Merge branch 'gwastro:master' into lisa-emri-pe

.github/workflows/basic-tests.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         test-type: [unittest, search, docs]
     steps:
     - uses: actions/checkout@v3
@@ -50,7 +50,7 @@ jobs:
         export LAL_DATA_PATH=$PWD
         tox -e py-inference
     - name: store documentation page
-      if: matrix.test-type == 'docs' && matrix.python-version == '3.8'
+      if: matrix.test-type == 'docs' && matrix.python-version == '3.12'
       uses: actions/upload-artifact@v2
       with:
         name: documentation-page

.github/workflows/distribution.yml

@@ -20,13 +20,13 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
+          CIBW_BUILD: cp39-* cp310-* cp311-* cp312-*
           CIBW_SKIP: "*musllinux*"
           CIBW_ARCHS_MACOS: x86_64 arm64
       - uses: actions/upload-artifact@v2
@@ -40,10 +40,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - uses: actions/download-artifact@v2
       with:
         path: ./

.github/workflows/inference-workflow.yml

@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
@@ -25,7 +25,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |

.github/workflows/mac-test.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [macos-12]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -25,5 +25,4 @@ jobs:
         pip install --upgrade pip setuptools "tox<4.0.0"
     - name: run basic pycbc test suite
       run: |
-        sudo chmod -R 777 /usr/local/miniconda/
         tox -e py-unittest

.github/workflows/search-workflow.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
@@ -30,7 +30,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |

.github/workflows/tmpltbank-workflow.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
@@ -29,7 +29,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |

.github/workflows/tut-test.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/workflow-tests.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
@@ -34,7 +34,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |

.gitignore

@@ -4,8 +4,18 @@
 *.log
 dist/
 html/
-pycbc_inspiralc
 build/
 *.pyc
 docs/Makefile
-PyCBC.egg-info
+PyCBC.egg-info/
+pycbc/events/eventmgr_cython.cpp
+pycbc/events/simd_threshold_cython.cpp
+pycbc/fft/fftw_pruned_cython.cpp
+pycbc/filter/matchedfilter_cpu.cpp
+pycbc/filter/simd_correlate_cython.cpp
+pycbc/inference/models/relbin_cpu.cpp
+pycbc/types/array_cpu.cpp
+pycbc/vetoes/chisq_cpu.cpp
+pycbc/waveform/decompress_cpu_cython.cpp
+pycbc/waveform/spa_tmplt_cpu.cpp
+pycbc/waveform/utils_cpu.cpp

bin/all_sky_search/pycbc_add_statmap

@@ -26,8 +26,6 @@ def get_ifo_string(fi):
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
     help="List of coinc files to be combined")
 parser.add_argument('--background-files', nargs='+', default=None,

bin/all_sky_search/pycbc_apply_rerank

@@ -10,8 +10,6 @@ from shutil import copyfile
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--stat-files', nargs='+',
     help="Statistic files produced by candidate followup codes")
 parser.add_argument('--followup-file',

bin/all_sky_search/pycbc_average_psd

@@ -26,13 +26,11 @@ import argparse
 import numpy as np
 import pycbc
 from pycbc.io import HFile
-from pycbc.version import git_verbose_msg as version
 from pycbc.types import MultiDetOptionAction, FrequencySeries
 
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument('--input-files', nargs='+', required=True, metavar='PATH',
                     help='HDF5 files from pycbc_calculate_psd (one per '
                          'detector) containing the input PSDs to average.')

bin/all_sky_search/pycbc_bin_templates

@@ -8,12 +8,10 @@ import numpy as np
 
 import pycbc
 import pycbc.pnutils
-from pycbc.version import git_verbose_msg as version
 from pycbc.events import background_bin_from_string
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--ifo", type=str, required=True)
 parser.add_argument("--f-lower", type=float, default=15.,
                     help='Enforce a uniform low frequency cutoff to '

bin/all_sky_search/pycbc_bin_trigger_rates_dq

@@ -16,11 +16,9 @@ from pycbc.events.veto import (select_segments_by_definer,
                                segments_to_start_end)
 from pycbc.types.optparse import MultiDetOptionAction
 from pycbc.io.hdf import SingleDetTriggers
-from pycbc.version import git_verbose_msg as version
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--template-bins-file", required=True)
 parser.add_argument("--trig-file", required=True)
 parser.add_argument("--flag-file", required=True)

bin/all_sky_search/pycbc_calculate_psd

@@ -5,15 +5,13 @@ import logging, argparse, numpy, multiprocessing, time, copy
 from six.moves import zip_longest
 import pycbc, pycbc.psd, pycbc.strain, pycbc.events
 from pycbc.io import HFile
-from pycbc.version import git_verbose_msg as version
 from pycbc.fft.fftw import set_measure_level
 from pycbc.workflow import resolve_td_option
 from ligo.segments import segmentlist, segment
 set_measure_level(0)
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--low-frequency-cutoff", type=float, required=True,
                     help="The low frequency cutoff to use for filtering (Hz)")
 parser.add_argument("--analysis-segment-file",  required=True,

bin/all_sky_search/pycbc_coinc_findtrigs

@@ -2,8 +2,8 @@
 import copy, argparse, logging, numpy, numpy.random
 import shutil, uuid, os.path, atexit
 from ligo.segments import infinity
+import pycbc
 from pycbc.events import veto, coinc, stat, ranking, cuts
-import pycbc.version
 from pycbc.io import HFile
 from pycbc import pool, init_logging
 from numpy.random import seed, shuffle
@@ -12,7 +12,6 @@ from pycbc.types.optparse import MultiDetOptionAction
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument("--veto-files", nargs='*', action='append', default=[],
                     help="Optional veto file. Triggers within veto segments "
                          "contained in the file are ignored")

bin/all_sky_search/pycbc_coinc_hdfinjfind

@@ -6,12 +6,12 @@ files.
 import argparse, logging, types, numpy, os.path
 from ligo.lw import lsctables, utils as ligolw_utils
 from ligo import segments
+import pycbc
 from pycbc import events, init_logging
 from pycbc.events import indices_within_segments
 from pycbc.types import MultiDetOptionAction
 from pycbc.inject import CBCHDFInjectionSet
 from pycbc.io import HFile
-import pycbc.version
 from pycbc.io.ligolw import LIGOLWContentHandler
 
 
@@ -57,8 +57,6 @@ def xml_to_hdf(table, hdf_file, hdf_key, columns):
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--trigger-files', nargs='+', required=True)
 parser.add_argument('--injection-files', nargs='+', required=True)
 parser.add_argument('--veto-file')

bin/all_sky_search/pycbc_coinc_mergetrigs

@@ -4,9 +4,8 @@
 """
 
 import numpy, argparse, h5py, logging
-import pycbc.version
 from pycbc.io import HFile
-from pycbc import init_logging
+from pycbc import add_common_pycbc_options, init_logging
 
 def changes(arr):
     l = numpy.where(arr[:-1] != arr[1:])[0]
@@ -31,9 +30,7 @@ def region(f, key, boundaries, ids):
                      dtype=h5py.special_dtype(ref=h5py.RegionReference))
 
 parser = argparse.ArgumentParser()
-pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
+add_common_pycbc_options(parser)
 parser.add_argument('--trigger-files', nargs='+')
 parser.add_argument('--output-file', required=True)
 parser.add_argument('--bank-file', required=True)

bin/all_sky_search/pycbc_coinc_statmap

@@ -10,7 +10,7 @@ the FANs of any other gravitational waves in the dataset.
 import argparse, itertools
 import lal, logging, numpy
 from pycbc.events import veto, coinc, significance
-import pycbc.version, pycbc.pnutils, pycbc.io
+import pycbc.pnutils, pycbc.io
 import sys
 import pycbc.conversions as conv
 
@@ -35,8 +35,6 @@ class fw(object):
 parser = argparse.ArgumentParser()
 # General required options
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--coinc-files', nargs='+',
                     help='List of coincidence files used to calculate the '
                          'FAP, FAR, etc.')

bin/all_sky_search/pycbc_coinc_statmap_inj

@@ -6,15 +6,12 @@ with producing the combined foreground and background triggers
 """
 import argparse, logging, itertools, copy, pycbc.io, numpy, lal
 from pycbc.events import veto, coinc, significance
-import pycbc.version
 import pycbc.conversions as conv
 from pycbc import init_logging
 
 parser = argparse.ArgumentParser()
 # General required options
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--cluster-window', type=float, default=10,
                     help='Length of time window in seconds to cluster coinc '
                          'events [default=10s]')

bin/all_sky_search/pycbc_combine_coincident_events

@@ -9,7 +9,6 @@ import logging
 
 import pycbc
 from pycbc.io import HFile
-import pycbc.version
 
 def com(f, files, group):
     """ Combine the same column from multiple files into another file f"""
@@ -56,7 +55,6 @@ def com_with_detector_key(f, files, group):
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
                     help="List of coinc files to be redistributed")
 parser.add_argument('--output-file', help="name of output file")

bin/all_sky_search/pycbc_combine_statmap

@@ -5,12 +5,10 @@ significant foreground, but leaves the background triggers alone.
 """
 
 import numpy, argparse, logging, pycbc, pycbc.events, pycbc.io, lal
-import pycbc.version
 from ligo import segments
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
                     help="List of coinc files to be redistributed")
 parser.add_argument('--cluster-window', type=float)

bin/all_sky_search/pycbc_cut_merge_triggers_to_tmpltbank

@@ -21,18 +21,15 @@ Reduce a MERGE triggers file to a reduced template bank
 """
 
 import logging
-import imp
 import argparse
 import numpy
 import h5py
 import pycbc
-import pycbc.version
 from pycbc.io import HFile
+from pycbc import load_source
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument("--input-file", required=True,
                     help="Input merge triggers HDF file.")
 parser.add_argument("--output-file", required=True,
@@ -53,7 +50,7 @@ pycbc.init_logging(opt.verbose)
 
 bank_fd = HFile(opt.full_template_bank, 'r')
 
-modl = imp.load_source('filter_func', opt.filter_func_file)
+modl = load_source('filter_func', opt.filter_func_file)
 func = modl.filter_tmpltbank
 bool_arr = func(bank_fd)