Change build backend to scikit_build "core" (#1284)

* move most setup from setup.cfg to pyproject.toml
* Update CMakeLists to install compiled products.
  (Needed so that they end up in wheels.)
* Update CI and deployment work flows.

.github/workflows/macos_x86.yml

@@ -65,3 +65,21 @@ jobs:
           python -m pytest -n 4 tests
           python -m pytest -n 2 tests_with_cpp
 
+      - name: Clean up build and venv
+        run: |
+          rm -rf build venv
+
+      - name: Test pip install from dist in fresh venv
+        run: |
+            python -m pip install build
+            python -m build -o dist -w .
+            cd dist
+            python -m venv venv
+            source venv/bin/activate
+            which python
+            python -m pip install --no-cache-dir ./fwdpy11*.whl
+            python -m fwdpy11 --includes
+            python -c "import fwdpy11;print(fwdpy11.__version__)"
+            python -c "import fwdpy11;print(fwdpy11.__file__)"
+
+

.github/workflows/ubuntu.yml

@@ -120,6 +120,10 @@ jobs:
         run: |
           cmake --build build -t test
 
+      - name: Clean cmake build
+        run: |
+          rm -rf build
+
       - name: Manualy run setuptools_scm
         run: |
           python -m setuptools_scm
@@ -148,15 +152,16 @@ jobs:
 
       - name: Test pip install from dist in fresh venv
         run: |
-            python -m pip install --upgrade setuptools pip wheel build
-            python -m build . --config-setting=--disable_lto
+            python -m pip install build
+            python -m build -o dist -w .
             cd dist
             python -m venv venv
             source venv/bin/activate
             which python
             # The CPPFLAGS contain stuff for C++ that makes no sense for C.
             # The flags are also too strict for tskit to build under Py 3.12
-            CPPFLAGS= python -m pip install --no-cache-dir ./fwdpy11*-linux*.whl
+            ls
+            CPPFLAGS= python -m pip install --no-cache-dir ./fwdpy11*-*linux*.whl
             python -m fwdpy11 --includes
             python -c "import fwdpy11;print(fwdpy11.__version__)"
             python -c "import fwdpy11;print(fwdpy11.__file__)"

MANIFEST.in

@@ -14,3 +14,4 @@ include doc/fwdpp.doxygen
 include doc/Makefile
 recursive-include doc *.md *.png
 recursive-include tests *.yaml
+recursive-include tests_with_cpp *.txt *.cc *.py

cpp/CMakeLists.txt

@@ -132,3 +132,5 @@ if (ENABLE_PROFILING)
     set_target_properties(_fwdpy11 PROPERTIES CXX_VISIBILITY_PRESET "default")
 endif()
 target_link_libraries(_fwdpy11 PRIVATE GSL::gsl GSL::gslcblas fwdpy11core)
+# The install directory is the output (wheel) directory
+install(TARGETS _fwdpy11 DESTINATION fwdpy11)

deployment/linux_wheels/wheel_workflow.sh

@@ -27,12 +27,12 @@ git config --global --add safe.directory /project
 
 # BUILD WHEEL INSIDE A VENV
 
-$(which $PYTHON) -m venv venv
-source venv/bin/activate
+$(which $PYTHON) -m venv /venv
+source /venv/bin/activate
 python -m pip install --upgrade pip setuptools build
 python -m build .
 deactivate
-rm -rf build venv
+rm -rf build /venv
 
 cd dist
 for whl in *.whl; do
@@ -45,8 +45,8 @@ cd ..
 
 # INSTALL WHEEL INTO VENV FOR TESTING
 
-$(which $PYTHON) -m venv venv
-source venv/bin/activate
+$(which $PYTHON) -m venv /venv
+source /venv/bin/activate
 python -m pip install --upgrade pip
 python -m pip install wheel
 python -m pip install fwdpy11 --pre --no-cache-dir --only-binary fwdpy11 --find-links dist/wheelhouse
@@ -67,4 +67,4 @@ python -m pytest tests -n 4
 rm -rf $TESTDIR
 cd ..
 deactivate
-rm -rf venv
+rm -rf /venv

fwdpy11/_types/tree_iterator.py

@@ -71,7 +71,7 @@ def __init__(
         update_samples: bool = False,
         ancient_samples: Union[List[int], np.ndarray] = None,
         begin: float = 0.0,
-        end: Optional[float] = None
+        end: Optional[float] = None,
     ):
         _end = end
         if _end is None:

fwdpy11/_types/variant_iterator.py

@@ -74,7 +74,7 @@ def __init__(
         begin: float = 0.0,
         end: Optional[float] = None,
         include_neutral_variants: bool = True,
-        include_selected_variants: bool = True
+        include_selected_variants: bool = True,
     ):
         if end is not None:
             _end = end

fwdpy11/discrete_demography.py

@@ -30,7 +30,7 @@ def from_demes(
     dg: typing.Union[str, demes.Graph],
     burnin: int = 10,
     *,
-    round_non_integer_sizes: typing.Optional[bool] = None
+    round_non_integer_sizes: typing.Optional[bool] = None,
 ) -> DemographicModelDetails:
     """
     Build a :class:`fwdpy11.DemographicModelDetails` object using demes.

fwdpy11/tskit_tools/metadata.py

@@ -94,7 +94,7 @@ def from_table_row(cls, ind: tskit.IndividualTableRow):
             **ind.metadata,
             alive=alive,
             preserved=preserved,
-            first_generation=first_generation
+            first_generation=first_generation,
         )
 
 

lib/CMakeLists.txt

@@ -35,3 +35,5 @@ add_library(fwdpy11core SHARED ${ALL_SOURCES})
 add_dependencies(fwdpy11core cargo-build_fp11rust header)
 target_link_libraries(fwdpy11core LINK_PRIVATE ${CMAKE_BINARY_DIR}/rust/libfp11rust.a)
 target_link_libraries(fwdpy11core PRIVATE GSL::gsl GSL::gslcblas)
+# The install directory is the output (wheel) directory
+install(TARGETS fwdpy11core DESTINATION fwdpy11)

pyproject.toml

@@ -1,13 +1,49 @@
 [build-system]
 # We need setup.cfg support, which setuptools indtroduced in 30.3.0.
 requires = [
-    "setuptools>=30.3.0",
-    "wheel",
-    "setuptools_scm<8",
+    "scikit-build-core>=0.3.3",
+    "setuptools_scm>=8",
     "pybind11[global]==2.11.1",
     "cmake>=3.27.2"
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "fwdpy11"
+authors = [
+    {name = "Kevin R. Thornton", email =  "krthornt@uci.edu"}
+]
+license = {text = "GNU GPL3+"}
+description = "Forward-time population genetic simulation in Python"
+readme = {file = "README.rst", content-type = "text/x-rst"}
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+]
+dynamic = ["version"]
+dependencies = [
+    "attrs >= 20.3.0",
+    "black",
+    "numpy < 2.0",
+    "scipy",
+    "tskit >= 0.5.6",
+    "demes ~= 0.2.2",
+    "Deprecated",
+]
+requires-python = ">=3.8, <3.13"
+
+[project.scripts]
+fwdpy11 = "fwdpy11.__main__:main"
+
+[project.urls]
+Repository = "https://github.com/molpopgen/fwdpy11"
+Issues = "https://github.com/molpopgen/fwdpy11/issues"
+Documentation = "https://molpopgen.github.io/fwdpy11"
+
+[tool.scikit-build]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["fwdpy11/_version.py"]
 
 [tool.setuptools_scm]
 write_to = "fwdpy11/_version.py"

setup.cfg

@@ -1,39 +1,6 @@
-[metadata]
-name = fwdpy11
-author = Kevin R. Thornton
-author_email = krthornt@uci.edu
-license = GNU GPL3+
-description = Forward-time population genetic simulation in Python
-long_description = file: README.rst
-long_description_content_type = text/x-rst
-url = https://github.com/molpopgen/fwdpy11
-classifiers = 
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Bio-Informatics
-    License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-
 [options]
 zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
 include_package_data = True
-python_requires = >=3.8, <3.13
-# NOTE: any pinning should also be coordinated
-# with requirements.in and doc/requirements.in
-# and may require regenerating the .txt files.
-install_requires =
-    attrs >= 20.3.0 
-    black
-    numpy < 2.0
-    scipy
-    tskit >= 0.5.6
-    demes ~= 0.2.2
-    Deprecated
-setup_requires =
-    setuptools
-    setuptools_scm
-
-[options.entry_points]
-console_scripts =
-    fwdpy11 = fwdpy11.__main__:main
 
 [mypy]
 files = fwdpy11