v1.0.0 develop into main

v1.0.0
# MHKiT v1.0.0
## New Features
* Sound Exposure Level by @jmcvey3 in MHKiT-Software#388
* Add discharge function to MHKiT by @jmcvey3 in MHKiT-Software#385

## Functionality enhancements
* Fix for corrupted Nortek files by @jmcvey3 in MHKiT-Software#372
* Update integral length scale function by @jmcvey3 in MHKiT-Software#376
* Fix ever-changing RDI RiverPro depth bin ranges by @jmcvey3 in MHKiT-Software#378
* Allow clean functions to handle _avg variables by @jmcvey3 in MHKiT-Software#377
* IEC TS 62600 updates by @akeeste in MHKiT-Software#382
* MLER explanation updates/corrections by @rgcoe in MHKiT-Software#393
* Improve Nortek2 index file creator functions by @jmcvey3 in MHKiT-Software#397
* Read Sentinel V specific data packets by @jmcvey3 in MHKiT-Software#396
* Short list of VMDAS updates by @jmcvey3 in MHKiT-Software#405
* Allow user to specify universal Kolmogorov constant for TKE dissipation rate function by @jmcvey3 in MHKiT-Software#406
* Nortek Dual Profile Dataset Rotation by @jmcvey3 in MHKiT-Software#414

## Source code improvements
* Lint Tidal by @ssolson in MHKiT-Software#386
* Lint river module by @ssolson in MHKiT-Software#389
* Lint hindcast by @ssolson in MHKiT-Software#398
* Modernize Package Configuration by @ssolson in MHKiT-Software#400
* Configure specific warnings by @ssolson in MHKiT-Software#401

## Bug fixes
* Avoid failing to scan very large files by @jmcvey3 in MHKiT-Software#371
* Acoustics SPL bugfix by @jmcvey3 in MHKiT-Software#379
* DOLfYN/RDI: Set  `fs` to NaN when typical calculation methods yield error (MHKiT-Software#408) by @simmsa in MHKiT-Software#409

## Testing and Continuous Integration Updates
* Fix Jupyter Notebook tests running Python 3.13 by @ssolson in MHKiT-Software#380
* CI Test Clean Up: Mock USGS, Acoustic Tolerances by @ssolson in MHKiT-Software#404
* Speed up tests with concurrency checks to prevent duplicate workflows on PRs from develop into main or from main into develop by @akeeste
* Define MPLBACKEND to decrease intermittent matplotlib errors in tests by @akeeste

## Documentation and Examples
* Add WEC-Sim power performance example  by @akeeste in MHKiT-Software#395
* Update dolfyn function docstrings and associated notebooks by @jmcvey3 in MHKiT-Software#412
* Update examples by @akeeste in MHKiT-Software#417
* Update installation instructions in README.md by @akeeste
* Adjust acoustics test tolerances by @akeeste in MHKiT-Software#420

**Full Changelog**: MHKiT-Software/MHKiT-Python@v0.9.0...v1.0.0

Author: akeeste

.github/workflows/main.yml

@@ -1,15 +1,19 @@
 name: Py 3.10, 3.11, 3.12 | Windows Mac Linux
 
 on:
-  push:
+  pull_request:
     branches:
       - main
       - develop
-  pull_request:
+  push:
     branches:
       - main
       - develop
 
+concurrency:
+  group: ${{ github.event.pull_request.number }}  # Use the pull request number as the concurrency group
+  cancel-in-progress: true # Cancel any in-progress jobs for the same group. Prevents duplicate workflows on PRs from develop into main or from main into develop.
+
 jobs:
   set-os:
     runs-on: ubuntu-latest
@@ -83,7 +87,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare non-hindcast API data
         shell: bash -l {0}
@@ -134,7 +138,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare Wave Hindcast data
         shell: bash -l {0}
@@ -183,7 +187,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Prepare Wind Hindcast data
         shell: bash -l {0}
@@ -286,7 +290,7 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          pip install -e  ".[all,dev]"
 
       - name: Install setuptools for Python 3.12
         if: matrix.python-version == '3.12'
@@ -354,7 +358,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Download Wave Hindcast data from artifact
         uses: actions/download-artifact@v4
@@ -390,6 +394,41 @@ jobs:
           parallel: true
           path-to-lcov: ./coverage.lcov
 
+  test-optional-pip-dependencies:
+    needs: [set-os, prepare-nonhindcast-cache]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        module:
+          [wave, tidal, river, dolfyn, power, loads, mooring, acoustics, utils]
+        python-version: ['3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Download non-hindcast data
+        uses: actions/download-artifact@v4
+        with:
+          name: data
+          path: ~/.cache/mhkit
+
+      - name: Install MHKiT with optional dependency
+        run: |
+          python -m pip install --upgrade pip
+          pip install "mhkit[${{ matrix.module }}]"
+          pip install pytest
+
+      - name: Run tests for ${{ matrix.module }}
+        env:
+          MPLBACKEND: Agg
+        run: |
+          python -m pytest -c .github/workflows/pytest.ini mhkit/tests/${{ matrix.module }}/
+
   notebook-matrix:
     runs-on: ubuntu-latest
     needs:
@@ -455,7 +494,8 @@ jobs:
         with:
           miniconda-version: 'latest'
           auto-update-conda: true
-          python-version: '3.11'
+          python-version: '3.12'
+          channels: conda-forge
           activate-environment: TESTconda
           use-only-tar-bz2: false
 
@@ -475,7 +515,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate mhkit-env
-          pip install -e . --no-deps
+          pip install -e  ".[all,dev]" --no-deps
 
       - name: Download non-hindcast data
         uses: actions/download-artifact@v4

.github/workflows/pylint.yml

@@ -18,8 +18,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
-          pip install pylint
-          pip install .
+          pip install ".[all,dev]"
 
       - name: Run Pylint on mhkit/loads/
         run: |
@@ -36,3 +35,15 @@ jobs:
       - name: Run Pylint on mhkit/acoustics/
         run: |
           pylint mhkit/acoustics/
+
+      - name: Run Pylint on mhkit/tidal/
+        run: |
+          pylint mhkit/tidal/
+
+      - name: Run Pylint on mhkit/river/
+        run: |
+          pylint --extension-pkg-allow-list=netCDF4 mhkit/river/
+
+      - name: Run Pylint on mhkit/wave/io/hindcast/
+        run: |
+          pylint  mhkit/wave/io/hindcast/

README.md

@@ -32,19 +32,54 @@ See the [MHKiT documentation](https://mhkit-software.github.io/MHKiT) for more i
 
 ## Installation
 
-MHKiT-Python requires Python (3.10, 3.11, 3.12) along with several Python
-package dependencies. MHKiT-Python can be installed using the Conda package manager:
+[MHKiT-Python](https://github.com/MHKiT-Software/MHKiT-Python) requires [Python (3.10-3.12)](https://www.python.org/).
+It is recommended to use the [Anaconda Python Distribution](https://www.anaconda.com/distribution/) (a fully featured Python installer with a GUI) 
+or [Miniconda](https://docs.anaconda.com/miniconda/#quick-command-line-install) (a lightweight installer with the ``conda`` command line utility).  
+Both will include most of MHKiT-Python's package dependencies. 
+MHKiT can be installed several ways:
+
+### Option 1: Install from Python
+
+This option is recommended as a fast installation for MHKiT-Python users.
+To install MHKiT-Python using ``conda``, in an Anaconda Prompt:
+
+```bash
+	conda install -c conda-forge mhkit
+```
+
+### Option 2: Clone Repository from GitHub
+
+This option is recommended for MHKiT-Python users who want access to example notebooks and developers.
+Download and install your preferred version of [git](https://git-scm.com/).
+To clone MHKiT-Python:
 
 ```bash
-conda install -c conda-forge mhkit
+	git clone https://github.com/MHKiT-Software/MHKiT-Python
+	cd MHKiT-Python
 ```
 
-MHKiT can alternatively be installed from PyPi using pip:
+To install a local, editable version of MHKiT-Python using [pip](https://pip.pypa.io/en/stable/):
 
 ```bash
-pip install mhkit
+	pip install -e .["all"]
 ```
 
+An [environment YAML file](https://github.com/MHKiT-Software/MHKiT-Python/blob/main/environment.yml) is also provided that can create the base environment required by MHKiT. 
+MHKiT can then be installed into that environment using any of the provided methods.
+
+### Option 3: Module-specific Install from Python
+
+A slim version of MHKiT-Python can be installed to reduce the number of dependencies and potential conflicts with other software. 
+This installation utilizes pip's optional dependencies installation. 
+To install a single MHKiT module, e.g. the wave module, and its dependencies, use:
+
+	pip install mhkit["wave"]
+
+Note that ``pip install mhkit`` only installs the base MHKiT dependencies and not the entire software.
+To install all MHKiT dependencies use:
+
+	pip install mhkit["all"]
+
 See [installation instructions](https://mhkit-software.github.io/MHKiT/installation.html) for more information.
 
 ## Copyright and license

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.10
+  - python>=3.10,<3.13
   - pip
   - numpy>=2.0.0
   - pandas>=2.2.2
@@ -25,3 +25,4 @@ dependencies:
   - matplotlib>=3.9.1
   - fatpack
   - nrel-rex
+  - cartopy