Update README/index (#1373)

leewujung · ctuguinay · web-flow · commit aa01b0277bb2 · 2024-08-08T09:42:31.000-07:00
* add FM to waveform_mode

* add v0.9.0 whats new

* update readme/index

* remove gsoc 2024

* include this PR to whats new

* Add changes from ctuguinay

Co-authored-by: Caesar Tuguinay &lt;87830138+ctuguinay@users.noreply.github.com&gt;

* fix typo

---------

Co-authored-by: Caesar Tuguinay &lt;87830138+ctuguinay@users.noreply.github.com&gt;
diff --git 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).
 
-## <img src="docs/source/images/GSoC-logo-horizontal.svg" alt="Google Summer of Code logo" width="300" style="padding-right: 50px; vertical-align: middle">
+<!-- ## <img src="docs/source/images/GSoC-logo-horizontal.svg" alt="Google Summer of Code logo" width="300" style="padding-right: 50px; vertical-align: middle">
 
 In collaboration with the [Integrated Ocean Observing System (IOOS)](https://ioos.noaa.gov/), the Echopype team aims to recruit talented [Google Summer of Code (GSoC)](https://summerofcode.withgoogle.com/)
 participants to help us upgrade the robustness and scalability of the Echopype package.
 
-If you are a GSoC 2024 contributor, please head over to [GSoC contributor's guide](gsoc_contrib_guide.md) to get more information specific to the program.
+If you are a GSoC 2024 contributor, please head over to [GSoC contributor's guide](gsoc_contrib_guide.md) to get more information specific to the program. -->
 
 
 
@@ -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
@@ -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
@@ -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
+<!-- ```{image} images/GSoC-logo-horizontal.svg
 :alt: Google Summer of Code logo
 :width: 300px
 ```
@@ -40,17 +41,23 @@ In collaboration with the [Integrated Ocean Observing System (IOOS)](https://ioo
 participants to help us upgrade the robustness and scalability of the Echopype package.
 
 If you are a GSoC 2024 contributor, please head over to [GSoC contributor's guide](https://github.com/OSOceanAcoustics/echopype/gsoc_contrib_guide.md) to get more information specific to the program.
-```
+``` -->
 
 ## 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
@@ -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
 

Original file line number	Diff line number	Diff line change
`@@ -238,7 +238,7 @@`
`238`	`238`	`"cell_type": "markdown",`
`239`	`239`	`"metadata": {},`
`240`	`240`	`"source": [`
`241`		- "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`)."
	`241`	+ "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`)."
`242`	`242`	`]`
`243`	`243`	`},`
`244`	`244`	`{`