Merge branch 'develop' into main

Author: akeeste

.github/workflows/main.yml

@@ -83,7 +83,7 @@ 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 +134,7 @@ 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 +183,7 @@ 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 +286,7 @@ 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 +354,7 @@ 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 +390,39 @@ 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 ${{ matrix.module }}
+        run: |
+          python -m pytest -c .github/workflows/pytest.ini mhkit/tests/${{ matrix.module }}/
+
   notebook-matrix:
     runs-on: ubuntu-latest
     needs:
@@ -455,7 +488,8 @@ 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 +509,7 @@ 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