Merge pull request #4 from Liam-Deacon/py311-support

Add Python 3.11 support for pip install

.gitignore

@@ -7,6 +7,7 @@ MANIFEST
 # cache
 *.pyc
 **/__pycache__
+_skbuild/
 
 # built binary objects
 *.so

CMakeLists.txt

@@ -0,0 +1,101 @@
+# Modified from https://numpy.org/doc/stable/f2py/buildtools/skbuild.html#cmake-modules-only
+
+### setup project ###
+cmake_minimum_required(VERSION 3.9)
+
+project(phaseshifts
+  VERSION 0.1.7
+  DESCRIPTION "LIBPHSH module"
+  LANGUAGES C Fortran
+  )
+
+# Safety net
+if(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
+  message(
+    FATAL_ERROR
+      "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n"
+  )
+endif()
+
+# Ensure scikit-build modules
+if (NOT SKBUILD)
+  find_package(PythonInterp 3.12 REQUIRED)
+  # If skbuild is not the driver; include its utilities in CMAKE_MODULE_PATH
+  execute_process(
+    COMMAND "${PYTHON_EXECUTABLE}"
+    -c "import os, skbuild; print(os.path.dirname(skbuild.__file__))"
+    OUTPUT_VARIABLE SKBLD_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+  list(APPEND CMAKE_MODULE_PATH "${SKBLD_DIR}/resources/cmake")
+  message(STATUS "Looking in ${SKBLD_DIR}/resources/cmake for CMake modules")
+endif()
+
+# scikit-build style includes
+find_package(PythonExtensions REQUIRED) # for ${PYTHON_EXTENSION_MODULE_SUFFIX}
+
+# Grab the variables from a local Python installation
+# NumPy headers
+execute_process(
+  COMMAND "${PYTHON_EXECUTABLE}"
+  -c "import numpy; print(numpy.get_include())"
+  OUTPUT_VARIABLE NumPy_INCLUDE_DIRS
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+# F2PY headers
+execute_process(
+  COMMAND "${PYTHON_EXECUTABLE}"
+  -c "import numpy.f2py; print(numpy.f2py.get_include())"
+  OUTPUT_VARIABLE F2PY_INCLUDE_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# Prepping the module
+set(f2py_module_name "libphsh")
+set(f2py_module_dirpath "phaseshifts/lib")
+set(fortran_src_file "${CMAKE_SOURCE_DIR}/${f2py_module_dirpath}/${f2py_module_name}.f")
+set(f2py_module_c "${f2py_module_name}module.c")
+set(f2py_wrapper_f "${f2py_module_name}-f2pywrappers.f")
+
+# Target for enforcing dependencies
+add_custom_target(genpyf
+  DEPENDS "${fortran_src_file}"
+)
+add_custom_command(
+  OUTPUT "${f2py_module_c}" "${f2py_wrapper_f}"
+  COMMAND ${PYTHON_EXECUTABLE} -m "numpy.f2py"
+      -m "${f2py_module_name}"
+      --lower # Important
+      "${fortran_src_file}"
+  DEPENDS "${fortran_src_file}" # Fortran source
+)
+
+add_library("${f2py_module_name}" MODULE
+            "${f2py_wrapper_f}"
+            "${f2py_module_c}"
+            "${F2PY_INCLUDE_DIR}/fortranobject.c"
+            "${fortran_src_file}")
+
+target_include_directories("${f2py_module_name}" PUBLIC
+                           ${F2PY_INCLUDE_DIR}
+                           ${NumPy_INCLUDE_DIRS}
+                           ${PYTHON_INCLUDE_DIRS})
+
+set_target_properties("${f2py_module_name}" PROPERTIES SUFFIX "${PYTHON_EXTENSION_MODULE_SUFFIX}")
+set_target_properties("${f2py_module_name}" PROPERTIES PREFIX "")
+
+
+
+if (UNIX)
+  if (APPLE)
+    set_target_properties("${f2py_module_name}" PROPERTIES
+    LINK_FLAGS  '-Wl,-dylib,-undefined,dynamic_lookup')
+  else()
+    set_target_properties("${f2py_module_name}" PROPERTIES
+  LINK_FLAGS  '-Wl,--allow-shlib-undefined')
+  endif()
+endif()
+
+add_dependencies("${f2py_module_name}" genpyf)
+
+install(TARGETS "${f2py_module_name}" DESTINATION phaseshifts/lib/)

MANIFEST.in

@@ -8,4 +8,7 @@ recursive-include phaseshifts/plugins *.py *.txt *.rst
 recursive-include phaseshifts/lib *.f *.c *.cpp *.h *.for *.py *.pyx
 recursive-exclude phaseshifts/build *
 recursive-exclude phaseshifts/dist *
-recursive-include phaseshifts/res *
+recursive-include phaseshifts/res *
+
+# TODO: Remove shared libraries from source distribution includes once numpy.distutils migration is stable 
+recursive-include phaseshifts/lib  *.so *.pyd

Makefile

@@ -1,5 +1,40 @@
-wheel: deps
-	NPY_DISABLE_CPU_FEATURES="AVX512F AVX512_SKX" python setup.py build bdist_wheel
+# Makefile for assisting with some common development activities
 
-deps:
-	pip install wheel numpy setuptools
+PYTHON ?= $(shell pyenv which python 2>/dev/null || echo python)
+
+.PHONY: wheel install-deps libphsh check test clean
+
+#: Quickly generate binary wheel
+wheel: install-deps
+	$(PYTHON) setup.py build bdist_wheel
+
+#: Install dependencies
+install-deps:
+	$(PYTHON) -m pip install wheel numpy setuptools meson ninja pytest scikit-build
+
+#: Install library into current virtualenv
+install:
+	$(PYTHON) -m pip install .
+
+libphsh.cmake:
+	cmake -S . -B build \
+		-DPYTHON_INCLUDE_DIR="$$($(PYTHON) -c "import sysconfig; print(sysconfig.get_path('include'))")"  \
+		-DPYTHON_LIBRARY="$$($(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")"
+	FFLAGS="-fallow-argument-mismatch -std=f95" \
+		cmake --build build
+
+#: Build the f2py wrapped libphsh shared library within source tree  
+libphsh:
+	$(PYTHON) setup.py build_ext --inplace
+
+#: Perform checks
+check: libphsh
+	$(PYTHON) -m pytest tests/
+
+test: check
+
+#: Remove any artifacts
+clean:
+	rm -rf build dist _skbuild \
+		phaseshifts/lib/libphshmodule.c phaseshifts/lib/libphsh-f2pywrappers.f \
+		phaseshifts/lib/libphsh*.so phaseshifts/lib/libphsh*.pyd

README.rst

@@ -31,8 +31,20 @@ information please read the documentation at `<http://pythonhosted.org//phaseshi
 Install
 =======
 
+TDLR;
+-----
+
+For python 3.11 or older::
+
+  pip install wheel numpy setuptools
+  pip install -e .
+  phsh --help
+
+Details
+-------
+
 The `phaseshifts <http://https://pypi.python.org/pypi/phaseshifts/>`_ package 
-requires CPython 2.6 or later and also uses the `numpy 
+requires CPython 2.7 or later and also uses the `numpy 
 <http://www.scipy.org/scipylib/download.html>`_, `scipy 
 <http://www.scipy.org/scipylib/download.html>`_ and `periodictable 
 <http://https://pypi.python.org/pypi/periodictable>`_ packages. 

phaseshifts/__init__.py

@@ -1,11 +1,4 @@
-from pkg_resources import get_distribution, DistributionNotFound
+__project__ = "phaseshifts"
+__version__ = "0.1.7"
 
-__project__ = 'phaseshifts'
-__version__ = None  # required for initial installation
-
-try:
-    __version__ = get_distribution(__project__).version
-except DistributionNotFound:
-    VERSION = __project__ + '-' + '(local)'
-else:
-    VERSION = __project__ + '-' + __version__
+VERSION = __project__ + "-" + __version__

phaseshifts/lib/__init__.py

@@ -0,0 +1,6 @@
+"""The subpackage is for library code, likely compiled from Fortran or C sources."""
+from ._fortran_lib import is_module_importable, compile_f2py_shared_library, FORTRAN_LIBS, LIBPHSH_MODULE
+
+# NOTE: Attempt to compile libphsh library on import if not already available, useful when installing from source dist
+if not is_module_importable(LIBPHSH_MODULE):
+    compile_f2py_shared_library(**FORTRAN_LIBS[LIBPHSH_MODULE])

phaseshifts/lib/_fortran_lib.py

@@ -0,0 +1,59 @@
+"""This module can be used for checking whether Fortran wrapped libraries such as `libphsh` hve compiled successfully.
+
+Notes
+-----
+
+The functionality currently targets `libphsh.f` by default and provides utilities to check for the
+compiled wrapped `libphsh` fortran shared library and adds the ability to crudely compile
+on the fly (useful when installing this package from source distribution).
+"""
+import importlib
+import os
+import subprocess
+import sys
+from typing import Optional
+
+LIBPHSH_MODULE = "phaseshifts.lib.libphsh"
+
+FORTRAN_LIBS = {
+    LIBPHSH_MODULE: {"source": "libphsh.f", "module_name": LIBPHSH_MODULE},
+}
+
+
+def is_module_importable(module: str) -> bool:
+    """Determine whether `module` is importable."""
+    try:
+        is_importable = bool(importlib.import_module(module))
+    except ModuleNotFoundError:
+        is_importable = False
+    return is_importable
+
+
+def compile_f2py_shared_library(
+    source: str,
+    module_name: Optional[str] = None,
+    **f2py_kwargs,
+) -> int:
+    """Compile `source` into f2py wrapped shared library given by `module_name`.
+
+    Examples
+    --------
+    >>> compile_f2py_shared_library(**FORTRAN_LIBS[LIBPHSH_MODULE])
+
+    See Also
+    --------
+    numpy.f2py
+    """
+    return subprocess.check_call(
+        [
+            sys.executable,
+            "-m",
+            "numpy.f2py",
+            source,
+            "-m",
+            module_name or os.path.basename(source),
+            "-c",
+            *[f"--{key}={val!r}" for key, val in f2py_kwargs.items()],
+        ],
+        cwd=os.path.dirname(__file__),
+    )