https://github.com/gwastro/pycbc

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Revision Author Date Message Commit Date
13b15d5 Set for 1.9.0 release (#2031) 20 December 2017, 16:25:46 UTC
6c72769 Add sbank scripts to released virtualenvs (#2028) * Add sbank scripts to released virtualenvs * Needs full make && make install; also, avoid transferring the entire lalsuite history 19 December 2017, 21:03:20 UTC
369870a Check InferenceFile integrity (#2027) * turn on checkpointing in datasets * add check_integrity function * try to please codacy * whitespace 18 December 2017, 18:18:36 UTC
1755721 Avoid trying to do scatter plot if not enough parameters (#2010) * Avoid scatter point if can't plot scatter plot. * Change to one-liner. 18 December 2017, 14:16:16 UTC
7fd6e84 BUGFIX log terms in template bank, and add tidal terms support (#1941) * Template bank add tidal terms * Adding another get_chirp_params function * Fix issues in log terms for metric computation * Remove unused code now * Updating test cases * Remove unused imports * Add new test of metric match vs actual match * Codacy 15 December 2017, 13:55:44 UTC
8fbdcca Fix error in Travis lalsuite update, update lalsuite for Docker images (#2026) * Fix error in Travis lalsuite update * Also update lalsuite for Docker images * Try to patch the psycopg2 bug * Investigate why pg_config is still around * DIE PG_CONFIG!!! * Missing sudo 15 December 2017, 08:57:49 UTC
ca3872a Typo fix (#2025) 14 December 2017, 18:57:27 UTC
d02bdd9 remove phenomb_chi (#2023) * update triggers.py to use conversions module * remove references to phenomb_chi 14 December 2017, 10:43:59 UTC
5c942f7 Update lalsuite to enable merging #1941 (#2024) 14 December 2017, 10:36:38 UTC
4e8b65f Randomize optimal_SNR (#2022) * Randomize optimal_SNR * Use numpy's random 13 December 2017, 16:16:07 UTC
157d086 remove optimal snr kludge (#2018) 13 December 2017, 14:27:29 UTC
7c51d8c Fix label warning in Sphinx (#2021) * Fix label warning in Sphinx * Remove legend 13 December 2017, 11:22:37 UTC
c5ff007 fix some bugs in mcmc (#2019) 13 December 2017, 10:18:49 UTC
00fb627 Option to specify url type in frame_paths (#2016) * Added urltype option to frame.frame_paths * Fixes urltype default 12 December 2017, 15:09:36 UTC
bcee1a5 Mcmc sampler (#1960) * initial set-up * first working version * Bug fixes * Added normed=True to histogram plotting * removed unnecessary verbose argument * Updated simple MCMC sampler to inherit BaseMCMCSampler, with nwalkers set to 1 * removed "from pycbc.io import FieldArray" 12 December 2017, 13:10:45 UTC
effc83d Move PriorEvaluator and rename to JointDistribution (#2005) * move priorevaluator to distributions * rename to Joint Distribution * ws * remove import * forgotten import * move joint distribution to its own module * update help * add missing imports * remove some unused imports * simplify import test for jointdistribution 11 December 2017, 18:12:59 UTC
00877eb Add metadata to posterior plot. (#2013) 11 December 2017, 18:06:23 UTC
c841421 Call from class. (#2011) 11 December 2017, 16:51:56 UTC
9e057e1 rescale test_volcano likelihood evaluator (#2012) * rescale volcano center * update test_volcano documentation 11 December 2017, 13:38:23 UTC
5197e31 Bug-fix for pycbc_page_foreground (#2014) Not sure how this happened or didn't get picked up in automated tests, but `pycbc_page_foreground` is not currently a python executable. 11 December 2017, 07:17:34 UTC
c4e3849 Fix error in Travis test script (#2008) 06 December 2017, 18:06:16 UTC
9003d00 Fix import error in setup.py under Python 3 (#2007) `trace.fullmodname` was undocumented in Python 2 and actually became an internal function in Python 3. We should not depend on it. 04 December 2017, 17:54:04 UTC
5009f90 Add analytic distribution to travis test suite (#2006) * add inference test * test * update 02 December 2017, 18:57:44 UTC
a3f0363 remove pycbc-glue develop doc (#2004) 01 December 2017, 19:30:23 UTC
83f9bef make the pycbc inference docs a bit more heirarchical (#2003) * show more of the inference items in the top-level page * update to be more heirarchical 01 December 2017, 09:47:58 UTC
b1a9efa Do not raise an error if an unrecognized parameter is passed to the CBC generator (#2001) * warn user about unused parameters instead of raising error * edit message 30 November 2017, 21:09:33 UTC
056ffdf Fix the psd start/end times in the inference docs (#2000) @micamu just pointed out to me that the PSD start/end times in the inference docs are using a larger time than expected. The PSD start time should be the trigger time +/- the desired PSD data length (1024s) / 2. The way the script sets it up now, however, it uses the gps start/end time -/+ the data length / 2, giving a total data length of 1024s + 16s. This isn't terrible, it just results in using slightly more time than what you might expect. Still, better to fix to be obvious. 29 November 2017, 15:48:44 UTC
a0aca18 Update inference docs (#1998) * switch to using n-independent-samples, burn in function * add documentation about sampling and waveform transforms * add documentation about the analytic distributions * add more about likelihood evaluators * added n_samples env variable * fix typos * fix typo 29 November 2017, 13:47:05 UTC
42e5148 Add some basic documentation on using the merger catalog interface (#1992) * update install directions * add catalog examples * add catalog.rst 22 November 2017, 22:53:45 UTC
1d7aeaf Add intervals plot for inference injection run (#1990) * Add intervals plot exe. * Rebase. * Fix typo. 22 November 2017, 15:41:18 UTC
d7aeabc Add recovery plot for inference injection runs (#1989) * Add plotting script. * Fix typo in logging statement. * Rebase. * Move 1:1 line to 0. * Fix typo. * Add help message. 22 November 2017, 15:40:59 UTC
7317a34 add test volcano likelihood (#1983) * add TestVolcano * simplify parameterization * revert last change * fix typo in TestVolcano doc 20 November 2017, 16:06:11 UTC
e42285a Allow group of HDF injection file to be changed. (#1988) 20 November 2017, 15:03:59 UTC
417e88e Save injection parameters to InferenceFile (#1985) * Save injection parameters to InferenceFile * Write injections for each IFO. * Remove import. 18 November 2017, 19:38:09 UTC
577a1a7 set back to dev (#1987) 18 November 2017, 18:51:45 UTC
811e3d4 set to release (#1986) 18 November 2017, 17:39:21 UTC
7343a33 add gw170608 to catalog (#1984) 18 November 2017, 17:35:00 UTC
f76b2ee down-select temps in memory (#1981) 16 November 2017, 23:48:40 UTC
7c373d5 add check integrity option to query and read (#1978) 14 November 2017, 18:54:36 UTC
a20b59c Has pycbc_live only check access to GraceDB if upload enabled (#1980) * Has pycbc_live only check access to GraceDB if upload enabled * Only requires gracedb_upload arg to be called 14 November 2017, 16:53:38 UTC
f641491 be explicity about not using a relative import (#1977) * be explicity about not using a relative import * fix typo 14 November 2017, 14:25:25 UTC
605b5a7 add test Rosenbrock likelihood (#1979) * add TestRosenbrock * fix typo 14 November 2017, 12:06:28 UTC
2b57913 add detrend method to timeseries (#1969) 13 November 2017, 23:06:36 UTC
4085224 add test eggbox likelihood (#1974) * add TestEggbox * change docstring formatting and fix loglikelihood * retry travis 13 November 2017, 22:34:18 UTC
ccd1e3e Write samples to arrays instead of groups (#1967) * store samples as multi-dimensional arrays instead of as groups * fix typos * change how acls are written * change how acls written again; update emcee_pt * update deprecation warning * fix bugs in reading acls 13 November 2017, 20:41:07 UTC
54413c4 Simplify writing samples to inference file (#1964) * always write all data in memory to file * always write all data to end of datasets * typos * whitespace * more whitespace 10 November 2017, 15:02:19 UTC
e35668c Add option to choose percentiles in pycbc_inference_plot_posterior (#1963) * Add option to choose percentiles in pycbc_inference_plot_posterior * Change option name 10 November 2017, 11:23:26 UTC
41c4e60 Add save state support for emcee (#1961) * move read/write state to BaseSampler * optionally specify state to write * set emcee's internal random number generator state * fix emcee to version 2.2.1 * move reading samples to set_p0 * fix typo 10 November 2017, 11:02:14 UTC
a4b80ab add notch filter (#1948) * add notch filter * Update resample.py * Update timeseries.py * Update resample.py * Update timeseries.py * update comments * more text * ws 08 November 2017, 13:57:01 UTC
4e69fde add unit test for transforms (#1889) * Add KL divergence module. * Add transforms test. * Ignore some transforms. * Remove other PR. * Change funtion for arrays. * Revert transform change. * Fix transforms. * Switch super and sub class. * Require that returned spins match masses. * PEP-8. * Ensure primary/secondary for mass-spin transforms. * Add chirp_distance to set of ranges. * Remove import. * Use isinstance. 08 November 2017, 02:09:31 UTC
4bf922f add option to return and interpolate complex qtiles (#1959) * add option to return and interpolate complex qtiles * update naming * renaming 07 November 2017, 20:53:07 UTC
c94f4e2 Add time-domain ringdown class in waveform generator module (#1951) 07 November 2017, 13:25:45 UTC
d5bd40b splitbank: add mchirp sort option (#1958) * splitbank: add mchirp sort option * fixup splitbank * fixup splitbank - remove redundant lines 01 November 2017, 19:26:33 UTC
137a08b Allow fields to be added that are a single value (#1957) * allow fields to be added that are a single value * use function to ensure list of arrays * remove if statement * put if statement back 01 November 2017, 18:30:25 UTC
2ac88b2 Give meaningful error when priors section missing (#1956) * give meaningful error when priors section missing * comment out unused variables in example ini file * fix update for travis 31 October 2017, 08:03:33 UTC
e3b8d4a Simplify, add log spacing image interpolation (#1954) 30 October 2017, 11:27:28 UTC
c9b9c2f Add function to perform the KS test to indicate if chains are burned in (#1952) * Add a function to perform the KS test to find the point of burn in * Fix doc * Sorting the array of samples is not required if we use scipy.ks_2samp * remove unused import * Move imports to top of the module and remove unused import * Shortcut to check the p-value criteria * Fill up burn in arrays after determining if chains have burned in 27 October 2017, 09:51:58 UTC
b175539 Add test gaussian likelihood (#1953) * move data/waveform gen to BaseLikelihood; add TestNormal * rearrange kwargs * add support to pycbc_inference * fix bug in multivariate init * allow for no static args * fix bugs in implementation * remove static args * remove expectation of waveform_generator, ifos, static_args * fix bugs * update travis test * whitespace 27 October 2017, 09:21:30 UTC
eaf3600 Save burn-in state to file (#1946) * save burn in state to file * only count samples if sampler is burned in * fix bugs * fix bug causing all false to always be returned 25 October 2017, 08:59:37 UTC
620d139 E@H: compile own Python on Debian 4 (#1949) - It gets increasingly difficult to work with the system's Python (and pip) that's linked with a pretty ancient version of libssl. So build an own Python with a newer openssl version. - pyOpenSSL was probably pinned to version 0.13 by requirements of Pegasus, which are now obsolete, so is the pinning - If pyssl_from=tarball, pyOpenSSL 0.13 and matching openssl-1.01p will be installed. Otherwise openssl-1.0.2l will be compiled and the latest available versiomn of pyOpenSSL will b einstalled (via pip). - Python compilation: rehash to make sure to use the newly built versions of python and pip, check for dbhas early as if it's missing, something must have gone wrong already during Pythoni compilation / installation 24 October 2017, 12:38:03 UTC
cdf3255 add indoc attribute if xmldoc is loaded (#1945) 24 October 2017, 09:39:34 UTC
ef3e60d bump M2Crypto version 23 October 2017, 06:46:33 UTC
b82ee4e add openssl for debian 20 October 2017, 19:19:50 UTC
dc4153d install swig for debian 20 October 2017, 18:51:49 UTC
5ab7f1c Install the current LDG version of M2Crypto 20 October 2017, 18:22:29 UTC
9895f71 Add new waveform example (#1943) 20 October 2017, 11:10:54 UTC
3bc36e7 Numpy scheme (#1942) * Add start of numpy scheme * Add matchedfilter_numpy * Bugfix * Rename function 19 October 2017, 09:08:35 UTC
5a53139 add gw170817 to catalog update to losc urls which work on azure (#1940) 17 October 2017, 17:10:26 UTC
8a843b0 debug debian build 16 October 2017, 21:20:38 UTC
af803b1 Allow extract samples to write CSV. (#1921) * Allow extract samples to write CSV. * Change plot to load. * Remove --csv. * Indent. * Copy over likelihood stats. * Change docstring. 16 October 2017, 17:34:07 UTC
a0b49bb add gw170814, use requests which is more robust (#1939) 10 October 2017, 17:05:01 UTC
be8982d Distance to chirp distance transform (#1932) * Add a chirp dist and mchirp to lum dist function * Add luminosity dist to chirp dist transform * Add chirp_distance to location parameters list * ws * Tried to make the dquad module easier to read * Make mchirp an input in forward and reverse transforms for chirp distance transform * Make ref_mass an attribute of the class * Make _inputs and _outputs to be class attributes inside __init__ * Fixed docs * Added blank lines where required * Added more blank lines where required * Fix label for chirp distance * fix doc for dquadmon 10 October 2017, 17:04:08 UTC
ff7e04a Gate template along with data (#1862) * add ability to apply gates to generator * apply gates to templates * remove logging message * resize to power 2 to prevent memory growth * use for loop instead of list comprehension * remove logging message 10 October 2017, 15:00:51 UTC
31c3acd fix nans in noise generator (#1938) * noise gen fixes * ws 10 October 2017, 03:12:17 UTC
5261264 remove cuda tf2 (#1934) 10 October 2017, 03:08:55 UTC
a8107bb upload_xml_to_gracedb: allow thresholding on IFAR (#1904) 06 October 2017, 19:56:11 UTC
f9e80d9 Add an ifos argument to plot_psd (#1917) * add ifos argument to plot psd * help doc 06 October 2017, 19:07:02 UTC
d52a414 fix tiny bug in hexplots (#1915) 06 October 2017, 18:20:27 UTC
6735bca add image to readme to make it less dry. (#1936) * update readme * mistake * add flash image * update readme 04 October 2017, 09:46:10 UTC
2bdb0a4 add some basic classes for accessing information about cbc events (#1933) * add a basic gw catalog access * update codacy 03 October 2017, 21:40:16 UTC
0ec70ee add function to align waveforms (#1929) * add function to align waveforms * add extra * fix typo * ws * round to power 2, and add warning about waveforms split across boundary * allow to turn off resizing, add warning * Update utils.py 03 October 2017, 15:23:32 UTC
4a40f13 Minor change to fix display of FAP for PyGRB results (#1930) 03 October 2017, 15:20:48 UTC
2b5a028 add nl tides modification to phase (#1931) * add nl tides model * add nl tides * nl * touch * ws * Typo in documentation 01 October 2017, 11:30:53 UTC
7122717 remove unused test (#1935) 01 October 2017, 08:45:11 UTC
6df24ad fix for multi file changes, and for multi-tempered sampler (#1926) 27 September 2017, 20:11:20 UTC
7d318e9 add fir convenience functions (#1928) 25 September 2017, 16:48:08 UTC
e8bf153 New banksim skymax code (#1899) 23 September 2017, 00:20:46 UTC
ebb9ffa Update inspiral_skymax (#1898) 23 September 2017, 00:20:25 UTC
bd4d712 add mode_array support for get_td_waveform (#1925) * add mode_array support for get_td_waveform mode_array was introduced in lalsimulation in this redmine issue https://bugs.ligo.org/redmine/issues/5592 see example python script: https://bugs.ligo.org/redmine/attachments/5911/mode-array-example.py It is a method that allows the user to specify the exact (l,m) modes to use when generating a waveform. Currently on the NR waveforms are supported. This patch adds the mode_array parameter to get_td_waveform Note: the default behaviour is completely unchanged. edit input to int list of 2-tupples waveform.py : add try except for modearray waveform.py trying to fix bkwrd comp for modearray simplify implementation change from None to 0 Signed-off-by: Sebastian Khan <Sebastian.Khan@LIGO.org> * waveform.py: remove try/exp 20 September 2017, 08:03:43 UTC
8f7e735 Finalize matched-filter higher-order modes 19 September 2017, 12:50:07 UTC
cd11b5a Coded up u_value function 19 September 2017, 12:50:07 UTC
a09371a Add HOM matched-filter 19 September 2017, 12:50:07 UTC
c849004 Add unit test for distributions (#1883) * Add KL divergence module. * Add example configuration file. * Add distributions unit test. * Check that all designated distributions are being checked. * Add KL divergence unit test for rvs and pdf. * Add in unit test for power law distributions. * Remove extras. * Add unit test to cross check the logpdf and pdf functions. * Add solid angle test. * More verbose error. * Replace kl module with entropy module. * Replace one more call. * Address codacy. 18 September 2017, 14:18:36 UTC
5ce69bc allow for different sized kde (#1908) 18 September 2017, 14:16:49 UTC
ba0dc5d Add waveform transforms, and CustomTransform (#1920) * first pass at adding CustomTransform class * add functions * add from config, remove inverse for now * add waveform transforms to likelihood * add waveform transforms to pycbc_inference * fix bugs * fix more bugs * fix doc 16 September 2017, 22:10:52 UTC
5c16927 add iloveq conversion (#1919) * add iloveq conversion * Update conversions.py * Update conversions.py * Update conversions.py 16 September 2017, 15:23:15 UTC
cdff0d7 Use recent version of pyOpenSSL (#1918) (cherry picked from commit 32a4bb23e44592f69551570004c476fbd47a29ac) 16 September 2017, 09:52:40 UTC
aae0849 Fix bug when plotting colorbar (#1916) * fix zarg, zlabel in plot_posterior * don't break multiple files 13 September 2017, 13:26:22 UTC
a3edbe7 Allow multiple posteriors overlaid on each other (#1892) * Add multiple plotting posteriors. * Remove unused LaTeX package. 11 September 2017, 11:46:20 UTC
bf1c3e1 Set back to development 10 September 2017, 14:16:31 UTC
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