skpkg: package update command with no manual edits.

Author: stevenhua0320

setup.py

@@ -1,207 +1,34 @@
 #!/usr/bin/env python
 
 # Extensions script for diffpy.pdffit2
-"""PDFfit2 - real space structure refinement engine
-
-Packages:   diffpy.pdffit2
-Scripts:    pdffit2
-"""
 
 import glob
-import os
-import re
-import shutil
-import sys
-import warnings
-from pathlib import Path
+import os  # noqa
+import re  # noqa
+import sys  # noqa
 
 from setuptools import Extension, setup
-from setuptools.command.build_ext import build_ext
-
-# Use this version when git data are not available, like in git zip archive.
-# Update when tagging a new release.
-FALLBACK_VERSION = "1.4.3"
-
-MYDIR = str(Path(__file__).parent.resolve())
-
-# Helper functions -----------------------------------------------------------
-
-
-def get_compiler_type():
-    """Return the compiler type used during the build."""
-    cc_arg = [a for a in sys.argv if a.startswith("--compiler=")]
-    if cc_arg:
-        return cc_arg[-1].split("=", 1)[1]
-    from distutils.ccompiler import new_compiler
-
-    return new_compiler().compiler_type
-
-
-def get_gsl_config():
-    """
-    Determine the GSL include and library directories by trying in order:
-      1) CONDA_PREFIX,
-      2) GSL_PATH,
-      3) gsl-config (for Unix-like systems).
-    Raises EnvironmentError if none are found.
-    """
-    rv = {"include_dirs": [], "library_dirs": []}
-
-    # 1. Check using CONDA_PREFIX.
-    conda_prefix = os.environ.get("CONDA_PREFIX", "")
-    if conda_prefix:
-        if os.name == "nt":
-            inc = Path(conda_prefix) / "Library" / "include"
-            lib = Path(conda_prefix) / "Library" / "lib"
-        else:
-            inc = Path(conda_prefix) / "include"
-            lib = Path(conda_prefix) / "lib"
-        if inc.is_dir() and lib.is_dir():
-            rv["include_dirs"].append(str(inc))
-            rv["library_dirs"].append(str(lib))
-            return rv
-        else:
-            warnings.warn(
-                f"CONDA_PREFIX is set to {conda_prefix}, "
-                "but GSL not found at those paths. Proceeding..."
-            )
 
-    # 2. Check using GSL_PATH.
-    gsl_path = os.environ.get("GSL_PATH", "")
-    if gsl_path:
-        inc = Path(gsl_path) / "include"
-        lib = Path(gsl_path) / "lib"
-        if inc.is_dir() and lib.is_dir():
-            rv["include_dirs"].append(str(inc))
-            rv["library_dirs"].append(str(lib))
-            return rv
-        else:
-            raise EnvironmentError(
-                f"GSL_PATH={gsl_path} is set, but {inc} or {lib} not found. "
-                "Please verify your GSL_PATH."
-            )
-
-    # 3. Try using the gsl-config executable (only on Unix-like systems).
-    if os.name != "nt":
-        path_dirs = os.environ.get("PATH", "").split(os.pathsep)
-        gslcfg_paths = [Path(p) / "gsl-config" for p in path_dirs if p]
-        gslcfg_paths = [p for p in gslcfg_paths if p.is_file()]
-        if gslcfg_paths:
-            gslcfg = gslcfg_paths[0]
-            txt = gslcfg.read_text()
-            prefix_match = re.search(r"(?m)^prefix=(.+)", txt)
-            include_match = re.search(r"(?m)^[^#]*\s-I(\S+)", txt)
-            lib_match = re.search(r"(?m)^[^#]*\s-L(\S+)", txt)
-            if prefix_match:
-                prefix_path = Path(prefix_match.group(1))
-                inc_dir = (
-                    include_match.group(1)
-                    if include_match
-                    else (prefix_path / "include")
-                )
-                lib_dir = (
-                    lib_match.group(1) if lib_match else (prefix_path / "lib")
-                )
-                rv["include_dirs"].append(str(inc_dir))
-                rv["library_dirs"].append(str(lib_dir))
-                return rv
-            else:
-                raise RuntimeError(f"Cannot parse 'prefix=' from {gslcfg}.")
-        else:
-            warnings.warn(
-                "No gsl-config found in PATH. GSL may not be installed or not in PATH. "
-                "Proceeding without GSL configuration."
-            )
-
-    # 4. Nothing found: raise error.
-    raise EnvironmentError(
-        "Unable to locate GSL:\n"
-        "1) CONDA_PREFIX not set or no GSL there\n"
-        "2) GSL_PATH not set or invalid\n"
-        "3) gsl-config not available\n"
-        "Please set GSL_PATH or use a conda environment with GSL."
-    )
-
-
-class CustomBuildExt(build_ext):
-    def run(self):
-        # Retrieve the GSL library directories and append them to each extension.
-        gsl_cfg = get_gsl_config()
-        lib_dirs = gsl_cfg.get("library_dirs", [])
-        for ext in self.extensions:
-            # Add gsl lib for linking.
-            ext.library_dirs.extend(lib_dirs)
-            # Embed RPATH flags, runtime linking without LD_LIBRARY_PATH.
-            ext.extra_link_args = ext.extra_link_args or []
-            for lib in lib_dirs:
-                ext.extra_link_args.append(f"-Wl,-rpath,{lib}")
-        super().run()
-        # Avoid dll error
-        gsl_path = (
-            Path(os.environ.get("GSL_PATH"))
-            if os.environ.get("GSL_PATH")
-            else Path(os.environ.get("CONDA_PREFIX", "")) / "Library"
-        )
-        bin_path = gsl_path / "bin"
-        dest_path = Path(self.build_lib) / "diffpy" / "pdffit2"
-        dest_path.mkdir(parents=True, exist_ok=True)
-        for dll_file in bin_path.glob("gsl*.dll"):
-            shutil.copy(str(dll_file), str(dest_path))
+# Define extension arguments here
+ext_kws = {
+    "libraries": [],
+    "extra_compile_args": [],
+    "extra_link_args": [],
+    "include_dirs": [],
+}
 
 
 def create_extensions():
-    """Create the list of Extension objects for the build."""
-    # lazy evaluation prevents build sdist failure
-    try:
-        gcfg = get_gsl_config()
-    except EnvironmentError:
-        return []
-
-    libraries = ["gsl"]
-
-    include_dirs = [MYDIR] + gcfg["include_dirs"]
-    library_dirs = gcfg["library_dirs"]
-    define_macros = []
-    extra_objects = []
-    extra_compile_args = []
-    extra_link_args = []
-
-    compiler_type = get_compiler_type()
-    if compiler_type in ("unix", "cygwin", "mingw32"):
-        extra_compile_args = [
-            "-std=c++11",
-            "-Wall",
-            "-Wno-write-strings",
-            "-O3",
-            "-funroll-loops",
-            "-ffast-math",
-        ]
-    elif compiler_type == "msvc":
-        define_macros += [("_USE_MATH_DEFINES", None)]
-        extra_compile_args = ["/EHs"]
-
-    # Extension keyword arguments.
-    ext_kws = {
-        "include_dirs": include_dirs,
-        "libraries": libraries,
-        "library_dirs": library_dirs,
-        "define_macros": define_macros,
-        "extra_compile_args": extra_compile_args,
-        "extra_link_args": extra_link_args,
-        "extra_objects": extra_objects,
-    }
+    "Initialize Extension objects for the setup function."
     ext = Extension(
-        "diffpy.pdffit2.pdffit2",
-        glob.glob("src/extensions/**/*.cc"),
-        **ext_kws,
+        "diffpy.pdffit2.pdffit2", glob.glob("src/extensions/*.cpp"), **ext_kws
     )
     return [ext]
 
 
 # Extensions not included in pyproject.toml
 setup_args = dict(
     ext_modules=[],
-    cmdclass={"build_ext": CustomBuildExt},
 )
 
 

tests/conftest.py

@@ -1,12 +1,8 @@
-import io
 import json
 from pathlib import Path
 
 import pytest
 
-import diffpy.pdffit2
-import diffpy.pdffit2.output  # assuming this is the correct import path
-
 
 @pytest.fixture
 def user_filesystem(tmp_path):
@@ -21,30 +17,3 @@ def user_filesystem(tmp_path):
         json.dump(home_config_data, f)
 
     yield tmp_path
-
-
-@pytest.fixture
-def datafile():
-    """Fixture to dynamically load any test file."""
-
-    def _load(filename):
-        return "tests/testdata/" + filename
-
-    return _load
-
-
-@pytest.fixture
-def capture_output():
-    """Capture output from pdffit2 engine produced in function call."""
-
-    def _capture(f, *args, **kwargs):
-        savestdout = diffpy.pdffit2.output.stdout
-        fp = io.StringIO()
-        diffpy.pdffit2.redirect_stdout(fp)
-        try:
-            f(*args, **kwargs)
-        finally:
-            diffpy.pdffit2.redirect_stdout(savestdout)
-        return fp.getvalue()
-
-    return _capture