Restructures project under src and adds support for cibuildwheel

.github/workflows/python-package.yml

@@ -1,5 +1,6 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+# This workflow builds binary wheels using cibuildwheel and a source distribution.
+# cibuildwheel handles manylinux and Windows wheel building across Python versions.
+# Publishes to TestPyPI on pushes to dev, and PyPI on pushes to main.
 
 name: Build Packages
 
@@ -10,80 +11,167 @@ on:
     branches: [ "main", "dev" ]
 
 jobs:
-  build:
-
+  make-wheels:
+    name: Build wheels on ${{ matrix.os }} (compiler ${{ matrix.compiler-version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10","3.11","3.12","3.13"]
-        os: [ubuntu-latest, windows-latest] #, macos-latest]
-        compiler: [gcc]
-        compiler-version: [13, 15]
-        exclude:
-          - os: windows-latest
-            compiler-version: 15
+        include:
           - os: ubuntu-latest
+            compiler: gcc
+            compiler-version: 15
+          - os: windows-latest
+            compiler: gcc
             compiler-version: 13
 
     steps:
     - name: Fortran Setup
       uses: fortran-lang/setup-fortran@v1
       id: setup-fortran
       with:
-        compiler: ${{ matrix.toolchain.compiler }}
-        version: ${{ matrix.toolchain.version }}
+        compiler: ${{ matrix.compiler }}
+        version: ${{ matrix.compiler-version }}
 
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         submodules: recursive
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        architecture: 'x64'
-        cache: 'pip'
-
-    - name: show-versions
+        fetch-depth: 0
+
+    - name: Show compiler versions
       run: |
         gcc --version
         gfortran --version
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install click numpy pandas matplotlib build wheel setuptools setuptools_scm meson-python pytest ninja
 
-    - name: Install Patchelf
-      if: runner.os == 'Linux'
-      run: |
-        python -m pip install patchelf
-
-    - name: Build and package
-      run: |
-        python -m build --no-isolation
-
-    - name: Store Wheel
-      uses: actions/upload-artifact@v4
+    - name: Build wheels
+      uses: pypa/cibuildwheel@v3.4.1
+      env:
+        # Build for Python 3.10–3.13, 64-bit only
+        CIBW_BUILD: cp310-* cp311-* cp312-* cp313-* cp314-*
+        CIBW_SKIP: "*-win32 *-manylinux_i686 *-musllinux*"
+        CIBW_ARCHS_LINUX: x86_64
+        CIBW_ARCHS_WINDOWS: AMD64
+
+        # Use manylinux_2_28 to get a gfortran-15-capable image
+        CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/manylinux_2_28_x86_64
+
+        # Install build dependencies inside the wheel-build environment
+        CIBW_BEFORE_BUILD_LINUX: |
+          dnf install -y gcc-gfortran ninja-build &&
+          pip install click numpy pandas build wheel setuptools setuptools_scm meson-python ninja patchelf
+
+        CIBW_BEFORE_BUILD_WINDOWS: |
+          pip install click numpy pandas build wheel setuptools setuptools_scm meson-python ninja
+
+        CIBW_BUILD_FRONTEND: "build"
+        CIBW_BUILD_VERBOSITY: 1
+
       with:
-        name: pyfvs-${{ runner.os }}-py${{ matrix.python-version }}-wheels
+        output-dir: dist
+
+    - name: Store wheels
+      uses: actions/upload-artifact@v7
+      with:
+        name: pyfvs-${{ matrix.os }}-wheels
         path: dist/*.whl
         if-no-files-found: warn
         overwrite: true
-
-    - name: Store Sdist
-      uses: actions/upload-artifact@v4
+
+  make-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v6
+      with:
+        submodules: recursive
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.13"
+        architecture: x64
+        cache: pip
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install click numpy pandas build wheel \
+          setuptools setuptools_scm meson-python ninja patchelf
+
+    - name: Create sdist
+      run: python -m build --sdist --no-isolation
+
+    - name: Store sdist
+      uses: actions/upload-artifact@v7
       with:
         name: pyfvs-sdist
         path: dist/*.tar.gz
         if-no-files-found: warn
         overwrite: true
 
-    - name: Test with pytest
-      working-directory: .
-      run: |
-        pip install confuse typing-extensions openpyxl
-        pip install dist/*.whl
-        pytest
+  publish-testpypi:
+    name: Publish to TestPyPI (dev branch)
+    if: github.event_name == 'push' && github.ref == 'refs/heads/dev'
+    needs: [ make-wheels, make-sdist ]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/pyfvs
+    permissions:
+      id-token: write  # Required for OIDC trusted publishing
+
+    steps:
+    - name: Download all wheels
+      uses: actions/download-artifact@v4
+      with:
+        pattern: pyfvs-*-wheels
+        path: dist
+        merge-multiple: true
+
+    - name: Download sdist
+      uses: actions/download-artifact@v4
+      with:
+        name: pyfvs-sdist
+        path: dist
+
+    - name: Publish to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        skip-existing: true
+        verbose: true
+
+  publish-pypi:
+    name: Publish to PyPI (main branch)
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    needs: [ make-wheels, make-sdist ]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyfvs
+    permissions:
+      id-token: write  # Required for OIDC trusted publishing
+
+    steps:
+    - name: Download all wheels
+      uses: actions/download-artifact@v4
+      with:
+        pattern: pyfvs-*-wheels
+        path: dist
+        merge-multiple: true
+
+    - name: Download sdist
+      uses: actions/download-artifact@v4
+      with:
+        name: pyfvs-sdist
+        path: dist
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip-existing: true
+        verbose: true

README.md

@@ -16,6 +16,15 @@ Python wrappers and utilities for using the Forest Vegetation Simulator
 
 The PyFVS [FVS source code](https://github.com/forest-modeling/ForestVegetationSimulator/tree/open-dev) is forked from the [USFS FVS GitHub](https://github.com/USDAForestService/ForestVegetationSimulator) repository, [open-dev](https://github.com/USDAForestService/ForestVegetationSimulator/tree/open-dev) branch
 
+  _____            ______ __      __  _____ 
+ |  __ \          |  ____|\ \    / / / ____|
+ | |__) | _    _  | |__    \ \  / / | (____  
+ |  ___/ | |  | | |  __|    \ \/ /   \___  \ 
+ | |     | |__| | | |        \  /    ____) |
+ |_|      \____ | |_|         \/    |______/ 
+            __/ |                            
+           |___/
+
 ## Documentation
 
 Check out the new AI generated documentation [wiki](https://deepwiki.com/forest-modeling/PyFVS).

meson.build

@@ -358,8 +358,8 @@ foreach variant : variants
     variant_args += '-DFVS_MORTS_WRAP'
 
     # Add the wrappers to the file lists
-    f_sources += 'api/variant/@0@/morts_fvs.f'.format(variant)
-    f90_sources += 'api/morts_wrap.f90'
+    f_sources += 'src/api/variant/@0@/morts_fvs.f'.format(variant)
+    f90_sources += 'src/api/morts_wrap.f90'
 
   endif
 
@@ -368,7 +368,7 @@ foreach variant : variants
   conf_data = configuration_data()
   conf_data.set('variant', variant)
   configure_file(
-    input: 'api/globals.f90.in',
+    input: 'src/api/globals.f90.in',
     output: variant + '_globals.f90',
     configuration: conf_data
   )
@@ -377,26 +377,26 @@ foreach variant : variants
   f90_sources += join_paths(meson.project_build_root(), variant + '_globals.f90')
 
   # Additional API files to compile
-  # f90_sources += 'api/apisubs.f90'
-
-  f90_sources += 'api/version.f90'
-  f90_sources += 'api/fvs_api.f90'
-  # f90_sources += 'api/sim_monitor.f90'
-  # f90_sources += 'api/initialize.f90'
-  f90_sources += 'api/inventory_trees.f90'
-  f90_sources += 'api/fvs_step.f90'
-  f90_sources += 'api/tree_data.f90'
-  f90_sources += 'api/snag_data.f90'
-  f90_sources += 'api/carbon_data.f90'
-  f90_sources += 'api/downwood_data.f90'
-  # f90_sources += 'api/step_tregro.f90'
-  f90_sources += 'api/prtrls_wrap.f90'
-  # f90_sources += 'api/stop_wrap.f90'
-  # f90_sources += 'api/foo.f90'
-  # f90_sources += 'api/test.f90'
+  # f90_sources += 'src/api/apisubs.f90'
+
+  f90_sources += 'src/api/version.f90'
+  f90_sources += 'src/api/fvs_api.f90'
+  # f90_sources += 'src/api/sim_monitor.f90'
+  # f90_sources += 'src/api/initialize.f90'
+  f90_sources += 'src/api/inventory_trees.f90'
+  f90_sources += 'src/api/fvs_step.f90'
+  f90_sources += 'src/api/tree_data.f90'
+  f90_sources += 'src/api/snag_data.f90'
+  f90_sources += 'src/api/carbon_data.f90'
+  f90_sources += 'src/api/downwood_data.f90'
+  # f90_sources += 'src/api/step_tregro.f90'
+  f90_sources += 'src/api/prtrls_wrap.f90'
+  # f90_sources += 'src/api/stop_wrap.f90'
+  # f90_sources += 'src/api/foo.f90'
+  # f90_sources += 'src/api/test.f90'
 
   # ## TODO: Auto-generate F90 includes from F77
-  # f90_inc_dirs += 'api/gen/@0@/include'.format(variant)
+  # f90_inc_dirs += 'src/api/gen/@0@/include'.format(variant)
 
   # # Add the include folders as a dependency to trigger
   # inc_dep = declare_dependency(
@@ -537,4 +537,4 @@ foreach variant : variants
 # End variant loop
 endforeach
 
-subdir('pyfvs')
+subdir('src/pyfvs')

meson_options.txt

@@ -1,9 +1,9 @@
 option('fvsvariants', type: 'array',
   choices: ['pn','wc','so','op','oc','ec','ca','nc','bm','ie','ci','ak','ws'], #,'em','tt','cr','ut','ls','cs','sn','ne'],
-  value:   ['pn','wc','so','op','oc','ec','ca','nc','bm','ie','ci','ak','ws'], #,'em','tt','cr','ut','ls','cs','sn','ne'],
+  # value:   ['pn','wc','so','op','oc','ec','ca','nc','bm','ie','ci','ak','ws'], #,'em','tt','cr','ut','ls','cs','sn','ne'],
   # value:   ['pn','wc','so','op','oc','ec','ca','nc','bm'],
   # value: ['ie','ci','ak',],
-  # value: ['pn',],
+  value: ['pn',],
   # value: ['ws',],
   description: 'FVS variants to build'
   )