update pip.yml for building wheels for PyPI

.github/workflows/cd.yml

@@ -60,7 +60,7 @@ jobs:
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - name: checkout vcell-solvers repo
+      - name: checkout vcell-fvsolvers repo
         uses: actions/checkout@v4
         with:
           submodules: true
@@ -104,6 +104,42 @@ jobs:
           brew info boost
           brew info hdf5
 
+      - name: Install Windows Dependencies
+        if: matrix.platform == 'windows-latest'
+        uses: msys2/setup-msys2@v2
+        with:
+          msystem: CLANG64
+          update: true
+          install: >
+            zip
+            git
+            mingw-w64-clang-x86_64-curl
+            mingw-w64-clang-x86_64-toolchain
+            mingw-w64-clang-x86_64-flang
+            mingw-w64-clang-x86_64-cmake
+            mingw-w64-clang-x86_64-boost
+            mingw-w64-clang-x86_64-hdf5
+            mingw-w64-clang-x86_64-libzip
+            mingw-w64-clang-x86_64-zlib
+            mingw-w64-clang-x86_64-libaec
+
+      - name: Install Linux Dependencies
+        if: matrix.platform == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libboost-all-dev
+          sudo apt-get install -y libhdf5-dev
+          sudo apt-get install -y libzip-dev
+          sudo apt-get install -y ninja-build
+
+          gcc --version
+          gfortran --version
+          cmake --version
+          dpkg -s libboost-all-dev
+          dpkg -s libhdf5-dev
+
+
+
       - name: Build Macos ARM
         if: matrix.platform == 'macos-14'
         run: |
@@ -182,25 +218,6 @@ jobs:
 #          limit-access-to-actor: false
 
 
-      - name: Install Windows Dependencies
-        if: matrix.platform == 'windows-latest'
-        uses: msys2/setup-msys2@v2
-        with:
-          msystem: CLANG64
-          update: true
-          install: >
-            zip
-            git
-            mingw-w64-clang-x86_64-curl
-            mingw-w64-clang-x86_64-toolchain
-            mingw-w64-clang-x86_64-flang
-            mingw-w64-clang-x86_64-cmake
-            mingw-w64-clang-x86_64-boost
-            mingw-w64-clang-x86_64-hdf5
-            mingw-w64-clang-x86_64-libzip
-            mingw-w64-clang-x86_64-zlib
-            mingw-w64-clang-x86_64-libaec
-
 #      - name: Setup tmate session
 #        uses: mxschmitt/action-tmate@v3
 #        with:
@@ -249,21 +266,6 @@ jobs:
           ./bin/FiniteVolume_x64 || true
           echo
 
-      - name: Install Linux Dependencies
-        if: matrix.platform == 'ubuntu-latest'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libboost-all-dev
-          sudo apt-get install -y libhdf5-dev
-          sudo apt-get install -y libzip-dev
-          sudo apt-get install -y ninja-build
-
-          gcc --version
-          gfortran --version
-          cmake --version
-          dpkg -s libboost-all-dev
-          dpkg -s libhdf5-dev
-
       - name: Build Linux
         if: matrix.platform == 'ubuntu-latest'
         run: |

.github/workflows/pip.yml

@@ -37,25 +37,27 @@ jobs:
       run: |
         brew install boost
         brew install hdf5
+          brew install libzip
         brew install ninja
         
         brew install llvm
         echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
         source /Users/runner/.bash_profile
+          ln -s $(which gfortran-14) /usr/local/bin/gfortran
         
         gcc --version
         gfortran --version
         cmake --version
         brew info boost
         brew info hdf5
 
-
     - name: Install ARM MacOS dependencies
       if: matrix.platform == 'macos-14'
       shell: bash
       run: |
         brew install boost
         brew install hdf5
+        brew install libzip
         brew install ninja
         
         brew install llvm
@@ -68,7 +70,6 @@ jobs:
         brew info boost
         brew info hdf5
 
-
     - name: Install Windows Dependencies
       if: matrix.platform == 'windows-latest'
       uses: msys2/setup-msys2@v2
@@ -93,28 +94,31 @@ jobs:
       with:
         python-version: "${{ matrix.python-version }}"
 
-    - name: Build and install macos-13
+
+    - name: Build and install macos-14
+      if: matrix.platform == 'macos-14'
       run: |
-        export MACOSX_DEPLOYMENT_TARGET=13.0
-        PATH="/usr/local/opt/llvm/bin:$PATH"
+        PATH="/opt/homebrew/opt/llvm/bin:$PATH"
         pip wheel . -w dist
         ls -al dist
         pip install delocate
         delocate-listdeps dist/*.whl
         delocate-wheel -v dist/*.whl
         pip install dist/*.whl
-      if: matrix.platform == 'macos-13'
 
-    - name: Build and install macos-14
+
+    - name: Build and install macos-13
+      if: matrix.platform == 'macos-13'
       run: |
-        PATH="/opt/homebrew/opt/llvm/bin:$PATH"
+        export MACOSX_DEPLOYMENT_TARGET=13.0
+        PATH="/usr/local/opt/llvm/bin:$PATH"
         pip wheel . -w dist
         ls -al dist
         pip install delocate
         delocate-listdeps dist/*.whl
         delocate-wheel -v dist/*.whl
         pip install dist/*.whl
-      if: matrix.platform == 'macos-14'
+
 
     - name: Build and install windows-latest
       shell: msys2 {0}
@@ -134,7 +138,7 @@ jobs:
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
            /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -146,7 +150,7 @@ jobs:
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
            /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -158,7 +162,7 @@ jobs:
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
            /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -170,7 +174,7 @@ jobs:
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
            /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"

Dockerfile

@@ -1,8 +1,18 @@
 FROM ubuntu:22.04
 
-RUN apt-get -y update && apt-get install -y apt-utils && \
-    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran \
-    libhdf5-dev libzip-dev ninja-build libcurl4-openssl-dev libboost-all-dev libbz2-dev cmake python3
+RUN apt-get -y update && \
+    apt-get install -y apt-utils && \
+    apt-get install -y -qq -o=Dpkg::Use-Pty=0 \
+        build-essential \
+        cmake \
+        ninja-build \
+        gfortran \
+        libcurl4-openssl-dev \
+        libhdf5-dev \
+        libzip-dev \
+        libboost-all-dev \
+        libbz2-dev \
+        python3
 
 # Install an alternative Fortran compiler
 RUN apt-get install -y gfortran-10