bilby_pipe merge requestshttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests2019-01-04T05:41:41Zhttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/18WIP: Rework singularity2019-01-04T05:41:41ZGregory Ashtongregory.ashton@ligo.orgWIP: Rework singularitySingularity offers "apps" these could potentially enable use like the following.
New users could get up and running with
```bash
$ singularity pull shub://lscsoft/bilby_pipe:dev
./lscsoft_-bilby_pipe-master.simg --help
```
I.e., `./ls...Singularity offers "apps" these could potentially enable use like the following.
New users could get up and running with
```bash
$ singularity pull shub://lscsoft/bilby_pipe:dev
./lscsoft_-bilby_pipe-master.simg --help
```
I.e., `./lscsoft_-bilby_pipe-master.simg` would act like the `bilby_pipe` executable. Then apps for "generation" and "analysis" would be used under the hood. In practise this is failing because it isn't clear how to pass the "singularity_image" file into the program.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/30WIP: Resolve "Expose bilby data-setting methods"2019-02-05T10:14:34ZGregory Ashtongregory.ashton@ligo.orgWIP: Resolve "Expose bilby data-setting methods"Closes #42Closes #42https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/35Added BNS example2019-02-19T22:44:38ZFrancisco HernandezAdded BNS exampleCloses #52Closes #52https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/43Change the extension of the default injection file2019-03-04T07:07:02ZSerguei OssokineChange the extension of the default injection filePreviosuly the default injection file had an extension .h5.
Now that the injections are dumped to json, the extension
is changed to .jsonPreviosuly the default injection file had an extension .h5.
Now that the injections are dumped to json, the extension
is changed to .jsonhttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/44inital attempt at adding compute roq weights2019-04-17T11:21:18ZColm Talbotcolm.talbot@ligo.orginital attempt at adding compute roq weightsThis attempts to add an additional stage in the pipeline between generation and analysis to compute ROQ weights.
I've no idea how to actually make this work though... @gregory.ashtonThis attempts to add an additional stage in the pipeline between generation and analysis to compute ROQ weights.
I've no idea how to actually make this work though... @gregory.ashtonGregory Ashtongregory.ashton@ligo.orgGregory Ashtongregory.ashton@ligo.orghttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/58WIP: Fix Checkpointing for cpnest2019-04-23T07:43:52ZMoritz HuebnerWIP: Fix Checkpointing for cpnestThis is supposed to fix the checkpointing by adding in automated self eviction.This is supposed to fix the checkpointing by adding in automated self eviction.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/61WIP: Add periodic eviction of jobs2019-04-24T07:03:10ZGregory Ashtongregory.ashton@ligo.orgWIP: Add periodic eviction of jobshttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/78WIP: Add pe workflow2019-05-27T23:26:09ZShanika GalaudageWIP: Add pe workflowadd workflow to select prior based on chirp mass which is read in from gracedbadd workflow to select prior based on chirp mass which is read in from gracedbhttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/83WIP: Add flag to pass and method to read coinc file2019-05-27T23:27:09ZShanika GalaudageWIP: Add flag to pass and method to read coinc fileAdds flag to pass the path of a json format coinc file.
GraceDB function can now read this file if it exists.Adds flag to pass the path of a json format coinc file.
GraceDB function can now read this file if it exists.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/90hack for injection test2019-05-31T02:00:57ZAvi Vajpeyiavi.vajpeyi@ligo.orghack for injection testThe `test_injections` in `tests.data_generation_test.TestDataGenerationInput` was failing due to the following import issue:
``` python
waveform_approximant = 'IMRPhenomPv2'
def lalsim_GetApproximantFromString(waveform_approxi...The `test_injections` in `tests.data_generation_test.TestDataGenerationInput` was failing due to the following import issue:
``` python
waveform_approximant = 'IMRPhenomPv2'
def lalsim_GetApproximantFromString(waveform_approximant):
if isinstance(waveform_approximant, str):
> return lalsim.GetApproximantFromString(waveform_approximant)
E NameError: name 'lalsim' is not defined
/opt/conda/lib/python3.6/site-packages/bilby/gw/utils.py:675: NameError
```
Came up with a hacky fix by checking
```python
if "lalsimulation" in sys.modules
```
is true, and only then executing the portion of the injection test with the `lalsimulation` import.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/152Adds make and gcc etc to the Docker image2019-07-25T01:44:20ZGregory Ashtongregory.ashton@ligo.orgAdds make and gcc etc to the Docker imagehttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/141add checking of roq parameters2019-07-25T04:04:00ZColm Talbotcolm.talbot@ligo.orgadd checking of roq parametersThis MR adds checking of the ROQ bounds, this should partially address https://git.ligo.org/lscsoft/bilby/issues/320.
@gregory.ashton @cjhaster @michael.puerrerThis MR adds checking of the ROQ bounds, this should partially address https://git.ligo.org/lscsoft/bilby/issues/320.
@gregory.ashton @cjhaster @michael.puerrerhttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/148Output slurm submit files2019-08-16T01:10:11ZMonica RizzoOutput slurm submit filesAdded methods to main.py and command line options to parser to output slurm submission scriptsAdded methods to main.py and command line options to parser to output slurm submission scripts0.2.4https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/85WIP: Custom likelihood2019-08-20T02:06:41ZAvi Vajpeyiavi.vajpeyi@ligo.orgWIP: Custom likelihood# Custom likelihood feature
Added feature to provide bilby-pipe with a `.py` script containing a custom likelihood.
# Refactoring
* refactored `parser.py` into several functions based on the parser argument groups
# New Fixmes
...# Custom likelihood feature
Added feature to provide bilby-pipe with a `.py` script containing a custom likelihood.
# Refactoring
* refactored `parser.py` into several functions based on the parser argument groups
# New Fixmes
Added a few `FIXME` (described below) that I would like to discuss with the bilby-pipe developers before working on.
* `BilbyArgParser`: has several `if` statements that can be merged to one line to improve readability
* `BilbyArgParser`: `parse_known_args` has a lot of code in it, which could be broken into several smaller functions to make a little easier to read+test
* `MainInput`: too much code in one file, making it difficult to follow. Suspect that it could be broken into a few smaller classes
* `create_main_parser`: this is a function which just calls another function... unnecessary wrapping since `create_main_parser` does no real work other than calling another function.
* `parse_args`: this function might belong in `parser.py` rather than in `utils.py`https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/183WIP: Resolve "Redesign main interface"2019-10-02T02:40:16ZGregory Ashtongregory.ashton@ligo.orgWIP: Resolve "Redesign main interface"Closes #115Closes #115Futurehttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/142WIP: make calibration prior be saved2019-10-03T08:05:50ZColm Talbotcolm.talbot@ligo.orgWIP: make calibration prior be savedThis MR saves the calibration prior (if used) to disk. This will make it easier to inspect the calibration being used.
I had to change some defaults from `None` to `dict` to stop it falling over.
I suspect this will fail when using...This MR saves the calibration prior (if used) to disk. This will make it easier to inspect the calibration being used.
I had to change some defaults from `None` to `dict` to stop it falling over.
I suspect this will fail when using the coherence test, so we should be wary of that.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/166Adds a method to read in time-series data from txt files2019-10-15T23:40:24ZGregory Ashtongregory.ashton@ligo.orgAdds a method to read in time-series data from txt fileshttps://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/202Update PESummary call2019-11-01T00:58:52ZCharlie HoyUpdate PESummary callThe purpose of this MR is to update the PESummary call. See issue #128.The purpose of this MR is to update the PESummary call. See issue #128.0.3.2https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/208WIP: Add pesummary ci test2019-11-01T01:11:00ZGregory Ashtongregory.ashton@ligo.orgWIP: Add pesummary ci testAdds a pesummary complete run to the C.I.Adds a pesummary complete run to the C.I.https://git.ligo.org/lscsoft/bilby_pipe/-/merge_requests/205Charlie.hoy/bilby pipe issue1282019-11-02T12:51:08ZGregory Ashtongregory.ashton@ligo.orgCharlie.hoy/bilby pipe issue128