diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c7933b7681060dfd53efaf203647b2a52f195956..a19412a78c0974cbf6e095ef4935b39e0e74d3a2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,11 +45,10 @@ basic-3.7:
# test example on python 3.7
python-3.7:
stage: test
+ needs: ["basic-3.7", "precommits-py3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python37
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
# Run pyflakes
- flake8 .
@@ -66,13 +65,12 @@ python-3.7:
docs:
stage: docs
+ needs: ["basic-3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python37
script:
# Make the documentation
- apt-get -yqq install pandoc
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
- cd docs
- pip install ipykernel ipython jupyter
- cp ../examples/tutorials/*.ipynb ./
@@ -90,33 +88,30 @@ docs:
# test example on python 3.8
python-3.8:
stage: test
+ needs: ["basic-3.7", "precommits-py3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python38
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
- pytest
# test example on python 3.6
python-3.6:
stage: test
+ needs: ["basic-3.7", "precommits-py3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python36
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
- pytest
# test samplers on python 3.7
python-3.7-samplers:
stage: test
+ needs: ["basic-3.7", "precommits-py3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python37
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
- pytest test/integration/sampler_run_test.py --durations 10
- pytest test/integration/sample_from_the_prior_test.py
@@ -124,11 +119,10 @@ python-3.7-samplers:
# test samplers on python 3.6
python-3.6-samplers:
stage: test
+ needs: ["basic-3.7", "precommits-py3.7"]
image: quay.io/bilbydev/v2-dockerfile-test-suite-python36
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
- pytest test/integration/sampler_run_test.py
@@ -151,8 +145,6 @@ scheduled-python-3.7:
- schedules
script:
- python -m pip install .
- # temporary fix for broken astropy version
- - pip install pyerfa==1.7.1.1
# Run tests which are only done on schedule
- pytest test/integration/example_test.py
@@ -177,6 +169,7 @@ authors:
pages:
stage: deploy
+ needs: ["docs", "python-3.7"]
dependencies:
- docs
- python-3.7
diff --git a/bilby/core/prior/dict.py b/bilby/core/prior/dict.py
index f05f7d3d398328b90d97d5c7c87e4be53cafbca6..fc9918b04e37054a309b47390c588128c55648c8 100644
--- a/bilby/core/prior/dict.py
+++ b/bilby/core/prior/dict.py
@@ -155,7 +155,7 @@ class PriorDict(dict):
@classmethod
def _get_from_json_dict(cls, prior_dict):
try:
- cls == getattr(
+ cls = getattr(
import_module(prior_dict["__module__"]),
prior_dict["__name__"])
except ImportError:
@@ -231,9 +231,19 @@ class PriorDict(dict):
"= {}. Error message {}".format(key, val, e)
)
elif isinstance(val, dict):
- logger.warning(
- 'Cannot convert {} into a prior object. '
- 'Leaving as dictionary.'.format(key))
+ try:
+ _class = getattr(
+ import_module(val.get("__module__", "none")),
+ val.get("__name__", "none"))
+ dictionary[key] = _class(**val.get("kwargs", dict()))
+ except ImportError:
+ logger.debug("Cannot import prior module {}.{}".format(
+ val.get("__module__", "none"), val.get("__name__", "none")
+ ))
+ logger.warning(
+ 'Cannot convert {} into a prior object. '
+ 'Leaving as dictionary.'.format(key))
+ continue
else:
raise TypeError(
"Unable to parse prior, bad entry: {} "
diff --git a/bilby/core/result.py b/bilby/core/result.py
index d4f544d5ed892a5a47ba233b5b668769dac4211c..7dcb4b04f426e461f6aebfb1ecf5b818b99f39f5 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -3,9 +3,11 @@ import os
from collections import OrderedDict, namedtuple
from copy import copy
from distutils.version import LooseVersion
+from importlib import import_module
from itertools import product
import corner
+import h5py
import json
import matplotlib
import matplotlib.pyplot as plt
@@ -22,7 +24,9 @@ from .utils import (
latex_plot_format, safe_save_figure,
BilbyJsonEncoder, load_json,
move_old_file, get_version_information,
- decode_bilby_json,
+ decode_bilby_json, docstring,
+ recursively_save_dict_contents_to_group,
+ recursively_load_dict_contents_from_group,
)
from .prior import Prior, PriorDict, DeltaFunction
@@ -88,6 +92,8 @@ def read_in_result(filename=None, outdir=None, label=None, extension='json', gzi
result = Result.from_json(filename=filename)
elif ('hdf5' in extension) or ('h5' in extension):
result = Result.from_hdf5(filename=filename)
+ elif ("pkl" in extension) or ("pickle" in extension):
+ result = Result.from_pickle(filename=filename)
elif extension is None:
raise ValueError("No filetype extension provided")
else:
@@ -336,8 +342,8 @@ class Result(object):
self._kde = None
@classmethod
- def from_hdf5(cls, filename=None, outdir=None, label=None):
- """ Read in a saved .h5 data file
+ def _from_hdf5_old(cls, filename=None, outdir=None, label=None):
+ """ Read in a saved .h5 data file in the old format.
Parameters
==========
@@ -374,7 +380,10 @@ class Result(object):
priordict = PriorDict()
for key, value in dictionary["priors"].items():
if key not in ["__module__", "__name__", "__prior_dict__"]:
- priordict[key] = decode_bilby_json(value)
+ try:
+ priordict[key] = decode_bilby_json(value)
+ except AttributeError:
+ continue
dictionary["priors"] = priordict
except Exception as e:
raise IOError(
@@ -391,27 +400,62 @@ class Result(object):
else:
raise IOError("No result '{}' found".format(filename))
- @classmethod
- def from_json(cls, filename=None, outdir=None, label=None, gzip=False):
- """ Read in a saved .json data file
+ _load_doctstring = """ Read in a saved .{format} data file
- 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
+ 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
+ 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
+ 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
- """
+ """
+
+ @staticmethod
+ @docstring(_load_doctstring.format(format="pickle"))
+ def from_pickle(filename=None, outdir=None, label=None):
+ filename = _determine_file_name(filename, outdir, label, 'hdf5', False)
+ import dill
+ with open(filename, "rb") as ff:
+ return dill.load(ff)
+
+ @classmethod
+ @docstring(_load_doctstring.format(format="hdf5"))
+ def from_hdf5(cls, filename=None, outdir=None, label=None):
+ 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)
+ )
+ try:
+ cls = getattr(import_module(data['__module__']), data['__name__'])
+ except ImportError:
+ logger.debug(
+ "Module {}.{} not found".format(data["__module__"], data["__name__"])
+ )
+ except KeyError:
+ logger.debug("No class specified, using base Result.")
+ for key in ["__module__", "__name__"]:
+ if key in data:
+ del data[key]
+ return cls(**data)
+
+ @classmethod
+ @docstring(_load_doctstring.format(format="json"))
+ def from_json(cls, filename=None, outdir=None, label=None, gzip=False):
filename = _determine_file_name(filename, outdir, label, 'json', gzip)
if os.path.isfile(filename):
@@ -592,7 +636,10 @@ class Result(object):
def save_to_file(self, filename=None, overwrite=False, outdir=None,
extension='json', gzip=False):
"""
- Writes the Result to a json or deepdish h5 file
+
+ Writes the Result to a file.
+
+ Supported formats are: `json`, `hdf5`, `arviz`, `pickle`
Parameters
==========
@@ -631,8 +678,8 @@ class Result(object):
try:
# convert priors to JSON dictionary for both JSON and hdf5 files
- dictionary["priors"] = dictionary["priors"]._get_json_dict()
if extension == 'json':
+ dictionary["priors"] = dictionary["priors"]._get_json_dict()
if gzip:
import gzip
# encode to a string
@@ -643,16 +690,25 @@ class Result(object):
with open(filename, 'w') as file:
json.dump(dictionary, file, indent=2, cls=BilbyJsonEncoder)
elif extension == 'hdf5':
- import deepdish
- for key in dictionary:
- if isinstance(dictionary[key], pd.DataFrame):
- dictionary[key] = dictionary[key].to_dict()
- deepdish.io.save(filename, dictionary)
+ dictionary["__module__"] = self.__module__
+ dictionary["__name__"] = self.__class__.__name__
+ with h5py.File(filename, 'w') as h5file:
+ recursively_save_dict_contents_to_group(h5file, '/', dictionary)
+ elif extension == 'pkl':
+ import dill
+ with open(filename, "wb") as ff:
+ dill.dump(self, ff)
else:
raise ValueError("Extension type {} not understood".format(extension))
except Exception as e:
- logger.error("\n\n Saving the data has failed with the "
- "following message:\n {} \n\n".format(e))
+ import dill
+ filename = ".".join(filename.split(".")[:-1]) + ".pkl"
+ with open(filename, "wb") as ff:
+ dill.dump(self, ff)
+ logger.error(
+ "\n\nSaving the data has failed with the following message:\n"
+ "{}\nData has been dumped to {}.\n\n".format(e, filename)
+ )
def save_posterior_samples(self, filename=None, outdir=None, label=None):
""" Saves posterior samples to a file
diff --git a/bilby/core/utils.py b/bilby/core/utils.py
index f0a8b2ff5c8fb2d115170c727e3af30e8f8797b9..7bfb1faa98f6112e02498eb17ed3c0e7eacd843b 100644
--- a/bilby/core/utils.py
+++ b/bilby/core/utils.py
@@ -1314,3 +1314,167 @@ class tcolors:
VALUE = '\033[91m'
HIGHLIGHT = '\033[95m'
END = '\033[0m'
+
+
+def decode_from_hdf5(item):
+ """
+ Decode an item from HDF5 format to python type.
+
+ This currently just converts __none__ to None and some arrays to lists
+
+ .. versionadded:: 1.0.0
+
+ Parameters
+ ----------
+ item: object
+ Item to be decoded
+
+ Returns
+ -------
+ output: object
+ Converted input item
+ """
+ if isinstance(item, str) and item == "__none__":
+ output = None
+ elif isinstance(item, bytes) and item == b"__none__":
+ output = None
+ elif isinstance(item, (bytes, bytearray)):
+ output = item.decode()
+ elif isinstance(item, np.ndarray):
+ if "|S" in str(item.dtype) or isinstance(item[0], bytes):
+ output = [it.decode() for it in item]
+ else:
+ output = item
+ else:
+ output = item
+ return output
+
+
+def encode_for_hdf5(item):
+ """
+ Encode an item to a HDF5 savable format.
+
+ .. versionadded:: 1.1.0
+
+ Parameters
+ ----------
+ item: object
+ Object to be encoded, specific options are provided for Bilby types
+
+ Returns
+ -------
+ output: object
+ Input item converted into HDF5 savable format
+ """
+ from .prior.dict import PriorDict
+ if isinstance(item, np.int_):
+ item = int(item)
+ elif isinstance(item, np.float_):
+ item = float(item)
+ elif isinstance(item, np.complex_):
+ item = complex(item)
+ if isinstance(item, (np.ndarray, int, float, complex, str, bytes)):
+ output = item
+ elif item is None:
+ output = "__none__"
+ elif isinstance(item, list):
+ if len(item) == 0:
+ output = item
+ elif isinstance(item[0], (str, bytes)) or item[0] is None:
+ output = list()
+ for value in item:
+ if isinstance(value, str):
+ output.append(value.encode("utf-8"))
+ elif isinstance(value, bytes):
+ output.append(value)
+ else:
+ output.append(b"__none__")
+ elif isinstance(item[0], (int, float, complex)):
+ output = np.array(item)
+ elif isinstance(item, PriorDict):
+ output = json.dumps(item._get_json_dict())
+ elif isinstance(item, pd.DataFrame):
+ output = item.to_dict(orient="list")
+ elif isinstance(item, pd.Series):
+ output = item.to_dict()
+ elif inspect.isfunction(item) or inspect.isclass(item):
+ output = dict(__module__=item.__module__, __name__=item.__name__)
+ elif isinstance(item, dict):
+ output = item.copy()
+ else:
+ raise ValueError(f'Cannot save {type(item)} type')
+ return output
+
+
+def recursively_load_dict_contents_from_group(h5file, path):
+ """
+ Recursively load a HDF5 file into a dictionary
+
+ .. versionadded:: 1.1.0
+
+ Parameters
+ ----------
+ h5file: h5py.File
+ Open h5py file object
+ path: str
+ Path within the HDF5 file
+
+ Returns
+ -------
+ output: dict
+ The contents of the HDF5 file unpacked into the dictionary.
+ """
+ import h5py
+ output = dict()
+ for key, item in h5file[path].items():
+ if isinstance(item, h5py.Dataset):
+ output[key] = decode_from_hdf5(item[()])
+ elif isinstance(item, h5py.Group):
+ output[key] = recursively_load_dict_contents_from_group(h5file, path + key + '/')
+ return output
+
+
+def recursively_save_dict_contents_to_group(h5file, path, dic):
+ """
+ Recursively save a dictionary to a HDF5 group
+
+ .. versionadded:: 1.1.0
+
+ Parameters
+ ----------
+ h5file: h5py.File
+ Open HDF5 file
+ path: str
+ Path inside the HDF5 file
+ dic: dict
+ The dictionary containing the data
+ """
+ for key, item in dic.items():
+ item = encode_for_hdf5(item)
+ if isinstance(item, dict):
+ recursively_save_dict_contents_to_group(h5file, path + key + '/', item)
+ else:
+ h5file[path + key] = item
+
+
+def docstring(docstr, sep="\n"):
+ """
+ Decorator: Append to a function's docstring.
+
+ This is required for e.g., :code:`classmethods` as the :code:`__doc__`
+ can't be changed after.
+
+ Parameters
+ ==========
+ docstr: str
+ The docstring
+ sep: str
+ Separation character for appending the existing docstring.
+ """
+ def _decorator(func):
+ if func.__doc__ is None:
+ func.__doc__ = docstr
+ else:
+ func.__doc__ = sep.join([func.__doc__, docstr])
+ return func
+ return _decorator
diff --git a/bilby/gw/detector/interferometer.py b/bilby/gw/detector/interferometer.py
index 9a0c5b9a80fd1f4c54d64ae7f34467434268e625..72a00168e5a4e1e08f3bc055f9c787ed199ea9d8 100644
--- a/bilby/gw/detector/interferometer.py
+++ b/bilby/gw/detector/interferometer.py
@@ -5,7 +5,7 @@ import numpy as np
from matplotlib import pyplot as plt
from ...core import utils
-from ...core.utils import logger
+from ...core.utils import docstring, logger
from .. import utils as gwutils
from ..utils import PropertyAccessor
from .calibration import Recalibrate
@@ -704,19 +704,35 @@ class Interferometer(object):
plt.close(fig)
@staticmethod
- def _hdf5_filename_from_outdir_label(outdir, label):
- return os.path.join(outdir, label + '.h5')
+ def _filename_from_outdir_label_extension(outdir, label, extension="h5"):
+ return os.path.join(outdir, label + f'.{extension}')
- def to_hdf5(self, outdir='outdir', label=None):
- """ Save the object to a hdf5 file
+ _save_ifo_docstring = """ Save the object to a {format} file
- Attributes
- ==========
- outdir: str, optional
- Output directory name of the file, defaults to 'outdir'.
- label: str, optional
- Output file name, is self.name if not given otherwise.
- """
+ {extra}
+
+ Attributes
+ ==========
+ outdir: str, optional
+ Output directory name of the file, defaults to 'outdir'.
+ label: str, optional
+ Output file name, is self.name if not given otherwise.
+ """
+
+ _load_docstring = """ Loads in an Interferometer object from a {format} file
+
+ Parameters
+ ==========
+ filename: str
+ If given, try to load from this filename
+
+ """
+
+ @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 sys.version_info[0] < 3:
raise NotImplementedError('Pickling of Interferometer is not supported in Python 2.'
@@ -724,19 +740,16 @@ class Interferometer(object):
if label is None:
label = self.name
utils.check_directory_exists_and_if_not_mkdir('outdir')
- filename = self._hdf5_filename_from_outdir_label(outdir, label)
- deepdish.io.save(filename, self)
+ 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):
- """ Loads in an Interferometer object from an hdf5 file
-
- Parameters
- ==========
- filename: str
- If given, try to load from this filename
-
- """
import deepdish
if sys.version_info[0] < 3:
raise NotImplementedError('Pickling of Interferometer is not supported in Python 2.'
@@ -746,3 +759,23 @@ class Interferometer(object):
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"
+ ))
+ def to_pickle(self, outdir="outdir", label=None):
+ import dill
+ utils.check_directory_exists_and_if_not_mkdir('outdir')
+ filename = self._filename_from_outdir_label_extension(outdir, label, extension="pkl")
+ with open(filename, "wb") as ff:
+ dill.dump(self, ff)
+
+ @classmethod
+ @docstring(_load_docstring.format(format="pickle"))
+ def from_pickle(cls, filename=None):
+ import dill
+ with open(filename, "rb") as ff:
+ res = dill.load(ff)
+ if res.__class__ != cls:
+ raise TypeError('The loaded object is not an Interferometer')
+ return res
diff --git a/bilby/gw/detector/networks.py b/bilby/gw/detector/networks.py
index 93dd11b350552b6e2b3e2fc7f830556528248201..8abd64c3f7ed1eac15f61a90925b8b323fb9efb4 100644
--- a/bilby/gw/detector/networks.py
+++ b/bilby/gw/detector/networks.py
@@ -217,38 +217,47 @@ class InterferometerList(list):
for interferometer in self}
@staticmethod
- def _hdf5_filename_from_outdir_label(outdir, label):
- return os.path.join(outdir, label + '.h5')
+ def _filename_from_outdir_label_extension(outdir, label, extension="h5"):
+ return os.path.join(outdir, label + f'.{extension}')
- def to_hdf5(self, outdir='outdir', label='ifo_list'):
- """ Saves the object to a hdf5 file
+ _save_docstring = """ Saves the object to a {format} file
- Parameters
- ==========
- outdir: str, optional
- Output directory name of the file
- label: str, optional
- Output file name, is 'ifo_list' if not given otherwise. A list of
- the included interferometers will be appended.
- """
+ {extra}
+
+ Parameters
+ ==========
+ outdir: str, optional
+ Output directory name of the file
+ label: str, optional
+ Output file name, is 'ifo_list' if not given otherwise. A list of
+ the included interferometers will be appended.
+ """
+
+ _load_docstring = """ Loads in an InterferometerList object from a {format} file
+
+ Parameters
+ ==========
+ filename: str
+ If given, try to load from this filename
+
+ """
+
+ def to_hdf5(self, outdir='outdir', label='ifo_list'):
import deepdish
if sys.version_info[0] < 3:
raise NotImplementedError('Pickling of InterferometerList is not supported in Python 2.'
'Use Python 3 instead.')
label = label + '_' + ''.join(ifo.name for ifo in self)
utils.check_directory_exists_and_if_not_mkdir(outdir)
- deepdish.io.save(self._hdf5_filename_from_outdir_label(outdir, label), self)
+ 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):
- """ Loads in an InterferometerList object from an hdf5 file
-
- Parameters
- ==========
- filename: str
- If given, try to load from this filename
-
- """
import deepdish
if sys.version_info[0] < 3:
raise NotImplementedError('Pickling of InterferometerList is not supported in Python 2.'
@@ -260,6 +269,33 @@ class InterferometerList(list):
raise TypeError('The loaded object is not a InterferometerList')
return res
+ def to_pickle(self, outdir="outdir", label="ifo_list"):
+ import dill
+ utils.check_directory_exists_and_if_not_mkdir('outdir')
+ label = label + '_' + ''.join(ifo.name for ifo in self)
+ filename = self._filename_from_outdir_label_extension(outdir, label, extension="pkl")
+ with open(filename, "wb") as ff:
+ dill.dump(self, ff)
+
+ @classmethod
+ def from_pickle(cls, filename=None):
+ import dill
+ with open(filename, "rb") as ff:
+ res = dill.load(ff)
+ if res.__class__ != cls:
+ 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")
+
class TriangularInterferometer(InterferometerList):
diff --git a/requirements.txt b/requirements.txt
index 3ef1d047adb45453f7f066322d58d4505684f519..50a9de636a5c35d515d796d8d9da423232bbaf50 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,8 @@ corner
numpy<1.20
matplotlib>=2.0
scipy>=0.16
-pandas<1.2
+pandas
mock
dill
tqdm
+h5py
diff --git a/setup.py b/setup.py
index f80072463619aa009986fe58fb371ff94382a166..9f49d130bd56acb7772cfaff7fd41bf59b8e686a 100644
--- a/setup.py
+++ b/setup.py
@@ -57,6 +57,12 @@ def get_long_description():
return long_description
+def get_requirements():
+ with open("requirements.txt", "r") as ff:
+ requirements = ff.readlines()
+ return requirements
+
+
# get version info from __init__.py
def readfile(filename):
with open(filename) as fp:
@@ -86,16 +92,7 @@ setup(name='bilby',
'bilby.gw.eos': ['eos_tables/*.dat'],
'bilby': [version_file]},
python_requires='>=3.5',
- install_requires=[
- 'dynesty>=1.0.0',
- 'emcee',
- 'corner',
- 'dill',
- 'numpy<1.20',
- 'matplotlib>=2.0',
- 'pandas<1.2',
- 'scipy',
- 'tqdm'],
+ install_requires=get_requirements(),
entry_points={'console_scripts':
['bilby_plot=cli_bilby.plot_multiple_posteriors:main',
'bilby_result=cli_bilby.bilby_result:main']
diff --git a/test/gw/detector/interferometer_test.py b/test/gw/detector/interferometer_test.py
index 0e5a51e032a6f3ce9ac11466b547eacbd596530a..d204d6cbc719ff87279b9828a57d199ae74232b8 100644
--- a/test/gw/detector/interferometer_test.py
+++ b/test/gw/detector/interferometer_test.py
@@ -1,11 +1,14 @@
import sys
import unittest
+import pytest
+from packaging import version
from shutil import rmtree
import deepdish as dd
import mock
import numpy as np
from mock import MagicMock, patch
+import pandas
import bilby
@@ -364,29 +367,47 @@ 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):
if sys.version_info[0] < 3:
with self.assertRaises(NotImplementedError):
self.ifo.to_hdf5(outdir="outdir", label="test")
else:
self.ifo.to_hdf5(outdir="outdir", label="test")
- filename = self.ifo._hdf5_filename_from_outdir_label(
- 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 or sys.version_info[0] < 3, reason=skip_reason)
def test_to_and_from_hdf5_wrong_class(self):
- if sys.version_info[0] < 3:
- pass
- else:
- bilby.core.utils.check_directory_exists_and_if_not_mkdir("outdir")
- dd.io.save("./outdir/psd.h5", self.power_spectral_density)
- filename = self.ifo._hdf5_filename_from_outdir_label(
- outdir="outdir", label="psd"
- )
- with self.assertRaises(TypeError):
- bilby.gw.detector.Interferometer.from_hdf5(filename)
+ 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"
+ recovered_ifo = bilby.gw.detector.Interferometer.from_pickle(filename)
+ self.assertEqual(self.ifo, recovered_ifo)
+
+ def test_to_and_from_pkl_wrong_class(self):
+ import dill
+ with open("./outdir/psd.pkl", "wb") as ff:
+ dill.dump(self.ifo.power_spectral_density, ff)
+ filename = self.ifo._filename_from_outdir_label_extension(
+ outdir="outdir", label="psd", extension="pkl"
+ )
+ with self.assertRaises(TypeError):
+ bilby.gw.detector.Interferometer.from_pickle(filename)
class TestInterferometerEquals(unittest.TestCase):
diff --git a/test/gw/detector/networks_test.py b/test/gw/detector/networks_test.py
index 3627db3ba65349979d34c9147cfe916018cd6883..4484cfb12d526ecb11940e390e78b2e10c9c21c7 100644
--- a/test/gw/detector/networks_test.py
+++ b/test/gw/detector/networks_test.py
@@ -1,11 +1,14 @@
import sys
import unittest
+import pytest
from shutil import rmtree
+from packaging import version
import deepdish as dd
import mock
import numpy as np
from mock import patch, MagicMock
+import pandas
import bilby
@@ -320,6 +323,10 @@ 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):
if sys.version_info[0] < 3:
with self.assertRaises(NotImplementedError):
@@ -330,16 +337,30 @@ class TestInterferometerList(unittest.TestCase):
recovered_ifo = bilby.gw.detector.InterferometerList.from_hdf5(filename)
self.assertListEqual(self.ifo_list, recovered_ifo)
+ @pytest.mark.skipif(pandas_version_test or sys.version_info[0] < 3, reason=skip_reason)
def test_to_and_from_hdf5_wrong_class(self):
- if sys.version_info[0] < 3:
- pass
- else:
- dd.io.save("./outdir/psd.h5", self.ifo_list[0].power_spectral_density)
- filename = self.ifo_list._hdf5_filename_from_outdir_label(
- outdir="outdir", label="psd"
- )
- with self.assertRaises(TypeError):
- bilby.gw.detector.InterferometerList.from_hdf5(filename)
+ 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"
+ recovered_ifo = bilby.gw.detector.InterferometerList.from_pickle(filename)
+ self.assertListEqual(self.ifo_list, recovered_ifo)
+
+ def test_to_and_from_pkl_wrong_class(self):
+ import dill
+ with open("./outdir/psd.pkl", "wb") as ff:
+ dill.dump(self.ifo_list[0].power_spectral_density, ff)
+ filename = self.ifo_list._filename_from_outdir_label_extension(
+ outdir="outdir", label="psd", extension="pkl"
+ )
+ with self.assertRaises(TypeError):
+ bilby.gw.detector.InterferometerList.from_pickle(filename)
def test_plot_data(self):
ifos = bilby.gw.detector.InterferometerList(["H1", "L1"])