* Switch FFTW/MKL order of preference

* Swap backend order and force gomp import

* FIx typo

* Do need openmpi in tox.ini

* Fix bug in MKL error function

* Force FFTW on this one.

* CC

* Requested Josh changes

* Add corner plotting script for template banks

* Comment where premerger duration has been subtracted from template duration in bank_conversions

* add premerger_duration to bank_conversions.py

* Move premerger duration into bank_conversions

* Use bank's approximant

* Dont plot signular values as default

* CC complaints

* docstring

* TDC comments

* Keep approximant kwarg as default, TDC comments 2

* Add a possibility for defaultvalues sections in config files

* do not allow [section] and [section-defaultvalues] options

* defaultvalues for top-level sections only

* underscore on add_ini_opts

* Replace LOSC with GWOSC

* Fix leftover Python 2-ism

* Try to improve codeclimate

* Try to fix codeclimate

* Try to fix codeclimate

* Try to fix codeclimate

* Exclude IFO sections when looping through the get_subsections for plots

* Add an example whihc would have previously failed into the search config

* Add single-detector options into workflow

* Fix a couple of isses which make results pages weird

* fix

* fix gen.sh to use correct workflow generator

* revert change made in error

* A couple of points which state coincident when it may not be

* unexpected events

* added temp-volume in cl

* added rejection sampling

* added indexing of mchirp in fit_param

* added compensation factor

* added corrections

* added more corrections

* added random number generator seed

* added mchirp instead of log(mchirp) in rejection samp

* Use probabilities to compensate downsampled kde

* Try to deal with flaky failures when apt-getting (#4384)

* Implement pre-cuts in fit_over_multiparam for efficiency (#4374)

* Make some efficiency savings in pycbc_fit_sngls_over_multiparam

* Missing logging line in once case

* Add in progress reporting, in case of silent failure

* I thought we needed some leeway, but we don't

* TD comments

* Simplify comment

* Migrate to new gwdatafind API (#4383)

* Migrate to new gwdatafind API

* CC and one regression fix

* One more style change

* Don't need these options now

* Revert "Don't need these options now"

This reverts commit 6f2ed1b.

* Add a Fisher distribution for sky locations (#4209)

* Update transforms.py

Adding new_z_to_euler and rotate_euler from pylal.sphericalutils

* Update sky_location.py

Added new class FisherDist for drawing from sky locations (in ra, dec)

* Update sky_location.py

Included help message for fisherDist

* Update sky_location.py

* Code climate issues

* Code climate issues

* Code-climate changes

* Code climate issues

* Code climate issues

* Update transforms.py

changed lal.PI to numpy.pi in new_z_to_euler

* Update transforms.py

minor changes

* Update sky_location.py

updated docstring, did changes to make the code look more simple

* Update sky_location.py

typos corrected

* Update sky_location.py

code climate changes

* Update sky_location.py

* Update sky_location.py

Included the definitions rvs_polaz and rvs_radec

* Update transforms.py

Included the definitions decra2polaz and polaz2decra

* Update sky_location.py

* Update transforms.py

code climate issues fixed

* Update sky_location.py

code climate issues fixed

* Update sky_location.py

code climate issues

* Update sky_location.py

fixed code climate issues

* Update sky_location.py

fixed code climate issues

* Update sky_location.py

* Update pycbc/distributions/sky_location.py

Co-authored-by: Tito Dal Canton <tito@dalcanton.it>

* Update sky_location.py

* Update sky_location.py

* Update transforms.py

modified polaz2decra to polaz2radec

* Update sky_location.py

* Update sky_location.py

Forgotten polaz2decra --> polaz2radec

* Update sky_location.py

Code climate fixes

* Update sky_location.py

Updated the code for checking the effectiveness of running from config file

* Create sky_location_old.py

* modified to include from config

* Modified to run from config file

* Added Fisher distribution to the lista of available distributions

* Delete sky_location_old.py

* Update sky_location.py

* Renamed Fisher to FisherSky

* Updated the name to FisherSky

* changed Fisher to FisherSky in __all__

* removed decra2polaz and polaz2radec to conversions

* Included def decra2polaz, polaz2radec in line 859

* Added angle_unit option

* removed decra2polaz and polaz2decra

* made carresction

* made corrections

* Corrected the typing error while removing recra2polaz

* Modified angle_unit and updated init file

* Empty line on 852 retrieved

* corrected

* Empty line on852 retrieved

* Fixed code climate issues

* Sigma conversion taken care of

* Fixed code climate issues

* Update sky_location.py

Codeclimate

* Update test_distributions.py

Adding fisher_sky to the list of distributions that do not undergo the distribution unittests.

* Update sky_location.py

Syntax fixed.

* Update sky_location.py complying to codeclimate

* Refactor using scipy's Rotation

* Improve docstring and make warning stricter

* Update pycbc/distributions/sky_location.py

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>

* Update pycbc/distributions/sky_location.py

right angle to correct angle

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>

* Update sky_location.py

logging issue solved

---------

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>
Co-authored-by: Tito Dal Canton <tito@dalcanton.it>
Co-authored-by: P Prasia <prasia.p@ldas-pcdev2.gw.iucaa.in>
Co-authored-by: Tito Dal Canton <tito.canton@ligo.org>

* add in several missing marginalization combinations (#4376)

* allow polarization marginalization with earth rotation

* add in missing marg combos

* fixes

* fixes

* fixes

* cleanup

* cc

* cc

* Try to fix CI tests (#4394)

* Switch FFTW/MKL order of preference

* Swap backend order and force gomp import

* FIx typo

* Do need openmpi in tox.ini

* Fix bug in MKL error function

* Force FFTW on this one.

* CC

* Requested Josh changes

* Add bank corner plot (#4339)

* Add corner plotting script for template banks

* Comment where premerger duration has been subtracted from template duration in bank_conversions

* add premerger_duration to bank_conversions.py

* Move premerger duration into bank_conversions

* Use bank's approximant

* Dont plot signular values as default

* CC complaints

* docstring

* TDC comments

* Keep approximant kwarg as default, TDC comments 2

* Added an OSError exception to MKL check (#4390)

* Add a possibility for defaultvalues sections in config files (#4385)

* Add a possibility for defaultvalues sections in config files

* do not allow [section] and [section-defaultvalues] options

* defaultvalues for top-level sections only

* underscore on add_ini_opts

* Remove default sections from get_subsections (#4399)

* Update setup-python action to v4 (#4400)

* Replace LOSC with GWOSC (#4401)

* Replace LOSC with GWOSC

* Fix leftover Python 2-ism

* Try to improve codeclimate

* Try to fix codeclimate

* Try to fix codeclimate

* Try to fix codeclimate

* Exclude IFO sections when looping through the get_subsections (#4402)

* Exclude IFO sections when looping through the get_subsections for plots

* Add an example whihc would have previously failed into the search config

* Offline singles in workflow (#4386)

* Add single-detector options into workflow

* Fix a couple of isses which make results pages weird

* fix

* fix gen.sh to use correct workflow generator

* revert change made in error

* A couple of points which state coincident when it may not be

---------

Co-authored-by: Thomas Dent <thomas.dent@usc.es>
Co-authored-by: Ian Harry <ian.harry@ligo.org>
Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org>
Co-authored-by: Prasia-Pankunni <116145091+Prasia-Pankunni@users.noreply.github.com>
Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>
Co-authored-by: Tito Dal Canton <tito@dalcanton.it>
Co-authored-by: P Prasia <prasia.p@ldas-pcdev2.gw.iucaa.in>
Co-authored-by: Tito Dal Canton <tito.canton@ligo.org>
Co-authored-by: Alex Nitz <alex.nitz@gmail.com>
Co-authored-by: Arthur Tolley <32394213+ArthurTolley@users.noreply.github.com>
Co-authored-by: Tito Dal Canton <tito.dalcanton@ijclab.in2p3.fr>

…ctionary (#4408)

Co-authored-by: KHUN PHUKON <khun.phukon@ligo.org>

* unexpected events

* added temp-volume in cl

* added injection kde

* retaining single ifo injection information

* Update pycbc_grb_inj_finder

Update according to requested changes from pull request review.

* Adding more specific comments

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>

* Adding more specific comments

out_dict changed to "output dictionary" in comment

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>

* Remove xlen

Removed xlen from cp_dataset_cont and instead calculated the length of xidentifier within the function.

* Reverting comment changes

* Remove extra comment

* Francesco's bug fix

Modified to simplify and correct where ifo information was jumbled together

* remove trig_dict and comment

* Removed extra lines

Removed line and datasets = {}

* Update to copyright comment and imports

Added our names and accounted for older python version.

---------

Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com>

Co-authored-by: Bhooshan Gadre <bhooshan.gadre@ligo.org>

* First part of moving venv build to igwn

* TESTING HACK. REVERT ME BEFORE MERGING!!!

* Try this

* Testing

* Revert "Testing"

This reverts commit c0b9ea0.

* Add new CVMFS commands

* Remove rsync filter which isn't working

* Add error wrap abort handler

* Update tools/venv_transfer_commands.sh

Co-authored-by: Duncan Macleod <duncan.macleod@ligo.org>

* Fix Ian's idiocy (attempt to) and HostChecking

* Set to abort for one last test

* One final publish test

* Add a chmod on the root CVMFS directory

* Prepare for merging

* Fix mistake

---------

Co-authored-by: Duncan Macleod <duncan.macleod@ligo.org>

#4176)

* Applying spin bounds based upon object mass~

* Updated reference to correct paper

* Adding spin bounds based on upper bounds of masses

* removing unnecessary additions

* Changing max mass2 to the right quantities

* Creating maxeta + reusing maxm1

* minor cleanup

* fixed min / max eta values

* fixed min / max eta

* Correcting maxm2 equation

* more readable/less redundant comment

---------

Co-authored-by: Thomas Dent <thomas.dent@usc.es>

* allow SNR optimizer to use the candidate point in the initial array of test points

* Update injection_smbhb.ini

* Update lisa_smbhb_relbin.ini

* Update lisa_smbhb_relbin.ini

* Update lisa_smbhb_relbin.ini

* Update lisa_smbhb_ldc_pe.rst

* Allow pycbc_multi_inspiral to search over a sky grid

* Adding the possibility to give either a sky grid or a sky position

* Change the names of the command lines --ra and --dec to --latitude and --longitude to match the changes made in pycbc_multi_inspiral and remove --processing-scheme because it makes the example crash

* Compute the antenna pattern only once for each sky position by keeping fp and fc together

* Replace the number of detectors from a hardcoded value to a variable

* add TDI AE PSD with confusion noise

* Update analytical_space.py

* fix cc issue

* Update analytical.py

* Space before colons in eos_utils.py help messages

* Enable extrapolation in eos_utils.py when NS is out of bounds

* Same check on shape in primary_mass and secondary mass

* Function to swap masses and spins of object 1 and object2

* Allow user to request for remnant_mass calculations: 1) extrapolation, 2) swapping object 1 and object 2 if mass2 > mass1, 3) treat as a (dark) BBH and NSBH with NS mass greater than a value probided by the user

* Renamned swap_companions to ensure_obj1_is_primary and generalized it

* codeclimate

* codeclimate

* Fixed line that was too long

* Fixed docstring and using keywords explicitly in all remnant_mass_* calls

* Renamed max_ns_mass as ns_bh_mass_boundary and improved help messages of functions

* Improved docstings

* Comprehensions in pycbc_brute_bank

* Complying to naming convention for spin components in spherical coordinates

* Update conversions.py

Fixing single code climate complaint.

* Prevent duplicates of the HLV page_ifar plot on the summary page

* Rename 'coincidences' as appropriate

…#4377)

* reset commit, add in high freqeuncy response to detector

* update

* fixes

* Revert "try pinning pegasus version (#4265)"

This reverts commit 398e135.

* Set for_planning flag for subworkflow output map

* Add version check so we don't break 5.0.3

* Also include 5.0.4

* update

* move long log into debug level, allow to set debug level

* fix workflow

* more explicit control of running external scripts for docs setup at same time

* fixes

* update

* try this

* try this ...

* update

* fixes

* update

* updates

* mistake in example search config file

* add failure if search runs too long

* unexpected events

* added temp-volume in cl

* setting the range for temp_kde

* setting min based on max kde

* logging for min template kde ratio

---------

Co-authored-by: Thomas Dent <thomas.dent@usc.es>

* Fixed indexing and autochisq argument in pycbc_multi_inspiral

* Only Hanford is labelled with a 1: avoiding pycbc_pygrb_plot_snr_timeseries failure.  trigs rather than trigs_or_injs as variable name in pycbc_pygrb_plot_coh_ifosnr

* Simplified and update pycbc_pygrb_plot_injs_results; adapted pycbc_pygrb_pp_workflow

* Forgotten comma

* Massive commit that stitches together pycbc_make_offline_grb_workflow and pycbc_pygrb_pp_workflow, by picking up the latter as a SubWorkflow.

* Massive commit that stitches together pycbc_make_offline_grb_workflow and pycbc_pygrb_pp_workflow, by picking up the latter as a SubWorkflow.

* Code-climate fixes

* More code-climate

* Import error flagged by code-climate

* Forgotten import fixes

* Minor cleanup of comments or commented out code lines

* Syntax fix

* Defining 2 empty file lists

* First part of PR 4288 review comments

* One more TODO

* opt_to_file is now configparser_value_to_file in pycbc/workflow/core.py

* Upgraded configparser_value_to_file with attrs keyword argument

* Using configparser_value_to_file throughout the PyGRB workflow generator

* Removing 2 unused PyGRB functions

* Removed LigolwCBCAlignTotalSpinExecutable, LigolwCBCJitterSkylocExecutable, and PycbcDarkVsBrightInjectionsExecutable support in general and removed LalappsInspinjExecutable support from PyGRB

* Codeclimate

* bank_veto_file variable needs to be a FileList, not a File

* Bug with tags for single IFO SNR plots workflow generator

* Fixing pycbc_pygrb_plot_coh_ifosnr

* Fixing layout of chi-square plots and section label for individual detector SNRs

* Codeclimate

* Codeclimate

* Codeclimate

* Removed FIXME for testing purposes

* First changes following up on PR review

* Second round of changes following up on PR review

* Flagging with an underscore grb utility functions not used outside the files they are defined in

* Flagging with an underscore grb utility functions not used outside the files they are defined in

* Removed _get_antenna_factors from PyGRB utily file

* Removed commented out function from pycbc_pygrb_plot_injs_results

* Substituted old unused code with a TODO

* Adding injection set name as an option in pycbc_pygrb_efficiency

* extend --> append for single files

* Documenting setup_pygrb_pp_workflow more appropriately

* Reverted name of _get_antenna_responses to get_antenna_responses; cleaner handling of bank-veto-bank-file for pycbc_multi_inspiral job setup.

* Line shortened

* Update analytical_space.py

* Update analytical_space.py

* Introduced a new arguement --skymap-only-ifos in pycbc_live

* Default skymap_only_ifos changed

* skymap_only_ifos as an attribute of LiveEventManager

* Test skymaps with V1 as skymap_only_ifos

* singles with skymap_only_ifos

* Removing commented lines etc

* A default seed for SNR opt

* Poking CI tests

I remove an unnecessary FIXME in the comments, but mostly doing this to restart the CI tests, which seem to have not linked up right.

---------

Co-authored-by: Souradeep Pal <souradeep.pal@ldas-pcdev4.ligo.caltech.edu>
Co-authored-by: Ian Harry <ian.harry@port.ac.uk>

* Fix the help message for stageout script

* Fix the help message for stageout and copy map scripts

---------

Co-authored-by: connor-mcisaac <connor.mcisaac@outlook.com>

…4350)

* more physical rwrap

* fix cc issues

* Update waveform.py

* Update companion.txt

* Update requirements.txt

* Update requirements.txt

* Update companion.txt

* 10 times tau

* Update companion.txt

* Update requirements.txt

* Update setup.py

* add check

* Update waveform.py

* allow user to choose rwarp

* fix cc issue

* set 0.2 as minimum rwrap

* Update waveform.py

* Remove most X509/globus links and hooks from PyCBC

* Need to update this one as well

* Don't need these options now

* Update docs/workflow/pycbc_make_coinc_search_workflow.rst

Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org>

---------

Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org>

* Allow pycbc inspiral to run with only numpy fft

* Remove Unneeded function from npfft.py

---------

Co-authored-by: Neeresh Kumar Perla <neereshkumarperla@Neereshs-MacBook-Pro.local>

* Add argument verification for singles

* Apply suggestions from code review

* remove --enable-single-detector-background

* Some more option-checking, and making fixed ifar option actually possible!

* fix options in example

* CC, typo

* CC

* Move versioning page generation into its own executable

* Allow duplicated executables

* 🤦

* CC changes

* CC

* save_fig_with_metadata cannot be imported from versioning

* Don't like spaces in arguments

* Ian's comments

* Dont pass executables as files

* Same type output from get_code_version_numbers

* bugfix - allow non-running of singles

* CC

* Revrt wrongly-added test chnages

* Add IMRPhenomXAS template duration

* removing assertion

* fixed fomatting for codeclimate

* Adding PhenomXAS duration and removing space fixes

* removing extra new line

---------

Co-authored-by: Bhooshan Gadre <bhooshan.gadre@ligo.org>

* dqsegdb2 update

* Update requirements-igwn.txt

Co-authored-by: Duncan Macleod <duncan.macleod@ligo.org>

---------

Co-authored-by: Ian Harry <ian.harry@ligo.org>
Co-authored-by: Duncan Macleod <duncan.macleod@ligo.org>