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This renames the input sftfilepath to sftfilepattern and adds
documentation on how that should be used, i.e. a colon separated list of
wildstring or exact matches. In globbing for all matches, the colon
split is added in. sftfilepath is still used by `Writer` since
an exact path is known.

Gregory Ashton authored Jul 17, 2017 and Gregory Ashton committed Jul 17, 2017

If there are multiple detectors, then multiple .sft files are generated.
This updates the attribute 'sftfilename' -> 'sftfilenames', a list of
those files while also updating 'sftpilpath' to a colon separated list
of the relevant sft files.

If there are multiple detectors, then multiple .sft files are generated.
This updates the attribute 'sftfilename' -> 'sftfilenames', a list of
those files while also updating 'sftpilpath' to a colon separated list
of the relevant sft files.

The command line argument is matched to formatting used by MFD to
reconstruct the argument (using .16g) formatting. Ideally, all REAL8
should use this formatting.

Removes the forced `int` for `fmin` in MFD. As noted by David, this
isn't required.

 -ported check from MCMC search
 -bug: for single-str SFT path, glob list comprehension
  was trying every single character

 -try-except wrapper for subprocess.check_output()
 -use this for MFDv5 call (properly terminate at error!)
 -and for other small utility calls
 -use unique variable names for cl strings too

 -first check $DISPLAY environment variable
 -then use non-interactive "AGG" backend if necessary

- Add peak detection utilities
- Move generate_loudest
- Add SSBprec pass through to MCMC searches
- Fix convergence stat (missing sqrt)
- Minor fixes to plot_walkers (put detection statistic behind walkers)

- Adds injectSources to a variety of other methods
- Adds conversion of injectSource to pfs_input

If the given tstart is before the minStartTime this will error - so
instead, select the minStartTime

Previously, if the data span was shorter than the requested tstart-tend,
the code would choke when attempting to calculate twoF over a range
without any data. Instead, the code now automatically only compute twoF
over a range with data in it.

1) Add ability to in F0s, F1s etc in grid search directly (use tuple as (is)
2) Update cumulative legend
3) Add option to produce pfs_input directly to calculate_pfs
4) Fix spelling mistake
5) Update transient example in the paper

- Adds option to underplot the preducted Fstat 1-sigma variation in
  twoF_cumulative plots
- Adds isolated function to predict Fstat (wrapper to lalapps function)
- Adds detector colours dictionary: use elsewhere

- Expose generate_loudest
- add check if par exists
- All read_par to read_loudest
- Make the default save_fig to be True in plot_corner

Makes this an optional module, adds it to the requirements and README.md

A hack fix for the internal error in LALSUITE - this should be reversed
once we have solved the fundamental issue: if the data contains no sfts
for that period, return 0 not nan

If SFTs where not loaded, i.e. if injectSources was used, no timestamps
are generated. In such a case don't attempt to used them.

- Adds debug information
- If no data is in a given segment, a nan will be produced. Rather than
  summing this, the code will now replace it with zero and spit out a
  debug message to the effect.

As far as I can tell this should not be here (transient=True) in this
case. Nevertheless, I'm leaving it commented as this is quite a core
routine and I wish to remind myself to investigate it further.

- Adds a simple interface to get grid search given uniform prior
- Fixes detector -> detectors bug (previous versions, the constrains
  where not actually set)
- Adds title functionality to plot2D

- Addresses incorrecelt named attributes and prevents error if
  sftfilepath is not specified

Also adds thetas_at_ref data to the Writer object

Now forces use of dtglitch = None for no glitches

1) Adds 'add_noise' option (defaults to true)
2) Better checking of Writer for if all glitch parameters have the same
length (avoid strange errors)
3) Fixes issue in which the tqdm ignore command was itself ignored