From 573dcf1b852868fdbb56efe760a64c233fa2ed62 Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Fri, 11 Feb 2022 19:40:15 +0000
Subject: [PATCH] remove deprecated functions
---
bilby/core/result.py | 61 -------------------------
bilby/core/utils/__init__.py | 1 -
bilby/core/utils/conversion.py | 53 ---------------------
bilby/core/utils/progress.py | 18 --------
bilby/gw/detector/interferometer.py | 26 -----------
bilby/gw/detector/networks.py | 31 -------------
bilby/gw/likelihood/base.py | 9 ----
test/gw/detector/interferometer_test.py | 26 -----------
test/gw/detector/networks_test.py | 23 ----------
9 files changed, 248 deletions(-)
delete mode 100644 bilby/core/utils/progress.py
diff --git a/bilby/core/result.py b/bilby/core/result.py
index 48797a4f1..e2608932e 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -422,65 +422,6 @@ class Result(object):
self.prior_values = None
self._kde = None
- @classmethod
- def _from_hdf5_old(cls, filename=None, outdir=None, label=None):
- """ Read in a saved .h5 data file in the old format.
-
- Parameters
- ==========
- filename: str
- If given, try to load from this filename
- outdir, label: str
- If given, use the default naming convention for saved results file
-
- Returns
- =======
- result: bilby.core.result.Result
-
- Raises
- =======
- ValueError: If no filename is given and either outdir or label is None
- If no bilby.core.result.Result is found in the path
-
- """
- import deepdish
- filename = _determine_file_name(filename, outdir, label, 'hdf5', False)
-
- if os.path.isfile(filename):
- dictionary = deepdish.io.load(filename)
- # Some versions of deepdish/pytables return the dictionary as
- # a dictionary with a key 'data'
- if len(dictionary) == 1 and 'data' in dictionary:
- dictionary = dictionary['data']
-
- if "priors" in dictionary:
- # parse priors from JSON string (allowing for backwards
- # compatibility)
- if not isinstance(dictionary["priors"], PriorDict):
- try:
- priordict = PriorDict()
- for key, value in dictionary["priors"].items():
- if key not in ["__module__", "__name__", "__prior_dict__"]:
- try:
- priordict[key] = decode_bilby_json(value)
- except AttributeError:
- continue
- dictionary["priors"] = priordict
- except Exception as e:
- raise IOError(
- "Unable to parse priors from '{}':\n{}".format(
- filename, e,
- )
- )
- try:
- if isinstance(dictionary.get('posterior', None), dict):
- dictionary['posterior'] = pd.DataFrame(dictionary['posterior'])
- return cls(**dictionary)
- except TypeError as e:
- raise IOError("Unable to load dictionary, error={}".format(e))
- else:
- raise IOError("No result '{}' found".format(filename))
-
_load_doctstring = """ Read in a saved .{format} data file
Parameters
@@ -516,8 +457,6 @@ class Result(object):
filename = _determine_file_name(filename, outdir, label, 'hdf5', False)
with h5py.File(filename, "r") as ff:
data = recursively_load_dict_contents_from_group(ff, '/')
- if list(data.keys()) == ["data"]:
- return cls._from_hdf5_old(filename=filename)
data["posterior"] = pd.DataFrame(data["posterior"])
data["priors"] = PriorDict._get_from_json_dict(
json.loads(data["priors"], object_hook=decode_bilby_json)
diff --git a/bilby/core/utils/__init__.py b/bilby/core/utils/__init__.py
index 85c3fb1f4..10509641a 100644
--- a/bilby/core/utils/__init__.py
+++ b/bilby/core/utils/__init__.py
@@ -9,7 +9,6 @@ from .introspection import *
from .io import *
from .log import *
from .plotting import *
-from .progress import *
from .samples import *
from .series import *
diff --git a/bilby/core/utils/conversion.py b/bilby/core/utils/conversion.py
index 978e34346..c89e2a9ec 100644
--- a/bilby/core/utils/conversion.py
+++ b/bilby/core/utils/conversion.py
@@ -1,6 +1,3 @@
-import warnings
-from math import fmod
-
import numpy as np
@@ -31,53 +28,3 @@ def theta_phi_to_ra_dec(theta, phi, gmst):
ra = phi + gmst
dec = np.pi / 2 - theta
return ra, dec
-
-
-def gps_time_to_gmst(gps_time):
- """
- Convert gps time to Greenwich mean sidereal time in radians
-
- This method assumes a constant rotation rate of earth since 00:00:00, 1 Jan. 2000
- A correction has been applied to give the exact correct value for 00:00:00, 1 Jan. 2018
- Error accumulates at a rate of ~0.0001 radians/decade.
-
- Parameters
- ----------
- gps_time: float
- gps time
-
- Returns
- -------
- float: Greenwich mean sidereal time in radians
-
- """
- warnings.warn(
- "Function gps_time_to_gmst deprecated, use "
- "lal.GreenwichMeanSiderealTime(time) instead",
- DeprecationWarning)
- omega_earth = 2 * np.pi * (1 / 365.2425 + 1) / 86400.
- gps_2000 = 630720013.
- gmst_2000 = (6 + 39. / 60 + 51.251406103947375 / 3600) * np.pi / 12
- correction_2018 = -0.00017782487379358614
- sidereal_time = omega_earth * (gps_time - gps_2000) + gmst_2000 + correction_2018
- gmst = fmod(sidereal_time, 2 * np.pi)
- return gmst
-
-
-def spherical_to_cartesian(radius, theta, phi):
- """ Convert from spherical coordinates to cartesian.
-
- Parameters
- ==========
- radius: float
- radial coordinate
- theta: float
- axial coordinate
- phi: float
- azimuthal coordinate
-
- Returns
- =======
- list: cartesian vector
- """
- return [radius * np.sin(theta) * np.cos(phi), radius * np.sin(theta) * np.sin(phi), radius * np.cos(theta)]
diff --git a/bilby/core/utils/progress.py b/bilby/core/utils/progress.py
deleted file mode 100644
index 9db1752b2..000000000
--- a/bilby/core/utils/progress.py
+++ /dev/null
@@ -1,18 +0,0 @@
-def get_progress_bar(module='tqdm'):
- """
- TODO: Write proper docstring
- """
- if module in ['tqdm']:
- try:
- from tqdm import tqdm
- except ImportError:
- def tqdm(x, *args, **kwargs):
- return x
- return tqdm
- elif module in ['tqdm_notebook']:
- try:
- from tqdm import tqdm_notebook as tqdm
- except ImportError:
- def tqdm(x, *args, **kwargs):
- return x
- return tqdm
diff --git a/bilby/gw/detector/interferometer.py b/bilby/gw/detector/interferometer.py
index 8447c16ef..06b298386 100644
--- a/bilby/gw/detector/interferometer.py
+++ b/bilby/gw/detector/interferometer.py
@@ -771,32 +771,6 @@ class Interferometer(object):
"""
- @docstring(_save_ifo_docstring.format(
- format="hdf5", extra=""".. deprecated:: 1.1.0
- Use :func:`to_pickle` instead."""
- ))
- def to_hdf5(self, outdir='outdir', label=None):
- import deepdish
- if label is None:
- label = self.name
- utils.check_directory_exists_and_if_not_mkdir('outdir')
- try:
- filename = self._filename_from_outdir_label_extension(outdir, label, "h5")
- deepdish.io.save(filename, self)
- except AttributeError:
- logger.warning("Saving to hdf5 using deepdish failed. Pickle dumping instead.")
- self.to_pickle(outdir=outdir, label=label)
-
- @classmethod
- @docstring(_load_docstring.format(format="hdf5"))
- def from_hdf5(cls, filename=None):
- import deepdish
-
- res = deepdish.io.load(filename)
- if res.__class__ != cls:
- raise TypeError('The loaded object is not an Interferometer')
- return res
-
@docstring(_save_ifo_docstring.format(
format="pickle", extra=".. versionadded:: 1.1.0"
))
diff --git a/bilby/gw/detector/networks.py b/bilby/gw/detector/networks.py
index db0d4743b..4f03b948b 100644
--- a/bilby/gw/detector/networks.py
+++ b/bilby/gw/detector/networks.py
@@ -272,31 +272,6 @@ class InterferometerList(list):
"""
- def to_hdf5(self, outdir="outdir", label="ifo_list"):
- import deepdish
-
- label = label + "_" + "".join(ifo.name for ifo in self)
- utils.check_directory_exists_and_if_not_mkdir(outdir)
- try:
- filename = self._filename_from_outdir_label_extension(outdir, label, "h5")
- deepdish.io.save(filename, self)
- except AttributeError:
- logger.warning(
- "Saving to hdf5 using deepdish failed. Pickle dumping instead."
- )
- self.to_pickle(outdir=outdir, label=label)
-
- @classmethod
- def from_hdf5(cls, filename=None):
- import deepdish
-
- res = deepdish.io.load(filename)
- if res.__class__ == list:
- res = cls(res)
- if res.__class__ != cls:
- raise TypeError("The loaded object is not a InterferometerList")
- return res
-
def to_pickle(self, outdir="outdir", label="ifo_list"):
import dill
@@ -318,15 +293,9 @@ class InterferometerList(list):
raise TypeError("The loaded object is not an InterferometerList")
return res
- to_hdf5.__doc__ = _save_docstring.format(
- format="hdf5",
- extra=""".. deprecated:: 1.1.0
- Use :func:`to_pickle` instead.""",
- )
to_pickle.__doc__ = _save_docstring.format(
format="pickle", extra=".. versionadded:: 1.1.0"
)
- from_hdf5.__doc__ = _load_docstring.format(format="hdf5")
from_pickle.__doc__ = _load_docstring.format(format="pickle")
diff --git a/bilby/gw/likelihood/base.py b/bilby/gw/likelihood/base.py
index 55845c093..d4d8eca34 100644
--- a/bilby/gw/likelihood/base.py
+++ b/bilby/gw/likelihood/base.py
@@ -936,15 +936,6 @@ class GravitationalWaveTransient(Likelihood):
"to use bilby.gw.utils.ln_i0"
)
- @staticmethod
- def _bessel_function_interped(xx):
- logger.warning(
- "The _bessel_function_interped method is deprecated and will be removed, "
- "please update the implementation of phase marginalization "
- "to use bilby.gw.utils.ln_i0"
- )
- return ln_i0(xx) + xx
-
def _setup_time_marginalization(self):
self._delta_tc = 2 / self.waveform_generator.sampling_frequency
self._times = \
diff --git a/test/gw/detector/interferometer_test.py b/test/gw/detector/interferometer_test.py
index 2a37830fc..3eea3c59d 100644
--- a/test/gw/detector/interferometer_test.py
+++ b/test/gw/detector/interferometer_test.py
@@ -3,13 +3,9 @@ from unittest import mock
import lal
import lalsimulation
-import pytest
-from packaging import version
from shutil import rmtree
-import deepdish as dd
import numpy as np
-import pandas
import bilby
@@ -371,28 +367,6 @@ class TestInterferometer(unittest.TestCase):
)
self.assertEqual(expected, repr(self.ifo))
- pandas_version_test = version.parse(pandas.__version__) >= version.parse("1.2.0")
- skip_reason = "Deepdish requires pandas < 1.2"
-
- @pytest.mark.skipif(pandas_version_test, reason=skip_reason)
- def test_to_and_from_hdf5_loading(self):
- self.ifo.to_hdf5(outdir="outdir", label="test")
- filename = self.ifo._filename_from_outdir_label_extension(
- outdir="outdir", label="test", extension="h5"
- )
- recovered_ifo = bilby.gw.detector.Interferometer.from_hdf5(filename)
- self.assertEqual(self.ifo, recovered_ifo)
-
- @pytest.mark.skipif(pandas_version_test, reason=skip_reason)
- def test_to_and_from_hdf5_wrong_class(self):
- bilby.core.utils.check_directory_exists_and_if_not_mkdir("outdir")
- dd.io.save("./outdir/psd.h5", self.power_spectral_density)
- filename = self.ifo._filename_from_outdir_label_extension(
- outdir="outdir", label="psd", extension="h5"
- )
- with self.assertRaises(TypeError):
- bilby.gw.detector.Interferometer.from_hdf5(filename)
-
def test_to_and_from_pkl_loading(self):
self.ifo.to_pickle(outdir="outdir", label="test")
filename = "outdir/test.pkl"
diff --git a/test/gw/detector/networks_test.py b/test/gw/detector/networks_test.py
index 971254b24..744d872a1 100644
--- a/test/gw/detector/networks_test.py
+++ b/test/gw/detector/networks_test.py
@@ -1,13 +1,9 @@
import unittest
from unittest import mock
-import pytest
from shutil import rmtree
-from packaging import version
from itertools import combinations
-import deepdish as dd
import numpy as np
-import pandas
import bilby
@@ -326,25 +322,6 @@ class TestInterferometerList(unittest.TestCase):
names = [ifo.name for ifo in self.ifo_list]
self.assertListEqual([self.ifo1.name, new_ifo.name, self.ifo2.name], names)
- pandas_version_test = version.parse(pandas.__version__) >= version.parse("1.2.0")
- skip_reason = "Deepdish requires pandas < 1.2"
-
- @pytest.mark.skipif(pandas_version_test, reason=skip_reason)
- def test_to_and_from_hdf5_loading(self):
- self.ifo_list.to_hdf5(outdir="outdir", label="test")
- filename = "outdir/test_name1name2.h5"
- recovered_ifo = bilby.gw.detector.InterferometerList.from_hdf5(filename)
- self.assertListEqual(self.ifo_list, recovered_ifo)
-
- @pytest.mark.skipif(pandas_version_test, reason=skip_reason)
- def test_to_and_from_hdf5_wrong_class(self):
- dd.io.save("./outdir/psd.h5", self.ifo_list[0].power_spectral_density)
- filename = self.ifo_list._filename_from_outdir_label_extension(
- outdir="outdir", label="psd", extension="h5"
- )
- with self.assertRaises(TypeError):
- bilby.gw.detector.InterferometerList.from_hdf5(filename)
-
def test_to_and_from_pkl_loading(self):
self.ifo_list.to_pickle(outdir="outdir", label="test")
filename = "outdir/test_name1name2.pkl"
--
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