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power spectrum pipeline v1 #151

Merged
merged 67 commits into from
Jul 18, 2018
Merged

power spectrum pipeline v1 #151

merged 67 commits into from
Jul 18, 2018

Commits on Jul 15, 2018

  1. modified: hera_pspec/utils.py

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  2. modified: hera_pspec/utils.py 

    	modified:   setup.py
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  3. added config_pspec_pipe function and tests

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  4. updated pspec_run for better handling of dset loading 

    and new PspecData capabilities
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  5. updated preprocess_data.py given new read_miriad_metadata func

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  6. made argparser in pspec_run handle lists of tuples

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  7. propagated pspec_run verbose to pspec

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  8. increased pspecdata test coverage

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  9. created container.merge_spectra func, and added pspec_type to uvpspec

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  10. first round of code edits for grouping.bootstrap_run function

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  11. modified: hera_pspec/utils.py

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  12. modified: hera_pspec/utils.py 

    	modified:   setup.py
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  13. added config_pspec_pipe function and tests

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  14. updated pspec_run for better handling of dset loading 

    and new PspecData capabilities
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  15. propagated pspec_run verbose to pspec

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  16. addressed pspec_run_config PR comments: added test for repeated dset … 

    …labels
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  17. fixed lots of PEP8 from analytic error PR. also fixed bug from analyt… 

    …ic err PR

where cov_array was not being propagated to pspec_run, and also wasn't being
loaded when read_from_group was called. added tests to check for these issues.
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  18. added store_cov and dsets_std to pspec_run_argparser [skip ci]

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  19. fixed how store_cov is assigned in uvpspec_utils._select

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  20. increased test_pspecdata coverage

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  21. added tests for container.merge_spectra

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  22. added tests for utils.get_blvec_reds

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  23. enabled testing.uvpspec_from_data to take bl_groups

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  24. added tests for grouping.bootstrap_run and bootstrap_resampled_error

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  25. updated config_pspec_blpairs output format

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  26. added glob-parsing to pspecdata._load_dsets

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  27. modified: hera_pspec/utils.py

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  28. updated label handling in PSpecData.add()

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  29. updated utils.log handling of traceback and updated load_config

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  30. added .coveragerc omitting tests directory from coveralls

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  31. another update to dset label handling in pspecdata

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  32. added pspec_pipe.py and pspec_pipe.yaml

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  33. added skeleton jacknife and bootstrap stages in pspec_pipe.py

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  34. added stats pipe to pspec_pipe.py and hera_stats dependency

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  35. added pspec_pipe.py to scripts in setup.py [skip ci]

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  36. condensed job monitoring to a single function in pspec_pipe.py

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  37. removed stats pipeline due to circular dependency: this should go in … 

    …hera_stats
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  38. added pspec_batch.sh for PBS run on NRAO [skip ci]

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  39. modified: pspec_batch.sh

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  40. removed hera_stats as optional dependency

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  41. added utils.job_monitor

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  42. updated preprocess_data.py for new utils.job_monitor

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  43. updated pspec_pipe.py for new utils.job_monitor

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  44. fixed line in testing.py after merge commit

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  45. modified: ../utils.py 

    	modified:   ../../pipelines/idr2_preprocessing/preprocess_data.py
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  46. added utils.job_monitor tests

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  47. split uvpspec.spw_array into spw_dly_array and spw_freq_array

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  48. updates to container.merge_spectra 

    	modified:   hera_pspec/container.py
	modified:   pipelines/pspec_pipeline/pspec_pipe.py
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  49. fixed bug in uvpspec.combine_uvpspec across blpts for scalar_array

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  50. created utils.get_reds and modified utils.calc_reds to use it

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  51. modified: pipelines/pspec_pipeline/pspec_batch.sh 

    	modified:   pipelines/pspec_pipeline/pspec_pipe.py
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  52. addressed power spectrum pipe v1 PR comments

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  53. rebase leftovers 

    more rebase leftovers
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Commits on Jul 16, 2018

  1. added stats_array to bootstrap_resample_error and fixed bug 

    in uvpspec.combine_uvpspec when concat across blpts
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  2. pep8 and docstrings

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  3. modified: pipelines/pspec_pipeline/pspec_pipe.py 

    	modified:   pipelines/pspec_pipeline/pspec_pipe.yaml
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  4. modified: pipelines/pspec_pipeline/pspec_pipe.py

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Commits on Jul 17, 2018

  1. added omit_flags kwarg to UVPSpec.get_* funcs to omit flagged data

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  2. modified: pipelines/pspec_pipeline/pspec_batch.sh

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  3. added basic unit tests for pipeline scripts

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Commits on Jul 18, 2018

  1. fixed tests in test_pspecdata

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  2. enforced numpy>=1.14 in travis

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  3. specified numpy=1.14 in travis

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  4. added conda update conda in .travis.yml

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  5. added multiprocess installation to travis

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  6. moved multiprocess install from conda to pip

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  7. modified: .travis.yml

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