using [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/), and when commits are on master, release with `doo release`.

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@@ -1,6 +1,7 @@
import logging import logging
from deepdog.meta import __version__ from deepdog.meta import __version__
from deepdog.bayes_run import BayesRun from deepdog.bayes_run import BayesRun
from deepdog.alt_bayes_run import AltBayesRun
from deepdog.diagnostic import Diagnostic from deepdog.diagnostic import Diagnostic
@@ -8,7 +9,7 @@ def get_version():
return __version__ return __version__
__all__ = ["get_version", "BayesRun", "Diagnostic"] __all__ = ["get_version", "BayesRun", "AltBayesRun", "Diagnostic"]
logging.getLogger(__name__).addHandler(logging.NullHandler()) logging.getLogger(__name__).addHandler(logging.NullHandler())

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deepdog/alt_bayes_run.py Normal file
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import pdme.inputs
import pdme.model
import pdme.measurement.input_types
import pdme.measurement.oscillating_dipole
import pdme.util.fast_v_calc
import pdme.util.fast_nonlocal_spectrum
from typing import Sequence, Tuple, List
import datetime
import csv
import multiprocessing
import logging
import numpy
# TODO: remove hardcode
CHUNKSIZE = 50
# TODO: It's garbage to have this here duplicated from pdme.
DotInput = Tuple[numpy.typing.ArrayLike, float]
_logger = logging.getLogger(__name__)
def get_a_result(input) -> int:
discretisation, dot_inputs, lows, highs, monte_carlo_count, max_frequency = input
sample_dipoles = discretisation.get_model().get_n_single_dipoles(monte_carlo_count, max_frequency)
vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
return numpy.count_nonzero(pdme.util.fast_v_calc.between(vals, lows, highs))
def get_a_result_using_pairs(input) -> int:
discretisation, dot_inputs, pair_inputs, local_lows, local_highs, nonlocal_lows, nonlocal_highs, monte_carlo_count, max_frequency = input
sample_dipoles = discretisation.get_model().get_n_single_dipoles(monte_carlo_count, max_frequency)
local_vals = pdme.util.fast_v_calc.fast_vs_for_dipoles(dot_inputs, sample_dipoles)
local_matches = pdme.util.fast_v_calc.between(local_vals, local_lows, local_highs)
nonlocal_vals = pdme.util.fast_nonlocal_spectrum.fast_s_nonlocal(pair_inputs, sample_dipoles)
nonlocal_matches = pdme.util.fast_v_calc.between(nonlocal_vals, nonlocal_lows, nonlocal_highs)
combined_matches = numpy.logical_and(local_matches, nonlocal_matches)
return numpy.count_nonzero(combined_matches)
class AltBayesRun():
'''
A single Bayes run for a given set of dots.
Parameters
----------
dot_inputs : Sequence[DotInput]
The dot inputs for this bayes run.
discretisations_with_names : Sequence[Tuple(str, pdme.model.Model)]
The models to evaluate.
actual_model_discretisation : pdme.model.Discretisation
The discretisation for the model which is actually correct.
filename_slug : str
The filename slug to include.
run_count: int
The number of runs to do.
'''
def __init__(self, dot_positions: Sequence[numpy.typing.ArrayLike], frequency_range: Sequence[float], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int = 100, low_error: float = 0.9, high_error: float = 1.1, pairs_high_error=None, pairs_low_error=None, monte_carlo_count: int = 10000, monte_carlo_cycles: int = 10, target_success: int = 100, max_monte_carlo_cycles_steps: int = 10, max_frequency: float = 20, end_threshold: float = None, chunksize: int = CHUNKSIZE, use_pairs: bool = False) -> 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.use_pairs = use_pairs
self.dot_pair_inputs = pdme.inputs.input_pairs_with_frequency_range(dot_positions, frequency_range)
self.dot_pair_inputs_array = pdme.measurement.input_types.dot_pair_inputs_to_array(self.dot_pair_inputs)
self.discretisations = [disc for (_, disc) in discretisations_with_names]
self.model_names = [name for (name, _) in discretisations_with_names]
self.actual_model = actual_model
self.model_count = len(self.discretisations)
self.monte_carlo_count = monte_carlo_count
self.monte_carlo_cycles = monte_carlo_cycles
self.target_success = target_success
self.max_monte_carlo_cycles_steps = max_monte_carlo_cycles_steps
self.run_count = run_count
self.low_error = low_error
self.high_error = high_error
if pairs_low_error is None:
self.pairs_low_error = self.low_error
else:
self.pairs_low_error = pairs_low_error
if pairs_high_error is None:
self.pairs_high_error = self.high_error
else:
self.pairs_high_error = pairs_high_error
self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"]
self.compensate_zeros = True
self.chunksize = chunksize
for name in self.model_names:
self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
self.probabilities = [1 / self.model_count] * self.model_count
timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
if self.use_pairs:
self.filename = f"{timestamp}-{filename_slug}.altbayes.pairs.csv"
else:
self.filename = f"{timestamp}-{filename_slug}.altbayes.csv"
self.max_frequency = max_frequency
if end_threshold is not None:
if 0 < end_threshold < 1:
self.end_threshold: float = end_threshold
self.use_end_threshold = True
_logger.info(f"Will abort early, at {self.end_threshold}.")
else:
raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
def go(self) -> None:
with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer.writeheader()
for run in range(1, self.run_count + 1):
rng = numpy.random.default_rng()
frequency = rng.uniform(1, self.max_frequency)
# Generate the actual dipoles
actual_dipoles = self.actual_model.get_dipoles(frequency)
dots = actual_dipoles.get_percent_range_dot_measurements(self.dot_inputs, self.low_error, self.high_error)
lows, highs = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(dots)
pair_lows, pair_highs = (None, None)
if self.use_pairs:
pair_measurements = actual_dipoles.get_percent_range_dot_pair_measurements(self.dot_pair_inputs, self.pairs_low_error, self.pairs_high_error)
pair_lows, pair_highs = pdme.measurement.input_types.dot_range_measurements_low_high_arrays(pair_measurements)
_logger.info(f"Going to work on dipole at {actual_dipoles.dipoles}")
results = []
_logger.debug("Going to iterate over discretisations now")
for disc_count, discretisation in enumerate(self.discretisations):
_logger.debug(f"Doing discretisation #{disc_count}")
with multiprocessing.Pool(multiprocessing.cpu_count() - 1 or 1) as pool:
cycle_count = 0
cycle_success = 0
cycles = 0
while (cycles < self.max_monte_carlo_cycles_steps) and (cycle_success <= self.target_success):
_logger.debug(f"Starting cycle {cycles}")
cycles += 1
current_success = 0
cycle_count += self.monte_carlo_count * self.monte_carlo_cycles
if self.use_pairs:
current_success = sum(
pool.imap_unordered(get_a_result_using_pairs, [(discretisation, self.dot_inputs_array, self.dot_pair_inputs_array, lows, highs, pair_lows, pair_highs, self.monte_carlo_count, self.max_frequency)] * self.monte_carlo_cycles, self.chunksize)
)
else:
current_success = sum(
pool.imap_unordered(get_a_result, [(discretisation, self.dot_inputs_array, lows, highs, self.monte_carlo_count, self.max_frequency)] * self.monte_carlo_cycles, self.chunksize)
)
cycle_success += current_success
results.append((cycle_count, cycle_success))
_logger.debug("Done, constructing output now")
row = {
"dipole_moment": actual_dipoles.dipoles[0].p,
"dipole_location": actual_dipoles.dipoles[0].s,
"dipole_frequency": actual_dipoles.dipoles[0].w
}
successes: List[float] = []
counts: List[int] = []
for model_index, (name, (count, result)) in enumerate(zip(self.model_names, results)):
row[f"{name}_success"] = result
row[f"{name}_count"] = count
successes.append(max(result, 0.5))
counts.append(count)
success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
self.probabilities = new_probabilities
for name, probability in zip(self.model_names, self.probabilities):
row[f"{name}_prob"] = probability
_logger.info(row)
with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer.writerow(row)
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

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@@ -41,7 +41,7 @@ class BayesRun():
run_count: int run_count: int
The number of runs to do. The number of runs to do.
''' '''
def __init__(self, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int, max_frequency: float = None) -> None: def __init__(self, dot_inputs: Sequence[DotInput], discretisations_with_names: Sequence[Tuple[str, pdme.model.Discretisation]], actual_model: pdme.model.Model, filename_slug: str, run_count: int, max_frequency: float = None, end_threshold: float = None) -> None:
self.dot_inputs = dot_inputs self.dot_inputs = dot_inputs
self.discretisations = [disc for (_, disc) in discretisations_with_names] self.discretisations = [disc for (_, disc) in discretisations_with_names]
self.model_names = [name for (name, _) in discretisations_with_names] self.model_names = [name for (name, _) in discretisations_with_names]
@@ -50,7 +50,6 @@ class BayesRun():
self.run_count = run_count self.run_count = run_count
self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"] self.csv_fields = ["dipole_moment", "dipole_location", "dipole_frequency"]
self.compensate_zeros = True self.compensate_zeros = True
for name in self.model_names: for name in self.model_names:
self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"]) self.csv_fields.extend([f"{name}_success", f"{name}_count", f"{name}_prob"])
@@ -60,6 +59,14 @@ class BayesRun():
self.filename = f"{timestamp}-{filename_slug}.csv" self.filename = f"{timestamp}-{filename_slug}.csv"
self.max_frequency = max_frequency self.max_frequency = max_frequency
if end_threshold is not None:
if 0 < end_threshold < 1:
self.end_threshold: float = end_threshold
self.use_end_threshold = True
_logger.info(f"Will abort early, at {self.end_threshold}.")
else:
raise ValueError(f"end_threshold should be between 0 and 1, but is actually {end_threshold}")
def go(self) -> None: def go(self) -> None:
with open(self.filename, "a", newline="") as outfile: with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix") writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
@@ -88,7 +95,8 @@ class BayesRun():
"dipole_location": dipoles.dipoles[0].s, "dipole_location": dipoles.dipoles[0].s,
"dipole_frequency": dipoles.dipoles[0].w "dipole_frequency": dipoles.dipoles[0].w
} }
successes: List[int] = [] successes: List[float] = []
counts: List[int] = []
for model_index, (name, result) in enumerate(zip(self.model_names, results)): for model_index, (name, result) in enumerate(zip(self.model_names, results)):
count = 0 count = 0
success = 0 success = 0
@@ -99,10 +107,11 @@ class BayesRun():
row[f"{name}_success"] = success row[f"{name}_success"] = success
row[f"{name}_count"] = count row[f"{name}_count"] = count
successes.append(max(success, 1)) successes.append(max(success, 0.5))
counts.append(count)
success_weight = sum([succ * prob for succ, prob in zip(successes, self.probabilities)]) success_weight = sum([(succ / count) * prob for succ, count, prob in zip(successes, counts, self.probabilities)])
new_probabilities = [succ * old_prob / success_weight for succ, old_prob in zip(successes, self.probabilities)] new_probabilities = [(succ / count) * old_prob / success_weight for succ, count, old_prob in zip(successes, counts, self.probabilities)]
self.probabilities = new_probabilities self.probabilities = new_probabilities
for name, probability in zip(self.model_names, self.probabilities): for name, probability in zip(self.model_names, self.probabilities):
row[f"{name}_prob"] = probability row[f"{name}_prob"] = probability
@@ -111,3 +120,9 @@ class BayesRun():
with open(self.filename, "a", newline="") as outfile: with open(self.filename, "a", newline="") as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix") writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect="unix")
writer.writerow(row) 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

View File

@@ -3,6 +3,7 @@ import pdme
from deepdog.bayes_run import DotInput from deepdog.bayes_run import DotInput
import datetime import datetime
import numpy import numpy
from dataclasses import dataclass
import logging import logging
from typing import Sequence, Tuple from typing import Sequence, Tuple
import csv import csv
@@ -16,6 +17,32 @@ def get_a_result(discretisation, dots, index):
return (index, discretisation.solve_for_index(dots, index)) return (index, discretisation.solve_for_index(dots, index))
@dataclass
class SingleDipoleDiagnostic():
model: str
index: Tuple
bounds: Tuple
actual_dipole: OscillatingDipole
result_dipole: OscillatingDipole
success: bool
def __post_init__(self) -> None:
self.p_actual_x = self.actual_dipole.p[0]
self.p_actual_y = self.actual_dipole.p[1]
self.p_actual_z = self.actual_dipole.p[2]
self.s_actual_x = self.actual_dipole.s[0]
self.s_actual_y = self.actual_dipole.s[1]
self.s_actual_z = self.actual_dipole.s[2]
self.p_result_x = self.result_dipole.p[0]
self.p_result_y = self.result_dipole.p[1]
self.p_result_z = self.result_dipole.p[2]
self.s_result_x = self.result_dipole.s[0]
self.s_result_y = self.result_dipole.s[1]
self.s_result_z = self.result_dipole.s[2]
self.w_actual = self.actual_dipole.w
self.w_result = self.result_dipole.w
class Diagnostic(): class Diagnostic():
''' '''
Represents a diagnostic for a single dipole moment given a set of discretisations. Represents a diagnostic for a single dipole moment given a set of discretisations.
@@ -40,10 +67,10 @@ class Diagnostic():
self.discretisations_with_names = discretisations_with_names self.discretisations_with_names = discretisations_with_names
self.model_count = len(self.discretisations_with_names) self.model_count = len(self.discretisations_with_names)
self.csv_fields = ["model", "index", "bounds", "actual_dipole_moment", "actual_dipole_position", "actual_dipole_freq", "success", "result"] self.csv_fields = ["model", "index", "bounds", "p_actual_x", "p_actual_y", "p_actual_z", "s_actual_x", "s_actual_y", "s_actual_z", "w_actual", "success", "p_result_x", "p_result_y", "p_result_z", "s_result_x", "s_result_y", "s_result_z", "w_result"]
timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S") timestamp = datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
self.filename = f"{timestamp}-{filename_slug}.csv" self.filename = f"{timestamp}-{filename_slug}.diag.csv"
def go(self): def go(self):
with open(self.filename, "a", newline="") as outfile: with open(self.filename, "a", newline="") as outfile:
@@ -59,22 +86,14 @@ class Diagnostic():
results = pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(self.dots), discretisation.all_indices())) results = pool.starmap(get_a_result, zip(itertools.repeat(discretisation), itertools.repeat(self.dots), discretisation.all_indices()))
with open(self.filename, "a", newline='') as outfile: with open(self.filename, "a", newline='') as outfile:
writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix') writer = csv.DictWriter(outfile, fieldnames=self.csv_fields, dialect='unix', extrasaction="ignore")
for idx, result in results: for idx, result in results:
bounds = discretisation.bounds(idx) bounds = discretisation.bounds(idx)
actual_success = result.success and result.cost <= 1e-10 actual_success = result.success and result.cost <= 1e-10
row = { diag_row = SingleDipoleDiagnostic(name, idx, bounds, self.dipoles.dipoles[0], discretisation.model.solution_as_dipoles(result.normalised_x)[0], actual_success)
"model": name, row = vars(diag_row)
"index": idx,
"bounds": bounds,
"actual_dipole_moment": self.dipoles.dipoles[0].p,
"actual_dipole_position": self.dipoles.dipoles[0].s,
"actual_dipole_freq": self.dipoles.dipoles[0].w,
"success": actual_success,
"result": result.normalised_x if actual_success else None,
}
_logger.debug(f"Writing result {row}") _logger.debug(f"Writing result {row}")
writer.writerow(row) writer.writerow(row)

4
do.sh
View File

@@ -16,6 +16,10 @@ test() {
poetry run pytest poetry run pytest
} }
release() {
./scripts/release.sh
}
htmlcov() { htmlcov() {
poetry run pytest --cov-report=html poetry run pytest --cov-report=html
} }

869
poetry.lock generated

File diff suppressed because it is too large Load Diff

View File

@@ -1,18 +1,19 @@
[tool.poetry] [tool.poetry]
name = "deepdog" name = "deepdog"
version = "0.1.5" version = "0.4.0"
description = "" description = ""
authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"] authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = "^3.8,<3.10" python = "^3.8,<3.10"
pdme = "^0.4.1" pdme = "^0.6.1"
[tool.poetry.dev-dependencies] [tool.poetry.dev-dependencies]
pytest = ">=6" pytest = ">=6"
flake8 = "^4.0.1" flake8 = "^4.0.1"
pytest-cov = "^3.0.0" pytest-cov = "^3.0.0"
mypy = "^0.931" mypy = "^0.942"
python-semantic-release = "^7.24.0"
[build-system] [build-system]
requires = ["poetry-core>=1.0.0"] requires = ["poetry-core>=1.0.0"]
@@ -32,3 +33,7 @@ module = [
"scipy.optimize" "scipy.optimize"
] ]
ignore_missing_imports = true ignore_missing_imports = true
[tool.semantic_release]
version_toml = "pyproject.toml:tool.poetry.version"
tag_format = "{version}"

3
renovate.json Normal file
View File

@@ -0,0 +1,3 @@
{
"$schema": "https://docs.renovatebot.com/renovate-schema.json"
}

View File

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

45
scripts/release.sh Normal file
View File

@@ -0,0 +1,45 @@
#!/usr/bin/env bash
set -Eeuo pipefail
if [ -z "$(git status --porcelain)" ]; then
branch_name=$(git symbolic-ref -q HEAD)
branch_name=${branch_name##refs/heads/}
branch_name=${branch_name:-HEAD}
if [ $branch_name != "master" ]; then
echo "The current branch is not master!"
echo "I'd feel uncomfortable releasing from here..."
exit 3
fi
release_needed=false
if \
{ git log "$( git describe --tags --abbrev=0 )..HEAD" --format='%s' | cut -d: -f1 | sort -u | sed -e 's/([^)]*)//' | grep -q -i -E '^feat|fix|perf|refactor|revert$' ; } || \
{ git log "$( git describe --tags --abbrev=0 )..HEAD" --format='%s' | cut -d: -f1 | sort -u | sed -e 's/([^)]*)//' | grep -q -E '\!$' ; } || \
{ git log "$( git describe --tags --abbrev=0 )..HEAD" --format='%b' | grep -q -E '^BREAKING CHANGE:' ; }
then
release_needed=true
fi
if ! [ "$release_needed" = true ]; then
echo "No release needed..."
exit 0
fi
# Working directory clean
echo "Doing a dry run..."
npx standard-version --dry-run
read -p "Does that look good? [y/N] " -n 1 -r
echo # (optional) move to a new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
# do dangerous stuff
npx standard-version
git push --follow-tags origin master
else
echo "okay, never mind then..."
exit 2
fi
else
echo "Can't create release, working tree unclean..."
exit 1
fi

View File

@@ -0,0 +1,11 @@
const pattern = /(\[tool\.poetry\]\nname = "deepdog"\nversion = ")(?<vers>\d+\.\d+\.\d)(")/mg;
module.exports.readVersion = function (contents) {
const result = pattern.exec(contents);
return result.groups.vers;
}
module.exports.writeVersion = function (contents, version) {
const newContents = contents.replace(pattern, `$1${version}$3`);
return newContents;
}