perf: improve gsl linking

news/setup.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* Added additional runtime linker flags in `CustomBuildExt.run` to embed the `RPATH` flags for the built extensions.
+* Support for retrieving GSL configuration from `CONDA_PREFIX`/ `GSL_PATH` on all platforms.
+
+**Changed:**
+
+* Merged the GSL configuration logic in `setup.py`.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

setup.py

@@ -28,7 +28,7 @@
 
 
 def get_compiler_type():
-    """Find compiler used for building extensions."""
+    """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]
@@ -38,48 +38,97 @@ def get_compiler_type():
 
 
 def get_gsl_config():
-    """Return dictionary with paths to GSL library."""
-    gslcfgpaths = [Path(p) / "gsl-config" for p in ([MYDIR] + os.environ["PATH"].split(os.pathsep))]
-    gslcfgpaths = [p for p in gslcfgpaths if p.is_file()]
+    """
+    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": []}
-    if not gslcfgpaths:
-        warnings.warn(f"Cannot find gsl-config in {MYDIR} nor in system PATH.")
-        return rv
-    gslcfg = gslcfgpaths[0]
-    txt = gslcfg.read_text()
-    mprefix = re.search(r"(?m)^prefix=(.+)", txt)
-    minclude = re.search(r"(?m)^[^#]*\s-I(\S+)", txt)
-    mlibpath = re.search(r"(?m)^[^#]*\s-L(\S+)", txt)
-    if not mprefix:
-        raise RuntimeError(f"Cannot find 'prefix=' line in {gslcfg}.")
-    p = Path(mprefix.group(1))
-    rv["include_dirs"].append(str(minclude.group(1) if minclude else p / "include"))
-    rv["library_dirs"].append(str(mlibpath.group(1) if mlibpath else p / "lib"))
-    return rv
-
-
-def get_gsl_config_win():
-    """Return dictionary with paths to GSL library on Windows."""
+
+    # 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"
-    else:
-        conda_prefix = os.environ.get("CONDA_PREFIX")
-        if conda_prefix:
-            inc = Path(conda_prefix) / "Library" / "include"
-            lib = Path(conda_prefix) / "Library" / "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(
-                "Neither GSL_PATH nor CONDA_PREFIX environment variables are set. "
-                "Please ensure GSL is installed and GSL_PATH is correctly set."
+                f"GSL_PATH={gsl_path} is set, but {inc} or {lib} not found. " "Please verify your GSL_PATH."
             )
-    return {"include_dirs": [str(inc)], "library_dirs": [str(lib)]}
+
+    # 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")
@@ -88,46 +137,44 @@ def run(self):
         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))
 
 
-# ----------------------------------------------------------------------------
+# Compile and link options----------------------------------------------------
 
-# Compile and link options
 os_name = os.name
-if os_name == "nt":
-    gcfg = get_gsl_config_win()
-else:
-    gcfg = get_gsl_config()
+gcfg = get_gsl_config()
 
+# On macOS, dynamic linking may not be needed
 if sys.platform == "darwin":
     libraries = []
 else:
     libraries = ["gsl"]
 
 include_dirs = [MYDIR] + gcfg["include_dirs"]
-library_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"]
-    extra_objects += [
+    # Check for static GSL libraries and add them if found.
+    static_libs = [
         os.path.join(p, "libgsl.a") for p in gcfg["library_dirs"] if os.path.isfile(os.path.join(p, "libgsl.a"))
     ]
+    if static_libs:
+        extra_objects += static_libs
+        # Use static linking: remove "-lgsl" to avoid dynamic linking conflicts.
+        libraries = []
 elif compiler_type == "msvc":
     define_macros += [("_USE_MATH_DEFINES", None)]
     extra_compile_args = ["/EHs"]
-    library_dirs += gcfg["library_dirs"]
-# add optimization flags for other compilers if needed
 
-# Define extension arguments
+# Extension keyword arguments.
 ext_kws = {
     "include_dirs": include_dirs,
     "libraries": libraries,
@@ -139,8 +186,8 @@ def run(self):
 }
 
 
-# Define extensions
 def create_extensions():
+    """Create the list of Extension objects for the build."""
     ext = Extension("diffpy.pdffit2.pdffit2", glob.glob("src/extensions/**/*.cc"), **ext_kws)
     return [ext]
 
@@ -153,5 +200,3 @@ def create_extensions():
 if __name__ == "__main__":
     setup_args["ext_modules"] = create_extensions()
     setup(**setup_args)
-
-# End of file