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Removed units from time headers in controllers. #1503

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merged 4 commits into from
Nov 21, 2023
Merged

Removed units from time headers in controllers. #1503

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41da58d
Removed units from time headers in controllers. Closes #1467.
MichaelClerx Nov 7, 2023
5affaaf
Updating tests and changelog
MichaelClerx Nov 7, 2023
fa17729
Updated tests for #1467.
MichaelClerx Nov 7, 2023
7e6d228
Reverted accidental notebook update
MichaelClerx Nov 7, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ All notable changes to this project will be documented in this file.
### Added
- [#1499](https://github.com/pints-team/pints/pull/1499) Added a log-uniform prior class.
### Changed
- [#1503](https://github.com/pints-team/pints/pull/1503) Stopped showing time units in controller logs, because the units change depending on the output type (see #1467).
### Deprecated
### Removed
### Fixed
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4 changes: 3 additions & 1 deletion pints/_abc/__init__.py
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Expand Up @@ -235,7 +235,9 @@ def run(self):
logger.add_counter('Eval.', max_value=max_eval_guess)
logger.add_float('Acceptance rate')
self._sampler._log_init(logger)
logger.add_time('Time m:s')
# Note: removed units from time field, see
# https://github.com/pints-team/pints/issues/1467
logger.add_time('Time')

# Start sampling
timer = pints.Timer()
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4 changes: 3 additions & 1 deletion pints/_mcmc/__init__.py
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Expand Up @@ -665,7 +665,9 @@ def run(self):
logger.add_counter('Eval.', max_value=max_eval_guess)
for sampler in self._samplers:
sampler._log_init(logger)
logger.add_time('Time m:s')
# Note: deleted time units from header, see
# https://github.com/pints-team/pints/issues/1467
logger.add_time('Time')

# Pre-allocate arrays for chain storage
# Note: we store the inverse transformed (to model space) parameters
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4 changes: 3 additions & 1 deletion pints/_nested/__init__.py
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Expand Up @@ -409,7 +409,9 @@ def _initialise_logger(self):
# Add fields to log
self._logger.add_counter('Iter.', max_value=self._iterations)
self._logger.add_counter('Eval.', max_value=self._iterations * 10)
self._logger.add_time('Time m:s')
# Note: removed units from time field, see
# https://github.com/pints-team/pints/issues/1467
self._logger.add_time('Time')
self._logger.add_float('Delta_log(z)')
self._logger.add_float('Acceptance rate')

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4 changes: 3 additions & 1 deletion pints/_optimisers/__init__.py
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Expand Up @@ -635,7 +635,9 @@ def run(self):
logger.add_float('Best')
logger.add_float('Current')
self._optimiser._log_init(logger)
logger.add_time('Time m:s')
# Note: No units shown in time field, for the reason why see
# https://github.com/pints-team/pints/issues/1467
logger.add_time('Time')

# Start searching
timer = pints.Timer()
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8 changes: 4 additions & 4 deletions pints/tests/test_abc_controller.py
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Expand Up @@ -18,7 +18,7 @@
LOG_SCREEN_1 = [
'Using Rejection ABC',
'Running in sequential mode.',
'Iter. Eval. Acceptance rate Time m:s',
'Iter. Eval. Acceptance rate Time ',
'1 127 0.00787401575 0:00.0',
'2 167 0.0119760479 0:00.0',
'3 209 0.014354067 0:00.0',
Expand All @@ -28,7 +28,7 @@
LOG_SCREEN_2 = [
'Using Rejection ABC',
'Running in parallel with 2 worker processess.',
'Iter. Eval. Acceptance rate Time m:s',
'Iter. Eval. Acceptance rate Time ',
'1 20 0.05 0:00.0',
'2 22 0.0909090909 0:00.0',
'3 144 0.0208333333 0:00.0',
Expand All @@ -38,15 +38,15 @@
]

LOG_FILE = [
'Iter. Eval. Acceptance rate Time m:s',
'Iter. Eval. Acceptance rate Time ',
'1 127 0.00787401575 0:00.0',
'2 167 0.0119760479 0:00.0',
'3 209 0.014354067 0:00.0',
'6 369 0.0162601626 0:00.0',
]

LOG_FILE_CSV = [
'"Iter.","Eval.","Acceptance rate","Time m:s"',
'"Iter.","Eval.","Acceptance rate","Time"',
'1,127,7.87401574803149595e-03,0:00.0',
'2,167,0.0119760479,0:00.0',
'3,209,0.014354067,0:00.0',
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2 changes: 1 addition & 1 deletion pints/tests/test_mcmc_adaptive.py
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Expand Up @@ -145,7 +145,7 @@ def test_logging(self):
self.assertIn('Accept.', text)
self.assertIn('Eval.', text)
self.assertIn('Iter.', text)
self.assertIn('Time m:s', text)
self.assertIn('Time', text)

def test_replace(self):
# Tests the replace() method
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12 changes: 8 additions & 4 deletions pints/tests/test_mcmc_controller.py
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Expand Up @@ -14,6 +14,7 @@
import unittest.mock
import numpy as np
import numpy.testing as npt
import warnings

from shared import StreamCapture, TemporaryDirectory

Expand All @@ -24,7 +25,7 @@
'Using Haario-Bardenet adaptive covariance MCMC',
'Generating 3 chains.',
'Running in sequential mode.',
'Iter. Eval. Accept. Accept. Accept. Time m:s',
'Iter. Eval. Accept. Accept. Accept. Time ',
'0 3 0 0 0 0:00.0',
'1 6 0 0 0.5 0:00.0',
'2 9 0 0 0.333 0:00.0',
Expand All @@ -35,7 +36,7 @@
]

LOG_FILE = [
'Iter. Eval. Accept. Accept. Accept. Time m:s',
'Iter. Eval. Accept. Accept. Accept. Time ',
'0 3 0 0 0 0:00.0',
'1 6 0 0 0.5 0:00.0',
'2 9 0 0 0.333 0:00.0',
Expand Down Expand Up @@ -791,8 +792,11 @@ def test_log_pdf_storage_in_memory_single_complex(self):

def test_deprecated_alias(self):

mcmc = pints.MCMCSampling(
self.log_posterior, 1, [self.real_parameters])
with warnings.catch_warnings(record=True) as w:
mcmc = pints.MCMCSampling(
self.log_posterior, 1, [self.real_parameters])
self.assertEqual(len(w), 1)
self.assertIn('deprecated', str(w[-1].message))
self.assertIsInstance(mcmc, pints.MCMCController)

def test_exception_on_multi_use(self):
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4 changes: 2 additions & 2 deletions pints/tests/test_nested_controller.py
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Expand Up @@ -160,7 +160,7 @@ def test_logging(self):
self.assertEqual(lines[1], 'Number of active points: 400')
self.assertEqual(lines[2], 'Total number of iterations: 20')
self.assertEqual(lines[3], 'Total number of posterior samples: 2')
self.assertEqual(lines[4], ('Iter. Eval. Time m:s Delta_log(z) ' +
self.assertEqual(lines[4], ('Iter. Eval. Time Delta_log(z) ' +
'Acceptance rate'))
pattern = re.compile('[0-9]+[ ]+[0-9]+[ ]+[0-9]{1}:[0-9]{2}.[0-9]{1}')
for line in lines[5:]:
Expand All @@ -182,7 +182,7 @@ def test_logging(self):
lines = f.read().splitlines()
self.assertEqual(c.text(), '')
self.assertEqual(len(lines), 23)
self.assertEqual(lines[0], ('Iter. Eval. Time m:s Delta_log(z) ' +
self.assertEqual(lines[0], ('Iter. Eval. Time Delta_log(z) ' +
'Acceptance rate'))
pattern = re.compile('[0-9]+[ ]+[0-9]+[ ]+[0-9]{1}:[0-9]{2}.[0-9]{1}')
for line in lines[5:]:
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18 changes: 9 additions & 9 deletions pints/tests/test_opt_adam.py
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Expand Up @@ -19,15 +19,15 @@
method = pints.Adam


log_1 = '''
Minimising error measure
Using Adam
Running in sequential mode.
Iter. Eval. Best Current b1 b2 Time m:s
0 1 0.02 0.02 0.9 0.999 0:00.0
1 2 5e-17 5e-17 0.81 0.998001 0:00.0
2 3 5e-17 0.00898 0.729 0.997003 0:00.0
'''.strip()
log_1 = '\n'.join((
'Minimising error measure',
'Using Adam',
'Running in sequential mode.',
'Iter. Eval. Best Current b1 b2 Time ',
'0 1 0.02 0.02 0.9 0.999 0:00.0',
'1 2 5e-17 5e-17 0.81 0.998001 0:00.0',
'2 3 5e-17 0.00898 0.729 0.997003 0:00.0',
))


class TestAdam(unittest.TestCase):
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4 changes: 2 additions & 2 deletions pints/tests/test_opt_controller.py
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Expand Up @@ -251,7 +251,7 @@ def test_logging(self):
self.assertEqual(lines[2], 'Running in sequential mode.')
self.assertEqual(lines[3], 'Population size: 6')
self.assertEqual(lines[4],
'Iter. Eval. Best Current Time m:s')
'Iter. Eval. Best Current Time ')
self.assertEqual(lines[5][:-3],
'0 3 -4.140462 -4.140462 0:0')
self.assertEqual(lines[6][:-3],
Expand Down Expand Up @@ -290,7 +290,7 @@ def test_logging(self):
self.assertEqual(lines[2], 'Running in sequential mode.')
self.assertEqual(lines[3], 'Population size: 4')
self.assertEqual(lines[4],
'Iter. Eval. Best Current Time m:s')
'Iter. Eval. Best Current Time ')
self.assertEqual(lines[5][:-3],
'0 4 6.471867 6.471867 0:0')
self.assertEqual(lines[6][:-3],
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38 changes: 19 additions & 19 deletions pints/tests/test_opt_irpropmin.py
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Expand Up @@ -19,25 +19,25 @@
method = pints.IRPropMin


log_1 = '''
Minimising error measure
Using iRprop-
Running in sequential mode.
Iter. Eval. Best Current Min. step Max. step Bound corr. Time m:s
0 1 0.02 0.02 0.12 0.12 0:00.0
1 2 0.0008 0.0008 0.06 0.06 0:00.0
'''.strip()

log_2 = '''
Minimising error measure
Using iRprop-
Running in sequential mode.
Iter. Eval. Best Current Min. step Max. step Bound corr. Time m:s
0 1 0.02 0.02 0.11 0.11 0:00.0
1 2 0.0002 0.0002 0.055 0.055 0:00.0
2 3 0.0002 0.0002 0.055 0.055 0:00.0
3 4 0.0002 0.00405 0.03 0.03 0:00.0
'''.strip()
log_1 = '\n'.join((
'Minimising error measure',
'Using iRprop-',
'Running in sequential mode.',
'Iter. Eval. Best Current Min. step Max. step Bound corr. Time ',
'0 1 0.02 0.02 0.12 0.12 0:00.0',
'1 2 0.0008 0.0008 0.06 0.06 0:00.0',
))

log_2 = '\n'.join((
'Minimising error measure',
'Using iRprop-',
'Running in sequential mode.',
'Iter. Eval. Best Current Min. step Max. step Bound corr. Time ',
'0 1 0.02 0.02 0.11 0.11 0:00.0',
'1 2 0.0002 0.0002 0.055 0.055 0:00.0',
'2 3 0.0002 0.0002 0.055 0.055 0:00.0',
'3 4 0.0002 0.00405 0.03 0.03 0:00.0',
))


class TestIRPropMin(unittest.TestCase):
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2 changes: 1 addition & 1 deletion pints/tests/test_opt_nelder_mead.py
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Expand Up @@ -170,7 +170,7 @@ def test_rosenbrock(self):
'Minimising error measure',
'Using Nelder-Mead',
'Running in sequential mode.',
'Iter. Eval. Best Current Time m:s',
'Iter. Eval. Best Current Time',
'0 3 865.9531 865.9531 0:00.0',
'1 4 832.5452 832.5452 0:00.0',
'2 5 832.5452 832.5452 0:00.0',
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4 changes: 2 additions & 2 deletions pints/tests/test_opt_pso.py
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Expand Up @@ -130,7 +130,7 @@ def test_logging(self):
self.assertEqual(
lines[2], 'Running in parallel with 4 worker processes.')
self.assertEqual(lines[3], 'Population size: 6')
self.assertEqual(lines[4], 'Iter. Eval. Best Current Time m:s')
self.assertEqual(lines[4], 'Iter. Eval. Best Current Time ')

pint = '[0-9]+[ ]+'
pflt = '[0-9.-]+[ ]+'
Expand Down Expand Up @@ -158,7 +158,7 @@ def test_logging(self):
self.assertEqual(
lines[0],
'Iter. Eval. Best Current f0 f1 f2 '
'f3 f4 f5 Time m:s'
'f3 f4 f5 Time '
)

pattern = re.compile(pint * 2 + pflt * 8 + ptim)
Expand Down
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