diff --git a/README.md b/README.md index fa4c564ba..2662460a9 100644 --- a/README.md +++ b/README.md @@ -59,12 +59,12 @@ Learn more about echopype in the official documentation at https://echopype.read You can find information about how to contribute to echopype at our [Contributing Page](https://echopype.readthedocs.io/en/latest/contributing.html). -## Google Summer of Code logo + @@ -81,9 +81,10 @@ Please report any bugs by [creating issues on GitHub](https://medium.com/nyc-pla Wu-Jung Lee ([@leewujung](https://github.com/leewujung)) founded the echopype project in 2018 and continue to be the primary contributor -together with Praneeth Ratna([@praneethratna](https://github.com/praneethratna)). +together with Caesar Tuguinay([@ctuguinay](https://github.com/ctuguinay)). Emilio Mayorga ([@emiliom](https://github.com/emiliom)), Landung "Don" Setiawan ([@lsetiawan](https://github.com/lsetiawan)), +Praneeth Ratna([@praneethratna](https://github.com/praneethratna)), Brandon Reyes ([@b-reyes](https://github.com/b-reyes)), Kavin Nguyen ([@ngkavin](https://github.com/ngkavin)) and Imran Majeed ([@imranmaj](https://github.com/imranmaj)) @@ -95,16 +96,24 @@ A complete list of direct contributors is on our [GitHub Contributors Page](http ## Acknowledgement +We thank all previous and current contributors to Echopype, +including those whose contributions do not include code. We thank Dave Billenness of ASL Environmental Sciences for providing the AZFP Matlab Toolbox as reference for developing support for the AZFP echosounder, -and Rick Towler ([@rhtowler](https://github.com/rhtowler)) +Rick Towler ([@rhtowler](https://github.com/rhtowler)) of the NOAA Alaska Fisheries Science Center for providing low-level file parsing routines for -Simrad EK60 and EK80 echosounders. +Simrad EK60 and EK80 echosounders, +and Alejandro Ariza ([@alejandro-ariza](https://github.com/alejandro-ariza)) +for developing NumPy implementation of +acoustic analysis functions via Echopy, which +we referenced for several Echopype functions. We also thank funding support from -the National Science Foundation and NOAA Ocean Exploration, +the National Science Foundation, +NOAA Ocean Exploration, +NOAA Fisheries, and software engineering support from the University of Washington Scientific Software Engineering Center (SSEC), as part of the Schmidt Futures Virtual Institute for Scientific Software (VISS) in 2023. diff --git a/docs/source/data-proc-func.ipynb b/docs/source/data-proc-func.ipynb index 5d70d3825..c9ee2b17c 100644 --- a/docs/source/data-proc-func.ipynb +++ b/docs/source/data-proc-func.ipynb @@ -238,7 +238,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Here, `waveform_mode=\"BB\"` indicates that the data you want to calibrate are the channels set to do broadband transmissions. `encode_mode=\"complex\"` indicates that these data are stored as complex samples. The function will raise an error if there are no broadband data found in the provided `EchoData` object (`ed`)." + "Here, `waveform_mode=\"BB\"` (or `\"FM\"`) indicates that the data you want to calibrate are the channels set to do broadband transmissions. `encode_mode=\"complex\"` indicates that these data are stored as complex samples. The function will raise an error if there are no broadband data found in the provided `EchoData` object (`ed`)." ] }, { diff --git a/docs/source/index.md b/docs/source/index.md index 2eb6d0ad3..f5d7d4b90 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -18,9 +18,10 @@ scientists to make discovery using these new data. Wu-Jung Lee ([@leewujung](https://github.com/leewujung)) founded the echopype project in 2018 and continue to be the primary contributor -together with Praneeth Ratna([@praneethratna](https://github.com/praneethratna)). +together with Caesar Tuguinay([@ctuguinay](https://github.com/ctuguinay)). Emilio Mayorga ([@emiliom](https://github.com/emiliom)), Landung "Don" Setiawan ([@lsetiawan](https://github.com/lsetiawan)), +Praneeth Ratna([@praneethratna](https://github.com/praneethratna)), Brandon Reyes ([@b-reyes](https://github.com/b-reyes)), Kavin Nguyen ([@ngkavin](https://github.com/ngkavin)) and Imran Majeed ([@imranmaj](https://github.com/imranmaj)) @@ -30,7 +31,7 @@ Valentina Staneva ([@valentina-s](https://github.com/valentina-s)) is also part A complete list of direct contributors is on our [GitHub Contributors Page](https://github.com/OSOceanAcoustics/echopype/graphs/contributors). -```{image} images/GSoC-logo-horizontal.svg + ## Acknowledgement +We thank all previous and current contributors to Echopype, +including those whose contributions do not include code. We thank Dave Billenness of ASL Environmental Sciences for providing the AZFP Matlab Toolbox as reference for developing support for the AZFP echosounder, -and Rick Towler ([@rhtowler](https://github.com/rhtowler)) +Rick Towler ([@rhtowler](https://github.com/rhtowler)) of the NOAA Alaska Fisheries Science Center for providing low-level file parsing routines for -Simrad EK60 and EK80 echosounders. +Simrad EK60 and EK80 echosounders, +and Alejandro Ariza ([@alejandro-ariza](https://github.com/alejandro-ariza)) +for developing NumPy implementation of +acoustic analysis functions via Echopy, which +we referenced for several Echopype functions. We also thank funding support from the National Science Foundation, diff --git a/docs/source/whats-new.md b/docs/source/whats-new.md index 9f8b6d98c..9b3bd59dc 100644 --- a/docs/source/whats-new.md +++ b/docs/source/whats-new.md @@ -4,7 +4,93 @@ What's new See [GitHub releases page](https://github.com/OSOceanAcoustics/echopype/releases) for the complete history. -# v0.8.3 (2024 December 24) +# v0.9.0 (2024/07/20) + +## 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](https://www.atlassian.com/continuous-delivery/continuous-integration/trunk-based-development) development workflow in this release. + +## New features +* Add noise and attenuation functions from Ryan et. al. 2015 and echopy by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1316 +* Add `.bot` and `.idx` files to EK60/EK80 parsing by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1318 +* Add index aggregation option for cleaning mask functions by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1326 +* Added alpha-version code for new AZFP6 format by @dash-uvic in https://github.com/OSOceanAcoustics/echopype/pull/1323 +* Use latest MRU parser version and enable `ep.consolidate.add_location` can be based off datagram type by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1359 + +## Enhancements +* Support lazy-loaded EK80 broadband-complex data by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1311 +* Allow `MVBS` into `ep.mask.apply_mask`, and add alignment check for target variable and mask by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1345 +* Enhance `ep.calibrate.compute_Sv` scalability by enabling EchoData chunking and removing eager computation by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1331 +* Use Echodata `Platform` and `Beam_group1` variables to compute depth for EK60/EK80 by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1319 +* Allow waveform mode "FM" in calibrate by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1363 +* Allow external arrays in `add_depth` and add an universal ping time alignment function by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1369 + +## Bug and warning fixes +* Fix duck array `RuntimeWarning` for EK60 `ep.open_raw` by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1337 +* Coding: `channel_mode` dtype from `float16` to `float32` by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1350 and https://github.com/OSOceanAcoustics/echopype/pull/1351 +* Fix problems in applying `compute_Sv` on combined `EchoData` object by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1328 +* Fix data type check for padding short complex pings by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1353 +* Update `xr.drop` to `xr.drop_vars` by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1364 + +## Documentation +* Update docs for visualization by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1347 +* Merge data processing level changes from `stable` by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1355 +* Add the Ping acoustic library to other resources by @gavinmacaulay in https://github.com/OSOceanAcoustics/echopype/pull/1362 +* Update contributing guide and README/index by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1356 and https://github.com/OSOceanAcoustics/echopype/pull/1373 + +## Others +* Remove the deprecated `visualize` subpackage by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1336 +* Temporarily skip datagrams generated by EC150 by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1357 +* Modify dask image in requirement.txt by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1361 + +## New Contributors +* @dash-uvic made their first contribution in https://github.com/OSOceanAcoustics/echopype/pull/1323 + +**Full Changelog**: https://github.com/OSOceanAcoustics/echopype/compare/v0.8.4...v0.9.0 + + + + + +# v0.8.4 (2024/04/24) + +## 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](https://www.atlassian.com/continuous-delivery/continuous-integration/trunk-based-development) development workflow in the next release to streamline new contributions. + +## Enhancements +* Upgrade `compress_pulse` to use parallelized convolution by @anantmittal in https://github.com/OSOceanAcoustics/echopype/pull/1208 +* Optimize `harmonize_env_param_time` by @anantmittal in https://github.com/OSOceanAcoustics/echopype/pull/1235 +* Optimize frequency differencing with dask by @anantmittal in https://github.com/OSOceanAcoustics/echopype/pull/1198 +* Optimize `get_vend_cal params_power` by @anujsinha3 in https://github.com/OSOceanAcoustics/echopype/pull/1285 +* `apply_mask` changes: Allow multi-channel masks, allow the `depth` dimension, and simplify fill value by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1230 +* Update `_calc_Sv_offset` for AZFP parsing by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1304 +* Move `compute_Sv_offset` to inside of AZFP parser by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1307 +* Support calibration of EK80 broadband complex data from sequential pinging by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1302 +* Add `skipna` argument to `compute_MVBS/NASC` to control mean behavior over NaN elements by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1269 + +## Bug fixes and warnings +* Fix error parsing integer in frequency-differencing equation by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1278 +* Fix time encoding to use int64 and "nanoseconds since 1970-01-01 00:00:00Z" by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1299 +* Add warnings and raised errors for `add_location` by @ctuguinay in https://github.com/OSOceanAcoustics/echopype/pull/1296 + +## Others +* One time `dev` merge to `main` to facilitate switching to trunk-based workflow by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1297 +* Engaging in Google Summer of Code 2024 program by @leewujung https://github.com/OSOceanAcoustics/echopype/pull/1266, https://github.com/OSOceanAcoustics/echopype/pull/1267, https://github.com/OSOceanAcoustics/echopype/pull/1274 +* Update Development roadmap by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1262 +* Deprecating `echopype.visualize` by @leewujung in https://github.com/OSOceanAcoustics/echopype/pull/1310 + +## New Contributors +* @anantmittal made their first contribution in https://github.com/OSOceanAcoustics/echopype/pull/1208 +* @anujsinha3 made their first contribution in https://github.com/OSOceanAcoustics/echopype/pull/1285 +* @ctuguinay made their first contribution in https://github.com/OSOceanAcoustics/echopype/pull/1230 + +**Full Changelog**: https://github.com/OSOceanAcoustics/echopype/compare/v0.8.3...v0.8.4 + + + + + +# v0.8.3 (2023/12/25) ## Overview