feat: enhance CI configuration and avoid setuptools

.github/workflows/ci.yml

@@ -6,13 +6,25 @@ env:
   CTEST_NO_TESTS_ACTION: error
 
 on:
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: 'Log level'
+        required: true
+        default: 'warning'
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
   push:
     paths:
       - "**/CMakeLists.txt"
       - "**.cmake"
       - "**.f90"
       - "**.py"
       - ".github/workflows/ci.yml"
+      - "pyproject.toml"
 
 
 jobs:
@@ -21,22 +33,28 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-24.04]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
         include:
         - os: macos-latest
           python-version: "3.10"
 
     runs-on: ${{ matrix.os }}
 
     env:
-      FC: gfortran-14
+      FC: gfortran
 
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - uses: fortran-lang/setup-fortran@v1
+      id: setup-fortran
+      with:
+        compiler: gcc
+        version: 14
+
     - run: pip install .[tests,lint]
 
     - run: flake8
@@ -47,11 +65,12 @@ jobs:
 
     - run: pytest
 
+    - run: pip install meson # required for cmake tests
     - run: cmake --workflow --preset default
 
   windows:
     runs-on: windows-latest
-    timeout-minutes: 10
+    timeout-minutes: 60
 
     steps:
     - uses: msys2/setup-msys2@v2
@@ -80,6 +99,7 @@ jobs:
 
     - run: pytest -v
 
+    - run: pip install meson # required for cmake tests
     - run: cmake -B build
       env:
         CMAKE_GENERATOR: "MinGW Makefiles"

.gitignore

@@ -6,8 +6,26 @@
 
 dist/
 
+build/
+cmake-build-*/
+CMakeFiles/
+CMakeCache.txt
+
 __pycache__/
 *.py[cod]
 *.so
 *.dylib
 *.egg-info/
+
+# Local virtual environments
+.venv/
+venv/
+
+# Ninja / CMake logs
+rules.ninja
+.ninja_log
+.ninja_deps
+
+# OS specific files
+.DS_Store
+Thumbs.db

README.md

@@ -21,7 +21,7 @@ See below for how to make these examples.
 
 Lowtran requires a Fortran compiler and CMake.
 We use `f2py` (part of `numpy`) to seamlessly use Fortran libraries from Python by special compilation of the Fortran library with auto-generated shim code.
-For Python 3.12, make sure to install setuptools using pip, i.e., `pip install setuptools` and make sure meson is available on the system.
+Make sure `meson` and the python devel headers & libraries are available on your system.
 
 If a Fortran compiler is not already installed, install Gfortran:
 

pyproject.toml

@@ -1,6 +1,10 @@
 [build-system]
-requires = ["setuptools>=61.0.0", "wheel", "numpy"]
-build-backend = "setuptools.build_meta"
+requires = [
+  "scikit-build-core>=0.9.0",
+  "numpy",
+  "meson"
+]
+build-backend = "scikit_build_core.build"
 
 [project]
 name = "lowtran"
@@ -16,16 +20,16 @@ classifiers = [
   "Programming Language :: Fortran",
   "Topic :: Scientific/Engineering :: Atmospheric Science"
 ]
-dynamic = ["readme"]
 requires-python = ">=3.9"
 dependencies = ["numpy", "xarray", "python-dateutil"]
 
 [project.optional-dependencies]
 tests = ["pytest"]
 lint = ["flake8", "flake8-bugbear", "flake8-builtins", "flake8-blind-except", "mypy", "types-python-dateutil"]
 
-[tool.setuptools.dynamic]
-readme = {file = ["README.md"], content-type = "text/markdown"}
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
 
 [tool.black]
 line-length = 100
@@ -34,3 +38,11 @@ line-length = 100
 files = ["src", "example"]
 allow_redefinition = true
 ignore_missing_imports = true
+
+# scikit-build-core configuration: out-of-source build and package discovery
+[tool.scikit-build]
+cmake.args = ["-GNinja"]
+editable.mode = "redirect"
+build-dir = "build/{wheel_tag}"
+wheel.packages = ["src/lowtran"]
+sdist.include = ["src/lowtran", "README.md", "LICENSE.txt", "MANIFEST.in"]

src/lowtran/base.py

@@ -3,52 +3,76 @@
 import xarray
 import numpy as np
 from typing import Any
-from pathlib import Path
-import importlib.util
-import distutils.sysconfig
+import importlib
+import sysconfig
 import os
+import sys
+from pathlib import Path
 from types import ModuleType
 
-from .cmake import build
-
 
 def check() -> ModuleType:
-    try:
-        lowtran7 = import_f2py_mod("lowtran7")
-    except ImportError:
-        src = Path(__file__).parent
-        build(source_dir=src, build_dir=src / "build")
-        lowtran7 = import_f2py_mod("lowtran7")
+    """Ensure the compiled lowtran7 extension is available.
 
-    return lowtran7
+    With scikit-build-core, the extension is built at install time and shipped in the wheel.
+    If it's missing, prompt the user to install the package (e.g., `pip install .`).
+    """
 
+    try:
+        return import_f2py_mod("lowtran7")
+    except ImportError as e:
+        raise ImportError(
+            "lowtran7 extension not found. Please install the package so the Fortran "
+            "extension is built (e.g., `pip install .` or `pip install lowtran`)."
+        ) from e
 
-def import_f2py_mod(name: str) -> ModuleType:
 
-    if os.name == "nt":
-        # https://github.com/space-physics/lowtran/issues/19
-        # code inspired by scipy._distributor_init.py for loading DLLs on Window
-        dll_path = (Path(__file__) / "../build/lowtran7/.libs").resolve()
-        if dll_path.is_dir():
-            # add the folder for Python 3.8 and above
-            logging.info(f"Adding {dll_path} to DLL search path")
-            os.add_dll_directory(dll_path)  # type: ignore
-        else:
-            logging.info(f"Could not find {dll_path} to add to DLL search path")
-
-    mod_name = name + distutils.sysconfig.get_config_var("EXT_SUFFIX")  # type: ignore
-    mod_file = Path(__file__).parent / mod_name
-    if not mod_file.is_file():
-        raise ModuleNotFoundError(mod_file)
-    spec = importlib.util.spec_from_file_location(name, mod_file)
-    if spec is None:
-        raise ModuleNotFoundError(f"{name} not found in {mod_file}")
-    mod = importlib.util.module_from_spec(spec)
-    if mod is None:
-        raise ImportError(f"could not import {name} from {mod_file}")
-    spec.loader.exec_module(mod)  # type: ignore
-
-    return mod
+def import_f2py_mod(name: str) -> ModuleType:
+    lib_name = name + sysconfig.get_config_var("EXT_SUFFIX")
+    lib_path = importlib.resources.files(__package__) / lib_name
+
+    if not lib_path.is_file():
+        # Assume editable install: navigate up to find the build directory
+        src_dir = Path(__file__).parent
+        project_root = src_dir.parent.parent  # Assuming src/lowtran structure
+
+        # scikit-build-core build directory pattern
+        build_base = project_root / "build"
+
+        if build_base.exists():
+            # Recursively search for the library file
+            matches = list(build_base.rglob(lib_name))
+            if matches:
+                lib_path = matches[0]  # Use the first match
+
+    if not lib_path.is_file():
+        raise ModuleNotFoundError(f"Module not found: {lib_path}")
+
+    # On Windows, add DLL search directories to fix loading issues
+    dll_dirs: list[Any] = []
+    if sys.platform == "win32" and hasattr(os, 'add_dll_directory'):
+        # Add common locations where your dependencies might be, i.e., system PATH and module dir
+        search_paths = os.environ.get('PATH', '').split(os.pathsep)
+        search_paths.append(os.fspath(lib_path.parent))
+
+        for path in search_paths:
+            try:
+                dll_dirs.append(os.add_dll_directory(path))
+            except OSError:
+                pass
+    try:
+        # Load the module from file path
+        spec = importlib.util.spec_from_file_location(name, lib_path)
+        if spec is None or spec.loader is None:
+            raise ImportError(f"Cannot load module from {lib_path}")
+
+        mod = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(mod)
+        return mod
+    finally:
+        # Clean up DLL directories
+        for dll_dir in dll_dirs:
+            dll_dir.close()
 
 
 def nm2lt7(short_nm: float, long_nm: float, step_cminv: float = 20) -> tuple[float, float, float]:

src/lowtran/cmake/f2py.cmake

@@ -1,10 +1,13 @@
 # f2py
 
-find_package(Python COMPONENTS Interpreter NumPy REQUIRED)
+set(Python3_FIND_VIRTUALENV FIRST)
+find_package(Python3 COMPONENTS Interpreter NumPy REQUIRED)
+message(STATUS "${PYTHON3_EXECUTABLE}")
+message(STATUS "${Python3_NumPy_VERSION}")
 
 if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU" AND
-   CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10 AND
-   Python_NumPy_VERSION VERSION_LESS 1.19)
+  CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10 AND
+  Python3_NumPy_VERSION VERSION_LESS 1.19)
   message(FATAL_ERROR "Numpy >= 1.19 required for GCC >= 10")
 endif()
 
@@ -15,26 +18,13 @@ if(f2py_suffix)
 endif()
 
 execute_process(
-COMMAND ${Python_EXECUTABLE} -c "import sysconfig; x=sysconfig.get_config_var('EXT_SUFFIX'); assert x is not None; print(x)"
+COMMAND ${Python3_EXECUTABLE} -c "import sysconfig; x=sysconfig.get_config_var('EXT_SUFFIX'); assert x is not None; print(x)"
 OUTPUT_STRIP_TRAILING_WHITESPACE
 RESULT_VARIABLE ret
 OUTPUT_VARIABLE out
 ERROR_VARIABLE err
 )
 
-if(NOT ret EQUAL 0)
-
-message(VERBOSE "${ret}: ${out}: ${err}")
-
-execute_process(
-COMMAND ${Python_EXECUTABLE} -c "import distutils.sysconfig; x=distutils.sysconfig.get_config_var('EXT_SUFFIX'); assert x is not None; print(x)"
-OUTPUT_STRIP_TRAILING_WHITESPACE
-RESULT_VARIABLE ret
-OUTPUT_VARIABLE out
-ERROR_VARIABLE err
-)
-
-endif()
 
 if(NOT ret EQUAL 0)
   message(FATAL_ERROR "${ret}: ${out}: ${err}: could not determine f2py output file suffix")