Introduces pyproject.toml, adds wheel build jobs to workflow, makes isfniycbozero more flexible

.github/workflows/build-test-wheel.yml

@@ -0,0 +1,202 @@
+name: Build and test UEDGE - write wheel files if tests pass
+
+
+on: [push, pull_request]
+
+jobs:
+  run-all-tests:
+    name: Runs test ${{ matrix.tests }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.9]
+        tests: [fulltests, unittests/D+C, unittests/D_mols, unittests/D_only, unittests/slab_D_only]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install pip dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install forthon mppl numpy h5py
+        python -m pip install flake8
+        python -m pip install pytest-isolate pytest-xdist
+    - name: Build UEDGE
+      run: |
+        pip install .
+    - name: Return to pytests branch
+      uses: actions/checkout@v4
+      with:
+        ref: pytests-develop
+        repository: LLNL/UEDGE 
+    - name: Test with pytest
+      run: |
+        # Create a clean UEDGE instance for every test
+        pytest --isolate --tb=native pytests/${{ matrix.tests }}
+
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }} for Python ${{ matrix.pyver }}
+    if: github.event_name == 'pull_request'
+    needs: run-all-tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-14] 
+        pyver: [cp37, cp38, cp39, cp310, cp311, cp312]
+
+    steps:
+      - name: Checks out repo
+        uses: actions/checkout@v4
+
+      - name: Symlink gfortran for x86 macOS
+        if: matrix.os == 'macos-13'
+        run: |
+          # make sure gfortran is available
+          ln -s /usr/local/bin/gfortran-13 /usr/local/bin/gfortran
+          gfortran --version
+
+
+      - name: Symlink gfortran for ARM macOS
+        if: matrix.os == 'macos-14'
+        run: |
+          # make sure gfortran is available
+          ln -s /opt/homebrew/bin/gfortran-13 /opt/homebrew/bin/gfortran
+          gfortran --version
+
+      - name: Build wheels
+        if: ${{ !(matrix.os == 'macos-14' && matrix.pyver == 'cp37') }}
+        uses: pypa/[email protected]
+        env:
+            CIBW_BUILD: ${{matrix.pyver}}-*
+            CIBW_ARCHS_LINUX: auto
+            CIBW_BEFORE_BUILD: pip install numpy forthon 'build<0.10.0'
+
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ matrix.pyver }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_wheels_pypy:
+    name: Build PyPy wheels on ${{ matrix.os }} 
+    if: github.event_name == 'pull_request'
+    needs: run-all-tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-14] 
+
+    steps:
+      - name: Checks out repo
+        uses: actions/checkout@v4
+
+      - name: Symlink gfortran for x86 macOS
+        if: matrix.os == 'macos-13'
+        run: |
+          # make sure gfortran is available
+          ln -s /usr/local/bin/gfortran-13 /usr/local/bin/gfortran
+          gfortran --version
+
+
+      - name: Symlink gfortran for ARM macOS
+        if: matrix.os == 'macos-14'
+        run: |
+          # make sure gfortran is available
+          ln -s /opt/homebrew/bin/gfortran-13 /opt/homebrew/bin/gfortran
+          gfortran --version
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+            CIBW_BUILD: pp*
+            CIBW_BEFORE_BUILD: pip install numpy forthon 'build<0.10.0'
+
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-pyp-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+
+  build_wheels_cross:
+    name: Build Linux cross-wheels
+    if: false
+#    needs: run-all-tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        pyver: [cp37, cp38, cp39, cp310, cp311, cp312]
+        arch: [aarch64, ppc64le]
+
+    steps:
+      - name: Checks out repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU for multi-arch build
+        uses: docker/setup-qemu-action@v2
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+            CIBW_BUILD: ${{matrix.pyver}}-*
+            CIBW_ARCHS: ${{matrix.arch}}
+            CIBW_BEFORE_BUILD: pip install numpy forthon 'build<0.10.0'
+
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-cross-wheels-${{ matrix.arch }}-${{ matrix.pyver }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_wheels_cross_pypy:
+    name: Build Linux PyPy cross-wheels
+    if: false
+#    needs: run-all-tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checks out repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU for multi-arch build
+        uses: docker/setup-qemu-action@v2
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+            CIBW_BUILD: pp*
+            CIBW_BEFORE_BUILD: pip install numpy forthon 'build<0.10.0'
+
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-cross-wheels-pypy-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+
+  gather_wheels:
+    name: Gather built wheels
+    needs: [build_wheels, build_wheels_pypy]
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download all Artifacts and merges them
+        uses: actions/download-artifact@v4
+        with: 
+          path: wheels
+          merge-multiple: true
+
+      - name: Upload all Artifacts in a single Archive
+        uses: actions/upload-artifact@v4
+        with:
+          name: all_wheels
+          path: wheels

MANIFEST.in

@@ -1,7 +1,8 @@
 include *
 recursive-include  pyscripts *
-recursive-include  pytests *
-recursive-include  jupyter *
+#recursive-include  pytests *
+#recursive-include  jupyter *
+recursive-include  buildscripts *
 recursive-include  aph *
 recursive-include  api *
 recursive-include  bbb *
@@ -10,6 +11,7 @@ recursive-include  flx *
 recursive-include  grd *
 recursive-include  svr *
 recursive-include  wdf *
+recursive-include  ncl *
 #recursive-include  dst *
 #recursive-include  idf *
 #recursive-include  psi *

Makefile.Forthon

@@ -13,7 +13,7 @@ all: mppl2f90 $(BUILDDIR)/compydep $(BUILDDIR)/grdpydep $(BUILDDIR)/flxpydep $(B
 	rm -f uedgeC.so
 
 mppl2f90:
-	(export PYTHONPATH=.:./pyscripts; $(MYPYTHON) convertor)
+	(export PYTHONPATH=.:./buildscripts; $(MYPYTHON) convertor)
 
 $(BUILDDIR)/compydep: com/blasext.F com/brent.F com/comutil.F com/misc.F com/mnbrak.F com/dsum.f com/dummy_py.f com/error.f com/getmsg.f com/ssum.f com/$(PETSC-COM) com/com.v
 	$(FORTHON) -a $(INSTALLARGS) -a $(FCOMP) $(DEBUG) --interfacefile com/com.v -f com/blasext.F com com/brent.F com/comutil.F com/misc.F com/mnbrak.F com/dsum.f com/dummy_py.f com/error.f com/getmsg.f com/ssum.f $(PETSC-COM)