PyCBC 2.8.5__tar.gz → 2.10.0__tar.gz

{PyCBC-2.8.5 → pycbc-2.10.0}/PKG-INFO

@@ -1,28 +1,64 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyCBC
-Version: 2.8.5
+Version: 2.10.0
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://pycbc.org/
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.8.5
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.10.0
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 Keywords: ligo,physics,gravity,signal processing,gravitational waves
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.16.0
+Requires-Dist: cython>=0.29
+Requires-Dist: numpy!=1.19.0,!=2.2.2,>=1.16.0
+Requires-Dist: scipy>=0.16.0
+Requires-Dist: astropy!=4.0.5,!=4.2.1,>=2.0.3
+Requires-Dist: matplotlib>=1.5.1
+Requires-Dist: mpld3>=0.3
+Requires-Dist: pillow
+Requires-Dist: h5py!=3.7.0,>=3.0.0
+Requires-Dist: jinja2
+Requires-Dist: Mako>=1.0.1
+Requires-Dist: beautifulsoup4>=4.6.0
+Requires-Dist: tqdm
+Requires-Dist: setuptools
+Requires-Dist: gwdatafind
+Requires-Dist: pegasus-wms.api>=5.1.1
+Requires-Dist: igwn-ligolw
+Requires-Dist: igwn-segments
+Requires-Dist: lalsuite!=7.2
+Requires-Dist: lscsoft-glue>=1.59.3
+Requires-Dist: pykerr
 Provides-Extra: cuda
+Requires-Dist: pycuda>=2015.1; extra == "cuda"
+Requires-Dist: scikit-cuda; extra == "cuda"
 Provides-Extra: igwn
-License-File: LICENSE
+Requires-Dist: ciecplib>=0.7.0; extra == "igwn"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
 

{PyCBC-2.8.5 → pycbc-2.10.0}/PyCBC.egg-info/PKG-INFO

@@ -1,28 +1,64 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyCBC
-Version: 2.8.5
+Version: 2.10.0
 Summary: Core library to analyze gravitational-wave data, find signals, and study their parameters.
 Home-page: http://pycbc.org/
-Download-URL: https://github.com/gwastro/pycbc/tarball/v2.8.5
+Download-URL: https://github.com/gwastro/pycbc/tarball/v2.10.0
 Author: The PyCBC team
 Author-email: alex.nitz@gmail.org
 Keywords: ligo,physics,gravity,signal processing,gravitational waves
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.16.0
+Requires-Dist: cython>=0.29
+Requires-Dist: numpy!=1.19.0,!=2.2.2,>=1.16.0
+Requires-Dist: scipy>=0.16.0
+Requires-Dist: astropy!=4.0.5,!=4.2.1,>=2.0.3
+Requires-Dist: matplotlib>=1.5.1
+Requires-Dist: mpld3>=0.3
+Requires-Dist: pillow
+Requires-Dist: h5py!=3.7.0,>=3.0.0
+Requires-Dist: jinja2
+Requires-Dist: Mako>=1.0.1
+Requires-Dist: beautifulsoup4>=4.6.0
+Requires-Dist: tqdm
+Requires-Dist: setuptools
+Requires-Dist: gwdatafind
+Requires-Dist: pegasus-wms.api>=5.1.1
+Requires-Dist: igwn-ligolw
+Requires-Dist: igwn-segments
+Requires-Dist: lalsuite!=7.2
+Requires-Dist: lscsoft-glue>=1.59.3
+Requires-Dist: pykerr
 Provides-Extra: cuda
+Requires-Dist: pycuda>=2015.1; extra == "cuda"
+Requires-Dist: scikit-cuda; extra == "cuda"
 Provides-Extra: igwn
-License-File: LICENSE
+Requires-Dist: ciecplib>=0.7.0; extra == "igwn"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 ![GW150914](https://raw.githubusercontent.com/gwastro/pycbc-logo/master/pycbc_logo_name.png)
 

{PyCBC-2.8.5 → pycbc-2.10.0}/PyCBC.egg-info/SOURCES.txt

@@ -104,6 +104,7 @@ bin/hwinj/pycbc_generate_hwinj_from_xml
 bin/hwinj/pycbc_insert_frame_hwinj
 bin/hwinj/pycbc_plot_hwinj
 bin/inference/pycbc_inference
+bin/inference/pycbc_inference_create_calibration_config
 bin/inference/pycbc_inference_create_fits
 bin/inference/pycbc_inference_extract_samples
 bin/inference/pycbc_inference_model_stats
@@ -125,6 +126,7 @@ bin/inference/pycbc_inference_plot_samples
 bin/inference/pycbc_inference_plot_skymap
 bin/inference/pycbc_inference_plot_thermodynamic_integrand
 bin/inference/pycbc_inference_pp_table_summary
+bin/inference/pycbc_inference_savage_dickey
 bin/inference/pycbc_inference_start_from_samples
 bin/inference/pycbc_inference_table_summary
 bin/inference/pycbc_validate_test_posterior
@@ -271,6 +273,8 @@ examples/inference/analytic-normal2d/run.sh
 examples/inference/bbh-injection/make_injection.sh
 examples/inference/bbh-injection/run.sh
 examples/inference/bbh-injection/run_test.sh
+examples/inference/calibration_configuration_files/download_calibration_uncertainty_files_o1_o2_o3.sh
+examples/inference/calibration_configuration_files/generate_calibration_config.sh
 examples/inference/gw150914/plot.sh
 examples/inference/gw150914/run.sh
 examples/inference/gw150914/run_test.sh
@@ -714,6 +718,7 @@ test/lalsim.py
 test/test_array.py
 test/test_array_lal.py
 test/test_autochisq.py
+test/test_bhspec.py
 test/test_calibration.py
 test/test_chisq.py
 test/test_coinc_stat.py
@@ -732,7 +737,7 @@ test/test_frame.py
 test/test_frequencyseries.py
 test/test_infmodel.py
 test/test_injection.py
-test/test_io_live.py
+test/test_io_gracedb.py
 test/test_live_coinc_compare.py
 test/test_matchedfilter.py
 test/test_noise.py

{PyCBC-2.8.5 → pycbc-2.10.0}/PyCBC.egg-info/requires.txt

@@ -13,11 +13,10 @@ beautifulsoup4>=4.6.0
 tqdm
 setuptools
 gwdatafind
-pegasus-wms.api==5.0.9
-pegasus-wms.common==5.0.9
-python-ligo-lw>=1.7.0
+pegasus-wms.api>=5.1.1
+igwn-ligolw
 igwn-segments
-lalsuite==7.25.1
+lalsuite!=7.2
 lscsoft-glue>=1.59.3
 pykerr
 

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_coinc_hdfinjfind

@@ -4,7 +4,7 @@ files.
 """
 
 import argparse, logging, types, numpy, os.path
-from ligo.lw import lsctables, utils as ligolw_utils
+from igwn_ligolw import lsctables, utils as ligolw_utils
 import igwn_segments as segments
 import pycbc
 from pycbc import events, init_logging

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_distribute_background_bins

@@ -43,7 +43,7 @@ logging.info('%s coinc triggers' % len(d))
 for name, outname in zip(names, args.output_files):
     # select the coincs from only this bin and save to a single combined file
     locs = locs_dict[name]
-    e = d.select(numpy.in1d(d.template_id, locs))
+    e = d.select(numpy.isin(d.template_id, locs))
     logging.info('%s coincs in mass bin: %s' % (len(e), name))
     e.save(outname)
     f = pycbc.io.HFile(outname)

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_fit_sngls_by_template

@@ -21,12 +21,32 @@ import pycbc
 from pycbc import events, init_logging
 from pycbc.events import triggers, trigger_fits as trstats
 from pycbc.events import stat as statsmod
+from pycbc.events import cuts
 from pycbc.types.optparse import MultiDetOptionAction
 from pycbc.io import HFile
 
 #### DEFINITIONS AND FUNCTIONS ####
 
-def get_stat(statname, trigs, threshold):
+def get_stat(args, trigs, threshold):
+    """
+    Select the triggers and calculate the single detector statistic.
+
+    Parameters
+    ----------
+    args: argparse.Namespace
+        The argparse object containing options and parameters.
+    trigs: dict
+        The dictionary of single detector trigger data.
+    threshold: float
+        The statistic threshold value for selecting triggers.
+
+    Returns
+    -------
+    np.concatenate(select): np.ndarray
+        A boolean array that selects the triggers.
+    np.concatenate(stat): np.ndarray
+        The statistic values of the selected triggers.
+    """
     # For now this is using the single detector ranking. If we want, this
     # could use the Stat classes in stat.py using similar code as in hdf/io.py
     # This requires additional options, so only change this if it's useful!
@@ -35,19 +55,32 @@ def get_stat(statname, trigs, threshold):
     select = []
     size = len(trigs['end_time'])
     s = 0
+    trigger_cut_dict, _ = cuts.ingest_cuts_option_group(args)
     while s < size:
         e = s + chunk_size if (s + chunk_size) <= size else size
 
         # read and format chunk of data so it can be read by key
         # as the stat classes expect.
         chunk = {k: trigs[k][s:e] for k in trigs if len(trigs[k]) == size}
-        
+        trigger_keep_bool = np.zeros(e-s, dtype=bool)
+
+        if len(trigger_cut_dict) > 0:
+            # Apply trigger cuts
+            trigger_keep_ids = cuts.apply_trigger_cuts(chunk, trigger_cut_dict)
+            chunk = {k: arr[trigger_keep_ids] for k, arr in chunk.items()}
+
         rank_method = statsmod.get_statistic_from_opts(args, [args.ifo])
         chunk_stat = rank_method.get_sngl_ranking(chunk)
 
         above = chunk_stat >= threshold
         stat.append(chunk_stat[above])
-        select.append(above)
+
+        if len(trigger_cut_dict) > 0:
+            trigger_keep_bool[trigger_keep_ids[above]] = True
+        else:
+            trigger_keep_bool[above] = True
+
+        select.append(trigger_keep_bool)
         s += chunk_size
 
     # Return boolean area that selects the triggers above threshold
@@ -119,6 +152,7 @@ parser.add_argument("--approximant", default="SEOBNRv4",
 
 statsmod.insert_statistic_option_group(parser,
     default_ranking_statistic='single_ranking_only')
+cuts.insert_cuts_option_group(parser)
 args = parser.parse_args()
 
 init_logging(args.verbose)

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_make_bayestar_skymap

@@ -22,7 +22,7 @@ import os
 import glob
 import tempfile
 
-from ligo.lw import lsctables, utils as ligolw_utils
+from igwn_ligolw import lsctables, utils as ligolw_utils
 
 import pycbc
 from pycbc.waveform import bank as wavebank

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_prepare_xml_for_gracedb

@@ -29,8 +29,8 @@ matplotlib.use('agg')
 
 import lal
 import lal.series
-from ligo.lw import lsctables
-from ligo.lw import utils as ligolw_utils
+from igwn_ligolw import lsctables
+from igwn_ligolw import utils as ligolw_utils
 from igwn_segments import segment, segmentlist
 
 import pycbc
@@ -131,11 +131,11 @@ for event in coinc_table:
 else:
     raise ValueError(f"event {args.event_id} not found in coinc table")
 
-coinc_event_table_curr = lsctables.New(lsctables.CoincTable)
+coinc_event_table_curr = lsctables.CoincTable.new()
 coinc_event_table_curr.append(event)
-coinc_inspiral_table_curr = lsctables.New(lsctables.CoincInspiralTable)
-coinc_event_map_table_curr = lsctables.New(lsctables.CoincMapTable)
-sngl_inspiral_table_curr = lsctables.New(lsctables.SnglInspiralTable)
+coinc_inspiral_table_curr = lsctables.CoincInspiralTable.new()
+coinc_event_map_table_curr = lsctables.CoincMapTable.new()
+sngl_inspiral_table_curr = lsctables.SnglInspiralTable.new()
 
 for coinc_insp in coinc_inspiral_table:
     if coinc_insp.coinc_event_id == event.coinc_event_id:

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_sngls_pastro

@@ -12,7 +12,7 @@ coincidences.
 
 import pycbc, pycbc.io, copy
 import argparse, logging, numpy as np
-from ligo.lw import lsctables, utils as ligolw_utils
+from igwn_ligolw import lsctables, utils as ligolw_utils
 from pycbc import conversions as conv
 from pycbc.events import veto
 from pycbc.io.ligolw import LIGOLWContentHandler

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/all_sky_search/pycbc_strip_injections

@@ -2,7 +2,7 @@
 import numpy, argparse, pycbc.pnutils, logging
 from pycbc.events import veto
 from pycbc.io.ligolw import LIGOLWContentHandler
-from ligo.lw import ligolw, table, utils as ligolw_utils
+from igwn_ligolw import ligolw, utils as ligolw_utils
 
 
 effd = {"H1":"eff_dist_h", "L1":"eff_dist_l", "V1":"eff_dist_v"}
@@ -26,7 +26,7 @@ pycbc.init_logging(args.verbose)
 
 logging.info('File: %s' % args.injection_file)
 indoc = ligolw_utils.load_filename(args.injection_file, False, contenthandler=LIGOLWContentHandler)
-sim_table = table.Table.get_table(indoc, 'sim_inspiral')
+sim_table = ligolw.Table.get_table(indoc, 'sim_inspiral')
 
 logging.info('%s Injections in file' % len(sim_table))
 

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/bank/pycbc_aligned_bank_cat

@@ -25,7 +25,7 @@ import logging
 import glob
 import argparse
 import numpy
-from ligo.lw import utils
+from igwn_ligolw import utils
 from pycbc import tmpltbank
 # Old ligolw output functions no longer imported at package level
 import pycbc.tmpltbank.bank_output_utils as bank_output

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/bank/pycbc_bank_verification

@@ -27,9 +27,9 @@ import logging
 import numpy
 import matplotlib
 matplotlib.use('Agg')
-import pylab
+from matplotlib import pyplot as plt
 
-from ligo.lw import lsctables, utils as ligolw_utils
+from igwn_ligolw import lsctables, utils as ligolw_utils
 
 import pycbc
 import pycbc.version
@@ -277,10 +277,10 @@ points_fittingfactor = numpy.array(points_fittingfactor)
 logging.info("Distances calculated.")
 
 if opts.histogram_output_file:
-    pylab.hist(points_fittingfactor, 100)
-    pylab.xlabel("Fitting factor")
-    pylab.ylabel("# of signals")
-    pylab.savefig(opts.histogram_output_file)
+    plt.hist(points_fittingfactor, 100)
+    plt.xlabel("Fitting factor")
+    plt.ylabel("# of signals")
+    plt.savefig(opts.histogram_output_file)
 
 if opts.print_distances:
     print()

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/bank/pycbc_geom_aligned_bank

@@ -31,8 +31,8 @@ import logging
 import configparser
 from scipy import spatial
 
-from ligo.lw import ligolw
-from ligo.lw import utils as ligolw_utils
+from igwn_ligolw import ligolw
+from igwn_ligolw import utils as ligolw_utils
 
 import pycbc
 import pycbc.psd

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/bank/pycbc_tmpltbank_to_chi_params

@@ -33,7 +33,7 @@ import argparse
 import logging
 import numpy
 
-from ligo.lw import lsctables, utils as ligolw_utils
+from igwn_ligolw import lsctables, utils as ligolw_utils
 
 from pycbc import tmpltbank, psd, strain
 from pycbc.io.ligolw import LIGOLWContentHandler

{PyCBC-2.8.5 → pycbc-2.10.0}/bin/hwinj/pycbc_generate_hwinj

@@ -22,10 +22,9 @@ import numpy
 import os
 import sys
 
-from ligo.lw import ligolw
-from ligo.lw import lsctables
-from ligo.lw import table
-from ligo.lw import utils
+from igwn_ligolw import ligolw
+from igwn_ligolw import lsctables
+from igwn_ligolw import utils
 
 import pycbc
 import pycbc.version
@@ -41,7 +40,7 @@ from pycbc.filter import sigmasq
 from pycbc.types import TimeSeries
 from pycbc.types.optparse import convert_to_process_params_dict
 from pycbc.io.ligolw import create_process_table
-from pycbc.waveform import get_td_waveform, td_approximants, taper_timeseries
+from pycbc.waveform import get_td_waveform, td_approximants
 
 def _empty_row(obj):
     """Create an empty sim_inspiral or sngl_inspiral row where the columns have
@@ -296,14 +295,15 @@ if opts.dquad_mon2 is not None:
 # You'd think that would it to redefine the table columns, but wait, it gets
 # worse!
 class SimInspiralNew(lsctables.SimInspiral):
-    __slots__ = tuple(map(table.Column.ColumnName,
+    __slots__ = tuple(map(ligolw.Column.ColumnName,
                           lsctables.SimInspiralTable.validcolumns))
 lsctables.SimInspiral = SimInspiralNew
 lsctables.SimInspiralTable.RowType = SimInspiralNew
 
 # create sim_inspiral table
-sim_table = lsctables.New(lsctables.SimInspiralTable,
-                          columns=lsctables.SimInspiralTable.validcolumns)
+sim_table = lsctables.SimInspiralTable.new(
+    columns=lsctables.SimInspiralTable.validcolumns
+)
 outdoc.childNodes[0].appendChild(sim_table)
 
 sim = _empty_row(lsctables.SimInspiral)
@@ -344,8 +344,9 @@ sim.waveform = waveform_string
 name, phase_order = legacy_approximant_name(sim.waveform)
 
 # create sngl_inspiral table
-sngl_table = lsctables.New(lsctables.SnglInspiralTable,
-                           columns=lsctables.SnglInspiralTable.validcolumns)
+sngl_table = lsctables.SnglInspiralTable.new(
+    columns=lsctables.SnglInspiralTable.validcolumns
+)
 outdoc.childNodes[0].appendChild(sngl_table)
 
 # create sngl_inspiral row for injection
@@ -426,7 +427,7 @@ for ifo in opts.instruments:
 
     # taper waveform
     logging.info('Tapering strain for %s', ifo)
-    strain = taper_timeseries(strain, tapermethod=sim.taper)
+    strain = strain.taper_timeseries(location=sim.taper)
 
     # FFT strain
     logging.info('FFT strain for %s', ifo)