From eae357eaf83c94fea2a1fa903b0b167a80a33820 Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Thu, 20 Nov 2025 15:26:17 -0500
Subject: [PATCH 01/11] skpkg: change version build file.

---
 src/diffpy/__init__.py         | 10 ------
 src/diffpy/pdffit2/__init__.py | 20 ++----------
 src/diffpy/pdffit2/version.py  | 57 ++++++----------------------------
 3 files changed, 12 insertions(+), 75 deletions(-)

diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index 2efe939..04d8ace 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -14,13 +14,3 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""diffpy - tools for structure analysis by diffraction.
-
-Blank namespace package for module diffpy."""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file
diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index 527477a..fceee94 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -16,24 +16,10 @@
 ##############################################################################
 """PDFfit2 - real space structure refinement program."""
 
-# WARNING: Do NOT remove the isort: off/on comments in this file.
-# These tags are used to prevent isort from reordering imports in this file.
-# __version__ must be initialized before importing C++ extensions.
+# package version
+from diffpy.pdffit2.version import __version__  # noqa
 
-# isort: off
-# Import the package version before C++ extensions are loaded.
-from diffpy.pdffit2.output import redirect_stdout
-from diffpy.pdffit2.version import __date__, __version__
-
-# Import C++ related modules since the __version__ attribute is used.
-from diffpy.pdffit2.pdffit import PdfFit
-from diffpy.pdffit2.pdffit2 import is_element
-
-# isort: on
-
-# Ensure all necessary components are imported and initialized
+# silence the pyflakes syntax checker
 assert __version__ or True
-assert __date__ or True
-assert all((PdfFit, redirect_stdout, is_element))
 
 # End of file
diff --git a/src/diffpy/pdffit2/version.py b/src/diffpy/pdffit2/version.py
index 8615928..0ade395 100644
--- a/src/diffpy/pdffit2/version.py
+++ b/src/diffpy/pdffit2/version.py
@@ -7,59 +7,20 @@
 # File coded by: Billinge Group members and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors
+# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
 """Definition of __version__."""
 
-import datetime
-import json
-import urllib.request
-from importlib.metadata import version
-from pathlib import Path
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
 
+# obtain version information
+from importlib.metadata import PackageNotFoundError, version
 
-def get_pypi_release_date(package_name, timeout=5):
-    package_file = Path(__file__).resolve()
-
-    try:
-        with open(package_file, "r", encoding="utf-8") as f:
-            lines = f.readlines()
-        for line in reversed(lines):
-            if line.startswith("# Release date:"):
-                return line.split(":", 1)[1].strip()
-
-        url = f"https://pypi.org/pypi/{package_name}/json"
-        with urllib.request.urlopen(url, timeout=timeout) as response:
-            data = json.loads(response.read().decode("utf-8"))
-
-        installed_version = version(package_name)
-        release_data = data["releases"].get(installed_version, [])
-        if not release_data:
-            raise ValueError(
-                f"No release data found for version {installed_version}"
-            )
-
-        release_date_str = release_data[-1]["upload_time"]
-        release_date = datetime.datetime.fromisoformat(release_date_str).date()
-
-        with open(package_file, "a", encoding="utf-8") as f:
-            f.write(f"\n# Release date: {release_date}")
-
-    except (ValueError, OSError) as e:
-        print(f"Warning: Could not fetch release date from PyPI: {e}")
-        release_date = datetime.datetime.fromtimestamp(
-            package_file.stat().st_ctime
-        ).isoformat()
-
-    return str(release_date)
-
-
-__version__ = version("diffpy.pdffit2")
-__date__ = get_pypi_release_date("diffpy.pdffit2")
-
-# End of file
-
-# Release date: 2025-02-07
+try:
+    __version__ = version("diffpy.pdffit2")
+except PackageNotFoundError:
+    __version__ = "unknown"

From 8b93472f93ce0f75a24a1f1539acae2eb3e8b23d Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Thu, 20 Nov 2025 20:26:12 -0500
Subject: [PATCH 02/11] skpkg: package update command with no manual edits.

---
 setup.py          | 197 +++-------------------------------------------
 tests/conftest.py |  31 --------
 2 files changed, 12 insertions(+), 216 deletions(-)

diff --git a/setup.py b/setup.py
index 9a334a8..9c1e69c 100644
--- a/setup.py
+++ b/setup.py
@@ -1,199 +1,27 @@
 #!/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]
 
@@ -201,7 +29,6 @@ def create_extensions():
 # Extensions not included in pyproject.toml
 setup_args = dict(
     ext_modules=[],
-    cmdclass={"build_ext": CustomBuildExt},
 )
 
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 6a14253..e3b6313 100644
--- a/tests/conftest.py
+++ b/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

From f7bc156cc7997be7f311034162ccd6328deb1cd4 Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 13:12:09 -0500
Subject: [PATCH 03/11] fix: revert setup.py and conftest.py to original

---
 setup.py          | 192 +++++++++++++++++++++++++++++++++++++++++++---
 tests/conftest.py |  31 ++++++++
 2 files changed, 211 insertions(+), 12 deletions(-)

diff --git a/setup.py b/setup.py
index 9c1e69c..d808441 100644
--- a/setup.py
+++ b/setup.py
@@ -3,25 +3,192 @@
 # 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]
 
@@ -29,6 +196,7 @@ def create_extensions():
 # Extensions not included in pyproject.toml
 setup_args = dict(
     ext_modules=[],
+    cmdclass={"build_ext": CustomBuildExt},
 )
 
 
diff --git a/tests/conftest.py b/tests/conftest.py
index e3b6313..6a14253 100644
--- a/tests/conftest.py
+++ b/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

From a8689bf450fcc6343a3958b30601c10c291bdc82 Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 13:52:20 -0500
Subject: [PATCH 04/11] chore: add docstring back to setup.py

---
 setup.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/setup.py b/setup.py
index d808441..9a334a8 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,11 @@
 #!/usr/bin/env python
 
 # Extensions script for diffpy.pdffit2
+"""PDFfit2 - real space structure refinement engine
+
+Packages:   diffpy.pdffit2
+Scripts:    pdffit2
+"""
 
 import glob
 import os

From 7293c68d63c908fbc550f12700a18535f85c91a6 Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 16:04:35 -0500
Subject: [PATCH 05/11] fix: change import directory

---
 tests/test_exceptions.py      | 3 ++-
 tests/test_pdffit.py          | 3 ++-
 tests/test_phase_fractions.py | 2 +-
 tests/test_shape_factors.py   | 3 ++-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/tests/test_exceptions.py b/tests/test_exceptions.py
index 83f2b37..07a4f4e 100644
--- a/tests/test_exceptions.py
+++ b/tests/test_exceptions.py
@@ -18,7 +18,8 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 class read_structExceptions(unittest.TestCase):
diff --git a/tests/test_pdffit.py b/tests/test_pdffit.py
index 7336f0e..54b1a1c 100644
--- a/tests/test_pdffit.py
+++ b/tests/test_pdffit.py
@@ -6,7 +6,8 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 from diffpy.structure import loadStructure
 
 # ----------------------------------------------------------------------------
diff --git a/tests/test_phase_fractions.py b/tests/test_phase_fractions.py
index ac33ec6..c86961e 100644
--- a/tests/test_phase_fractions.py
+++ b/tests/test_phase_fractions.py
@@ -6,7 +6,7 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 ##############################################################################
diff --git a/tests/test_shape_factors.py b/tests/test_shape_factors.py
index 110ce55..70424e5 100644
--- a/tests/test_shape_factors.py
+++ b/tests/test_shape_factors.py
@@ -8,7 +8,8 @@
 import numpy
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 def spherefactor(r, d):

From 3acf21ea80f8cb4d8ab450f4d4743ef42431c1da Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 17:34:12 -0500
Subject: [PATCH 06/11] fix: revert the get release date function.

---
 src/diffpy/pdffit2/__init__.py |  2 +-
 src/diffpy/pdffit2/version.py  | 44 ++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index fceee94..2e143ec 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -17,7 +17,7 @@
 """PDFfit2 - real space structure refinement program."""
 
 # package version
-from diffpy.pdffit2.version import __version__  # noqa
+from diffpy.pdffit2.version import __date__, __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True
diff --git a/src/diffpy/pdffit2/version.py b/src/diffpy/pdffit2/version.py
index 0ade395..7a1eaaa 100644
--- a/src/diffpy/pdffit2/version.py
+++ b/src/diffpy/pdffit2/version.py
@@ -17,8 +17,52 @@
 #  We do not use the other three variables, but can be added back if needed.
 #  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
 
+import datetime
+import json
+import urllib.request
+
 # obtain version information
 from importlib.metadata import PackageNotFoundError, version
+from pathlib import Path
+
+
+def get_pypi_release_date(package_name, timeout=5):
+    package_file = Path(__file__).resolve()
+
+    try:
+        with open(package_file, "r", encoding="utf-8") as f:
+            lines = f.readlines()
+        for line in reversed(lines):
+            if line.startswith("# Release date:"):
+                return line.split(":", 1)[1].strip()
+
+        url = f"https://pypi.org/pypi/{package_name}/json"
+        with urllib.request.urlopen(url, timeout=timeout) as response:
+            data = json.loads(response.read().decode("utf-8"))
+
+        installed_version = version(package_name)
+        release_data = data["releases"].get(installed_version, [])
+        if not release_data:
+            raise ValueError(
+                f"No release data found for version {installed_version}"
+            )
+
+        release_date_str = release_data[-1]["upload_time"]
+        release_date = datetime.datetime.fromisoformat(release_date_str).date()
+
+        with open(package_file, "a", encoding="utf-8") as f:
+            f.write(f"\n# Release date: {release_date}")
+
+    except (ValueError, OSError) as e:
+        print(f"Warning: Could not fetch release date from PyPI: {e}")
+        release_date = datetime.datetime.fromtimestamp(
+            package_file.stat().st_ctime
+        ).isoformat()
+
+    return str(release_date)
+
+
+__date__ = get_pypi_release_date("diffpy.pdffit2")
 
 try:
     __version__ = version("diffpy.pdffit2")

From 3ec420e41009ed61fd8147c533d15ddce13b24d7 Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 17:43:04 -0500
Subject: [PATCH 07/11] revert the import of redirect_stdout

---
 src/diffpy/pdffit2/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index 2e143ec..048588e 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -18,6 +18,7 @@
 
 # package version
 from diffpy.pdffit2.version import __date__, __version__  # noqa
+from diffpy.pdffit2.output import redirect_stdout
 
 # silence the pyflakes syntax checker
 assert __version__ or True

From 07635d0d1581c4e207de965f46ea1e92b17ae973 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 21 Nov 2025 22:43:22 +0000
Subject: [PATCH 08/11] [pre-commit.ci] auto fixes from pre-commit hooks

---
 src/diffpy/pdffit2/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index 048588e..f6f617f 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -16,9 +16,10 @@
 ##############################################################################
 """PDFfit2 - real space structure refinement program."""
 
+from diffpy.pdffit2.output import redirect_stdout
+
 # package version
 from diffpy.pdffit2.version import __date__, __version__  # noqa
-from diffpy.pdffit2.output import redirect_stdout
 
 # silence the pyflakes syntax checker
 assert __version__ or True

From ce191940c74e614ff0d58b91fef23bc16c7cdcfd Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 17:47:38 -0500
Subject: [PATCH 09/11] chore: suppress flake8 since it is used in C++

---
 src/diffpy/pdffit2/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index f6f617f..1b81823 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -16,7 +16,7 @@
 ##############################################################################
 """PDFfit2 - real space structure refinement program."""
 
-from diffpy.pdffit2.output import redirect_stdout
+from diffpy.pdffit2.output import redirect_stdout # noqa
 
 # package version
 from diffpy.pdffit2.version import __date__, __version__  # noqa

From 29005904ac9793d53ddf78284f1ea0e56d2af9a2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 21 Nov 2025 22:47:57 +0000
Subject: [PATCH 10/11] [pre-commit.ci] auto fixes from pre-commit hooks

---
 src/diffpy/pdffit2/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index 1b81823..f22d9cb 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -16,7 +16,7 @@
 ##############################################################################
 """PDFfit2 - real space structure refinement program."""
 
-from diffpy.pdffit2.output import redirect_stdout # noqa
+from diffpy.pdffit2.output import redirect_stdout  # noqa
 
 # package version
 from diffpy.pdffit2.version import __date__, __version__  # noqa

From d352c0964b621f964d50568099396a081acac24a Mon Sep 17 00:00:00 2001
From: stevenhua0320 <r.hua@mail.utoronto.ca>
Date: Fri, 21 Nov 2025 23:56:02 -0500
Subject: [PATCH 11/11] fix: revert original code to import

---
 src/diffpy/pdffit2/__init__.py | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/diffpy/pdffit2/__init__.py b/src/diffpy/pdffit2/__init__.py
index f22d9cb..527477a 100644
--- a/src/diffpy/pdffit2/__init__.py
+++ b/src/diffpy/pdffit2/__init__.py
@@ -16,12 +16,24 @@
 ##############################################################################
 """PDFfit2 - real space structure refinement program."""
 
-from diffpy.pdffit2.output import redirect_stdout  # noqa
+# WARNING: Do NOT remove the isort: off/on comments in this file.
+# These tags are used to prevent isort from reordering imports in this file.
+# __version__ must be initialized before importing C++ extensions.
 
-# package version
-from diffpy.pdffit2.version import __date__, __version__  # noqa
+# isort: off
+# Import the package version before C++ extensions are loaded.
+from diffpy.pdffit2.output import redirect_stdout
+from diffpy.pdffit2.version import __date__, __version__
 
-# silence the pyflakes syntax checker
+# Import C++ related modules since the __version__ attribute is used.
+from diffpy.pdffit2.pdffit import PdfFit
+from diffpy.pdffit2.pdffit2 import is_element
+
+# isort: on
+
+# Ensure all necessary components are imported and initialized
 assert __version__ or True
+assert __date__ or True
+assert all((PdfFit, redirect_stdout, is_element))
 
 # End of file