Skip to content

Feature: Add python 3.13 support - #445

Merged
akeeste merged 9 commits into
MHKiT-Software:developfrom
simmsa:feat_add_python_3_13_support
Jun 10, 2026
Merged

Feature: Add python 3.13 support#445
akeeste merged 9 commits into
MHKiT-Software:developfrom
simmsa:feat_add_python_3_13_support

Conversation

@simmsa

@simmsa simmsa commented Jun 9, 2026 •
edited
Loading

Copy link
Copy Markdown
Contributor

This PR verifies MHKiT-Python supports Python 3.13.

No python code changes were required.

README was updated to include Python 3.13

Actions were updated to include 3.13 in test matrices and for notebook tests (single version)

Action versions for setup-miniconda and download-artifact were update

@akeeste
akeeste self-requested a review June 10, 2026 13:56
@simmsa
simmsa marked this pull request as ready for review June 10, 2026 18:15
@simmsa

simmsa commented Jun 10, 2026

Copy link
Copy Markdown
Contributor Author

@akeeste, this is ready for review.

Python 3.13 did not require any major code changes and we didn't have any library issues here.

akeeste
akeeste approved these changes Jun 10, 2026
View reviewed changes

@akeeste akeeste left a comment •
edited
Loading

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Awesome, thanks @simmsa ! This looks good for the Python source. We'll have to update our documentation repo as well later on

@akeeste
akeeste merged commit 51e216e into MHKiT-Software:develop Jun 10, 2026
115 of 118 checks passed
@simmsa simmsa mentioned this pull request Jun 11, 2026
Closed
@akeeste akeeste linked an issue Jun 15, 2026 that may be closed by this pull request
Python Versions: Add support for Python 3.13 #441
Closed
@simmsa simmsa mentioned this pull request Jun 29, 2026
Merged
3 tasks
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
@simmsa simmsa mentioned this pull request Jul 8, 2026
Merged
simmsa added a commit to simmsa/MHKiT-Python that referenced this pull request Jul 10, 2026
@simmsa
Feature: Add python 3.13 support (MHKiT-Software#445)
b962f4c 
This PR verifies MHKiT-Python supports Python 3.13.

No python code changes were required.

README was updated to include Python 3.13

Actions were updated to include 3.13 in test matrices and for notebook
tests (single version)

Action versions for setup-miniconda and download-artifact were update
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
Feature: Add python 3.13 support (#445)
cddae38 
This PR verifies MHKiT-Python supports Python 3.13.

No python code changes were required.

README was updated to include Python 3.13

Actions were updated to include 3.13 in test matrices and for notebook
tests (single version)

Action versions for setup-miniconda and download-artifact were update
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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@akeeste akeeste akeeste approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Python Versions: Add support for Python 3.13

2 participants

@simmsa @akeeste