Pygama

What's Changed
* Fixed error in `DataLoader.get_iterator()` caused when no column is requested from a data tier by iguinn in https://github.com/legend-exp/pygama/pull/496
* Add more progress bars to `DataLoader` by gipert in https://github.com/legend-exp/pygama/pull/497
* Added DSPTutorial to teach development of new processors by iguinn in https://github.com/legend-exp/pygama/pull/498
* Let ``DataLoader`` default setters overwrite (not append) + `lgdo.Struct.int_dtype` by gracesong312 in https://github.com/legend-exp/pygama/pull/493


**Full Changelog**: https://github.com/legend-exp/pygama/compare/v1.3.1...v1.3.2

What's Changed
* Update `dsp/processor/__init__.py` to contain `interpolated_time_point_thresh()` by erin717 in https://github.com/legend-exp/pygama/pull/488
* Switch to pylegendtestdata package by gipert in https://github.com/legend-exp/pygama/pull/491
* Fix several `FileDB.from_disk()` issues by gipert in https://github.com/legend-exp/pygama/pull/495


**Full Changelog**: https://github.com/legend-exp/pygama/compare/v1.3.0...v1.3.1

What's Changed
* Pargen changes based on l200 data by ggmarshall in https://github.com/legend-exp/pygama/pull/446
* Remove hardcoded value from test for `ORRunDecoderForRun` by slwatkins in https://github.com/legend-exp/pygama/pull/447
* Fix for scipy bug/change by ggmarshall in https://github.com/legend-exp/pygama/pull/449
* Fix pre-commit.ci failure by gipert in https://github.com/legend-exp/pygama/pull/450
* Implemented CoMPASS DAQ data decoder by SamuelBorden in https://github.com/legend-exp/pygama/pull/357
* DataLoader: handling of non-scalar data by gracesong312 in https://github.com/legend-exp/pygama/pull/448
* Fix `build_dsp()` bug occurring when only one input JSON config is given by MoritzNeuberger in https://github.com/legend-exp/pygama/pull/452
* Fixed bug in the `overwrite` option in `write_object` by SamuelBorden in https://github.com/legend-exp/pygama/pull/453
* flush buffers before exiting on bad packet read by jasondet in https://github.com/legend-exp/pygama/pull/454
* Enhancement: ability to append columns to existing tables in lh5 files using `store.write_object` by SamuelBorden in https://github.com/legend-exp/pygama/pull/455
* Adding daq to raw validation code by slwatkins in https://github.com/legend-exp/pygama/pull/427
* update tcm documentation by jasondet in https://github.com/legend-exp/pygama/pull/456
* Allow using list of input table patterns for TCM setup by jasondet in https://github.com/legend-exp/pygama/pull/457
* Fix hardcoded dtype for output buffer by erin717 in https://github.com/legend-exp/pygama/pull/458
* New Orca/FlashCam keying convention, fix timestamp issue, draft status decoding by jasondet in https://github.com/legend-exp/pygama/pull/459
* Remove deprecated `flow.DataGroup` by gipert in https://github.com/legend-exp/pygama/pull/460
* improve raw buffer setup for multi-key-list decoders by jasondet in https://github.com/legend-exp/pygama/pull/461
* Option to pass filter coefficients to DPLMS processor by valerioda in https://github.com/legend-exp/pygama/pull/462
* Changes ready for p03 by ggmarshall in https://github.com/legend-exp/pygama/pull/463
* Fix `timestamp` in raw files by jasondet in https://github.com/legend-exp/pygama/pull/466
* Small fix for cal allowing larger range on euc_max by ggmarshall in https://github.com/legend-exp/pygama/pull/464
* Fix for ecal stability plots to check for nan values by ggmarshall in https://github.com/legend-exp/pygama/pull/467
* plotting fixes for when no pulser found by ggmarshall in https://github.com/legend-exp/pygama/pull/468
* Speed up `FileDB.scan_tables_columns()` by jasondet in https://github.com/legend-exp/pygama/pull/471
* Remove outdated tutorials directory. by erin717 in https://github.com/legend-exp/pygama/pull/469
* Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.4 by dependabot in https://github.com/legend-exp/pygama/pull/473
* chore: update pre-commit hooks by pre-commit-ci in https://github.com/legend-exp/pygama/pull/474
* DataLoader - attribute and error handling by gracesong312 in https://github.com/legend-exp/pygama/pull/472
* Expand `build_raw()` manual by gipert in https://github.com/legend-exp/pygama/pull/476
* Allow for running `FileDB.scan_files()` on a list of subfolders by gipert in https://github.com/legend-exp/pygama/pull/477
* Added linear slope diff processor for quality cuts and cleaned up some logging levels by ggmarshall in https://github.com/legend-exp/pygama/pull/478
* Reverted from `scipy.fftconvolve` to `numpy.convolve` as causing issues at LNGS by ggmarshall in https://github.com/legend-exp/pygama/pull/480
* Support chunked loading with `DataLoader.next()` by gipert in https://github.com/legend-exp/pygama/pull/475
* Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 by dependabot in https://github.com/legend-exp/pygama/pull/483
* Support chaining FileDB files and other improvements by gipert in https://github.com/legend-exp/pygama/pull/481
* Preparations for waveform and HDF5 built-in compression by gipert in https://github.com/legend-exp/pygama/pull/442
* Support nesting of `DataLoader` config in a JSON file by gipert in https://github.com/legend-exp/pygama/pull/485
* Add WaveformBrowser compatibility to DataLoader by iguinn in https://github.com/legend-exp/pygama/pull/484
* Properly substitute variables in `FileDB` and `DataLoader` configuration by gipert in https://github.com/legend-exp/pygama/pull/486
* Bug fix in `FileDB.from_disk()` by gipert in https://github.com/legend-exp/pygama/pull/487

New Contributors
* MoritzNeuberger made their first contribution in https://github.com/legend-exp/pygama/pull/452
* erin717 made their first contribution in https://github.com/legend-exp/pygama/pull/458

**Full Changelog**: https://github.com/legend-exp/pygama/compare/v1.2.0...v1.3.0

What's Changed
* Remove Sphinx mock imports (fixes 344) by gipert in https://github.com/legend-exp/pygama/pull/392
* Add links to badges in README by slwatkins in https://github.com/legend-exp/pygama/pull/393
* Disable multithreaded sphinx build by gipert in https://github.com/legend-exp/pygama/pull/398
* Fix `VectorOfVectors` read/write and add fancy indexing support by jasondet in https://github.com/legend-exp/pygama/pull/387
* Update `IntroToDSP.ipynb` tutorial to work with `pygama` 1.1.0 by slwatkins in https://github.com/legend-exp/pygama/pull/394
* Fixed a pretty big sign error by iguinn in https://github.com/legend-exp/pygama/pull/400
* Add `fixed_time_pickoff` unit test by slwatkins in https://github.com/legend-exp/pygama/pull/399
* add option to not use logger in orca_packet.py by jasondet in https://github.com/legend-exp/pygama/pull/403
* Ignore Flake8 error about print statement by gipert in https://github.com/legend-exp/pygama/pull/404
* Add missing `abstractmethod` decorator to `DataStreamer.close_stream()` by gipert in https://github.com/legend-exp/pygama/pull/405
* Add function to run both the numba and pure python versions of some function by slwatkins in https://github.com/legend-exp/pygama/pull/402
* Bug fixes and improvements to the waveform browser by iguinn in https://github.com/legend-exp/pygama/pull/401
* fix bool array read bug by jasondet in https://github.com/legend-exp/pygama/pull/409
* Fix for seaborn deprecation in matplotlib by iguinn in https://github.com/legend-exp/pygama/pull/412
* Update for new ORCA FlashCam waveform record format by jasondet in https://github.com/legend-exp/pygama/pull/419
* Fixed issue with cusp and zac filters, changed plots to output as a dict and cleaned them up by ggmarshall in https://github.com/legend-exp/pygama/pull/416
* Update path for the main branch build status badge by slwatkins in https://github.com/legend-exp/pygama/pull/424
* Add functionality for testing factory functions in DSP, Add discrete_wavelet_transform test by slwatkins in https://github.com/legend-exp/pygama/pull/425
* chore: update pre-commit hooks by pre-commit-ci in https://github.com/legend-exp/pygama/pull/420
* Add DPLMS DSP processor by valerioda in https://github.com/legend-exp/pygama/pull/411
* Fix check for if the decoded values were built in ORFlashCamADCWaveformDecoder by slwatkins in https://github.com/legend-exp/pygama/pull/426
* Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.4 by dependabot in https://github.com/legend-exp/pygama/pull/429
* chore: update pre-commit hooks by pre-commit-ci in https://github.com/legend-exp/pygama/pull/431
* Bound Pandas version to >=1.4.4 by gipert in https://github.com/legend-exp/pygama/pull/432
* Add an `LGDO` supertype by gipert in https://github.com/legend-exp/pygama/pull/430
* Fix decoding of data from the LEGEND muon-veto system by jasondet in https://github.com/legend-exp/pygama/pull/435
* Switch to GPLv3 license by gipert in https://github.com/legend-exp/pygama/pull/422
* Add Sphinx extension to handle Numba-decorated functions by gipert in https://github.com/legend-exp/pygama/pull/436
* Bugfixes and other improvements in pargen for l200 by ggmarshall in https://github.com/legend-exp/pygama/pull/437
* Implement multi-use decoders and auto-custom buffers by jasondet in https://github.com/legend-exp/pygama/pull/438
* Bug fix in `DataStreamer.open_stream()` by SamuelBorden in https://github.com/legend-exp/pygama/pull/439
* `processors.get_multi_local_extrema()`: new advanced search methods (+ unit tests) by patgo25 in https://github.com/legend-exp/pygama/pull/433
* `processors.histogram()`: check that bin edges array is +1 longer than weights array by patgo25 in https://github.com/legend-exp/pygama/pull/434
* Minor miscellaneous updates by gipert in https://github.com/legend-exp/pygama/pull/440
* Added data trimming to build_raw stage by SamuelBorden in https://github.com/legend-exp/pygama/pull/415
* Set lower bound to flake8-bugbear version by gipert in https://github.com/legend-exp/pygama/pull/441
* Created a temporary table for `buffer_processor()` to write to file during `build_raw()` by SamuelBorden in https://github.com/legend-exp/pygama/pull/443
* Add ORRunDecoderForRun to Orca decoders by slwatkins in https://github.com/legend-exp/pygama/pull/421

New Contributors
* slwatkins made their first contribution in https://github.com/legend-exp/pygama/pull/393

**Full Changelog**: https://github.com/legend-exp/pygama/compare/v1.1.0...v1.2.0

What's Changed
* Initial versions and updates of pargen scripts by ggmarshall in https://github.com/legend-exp/pygama/pull/341
* First implementation of `build_hit` by gipert in https://github.com/legend-exp/pygama/pull/340
* Update extract_tau.py by mmatteo in https://github.com/legend-exp/pygama/pull/346
* More advanced `build_hit` interface by gipert in https://github.com/legend-exp/pygama/pull/345
* Pargen updates for new build_hit by ggmarshall in https://github.com/legend-exp/pygama/pull/351
* Bare-bones class for setting global Numba options by gipert in https://github.com/legend-exp/pygama/pull/350
* Changes for better pulser handling by ggmarshall in https://github.com/legend-exp/pygama/pull/352
* Set Numba `cache=False` by default by gipert in https://github.com/legend-exp/pygama/pull/353
* Bugfix to keep snakemake happy by ggmarshall in https://github.com/legend-exp/pygama/pull/354
* Changes to pulser to handle more peaks by ggmarshall in https://github.com/legend-exp/pygama/pull/356
* pulser fixes by ggmarshall in https://github.com/legend-exp/pygama/pull/358
* LGDO's `__repr__()` and `__str__()` review by gipert in https://github.com/legend-exp/pygama/pull/359
* Adding `numpy.constants` parsing to `dsp.processing_chain` by patgo25 in https://github.com/legend-exp/pygama/pull/365
* `lgdo.Table.eval()` change to use NumExpr2 by patgo25 in https://github.com/legend-exp/pygama/pull/363
* Fix `build_hit()` `lh5_tables_config` initialization bug by patgo25 in https://github.com/legend-exp/pygama/pull/367
* Fix `build_hit()` file overwriting bug by patgo25 in https://github.com/legend-exp/pygama/pull/368
* Fixes to ProcessingChain by iguinn in https://github.com/legend-exp/pygama/pull/364
* Data Cleaning Processors by ggmarshall in https://github.com/legend-exp/pygama/pull/369
* fix flake8 errors on ABC usage. by jasondet in https://github.com/legend-exp/pygama/pull/373
* Added discrete wavelet transform processor by esleon97 in https://github.com/legend-exp/pygama/pull/349
* New DSP processors for SiPM waveforms by patgo25 in https://github.com/legend-exp/pygama/pull/355
* Add possibility to parse a list to the parameter entry of the DSP JSON by patgo25 in https://github.com/legend-exp/pygama/pull/371
* lh5_tables argument in build_dsp now accepts a single string by iguinn in https://github.com/legend-exp/pygama/pull/375
* Bump legend-testdata version and get it from PyPI by gipert in https://github.com/legend-exp/pygama/pull/376
* TCM docstring cosmetics by gipert in https://github.com/legend-exp/pygama/pull/378
* Improved handling of Numba default options, add `PYGAMA_*` shell variables by iguinn in https://github.com/legend-exp/pygama/pull/374
* Added interpolation option to `fixed_time_pickoff()` processor by iguinn in https://github.com/legend-exp/pygama/pull/360
* Updates to pargen scripts by ggmarshall in https://github.com/legend-exp/pygama/pull/379
* Tau bugfix by ggmarshall in https://github.com/legend-exp/pygama/pull/381
* Fixed time pickoff cache fix by ggmarshall in https://github.com/legend-exp/pygama/pull/382
* Enable wheels building in GitHub actions and set up PyPI uploads by gipert in https://github.com/legend-exp/pygama/pull/380
* Energy cal bugfix by ggmarshall in https://github.com/legend-exp/pygama/pull/385
* fix flake8 errors on ABC usage by jasondet in https://github.com/legend-exp/pygama/pull/386
* Add `lh5_store.show()` and new notebooks for the online docs by gipert in https://github.com/legend-exp/pygama/pull/383
* chore: update pre-commit hooks by pre-commit-ci in https://github.com/legend-exp/pygama/pull/384
* Implemented Struck SIS3316 DAQ (via ORCA) decoder by jbrowni2 in https://github.com/legend-exp/pygama/pull/339
* Install all extra dependencies in RTD build by gipert in https://github.com/legend-exp/pygama/pull/390
* Raise `RuntimeError` in `LH5Iterator` if no files could be found by iguinn in https://github.com/legend-exp/pygama/pull/391
* Data loading utilities, first implementation by gracesong312 in https://github.com/legend-exp/pygama/pull/337

New Contributors
* esleon97 made their first contribution in https://github.com/legend-exp/pygama/pull/349
* pre-commit-ci made their first contribution in https://github.com/legend-exp/pygama/pull/384
* jbrowni2 made their first contribution in https://github.com/legend-exp/pygama/pull/339

**Full Changelog**: https://github.com/legend-exp/pygama/compare/v1.0.1...v1.1.0