Merge pull request #122 from Tieqiong/win_memory

fix: win_py13 SystemError from pytest

Author: sbillinge

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -15,7 +15,7 @@ jobs:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.pdffit2
-      python_versions: "3.11, 3.12"
+      python_versions: "3.11, 3.12, 3.13"
       c_extension: true
       headless: false
     secrets:

.github/workflows/publish-docs-on-release.yml

@@ -14,4 +14,4 @@ jobs:
       project: diffpy.pdffit2
       c_extension: true
       headless: false
-      python_version: 3.12
+      python_version: 3.13

.github/workflows/tests-on-pr.yml

@@ -14,6 +14,6 @@ jobs:
       project: diffpy.pdffi2
       c_extension: true
       headless: false
-      python_version: 3.12
+      python_version: 3.13
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

README.rst

@@ -72,7 +72,7 @@ If you use diffpy.pdffit2 in a scientific publication, we would like you to cite
 Installation
 ------------
 
-diffpy.pdffit2 supports Python 3.11 and 3.12.
+diffpy.pdffit2 supports Python 3.11, 3.12, and 3.13.
 
 Windows, macOS (non-Arm64), Linux
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -102,7 +102,7 @@ macOS (Arm64)
 
 Create a new conda environment ``diffpy.pdffit2_env``: ::
 
-        conda create -n diffpy.pdffit2_env python=3.12
+        conda create -n diffpy.pdffit2_env python=3.13
 
 Activate the environment: ::
 
@@ -121,7 +121,7 @@ Build from source
 
 For advanced users, obtain the source archive, and in the ``diffpy.pdffit2`` directory, run ::
 
-        conda create -n diffpy.pdffit2_env python=3.12 \
+        conda create -n diffpy.pdffit2_env python=3.13 \
                 --file requirements/test.txt \
                 --file requirements/conda.txt \
                 --file requirements/build.txt

news/win_memory.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* Added `restore_stdout` function and wrapper.
+* Added Python 3.13 support.
+
+**Changed:**
+
+* Changed `pytest` `capture_output` fixture. Now automatically restores `sys.stdout`.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed `SystemError` when running `pytest` on Windows with Python 3.13.
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "PDFfit2 - real space structure refinement program."
 keywords = ["PDF", "structure refinement"]
 readme = "README.rst"
-requires-python = ">=3.11, <3.13"
+requires-python = ">=3.11, <3.14"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -27,6 +27,7 @@ classifiers = [
         'Operating System :: Unix',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]

src/diffpy/pdffit2/output.py

@@ -39,4 +39,13 @@ def redirect_stdout(dst):
     return
 
 
+def restore_stdout():
+    """Restore the standard output."""
+    from diffpy.pdffit2.pdffit2 import restore_stdout
+
+    restore_stdout()
+    global stdout
+    return
+
+
 #  End of file

src/extensions/pdffit2module/bindings.cc

@@ -330,6 +330,10 @@ struct PyMethodDef pypdffit2_methods[] = {
     {pypdffit2_redirect_stdout__name__, pypdffit2_redirect_stdout,
      METH_VARARGS, pypdffit2_redirect_stdout__doc__},
 
+    //restore_stdout
+    {pypdffit2_restore_stdout__name__, pypdffit2_restore_stdout,
+     METH_VARARGS, pypdffit2_restore_stdout__doc__},
+
     //is_element
     {pypdffit2_is_element__name__, pypdffit2_is_element,
      METH_VARARGS, pypdffit2_is_element__doc__},

src/extensions/pdffit2module/misc.cc

@@ -2201,6 +2201,36 @@ PyObject * pypdffit2_redirect_stdout(PyObject *, PyObject *args)
     return Py_None;
 }
 
+// restore_stdout
+char pypdffit2_restore_stdout__doc__[] =
+    "Restore engine output to the default stream (std::cout).";
+char pypdffit2_restore_stdout__name__[] =
+    "restore_stdout";
+
+PyObject * pypdffit2_restore_stdout(PyObject *, PyObject *args)
+{
+    // no arguments.
+    if (!PyArg_ParseTuple(args, ""))
+        return 0;
+
+    // If the global output stream pointer is not std::cout, then delete the custom stream.
+    if (NS_PDFFIT2::pout != &std::cout)
+    {
+        delete NS_PDFFIT2::pout;
+        NS_PDFFIT2::pout = &std::cout;
+    }
+
+    // Clean up the custom stream buffer
+    if (py_stdout_streambuf)
+    {
+        delete py_stdout_streambuf;
+        py_stdout_streambuf = nullptr;
+    }
+
+    Py_INCREF(Py_None);
+    return Py_None;
+}
+
 // is_element
 char pypdffit2_is_element__doc__[] = "Check if element or isotope is defined in the built-in periodic table.";
 char pypdffit2_is_element__name__[] = "is_element";

src/extensions/pdffit2module/misc.h

@@ -477,6 +477,12 @@ extern char pypdffit2_redirect_stdout__name__[];
 extern "C"
 PyObject * pypdffit2_redirect_stdout(PyObject *, PyObject *);
 
+// restore_stdout
+extern char pypdffit2_restore_stdout__doc__[];
+extern char pypdffit2_restore_stdout__name__[];
+extern "C"
+PyObject * pypdffit2_restore_stdout(PyObject *, PyObject *);
+
 // is_element
 extern char pypdffit2_is_element__doc__[];
 extern char pypdffit2_is_element__name__[];