Merge Seg fault related PRs and few fixes (#58)

* Merging pr 45

* merging pr 47

* Adding no-cache option to build

* let ngen build steps handle cpp test lib

* Update Dockerfile.ngen

* Added missing "

* Fix syntax error (#54)

* remove $ from build dir in build steps

* build wheel for new troute sub package

* use build module to build troute-config wheel

---------

Co-authored-by: Nels <nfrazier@lynker.com>
Co-authored-by: Arpita Patel <gagarp@gmail.com>

.github/action_templates/build-and-push/action.yaml

@@ -41,6 +41,7 @@ runs:
         tags: |
           awiciroh/${{ inputs.image-name}}:latest
         builder: mybuilder
+        no-cache: true
       env:
         DOCKER_BUILDKIT: 1
-        DOCKER_CLI_EXPERIMENTAL: enabled
+        DOCKER_CLI_EXPERIMENTAL: enabled

docker/Dockerfile.ngen

@@ -133,6 +133,7 @@ RUN cd ${WORKDIR}/ngen \
         -DNETCDF_LIBRARY=/usr/lib/libnetcdf.so \
         -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include \
         -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so ; \
+        cmake --build cmake_build_serial --target all -j $(nproc); \
     fi \
     && if [ "${BUILD_NGEN_PARALLEL}" == "true" ]; then \
         cmake -B cmake_build_parallel -S . \
@@ -149,21 +150,18 @@ RUN cd ${WORKDIR}/ngen \
         -DNETCDF_LIBRARY=/usr/lib/libnetcdf.so \
         -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include \
         -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so ; \
+        cmake --build cmake_build_parallel --target all -j $(nproc); \
     fi \
-    && ln -s $(if [ "${BUILD_NGEN_PARALLEL}" == "true" ]; then echo "cmake_build_parallel"; else echo "cmake_build_serial"; fi) cmake_build \
     # Build the required submodules/external libs needed for running the tests later \
     # C++ functionality isn't separate, so always build the test_bmi_cpp shared lib (also needed for test_bmi_multi) \
-    && ./build_sub extern/test_bmi_cpp \
+    # && ./build_sub extern/test_bmi_cpp \
     # For the external language BMI integrations, conditionally build the test packages/libraries and run tests \
     &&  if [ "${NGEN_ACTIVATE_C}" == "ON" ]; then \
             ./build_sub extern/test_bmi_c; \
         fi \
     &&  if [ "${NGEN_ACTIVATE_FORTRAN}" == "ON" ]; then \
             ./build_sub extern/test_bmi_fortran; \
         fi \
-    &&  for BUILD_DIR in $(if [ "${BUILD_NGEN_PARALLEL}" == "true" ]; then echo "cmake_build_parallel"; fi) $(if [ "${BUILD_NGEN_SERIAL}" == "true" ]; then echo "cmake_build_serial"; fi) ; do \
-        cmake --build $BUILD_DIR --target all -j $(nproc); \
-    done \
     # run the serial tests \
     && cd ${WORKDIR}/ngen \
     # && cmake --build cmake_build_serial --target test \ 

docker/Dockerfile.ngen-deps

@@ -301,7 +301,7 @@ RUN pip3 install --upgrade pip \
     && git submodule update --init --recursive \
     && python3 -m pip install -r requirements-build.txt \
     && pip3 install . \
-    && pip3 install numpy pandas pyyaml bmipy Cython netCDF4 wheel packaging \
+    && pip3 install numpy pandas pyyaml bmipy Cython==3.0.3 netCDF4==1.6.3 wheel packaging \
     && HDF5_DIR=/usr pip3 install -v --no-build-isolation tables \
     # Make aliases for convenience \
     && alias pip='pip3' \

docker/Dockerfile.t-route

@@ -36,6 +36,8 @@ ARG REPO_URL \
 COPY --chown=root --from=rocky_init_troute_repo ${WORKDIR}/t-route ${WORKDIR}/t-route
 
 RUN cp -s /usr/bin/python3 /usr/bin/python \
+    # Install the build package to build package wheel for troute-config
+    && pip install build \
     #&& python(){ /usr/bin/python3 \$@; } && export -f python \
     && cd ${WORKDIR}/t-route \
     && mkdir wheels \
@@ -50,6 +52,10 @@ RUN cp -s /usr/bin/python3 /usr/bin/python \
     && cd ../troute-routing \
     && python3 setup.py --use-cython bdist_wheel \
     && cp dist/*.whl ${WORKDIR}/t-route/wheels/ \
+    # troute-config doesn't use setup.py, use build to make the wheel
+    && cd ../troute-config \
+    && python3 -m build . \
+    && cp dist/*.whl ${WORKDIR}/t-route/wheels/ \
     && cd ../troute-nwm \
     && python3 setup.py bdist_wheel \
     && cp dist/*.whl ${WORKDIR}/t-route/wheels/