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Add method option to surface_elevation #126

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merged 7 commits into from
May 10, 2024
+330 −126
Merged

Add method option to surface_elevation #126

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af1b9c2
Test: add `surface_elevation` method option test
simmsa Apr 22, 2024
edb9155
Feat: Add method option to `surface_elevation`
simmsa Apr 22, 2024
1f814e9
MATLAB: Update add-on
simmsa Apr 22, 2024
0ef9e05
Test: Verify surface elevation using mean diff
simmsa Apr 26, 2024
c6b9c8c
Build: Update mltbx and version
simmsa Apr 26, 2024
763beab
Actions: Use macos-version that does not use arm
simmsa Apr 29, 2024
e364c9f
Actions: Use workflows from delft-3d-io branch
simmsa Apr 29, 2024
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155 changes: 92 additions & 63 deletions .github/workflows/unix_unit_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,43 +21,43 @@ jobs:
env:
mhkit-python-dir: "MHKiT-Python"
steps:
- name: Check out MHKiT-MATLAB
uses: actions/checkout@v4

- name: Check out MHKiT-Python
uses: actions/checkout@v4
with:
repository: "MHKiT-Software/MHKiT-Python"
path: ${{env.mhkit-python-dir}}

- name: Install & Setup Miniconda
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: latest
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: MHKIT_CONDA_ENV
activate-environment: mhkit_conda_env
channels: conda-forge

- name: Setup Python ${{ matrix.python-version }}
- name: "Conda install netcdf4, hdf5"
shell: bash -l {0}
run: |
conda create --name MHKIT_CONDA_ENV python=${{ matrix.python-version }} numpy cython pip pytest hdf5 libnetcdf cftime openssl --strict-channel-priority
conda activate MHKIT_CONDA_ENV
conda install -c conda-forge netcdf4
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install -e . --no-deps --force-reinstall
conda activate mhkit_conda_env
conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
# conda install netcdf4 hdf5
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config

- name: Check out MHKiT-MATLAB
uses: actions/checkout@v4

- name: Check out MHKiT-Python
uses: actions/checkout@v4
with:
repository: "MHKiT-Software/MHKiT-Python"
path: ${{env.mhkit-python-dir}}

- name: pip install mhkit module from source
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
pip install -e .
working-directory: ${{env.mhkit-python-dir}}

- name: pip install mhkit-python-utils module from source
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
pip install -e .

# Create the cache and add a dummy file
Expand All @@ -70,15 +70,15 @@ jobs:
echo "Hello World" > mhkit_webread_cache/test.txt

- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v1
uses: matlab-actions/setup-matlab@v2
with:
release: ${{ matrix.matlab-version }}

# OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu
- name: Configure MATLAB Python Environment
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") > run.m

- name: Add MATLAB test commands
Expand All @@ -98,13 +98,13 @@ jobs:
run: cat run.m

- name: Run MATLAB Unit Tests
uses: matlab-actions/run-command@v1
uses: matlab-actions/run-command@v2
with:
command: run
startup-options: -noFigureWindows

- name: Save mhkit_webread_cache directory as an artifact
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
# GitHub Action "Name" of artifact
name: mhkit_webread_cache
Expand All @@ -118,16 +118,16 @@ jobs:

# Expecting 2 * 4 * 7 - (13 * 2) = 30 jobs
matrix:
os: [macos-latest, ubuntu-latest]
os: [macos-13, ubuntu-latest]
python-version: [3.8, 3.9, "3.10", 3.11]
# Note: It is preferred to use an actual release name as opposed to 'latest'
matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b]
matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a]
exclude:
# cache_population job
- python-version: "3.10"
- python-version: "3.10" # cache_population job
matlab-version: R2022b
os: ubuntu-latest
# Non compatiable MATLAB/Python Versions according to Mathworks
- matlab-version: R2024a # Non compatiable versions of Python and MATLAB
python-version: 3.8
- matlab-version: R2023b
python-version: 3.8
- matlab-version: R2023a
Expand All @@ -154,9 +154,25 @@ jobs:
python-version: "3.10"
- matlab-version: R2020b
python-version: 3.9
# Combinations with failing tests that seem related to GitHub Actions
- matlab-version: R2023b
os: macos-latest
# Specific versions of tests that fail consistently. Most likely due to the GitHub actions environment
- matlab-version: R2024a # Python netcdf4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123413351
python-version: 3.11
os: macos-13
# - matlab-version: R2024a # Working!
# python-version: "3.10"
# os: macos-13
- matlab-version: R2024a # Java Segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411604
python-version: 3.9
os: macos-13
- matlab-version: R2023b # Python netcd4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412889
python-version: 3.11
os: macos-13
- matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412352
python-version: "3.10"
os: macos-13
- matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411335
python-version: 3.9
os: macos-13

runs-on: ${{ matrix.os }}

Expand All @@ -172,36 +188,35 @@ jobs:
repository: "MHKiT-Software/MHKiT-Python"
path: ${{env.mhkit-python-dir}}

# - name: Setup Conda
# uses: s-weigand/setup-conda@v1
# with:
# activate-conda: false
# conda-channels: conda-forge

- name: Install & Setup Miniconda
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: latest
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: MHKIT_CONDA_ENV
activate-environment: mhkit_conda_env
channels: conda-forge

- name: Setup Python ${{ matrix.python-version }}
# This is necessary to fix any issues with netcdf4 and hdf5 headers
- name: "Conda install netcdf4, hdf5"
shell: bash -l {0}
run: |
conda create --name MHKIT_CONDA_ENV python=${{ matrix.python-version }} numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
conda activate MHKIT_CONDA_ENV
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install -e . --no-deps --force-reinstall

# - name: Setup Python
# uses: actions/setup-python@v4
# with:
# python-version: ${{ matrix.python-version }}
conda activate mhkit_conda_env
conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4
# conda install netcdf4 hdf5
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config

# - name: Setup Python ${{ matrix.python-version }}
# shell: bash -l {0}
# run: |
# conda create --name mhkit_conda_env python=${{ matrix.python-version }} numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
# conda activate mhkit_conda_env
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
# pip install -e . --no-deps --force-reinstall

# - name: Setup MHKiT Dependencies on macOS
# if: ${{ matrix.os == 'macos-13' }}
# run: brew install hdf5 netcdf
# if: ${{ matrix.os == 'macos-latest' }}

# - name: Setup MHKiT Dependencies on ubuntu
# run: sudo apt install libhdf5-serial-dev libnetcdf-dev
Expand Down Expand Up @@ -231,48 +246,57 @@ jobs:
- name: Print Python executable
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
python -c "import sys; print(sys.executable)"

- name: Print Python Version
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
python --version

- name: pip install mhkit module from source
working-directory: ${{env.mhkit-python-dir}}
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install -e .

- name: pip upgrade netcdf4
working-directory: ${{env.mhkit-python-dir}}
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install --upgrade netcdf4

- name: pip install mhkit-python-utils module from source
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
pip install -e .

- name: List installed pip modules
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
pip freeze

- name: Print MHKiT-Python Version
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
python -c "import mhkit; print(mhkit.__version__)"

- name: Verify MHKiT-Python Operation
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
conda activate mhkit_conda_env
python -c "import mhkit; [ED, AP] = mhkit.river.performance.circular(30); print(ED); print(AP);"

- name: Download mhkit_webread_cache artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: mhkit_webread_cache
path: mhkit_webread_cache
Expand All @@ -282,16 +306,22 @@ jobs:
working-directory: .

- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v2-beta
uses: matlab-actions/setup-matlab@v2
with:
release: ${{ matrix.matlab-version }}

- name: Add Python Dir to Path
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
printf "getenv('path')\nsetenv('path', ['%s;', getenv('path')])\ngetenv('path')\n" $(python -c "import sys; import os; print(os.path.dirname(sys.executable))") >> run.m

# OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu
- name: Configure MATLAB Python Environment
shell: bash -l {0}
run: |
conda activate MHKIT_CONDA_ENV
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") > run.m
conda activate mhkit_conda_env
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") >> run.m

- name: Add MATLAB test commands
shell: bash
Expand All @@ -316,8 +346,7 @@ jobs:
# select-by-folder: mhkit/tests

- name: Run MATLAB Unit Tests
uses: matlab-actions/run-command@v1
uses: matlab-actions/run-command@v2
with:
command: run
startup-options: -noFigureWindows

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