Using local copies of LAPACK for easier packaging.

.github/tools/cibw_repair_wheel_command_windows.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -e
+set -x
+
+WHEEL=$1
+DEST_DIR=$2
+
+python -m pip install delvewheel
+python -m delvewheel show "$WHEEL" && python -m delvewheel repair -w "$DEST_DIR" "$WHEEL" --no-mangle-all

.github/workflows/CI_pyHAMS.yml

@@ -16,50 +16,63 @@ jobs:
             fail-fast: false #true
             matrix:
                 os: ["ubuntu-latest", "macOS-latest"] #, "windows-latest"]
-                python-version: ["3.9", "3.10", "3.11"]
+                python-version: ["3.9", "3.10", "3.11", "3.12"]
 
         steps:
             - name: Setup GNU Fortran
-            #  if: false == contains( matrix.os, 'windows')
-              uses: awvwgk/setup-fortran@v1 #modflowpy/install-intelfortran-action@v1 #
+              if: false == contains( matrix.os, 'windows')
+              uses: awvwgk/setup-fortran@v1
+
+            - name: Install compiler
+              if: false == contains( matrix.os, 'windows')
+              id: install_cc
+              uses: rlalik/setup-cpp-compiler@master
+              with:
+                  compiler: clang
+
+            - name: Install mingw-w64 on Windows
+              if: contains( matrix.os, 'windows')
+              uses: msys2/setup-msys2@v2
+              with:
+                  path-type: inherit
+                  update: true
+                  install: >-
+                      mingw-w64-x86_64-cmake
+                      mingw-w64-x86_64-pkg-config
+                      mingw-w64-x86_64-gcc
+                      mingw-w64-x86_64-gcc-libs
+                      mingw-w64-x86_64-gcc-fortran
 
             - name: checkout repository
               uses: actions/checkout@v4
+
+            - name: Mac openmp
+              if: contains( matrix.os, 'mac')
+              run: |
+                  brew install llvm
+
+            - name: Set compilers
+              if: false == contains( matrix.os, 'windows')
+              run: |
+                  echo "CC=${{ steps.install_cc.outputs.cc }}" >> $GITHUB_ENV
+                  echo "CXX=${{ steps.install_cc.outputs.cxx }}" >> $GITHUB_ENV
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               id: cp
               with:
                   python-version: ${{ matrix.python-version }}
                   update-environment: true
-
-            - name: Windows openblas
-              if: contains( matrix.os, 'windows')
-              run: |
-                  #vcpkg install openblas
-                  pacman -S mingw-w64-x86_64-openblas64 mingw-w64-lapack
-                  #'${{ steps.cp.outputs.python-path }}' -m pip install pylib-openblas
-
-            - name: Mac openblas
-              if: contains( matrix.os, 'mac')
-              run: |
-                  #export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig:$PKG_CONFIG_PATH"
-                  sudo ln -s /usr/local/opt/openblas/lib/libopenblas* /usr/local/lib/
-
-            - name: Linux openblas
-              if: contains( matrix.os, 'ubuntu')
-              run: |
-                  sudo apt-get install libopenblas-dev
-
-            #- name: Setup tmate session
-            #  if: contains( matrix.os, 'windows')
-            #  uses: mxschmitt/action-tmate@v3
 
             - name: Pip Install pyHAMS
               run: |
                   '${{ steps.cp.outputs.python-path }}' -m pip install --upgrade pip
-                  '${{ steps.cp.outputs.python-path }}' -m pip install meson-python meson numpy ninja wheel
+                  '${{ steps.cp.outputs.python-path }}' -m pip install meson-python meson numpy ninja wheel setuptools
                   '${{ steps.cp.outputs.python-path }}' -m pip install --no-build-isolation -e . -v
+
+            #- name: Setup tmate session
+            #  if: contains( matrix.os, 'windows')
+            #  uses: mxschmitt/action-tmate@v3
 
             - name: Test run
               run: |
@@ -78,7 +91,7 @@ jobs:
             fail-fast: false #true
             matrix:
                 os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
-                python-version: ["3.9", "3.10", "3.11"]
+                python-version: ["3.9", "3.10", "3.11", "3.12"]
 
         steps:
             - name: checkout repository
@@ -96,19 +109,22 @@ jobs:
                   auto-activate-base: false
 
             # Install dependencies of WISDEM specific to windows
-            # NOTE: If you install m2w64-toolchain, it includes m2w64-pkgconfig which supercedes the conda one
-            # The m2w64 pkgconfig fails to find openblas and the install fails
-            # By only includes these compiler packages, the build succeeds
             - name: Add dependencies windows specific
               if: contains( matrix.os, 'windows')
               run: |
-                  conda install -y m2w64-binutils m2w64-gcc m2w64-gcc-libgfortran m2w64-gcc-fortran libpython
+                  conda install -y m2w64-toolchain libpython
 
             # Install dependencies of WISDEM specific to windows
+            - name: Add dependencies unix specific
+              if: contains( matrix.os, 'ubuntu')
+              run: |
+                  conda install -y libgomp
+                  gfortran --version
+
             - name: Add dependencies mac specific
               if: contains( matrix.os, 'mac')
               run: |
-                  conda install -y compilers
+                  conda install -y compilers llvm-openmp
                   gfortran --version
 
             # Install 

.github/workflows/Publish_pyHAMS.yml

@@ -0,0 +1,125 @@
+name: Build and upload to PyPI
+# https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml
+# Best comparable example: https://github.com/pdfo/pdfo
+
+# Build on every pull request (no need for every push) and release change:
+on: [pull_request, release]
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-12, macos-13, macos-14]
+
+    steps:
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+
+      - name: Setup GNU Fortran
+        if: false == contains( matrix.os, 'windows')
+        uses: awvwgk/setup-fortran@v1
+
+      - name: Install compiler
+        if: false == contains( matrix.os, 'windows')
+        id: install_cc
+        uses: rlalik/setup-cpp-compiler@master
+        with:
+          compiler: clang
+
+      - name: Install mingw-w64 on Windows
+        if: contains( matrix.os, 'windows')
+        uses: msys2/setup-msys2@v2
+        with:
+          path-type: inherit
+          install: |
+            mingw-w64-x86_64-gcc
+            mingw-w64-x86_64-gcc-fortran
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build wheels linux
+        if: contains( matrix.os, 'ubuntu')
+        uses: pypa/cibuildwheel@v2.18.1
+        env:
+          CC: ${{ steps.install_cc.outputs.cc }}
+          CXX: ${{ steps.install_cc.outputs.cxx }}
+
+      - name: Build wheels mac-12
+        if: contains( matrix.os, 'macos-12')
+        uses: pypa/cibuildwheel@v2.18.1
+        env:
+          CC: ${{ steps.install_cc.outputs.cc }}
+          CXX: ${{ steps.install_cc.outputs.cxx }}
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="12.0"
+
+      - name: Build wheels mac-13
+        if: contains( matrix.os, 'macos-13')
+        uses: pypa/cibuildwheel@v2.18.1
+        env:
+          CC: ${{ steps.install_cc.outputs.cc }}
+          CXX: ${{ steps.install_cc.outputs.cxx }}
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="13.0"
+
+      - name: Build wheels mac-14
+        if: contains( matrix.os, 'macos-14')
+        uses: pypa/cibuildwheel@v2.18.1
+        env:
+          CC: ${{ steps.install_cc.outputs.cc }}
+          CXX: ${{ steps.install_cc.outputs.cxx }}
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET="14.0"
+
+      - name: Build wheels windows
+        if: contains( matrix.os, 'windows')
+        uses: pypa/cibuildwheel@v2.18.1
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    # upload to PyPI on every tag starting with 'v'
+    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    # alternatively, to publish when a GitHub Release is created, use the following rule:
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Upload to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        #with:
+        #  user: __token__
+        #  password: ${{ secrets.pypi_password }}
+        #  # To test: repository_url: https://test.pypi.org/legacy/
+

README.md

@@ -6,7 +6,7 @@ There is cylinder test case that demonstrates usage and outputs in ``test/test_c
 
 ## Prerequisites
 
-pyHAMS requires a Fortran compiler and OpenBLAS / MKL / LAPACK.  The python wrapper currently supports GNU and Intel compilers.  HAMS can be built with Flang, but that is not yet recognized by pyHAMS.
+pyHAMS requires a Fortran compiler and OpenBLAS / MKL / LAPACK.  We strongly recommend the [Miniforge](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge3) distribution of `conda` to satisfy package dependencies, as the traditional Anaconda distribution can be slow and struggle with mapping out dependencies.
 
 ## Install (as a library)
 
@@ -17,13 +17,17 @@ To install pyHAMS as a library that can be used by WEIS or RAFT in the backend,
 
 ## Install (from source)
 
-If you would like to build the project locally from source for easier access to the underlying methods and tests, do:
+If you would like to build the project locally from source for easier access to the underlying methods and tests, we still recommend using `conda` to satisfy dependencies.
 
     $ git clone https://github.com/WISDEM/pyHAMS.git
     $ cd pyHAMS
+    $ conda env create --name pyhams-env -f environment.yml
+    $ conda activate pyhams-env
+    $ conda install -y compilers                       # (Mac/Linux without other compilers)
+    $ conda install -y m2w64-toolchain libpython       # (Windows only)
     $ pip install .
 
-If developer/editable mode, do the same `git clone` step, but on install do:
+If developer/editable mode, replace the final step with:
 
     $ pip install --no-build-isolation -e .
 

environment.yml

@@ -8,8 +8,7 @@ dependencies:
   - meson-python
   - ninja
   - numpy
-  - openblas
-  - openmp
   - pip
   - pkg-config
   - python
+  - setuptools