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Package / Actions Cleanup - Continuation of #435 - #436

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simmsa merged 78 commits into
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simmsa:package-cleanup-v2
Apr 13, 2026
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Package / Actions Cleanup - Continuation of #435#436
simmsa merged 78 commits into
MHKiT-Software:developfrom
simmsa:package-cleanup-v2

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@simmsa simmsa commented Feb 25, 2026 •
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This is a continuation and refinement of #435

Highlights:

From #435

  • Actions version updates:
    • checkout - v4 to v6
    • setup-python - v2 to v6
  • cdip fixes

Dependencies

Module Dependencies

  • Pin pandas below version 3.0
    • There are some subtle bugs related to underlying pandas changes that we should address and possibly fix that are out of scope of this PR.
  • Refactor dependencies to move xarray, netcdf, and h5 dependencies into all
    • This helps standardize the versions for all modules, and behind the scenes xarray typically requires both netcdf and h5.

Conda and Conda-Forge Dependency Definitions

  • Move conda forge environment file into environment-dev.yml and create new conda-forge-build job to test the conda-forge specific no deps build

Actions

Linting

  • Add filter to only run black on files that have changed
    • Intent is to reduce noise in the tests. It is a non goal to have all files share the same formatting, we are just trying to enforce formatting on new or changed code
  • Add Development Installation section to readme detailing pip, conda, and conda forge installation pathways

Coveralls

  • Pin coveralls action at v2
  • Adds a switch at the top of main.yml to toggle reporting coveralls upload failures as test failures. Coveralls failures are of the 500 variant, Error: Bad response: 530 error code: 1016 per: https://status.coveralls.io/ and this implements the recommended fail-on-error: false fix
Update - Outage will be extended for at least several more hours. To avoid further disruption to your CI workflows, we recommend employing the fail-on-error: false input option available with all official coveralls integrations. See: https://docs.coveralls.io/integrations#official-integrations.
Feb 24, 2026 - 19:28 PST

We can incorporate this into #435 if that makes sense. My main goal here is to understand what changes are necessary in #435

jmcvey3 and others added 30 commits February 19, 2026 09:01
@jmcvey3
Update year in license file
8648bff
@akeeste @jmcvey3
fix upcrossing.py:upcrossing() for pandas 3.0
8862c89
@akeeste @jmcvey3
lint and black formatting for the last commit
70f58ce
@jmcvey3
Clean up package installation, remove pandas 'd' time warning
b0d41d9
@jmcvey3
Update github actions versions, install dependencies for hindcast prep
d9f98b0
@jmcvey3
Square up caching code to make it easier to read. Room for improvement
a5149ed
@jmcvey3
Remove all the extra code in cdip.py
b3ae816
@jmcvey3
Remove requirements-dev file, add black to toml reqs
b8edd87
@jmcvey3
Merge branch 'develop' into package-cleanup
81c14b0
@jmcvey3
Fix refactoring of cdip file
9f7b92e
@jmcvey3
Create second environment file to test conda-forge package
d88b07f
@simmsa
Dev: Move conda-forge env file into the root dir
c8dd965
@simmsa
Actions: Refine conda build name for user facing installs
9ff07e8
@simmsa
Actions: Add conda-forge build/test steps
59f30e6
@simmsa
Actions: Remove unnecessary miniconda setup from single job
ddcd1e8
@simmsa
Actions: Remove no deps from user-conda install
3db1575
@simmsa
Actions: Update coveralls with new build step names
54ab157
@simmsa
Docs: Add development installation section
335e7de
@simmsa
Actions: Temp support actions on different branch
ab464e0
@simmsa
Actions: Only run black on changed files
b0f799d
@simmsa
Actions: Add comment above set-os code to clarify purpose
e557e71
@simmsa
Actions: Only run all OS on PR's into main
540d289
@simmsa
Actions: Use stricter logic to only run hindcast tests or pull requests.
88e2182
@simmsa
Dev: Pin pandas below version 3.0
7aac110 
There is a bug where something in requiring pyarrow that is likely
related to pandas 3.0.

Adding pyarrow as a dependency is a reasonable fix, but managing the
pyarrow version should be handled by pandas and not mhkit.

This pins pandas below 3.0 to see if pyarrow dependencies are caused by
including >= 3.0 somewhere.
@simmsa
Dev: Remove adhoc branch for actions test
79f1b54
@simmsa
Dev: Revert unnecessary single to double quote changes
fc9f4a0
@simmsa
Actions: Add python 3.10 to test wheel build
05364cc
@simmsa
Actions: Fix "defaults" warning:
daf9c20 
```
prepare-nonhindcast-cache
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
```
@simmsa
Dev: Format with black
8215636
@simmsa
Actions: Fix, specify conda-forge as channel
ddf5b88
@simmsa
Env: Specify python 3.11 for reproducibility
492a7d2 
Previously we had `python>=3.10,<3.13` but this was likely legacy from
the conda-forge version of the conda config. This removes the ambiguous
python version, which relied on the solver, to a deterministic version
with the intent of providing reproducible builds for conda users.
jmcvey3
jmcvey3 reviewed Mar 17, 2026
View reviewed changes
Comment thread README.md
**Pip development** (no conda):

```bash
pip install -e ".[all,dev]"

@jmcvey3 jmcvey3 Mar 17, 2026

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Just adding a note to create and activate a venv environment here

@simmsa simmsa Mar 17, 2026

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Good call, will update accordingly. LMK if other areas don't make sense here either, or could be clarified.

@simmsa simmsa Apr 10, 2026

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This is also fixed.

simmsa added 18 commits April 1, 2026 13:48
@simmsa
Docs: Move user facing code sections into copyable blocks
c80c9ee
@simmsa
Docs: Add note about installing deps for examples
6326d92
@simmsa
Docs: Add more detail to VSCode environment usage
09b3236
@simmsa
Docs: Use steps for GitHub clone install
063bdb7
@simmsa
Docs: Add shell syntax highlights
75d2c26
@simmsa
Docs: Add details about module installation
77d5242
@simmsa
Docs: Add developer note about using venv and multiple venvs
fd85093
@simmsa
Docs: Fix typos
aea8426
@simmsa
Merge remote-tracking branch 'upstream/develop' into package-cleanup-v2
9a1c0dc
@simmsa
Wave: Revert cdip reader and test changes
a323de8 
These changes were a reaction to failing tests, but it is likely that
the failing tests were not caused by this code specifically, but pandas
3.0 updates.

This reverts these changes back to the develop branch as they are likely
unnecessary for the tests to pass when pandas is pinned below 3.0
@simmsa
Actions: Update checkout to v6
ceed641
@simmsa
DOLFyN: Use lowercase for filenames to appease actions tests on ubuntu
18e273c 
```
FAILED .github/workflows/test_read_adp.py::io_adp_testcase::test_io_nortek - FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/MHKiT-Python/MHKiT-Python/examples/data/dolfyn/AQD_HR.prf'
```
@simmsa
Actions: Update dorny/paths-filter version
96e4735
@simmsa
Actions: Update upload-artifact to v6
815d63b
@simmsa
Revert: Non critical changes to cdip_example
fd65176
@simmsa
Docs: Leverage sections to separate installation options.
0f2d577
@simmsa
Docs: Clarify collapsed installation headers
dbc8933
@simmsa
Docs: Clarify pip module install
600c980
@simmsa

simmsa commented Apr 13, 2026

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@jmcvey3, I removed the CDIP changes in this PR, and the tests now pass. This suggests the test failures you saw were related to the pandas 3.0 update. I plan to use your changes in the upcoming PR for pandas 3.0, but just wanted to give you a heads up.

@simmsa
simmsa merged commit 7e81457 into MHKiT-Software:develop Apr 13, 2026
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@simmsa simmsa mentioned this pull request Jun 29, 2026
Merged
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simmsa added a commit that referenced this pull request Jul 8, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (#449)
31f3c78 
# MHKiT-Python v1.1.0

## Additions

* Acoustics: Add millicdecade and WISPR instrument support
  * Added millidecade spectral conversion
  * Added a WISPR hydrophone reader
  * Added a voltage-based `export_audio` resampling option
  * Refactored band-averaging to avoid losing information at frequency-band boundaries
  * #447
  * Author: @jmcvey3
  * Reviewer: @simmsa
* DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support
  * Added DOLfYN support for reading Aquadopp instruments
  * Cleaned Nortek parsing code
  * Simplified handling of the non-cabled ADV orientation flag
  * #434
  * Author: @jmcvey3
  * Reviewer: @akeeste
* Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb`
  * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave.
  * #430
  * Author: @jmcvey3
  * Reviewer: @akeeste

## Improvements

### Acoustics

- Improved flexibility and robustness of the Acoustics module
  - Added a configurable FFT length for sound pressure PSDs
  - Renamed bin/windowing attributes for clarity
  - Fixed an incorrectly signed gain correction
  - #433
  - Author: @jmcvey3
  - Reviewer: @akeeste

### DOLfYN

- Refactored PSD calculations to use `scipy.signal.welch`
  - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch`
  - Removed the bin-based segment structure and added a `step` argument to control overlap
  - Dropped float32 casts in some functions in favor of float64
  - Removed `fft.py` and renamed `tools/misc.py` to `tools.py`
  - Breaking Changes:
    - NaNs are no longer tolerated in PSD calculations
    - DOLfYN defaults to 0% overlap to preserve existing array shapes
    - Acoustics defaults to 50% overlap
    - PSD output time dimension renamed to `time_psd`
  - #452
  - Author: @jmcvey3
  - Reviewer: @akeeste, @simmsa
- Improved handling of "averaged" profiles
  - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste
- Critical PSD bugfix
  - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste

### Examples

- Added histograms to ADCP example
  - #448
  - Author: @browniea
  - Reviewer: @akeeste


### River/IO

- Fixed Qhull interpolation and D3D coordinate-system errors
  - #448
  - Author: @browniea
  - Reviewer: @akeeste
  - Fixes: #442, #444
- Delft3D module updates
  - Added new Delft3D coordinate names
  - Added a new grid-convergence-index calculation function
  - Added support for xarray/netCDF4 input in the D3D module
  - #428
  - Author: @browniea
  - Reviewer: @akeeste

### Wave

- NDBC Directional Wave Units
  - Fixed NDBC directional wave spectrum output to return degrees instead of radians
  - Updated polar plots so 0 deg is at the top and increases clockwise
  - #437
  - Author: @jmcvey3
  - Reviewer: @akeeste
  - Fixes: #427

### Wave/Hindcast

- Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste

## Maintenance

- Added Python 3.13 support
  - #445
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #441
- Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support
  - Updated the pandas dependency to allow pandas 3.x
  - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes
  - Fixed a deprecated period alias in tests
  - #443
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #440
- Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies
  - Refactored optional dependencies
  - Standardized conda/conda-forge environment builds
  - Scoped black linting to changed files
  - #436
  - Author: @simmsa
  - Reviewer: @akeeste
- Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/)
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste
This was referenced Jul 8, 2026
Merged
Closed
simmsa added a commit to simmsa/MHKiT-Python that referenced this pull request Jul 10, 2026
@simmsa
Package / Actions Cleanup - Continuation of MHKiT-Software#435 (MHKiT…
cc6c570 
…-Software#436)

This is a continuation and refinement of MHKiT-Software#435

Highlights:

## From MHKiT-Software#435

* Actions version updates:
  * checkout - v4 to v6
  * setup-python - v2 to v6
* cdip fixes

## Dependencies

### Module Dependencies

* Pin pandas below version 3.0
  * There are some subtle bugs related to underlying pandas changes that we should address and possibly fix that are out of scope of this PR.
* Refactor dependencies to move xarray, netcdf, and h5 dependencies into `all`
  * This helps standardize the versions for all modules, and behind the scenes xarray typically requires both netcdf and h5.

### Conda and Conda-Forge Dependency Definitions

* Move conda forge environment file into environment-dev.yml and create new conda-forge-build job to test the conda-forge specific no deps build

## Actions

### Linting

* Add filter to only run `black` on files that have changed
* Add Development Installation section to readme detailing pip, conda, and conda forge installation pathways

### Coveralls

* Pin coveralls action at v2
* Add a switch in main.yml to toggle reporting coveralls upload failures as test failures (recommended `fail-on-error: false` fix)
simmsa added a commit to simmsa/MHKiT-Python that referenced this pull request Jul 10, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (MHKiT-Software#449)
80671f0 
# MHKiT-Python v1.1.0

## Additions

* Acoustics: Add millicdecade and WISPR instrument support
  * Added millidecade spectral conversion
  * Added a WISPR hydrophone reader
  * Added a voltage-based `export_audio` resampling option
  * Refactored band-averaging to avoid losing information at frequency-band boundaries
  * MHKiT-Software#447
  * Author: @jmcvey3
  * Reviewer: @simmsa
* DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support
  * Added DOLfYN support for reading Aquadopp instruments
  * Cleaned Nortek parsing code
  * Simplified handling of the non-cabled ADV orientation flag
  * MHKiT-Software#434
  * Author: @jmcvey3
  * Reviewer: @akeeste
* Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb`
  * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave.
  * MHKiT-Software#430
  * Author: @jmcvey3
  * Reviewer: @akeeste

## Improvements

### Acoustics

- Improved flexibility and robustness of the Acoustics module
  - Added a configurable FFT length for sound pressure PSDs
  - Renamed bin/windowing attributes for clarity
  - Fixed an incorrectly signed gain correction
  - MHKiT-Software#433
  - Author: @jmcvey3
  - Reviewer: @akeeste

### DOLfYN

- Refactored PSD calculations to use `scipy.signal.welch`
  - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch`
  - Removed the bin-based segment structure and added a `step` argument to control overlap
  - Dropped float32 casts in some functions in favor of float64
  - Removed `fft.py` and renamed `tools/misc.py` to `tools.py`
  - Breaking Changes:
    - NaNs are no longer tolerated in PSD calculations
    - DOLfYN defaults to 0% overlap to preserve existing array shapes
    - Acoustics defaults to 50% overlap
    - PSD output time dimension renamed to `time_psd`
  - MHKiT-Software#452
  - Author: @jmcvey3
  - Reviewer: @akeeste, @simmsa
- Improved handling of "averaged" profiles
  - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent.
  - MHKiT-Software#430
  - Author: @jmcvey3
  - Reviewer: @akeeste
- Critical PSD bugfix
  - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries.
  - MHKiT-Software#430
  - Author: @jmcvey3
  - Reviewer: @akeeste

### Examples

- Added histograms to ADCP example
  - MHKiT-Software#448
  - Author: @browniea
  - Reviewer: @akeeste


### River/IO

- Fixed Qhull interpolation and D3D coordinate-system errors
  - MHKiT-Software#448
  - Author: @browniea
  - Reviewer: @akeeste
  - Fixes: MHKiT-Software#442, MHKiT-Software#444
- Delft3D module updates
  - Added new Delft3D coordinate names
  - Added a new grid-convergence-index calculation function
  - Added support for xarray/netCDF4 input in the D3D module
  - MHKiT-Software#428
  - Author: @browniea
  - Reviewer: @akeeste

### Wave

- NDBC Directional Wave Units
  - Fixed NDBC directional wave spectrum output to return degrees instead of radians
  - Updated polar plots so 0 deg is at the top and increases clockwise
  - MHKiT-Software#437
  - Author: @jmcvey3
  - Reviewer: @akeeste
  - Fixes: MHKiT-Software#427

### Wave/Hindcast

- Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (MHKiT-Software#450) from other failures
  - MHKiT-Software#449
  - Author: @simmsa
  - Reviewer: @akeeste

## Maintenance

- Added Python 3.13 support
  - MHKiT-Software#445
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: MHKiT-Software#441
- Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support
  - Updated the pandas dependency to allow pandas 3.x
  - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes
  - Fixed a deprecated period alias in tests
  - MHKiT-Software#443
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: MHKiT-Software#440
- Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies
  - Refactored optional dependencies
  - Standardized conda/conda-forge environment builds
  - Scoped black linting to changed files
  - MHKiT-Software#436
  - Author: @simmsa
  - Reviewer: @akeeste
- Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/)
  - MHKiT-Software#449
  - Author: @simmsa
  - Reviewer: @akeeste
simmsa added a commit that referenced this pull request Jul 10, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (#449)
8aa27ee 
# MHKiT-Python v1.1.0

## Additions

* Acoustics: Add millicdecade and WISPR instrument support
  * Added millidecade spectral conversion
  * Added a WISPR hydrophone reader
  * Added a voltage-based `export_audio` resampling option
  * Refactored band-averaging to avoid losing information at frequency-band boundaries
  * #447
  * Author: @jmcvey3
  * Reviewer: @simmsa
* DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support
  * Added DOLfYN support for reading Aquadopp instruments
  * Cleaned Nortek parsing code
  * Simplified handling of the non-cabled ADV orientation flag
  * #434
  * Author: @jmcvey3
  * Reviewer: @akeeste
* Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb`
  * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave.
  * #430
  * Author: @jmcvey3
  * Reviewer: @akeeste

## Improvements

### Acoustics

- Improved flexibility and robustness of the Acoustics module
  - Added a configurable FFT length for sound pressure PSDs
  - Renamed bin/windowing attributes for clarity
  - Fixed an incorrectly signed gain correction
  - #433
  - Author: @jmcvey3
  - Reviewer: @akeeste

### DOLfYN

- Refactored PSD calculations to use `scipy.signal.welch`
  - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch`
  - Removed the bin-based segment structure and added a `step` argument to control overlap
  - Dropped float32 casts in some functions in favor of float64
  - Removed `fft.py` and renamed `tools/misc.py` to `tools.py`
  - Breaking Changes:
    - NaNs are no longer tolerated in PSD calculations
    - DOLfYN defaults to 0% overlap to preserve existing array shapes
    - Acoustics defaults to 50% overlap
    - PSD output time dimension renamed to `time_psd`
  - #452
  - Author: @jmcvey3
  - Reviewer: @akeeste, @simmsa
- Improved handling of "averaged" profiles
  - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste
- Critical PSD bugfix
  - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste

### Examples

- Added histograms to ADCP example
  - #448
  - Author: @browniea
  - Reviewer: @akeeste


### River/IO

- Fixed Qhull interpolation and D3D coordinate-system errors
  - #448
  - Author: @browniea
  - Reviewer: @akeeste
  - Fixes: #442, #444
- Delft3D module updates
  - Added new Delft3D coordinate names
  - Added a new grid-convergence-index calculation function
  - Added support for xarray/netCDF4 input in the D3D module
  - #428
  - Author: @browniea
  - Reviewer: @akeeste

### Wave

- NDBC Directional Wave Units
  - Fixed NDBC directional wave spectrum output to return degrees instead of radians
  - Updated polar plots so 0 deg is at the top and increases clockwise
  - #437
  - Author: @jmcvey3
  - Reviewer: @akeeste
  - Fixes: #427

### Wave/Hindcast

- Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste

## Maintenance

- Added Python 3.13 support
  - #445
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #441
- Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support
  - Updated the pandas dependency to allow pandas 3.x
  - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes
  - Fixed a deprecated period alias in tests
  - #443
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #440
- Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies
  - Refactored optional dependencies
  - Standardized conda/conda-forge environment builds
  - Scoped black linting to changed files
  - #436
  - Author: @simmsa
  - Reviewer: @akeeste
- Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/)
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste
simmsa added a commit that referenced this pull request Jul 10, 2026
@simmsa
Release: MHKiT v1.1.0
9fa9f9c 
# MHKiT-Python v1.1.0

## Additions

* Acoustics: Add millicdecade and WISPR instrument support
  * Added millidecade spectral conversion
  * Added a WISPR hydrophone reader
  * Added a voltage-based `export_audio` resampling option
  * Refactored band-averaging to avoid losing information at frequency-band boundaries
  * #447
  * Author: @jmcvey3
  * Reviewer: @simmsa
* DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support
  * Added DOLfYN support for reading Aquadopp instruments
  * Cleaned Nortek parsing code
  * Simplified handling of the non-cabled ADV orientation flag
  * #434
  * Author: @jmcvey3
  * Reviewer: @akeeste
* Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb`
  * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave.
  * #430
  * Author: @jmcvey3
  * Reviewer: @akeeste

## Improvements

### Acoustics

- Improved flexibility and robustness of the Acoustics module
  - Added a configurable FFT length for sound pressure PSDs
  - Renamed bin/windowing attributes for clarity
  - Fixed an incorrectly signed gain correction
  - #433
  - Author: @jmcvey3
  - Reviewer: @akeeste

### DOLfYN

- Refactored PSD calculations to use `scipy.signal.welch`
  - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch`
  - Removed the bin-based segment structure and added a `step` argument to control overlap
  - Dropped float32 casts in some functions in favor of float64
  - Removed `fft.py` and renamed `tools/misc.py` to `tools.py`
  - Breaking Changes:
    - NaNs are no longer tolerated in PSD calculations
    - DOLfYN defaults to 0% overlap to preserve existing array shapes
    - Acoustics defaults to 50% overlap
    - PSD output time dimension renamed to `time_psd`
  - #452
  - Author: @jmcvey3
  - Reviewer: @akeeste, @simmsa
- Improved handling of "averaged" profiles
  - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste
- Critical PSD bugfix
  - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries.
  - #430
  - Author: @jmcvey3
  - Reviewer: @akeeste

### Examples

- Added histograms to ADCP example
  - #448
  - Author: @browniea
  - Reviewer: @akeeste

### River/IO

- Fixed Qhull interpolation and D3D coordinate-system errors
  - #448
  - Author: @browniea
  - Reviewer: @akeeste
  - Fixes: #442, #444
- Delft3D module updates
  - Added new Delft3D coordinate names
  - Added a new grid-convergence-index calculation function
  - Added support for xarray/netCDF4 input in the D3D module
  - #428
  - Author: @browniea
  - Reviewer: @akeeste

### Wave

- NDBC Directional Wave Units
  - Fixed NDBC directional wave spectrum output to return degrees instead of radians
  - Updated polar plots so 0 deg is at the top and increases clockwise
  - #437
  - Author: @jmcvey3
  - Reviewer: @akeeste
  - Fixes: #427

### Wave/Hindcast

- Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste

## Maintenance

- Added Python 3.13 support
  - #445
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #441
- Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support
  - Updated the pandas dependency to allow pandas 3.x
  - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes
  - Fixed a deprecated period alias in tests
  - #443
  - Author: @simmsa
  - Reviewer: @akeeste
  - Fixes: #440
- Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies
  - Refactored optional dependencies
  - Standardized conda/conda-forge environment builds
  - Scoped black linting to changed files
  - #436
  - Author: @simmsa
  - Reviewer: @akeeste
- Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/)
  - #449
  - Author: @simmsa
  - Reviewer: @akeeste
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