Fix failing pip tests (#422)

Status: Ready

This is a fix for failing pip tests in main.yml:


https://github.com/MHKiT-Software/MHKiT-Python/actions/runs/18511807517/job/52754343805?pr=421

https://github.com/MHKiT-Software/MHKiT-Python/actions/runs/18511807517/job/52754343883?pr=421

There are lots of errors in both of these tests related to h5 and
netcdf4. One fix for this is installing the system h5 and nc binaries
and having pip rebuild against these binaries

---------

Co-authored-by: jmcvey3 <[email protected]>

Author: simmsa

.github/workflows/main.yml

@@ -282,12 +282,20 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Update and install packages
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip wheel
           pip install -e  ".[all,dev]"
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        if: runner.os == 'Linux'
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Install setuptools for Python 3.12
         if: matrix.python-version == '3.12'
         run: pip install setuptools
@@ -469,12 +477,18 @@ jobs:
           name: data
           path: ~/.cache/mhkit
 
+      - name: Install system dependencies
+        run: sudo apt-get install -y libhdf5-dev libnetcdf-dev
+
       - name: Install MHKiT with optional dependency
         run: |
           python -m pip install --upgrade pip
           pip install "mhkit[${{ matrix.module }}]"
           pip install pytest
 
+      - name: Reinstall h5py and netCDF4 with system libraries
+        run: "pip install --force-reinstall --no-binary=:all: h5py netCDF4"
+
       - name: Run tests for ${{ matrix.module }}
         env:
           MPLBACKEND: Agg