fix: revert setup.py and conftest.py to original

Author: stevenhua0320

setup.py

@@ -3,32 +3,200 @@
 # Extensions script for diffpy.pdffit2
 
 import glob
-import os  # noqa
-import re  # noqa
-import sys  # noqa
+import os
+import re
+import shutil
+import sys
+import warnings
+from pathlib import Path
 
 from setuptools import Extension, setup
+from setuptools.command.build_ext import build_ext
 
-# Define extension arguments here
-ext_kws = {
-    "libraries": [],
-    "extra_compile_args": [],
-    "extra_link_args": [],
-    "include_dirs": [],
-}
+# 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))
 
 
 def create_extensions():
-    "Initialize Extension objects for the setup function."
+    """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,
+    }
     ext = Extension(
-        "diffpy.pdffit2.pdffit2", glob.glob("src/extensions/*.cpp"), **ext_kws
+        "diffpy.pdffit2.pdffit2",
+        glob.glob("src/extensions/**/*.cc"),
+        **ext_kws,
     )
     return [ext]
 
 
 # Extensions not included in pyproject.toml
 setup_args = dict(
     ext_modules=[],
+    cmdclass={"build_ext": CustomBuildExt},
 )
 
 

tests/conftest.py

@@ -1,8 +1,12 @@
+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):
@@ -17,3 +21,30 @@ 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