v0.11.1a2 (release assets staging)

This pre-release is for staging new files in release assets in the upcoming release.

v0.11.1a1 (release assets staging)

This pre-release is for staging new files in release assets in the upcoming release.

v0.11.0

Overview

This release includes a number of major changes, in particular:

• additional functions for detecting transient noise, seafloor, and shoals
• upgrade to use Zarr >3, and along with this change, discontinue support for Python 3.10 and Zarr <3, and add support for Python 3.13

Thanks to @LOCEANlloydizard , @dbashford-NOAA , @shivam096, and @leewujung for their contributions!

New features

• Add weill to codespell ignore list by @LOCEANlloydizard in #1543
• Implementations of basic seafloor detection in mask subpackage by @LOCEANlloydizard in #1521
• Add Fielding and Matecho-like transient noise removal methods by @LOCEANlloydizard in #1544
• Shoals detection implementation by @LOCEANlloydizard in #1525

Enhancements

• Update apply_mask to only take in boolean or 0/1 masks by @shivam096 in #1502
• Add order agnostic dimension in masks by @shivam096 in #1503
• Moved the check for duplicate times to after NMEA selection by @dbashford-NOAA in #1511
• Support computing MVBS with frequency_nominal and fix some tests by @dbashford-NOAA in #1517

Bug fixes

• Fix utcnow by @shivam096 in #1497
• Add time decode by @shivam096 in #1499

Infrastructure

• Migrate to numpy v2 and zarr v3 by @dbashford-NOAA and @leewujung in #1531
• Add test to validate actual range calculations by @shivam096 in #1504
• Unpinning numpy and scipy by @LOCEANlloydizard in #1518
• Reverse unpinning numpy by @leewujung in #1519
• Update pr.yaml to run full test suite for all PR by @LOCEANlloydizard in #1524
• Modifications to match xarray update to v2025.9.1 by @LOCEANlloydizard in #1550
• fix(ci): free disk space to resolve "No space left on device" by @LOCEANlloydizard in #1556
• Remove python 3.10 support by @dbashford-NOAA in #1546
• Support python 3.13 by @dbashford-NOAA in #1553

Documentation

• Update contributing section in docs by @leewujung in #1489
• Update data processing docs and contributor guide by @leewujung in #1490
• Update docstrings for transient noise and shoal detection functions by @LOCEANlloydizard in #1554

New Contributors

• @shivam096 made their first contribution in #1497
• @LOCEANlloydizard made their first contribution in #1518
• @dbashford-NOAA made their first contribution in #1511

Full Changelog: v0.10.1...v0.11.0

v0.10.1

Overview

This release includes changes that improve performance of compute_Sv and compute_MVBS and fixes of a typo and a bug.

Enhancements

• Expand ping_time preemptively in get_vend_cal_params_power to avoid tiny chunks by @ctuguinay in #1483
• Enhance compute_MVBS feasibility via flox reindex=False changes by @ctuguinay in #1470

Bug fixes

• Use normalization to compute echo range scaling by @ctuguinay in #1463

Documentation

• docs: fix little typo by @jmeischner in #1471

New Contributors

• @jmeischner made their first contribution in #1471

Full Changelog: v0.10.0...v0.10.1

v0.10.0

Overview

This release includes critical updates to migration to support python 3.12, use the new xr.DataTree functionality, and many other changes to resolve deprecation warnings and small bugs. There are a number of pinned dependencies we are continuing to work on.

Enhancements

• Drop ping time duplicates by @ctuguinay in #1382
• Support Python 3.12 and partial migration to Xarray DataTree by @ctuguinay in #1419
• Fix tests that fail from new Xarray variable and attribute assignment updates by @ctuguinay in #1433
• Add backward compatibility of raw-converted dataset with xr.DataTree by @oftfrfbf @leewujung @ctuguinay in #1447
• Add assign actual range utility function by @ctuguinay in #1435

Bug and warning fixes

• Assemble AD2CP timestamp with nanosecond precision by @leewujung in #1436
• Use import_resources.files instead of the legacy open_text by @leewujung in #1434
• Replace pkg_resources.resource_string with importlib.resources.files by @leewujung in #1468
• Fix invalid \d warning by using raw string by @leewujung in #1448
• Check if there exist any swap files before cleaning them up by @ctuguinay in #1451
• Remove __setattr__ from EchoData by @leewujung in #1457
• Compute dask array before np array equal by @ctuguinay in #1452
• Dataset.dims to Dataset.sizes by @ctuguinay in #1453
• Chunks as dictionaries in _get_auto_chunk by @ctuguinay in #1454
• Set decode timedelta to False since it will default to this in later xarray version by @ctuguinay in #1462
• Fixed logic bug in AZFP6 parser in validating parameters by @ctuguinay @leewujung in #1450
• Fill in NaN for missing EK80 coefficients by @leewujung in #1458

Infrastructure

• Update workflows to use python 3.12 and ubuntu 22.04 by @leewujung in #1425 and #1466
• Bump codespell version, add exceptions by @leewujung in #1438
• Pin zarr and netcdf4 temporarily by @leewujung in #1429
• Add type-extensions to requirements.txt by @leewujung in #1440
• Add manual trigger to pypi workflow by @leewujung in #1442
• Pin scipy to temporarily ensure that rotation matrix calculation does not fail by @ctuguinay in #1460

Others

• Update cff citation file by @leewujung in #1443
• Replace previous arXiv citation with recent ICES paper citation by @ctuguinay in #1455

Full Changelog: v0.9.1...v0.10.0

v0.9.1

Overview

This release includes a number of small fixes and enhancements. An important component is to set the max supported python version to <3.12, before we fully migrate to using the new xarray.DataTree in the next release with breaking changes.

Enhancements

• Remove min max attributes for compute_MVBS by @ctuguinay in #1380
• Update setup-services.py by @spacetimeengineer in #1398
• Add support for AZFP 130kHz by @ctuguinay in #1412
• Update calibrate_base.py to include EA640 in backscatter size check. by @torsteinnh in #1407

Bug and warning fixes

• Handle NaN in apply_mask input mask by @leewujung in #1376
• EK60 Conversion: Drop channels that don't have power data by @ctuguinay in #1383
• Skip Parsing Invalid EK80 Environment Datagram(s) by @ctuguinay in #1387
• Fix 'Division by Zero' error when converting EK80 files without Sound Velocity Profile Depth value(s) by @ctuguinay in #1381
• Add error warning for all NaN lat/lon in get_distance_from_latlon by @leewujung in #1403
• Updated paths in test_align_to_ping_time_glider_azfp to use pytest fixture by @oftfrfbf in #1414

Documentation

• Update installation doc page by @leewujung in #1389

Others

• Set max python version <3.12 [all tests ci] by @leewujung in #1422

New Contributors

• @spacetimeengineer made their first contribution in #1398
• @oftfrfbf made their first contribution in #1414
• @torsteinnh made their first contribution in #1407

Full Changelog: v0.9.0...v0.9.1

v0.9.0

Overview

This release includes a number of new features and performance enhancements, as well as fixes for bugs and warnings. We have fully switched to using the trunk-based development workflow in this release.

New features

• Add noise and attenuation functions from Ryan et. al. 2015 and echopy by @ctuguinay in #1316
• Add .bot and .idx files to EK60/EK80 parsing by @ctuguinay in #1318
• Add index aggregation option for cleaning mask functions by @ctuguinay in #1326
• Added alpha-version code for new AZFP6 format by @dash-uvic in #1323
• Use latest MRU parser version and enable ep.consolidate.add_location can be based off datagram type by @ctuguinay in #1359

Enhancements

• Support lazy-loaded EK80 broadband-complex data by @leewujung in #1311
• Allow MVBS into ep.mask.apply_mask, and add alignment check for target variable and mask by @ctuguinay in #1345
• Enhance ep.calibrate.compute_Sv scalability by enabling EchoData chunking and removing eager computation by @ctuguinay in #1331
• Use Echodata Platform and Beam_group1 variables to compute depth for EK60/EK80 by @ctuguinay in #1319
• Allow waveform mode "FM" in calibrate by @ctuguinay in #1363
• Allow external arrays in add_depth and add an universal ping time alignment function by @ctuguinay in #1369

Bug and warning fixes

• Fix duck array RuntimeWarning for EK60 ep.open_raw by @ctuguinay in #1337
• Coding: channel_mode dtype from float16 to float32 by @ctuguinay in #1350 and #1351
• Fix problems in applying compute_Sv on combined EchoData object by @leewujung in #1328
• Fix data type check for padding short complex pings by @ctuguinay in #1353
• Update xr.drop to xr.drop_vars by @ctuguinay in #1364

Documentation

• Update docs for visualization by @leewujung in #1347
• Merge data processing level changes from stable by @leewujung in #1355
• Add the Ping acoustic library to other resources by @gavinmacaulay in #1362
• Update contributing guide and README/index by @leewujung in #1356 and #1373

Others

• Remove the deprecated visualize subpackage by @leewujung in #1336
• Temporarily skip datagrams generated by EC150 by @leewujung in #1357
• Modify dask image in requirement.txt by @leewujung in #1361

New Contributors

• @dash-uvic made their first contribution in #1323

Full Changelog: v0.8.4...v0.9.0

v0.8.4

Overview

This release includes a few performance enhancements, bug fixes, and improving warnings/error messages. We are also preparing to switch to using the trunk-based development workflow in the next release to streamline new contributions.

Enhancements

• Upgrade compress_pulse to use parallelized convolution by @anantmittal in #1208
• Optimize harmonize_env_param_time by @anantmittal in #1235
• Optimize frequency differencing with dask by @anantmittal in #1198
• Optimize get_vend_cal params_power by @anujsinha3 in #1285
• apply_mask changes: Allow multi-channel masks, allow the depth dimension, and simplify fill value by @ctuguinay in #1230
• Update _calc_Sv_offset for AZFP parsing by @leewujung in #1304
• Move compute_Sv_offset to inside of AZFP parser by @ctuguinay in #1307
• Support calibration of EK80 broadband complex data from sequential pinging by @ctuguinay in #1302
• Add skipna argument to compute_MVBS/NASC to control mean behavior over NaN elements by @ctuguinay in #1269

Bug fixes and warnings

• Fix error parsing integer in frequency-differencing equation by @leewujung in #1278
• Fix time encoding to use int64 and "nanoseconds since 1970-01-01 00:00:00Z" by @ctuguinay in #1299
• Add warnings and raised errors for add_location by @ctuguinay in #1296

Others

• One time dev merge to main to facilitate switching to trunk-based workflow by @leewujung in #1297
• Engaging in Google Summer of Code 2024 program by @leewujung #1266, #1267, #1274
• Update Development roadmap by @leewujung in #1262
• Deprecating echopype.visualize by @leewujung in #1310

New Contributors

• @anantmittal made their first contribution in #1208
• @anujsinha3 made their first contribution in #1285
• @ctuguinay made their first contribution in #1230

Full Changelog: v0.8.3...v0.8.4

v0.8.3

Overview

This release includes a bug fix for changes from the previous release and a few functionality enhancements.

Enhancements

• Add parser support for EK80 MRU1 datagram (#1242)
• Add support for consolidate subpackage functions to accept both in-memory or stored datasets (#1216)
• Add test for ES60 spare field decoding issue (#1233)
• Add test for EK80 missing receiver_sampling_freq error (#1234)

Bug fixes

• Fixed reshape bug in pad_shorter_ping that was remnant from use_swap full refactoring (#1234)

v0.8.2

Overview

This release includes a number of important performance enhancements, bug fixes, and under-the-hood refactoring to improve code readability.

Enhancements

• Full refactor of the functionality to directly storing parsed data to zarr before set_groups_* (#1185, #1218, #1070)
  • This avoids memory expansion during NaN padding across channel
• Improve compute_MVBS using flox (#1124)
• Revive and improve compute_NASC using flox (#1167)
• Refactor AZFP XML parser
  • Improved XML parsing by using xml.etree.ElementTree to be consistent with other XML parsers in echopype (#1135)
  • Parse more parameters and store in the resulting EchoData objects (#1135)
  • Add partial support for AZFP multiple phase settings (#1182)
• Overhaul AZFP Environment group
  • Set mandatory variables not in data to NaN (sounds_speed_indicative, absorption_indicative) (#1226)
  • Parse and store AZFP pressure data when exist (#1189, #1226)
• Add utils.misc.depth_from_pressure function for converting pressure to depth (#1207)
• Remove unused mechanism to selectively parse some EK datagrams (#1214)
• Enhancements of EchoData.update_platform method
  • Factor out utility functions to a submodule (#1209)
  • Auto-assign timestamp for fixed-location external data using first ping_time(#1196)
• Add support for consolidate subpackage functions to accept both in-memory or stored datasets (#1216) [NOT MERGED]

Bug fixes

• Fix EchoData.to_zarr encoding (#1128)
  • Eliminate preferred chunks
  • Ensuring chunk alignment and encoding only when handling dask arrays
• Fix scaling bugs in compute_NASC (#1167)
• Fix UnicodeDecodeError for ES60 files (#1215)
• Handle missing receiver_sampling_frequency for EK80 data (#1219)

Infrastructure and refactoring

• Add support for running individual test files (#1166)
• Add module based testing (#1180)
• Update CI to barebone python, without conda (#1192)