Minor adjustments to exception handling

.github/workflows/release.yaml

@@ -26,7 +26,7 @@ jobs:
       - name: Build sdist
         run:  python setup.py sdist
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4.4.3
         with:
           name: sdist
           path: ./dist/*.tar.gz
@@ -49,7 +49,7 @@ jobs:
       - name: Build wheels
         run:  bash ./.ci/build_wheels.sh
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4.4.3
         with:
           name: wheels
           path: ./dist/*.whl
@@ -76,7 +76,7 @@ jobs:
         run:  bash ./.ci/download_zlib.sh
       - name: Build wheels
         run:  bash ./.ci/build_wheels.sh
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4.4.3
         with:
           name: wheels
           path: ./dist/*.whl
@@ -105,7 +105,7 @@ jobs:
         uses: docker/setup-qemu-action@v3
       - name: Build wheels
         run:  bash ./.ci/build_wheels.sh
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4.4.3
         with:
           name: wheels
           path: ./dist/*.whl

CHANGELOG.md

@@ -1,6 +1,12 @@
 # `indexed_gzip` changelog
 
 
+## 1.9.0 (November 15th 2024)
+
+
+* Preserve exception information when reading from a Python file-like (#152).
+
+
 ## 1.8.8 (November 7th 2024)
 
 

README.md

@@ -311,6 +311,7 @@ Many thanks to the following contributors (listed chronologically):
  - Maximilian Knespel (@mxmlnkn) Change default read buffer size to
    improve performance (#90).
  - Ben Beasley (@musicinmybrain) Python 3.12 compatibility (#126).
+ - @camillol: Preserve exceptions raised by Python file-likes (#152).
 
 
 ## License

indexed_gzip/__init__.py

@@ -19,4 +19,4 @@
 """
 
 
-__version__ = '1.8.8'
+__version__ = '1.9.0'

indexed_gzip/indexed_gzip.pyx

@@ -9,36 +9,44 @@ random access to gzip files.
 """
 
 
-from libc.stdio     cimport (SEEK_SET,
-                             SEEK_CUR,
-                             SEEK_END,
-                             FILE,
-                             fopen,
-                             fdopen,
-                             fclose)
-
-from libc.stdint    cimport (uint8_t,
-                             uint32_t,
-                             uint64_t,
-                             int64_t)
-
-from cpython.mem    cimport (PyMem_Malloc,
-                             PyMem_Realloc,
-                             PyMem_Free)
-
-from cpython.buffer cimport (PyObject_GetBuffer,
-                             PyBuffer_Release,
-                             PyBUF_ANY_CONTIGUOUS,
-                             PyBUF_SIMPLE)
-
-from cpython.ref cimport PyObject, Py_XDECREF
-from cpython.exc cimport PyErr_Occurred, PyErr_Fetch, PyErr_NormalizeException
+from libc.stdio                 cimport (SEEK_SET,
+                                         SEEK_CUR,
+                                         SEEK_END,
+                                         FILE,
+                                         fopen,
+                                         fdopen,
+                                         fclose)
+
+from libc.stdint                cimport (uint8_t,
+                                         uint32_t,
+                                         uint64_t,
+                                         int64_t)
+
+from cpython.mem                cimport (PyMem_Malloc,
+                                         PyMem_Realloc,
+                                         PyMem_Free)
+
+from cpython.buffer             cimport (PyObject_GetBuffer,
+                                         PyBuffer_Release,
+                                         PyBUF_ANY_CONTIGUOUS,
+                                         PyBUF_SIMPLE)
+
+from cpython.ref                cimport (PyObject,
+                                         Py_XDECREF)
+from cpython.exc                cimport (PyErr_Fetch,
+                                         PyErr_Fetch,
+                                         PyErr_NormalizeException,
+                                         PyErr_Occurred)
+from indexed_gzip.set_traceback cimport  PyException_SetTraceback
+
 
 cimport indexed_gzip.zran as zran
 
+
 import            io
 import            os
 import os.path as op
+import            sys
 import            pickle
 import            logging
 import            warnings
@@ -55,6 +63,9 @@ instead.
 """
 
 
+PY3 = sys.version_info[0] >= 3
+
+
 log = logging.getLogger(__name__)
 
 
@@ -69,14 +80,28 @@ def open(filename=None, fileobj=None, *args, **kwargs):
     return IndexedGzipFile(filename, fileobj, **kwargs)
 
 
-cdef _get_python_exception():
+cdef get_python_exception():
+    """Checks to see if a Python exception has occurred. If so, returns a
+    reference to the exception object. Returns None otherwise.
+
+    This function is used so that, if an IndexedGzipFile object is reading
+    from a Python file-like, and the file-like raises an error, the
+    information about that error is not lost.
+    """
     cdef PyObject *ptype
     cdef PyObject *pvalue
     cdef PyObject *ptraceback
     if PyErr_Occurred():
         PyErr_Fetch(&ptype, &pvalue, &ptraceback)
         PyErr_NormalizeException(&ptype, &pvalue, &ptraceback)
+
+        # Populate traceback info for the original exception
+        if PY3 and (ptraceback != NULL):
+            PyException_SetTraceback(pvalue, ptraceback)
+
         exc = <object>pvalue
+        if PY3 and (ptraceback != NULL):
+            PyException_SetTraceback(pvalue, NULL)
         Py_XDECREF(ptype)
         Py_XDECREF(pvalue)
         Py_XDECREF(ptraceback)
@@ -759,7 +784,7 @@ cdef class _IndexedGzipFile:
 
                 # Unknown error
                 elif ret < 0:
-                    exc = _get_python_exception()
+                    exc = get_python_exception()
                     raise ZranError('zran_read returned error: {} (file: '
                                     '{})'.format(ZRAN_ERRORS.ZRAN_READ[ret],
                                                  self.errname)) from exc
@@ -818,7 +843,7 @@ cdef class _IndexedGzipFile:
 
         # see how the read went
         if ret == zran.ZRAN_READ_FAIL:
-            exc = _get_python_exception()
+            exc = get_python_exception()
             raise ZranError('zran_read returned error: {} (file: {})'
                             .format(ZRAN_ERRORS.ZRAN_READ[ret], self.errname)) from exc
 

indexed_gzip/set_traceback.pxd

@@ -0,0 +1,10 @@
+#
+# Cython declaration for the PyException_SetTraceback function.
+# This function is in the Python C API, but is not in the built-in
+# Cython declarations.
+#
+
+from cpython.ref cimport PyObject
+
+cdef extern from "Python.h":
+    PyObject* PyException_SetTraceback(PyObject* ex, PyObject* tb)

indexed_gzip/tests/test_indexed_gzip.py

@@ -510,7 +510,8 @@ def test_read_beyond_end(concat, drop):
 
 
 def test_read_exception(testfile, nelems):
-    """When wrapping a python file object, if it raises an exception it should be preserved.
+    """When wrapping a python file object, if it raises an exception
+    it should be preserved.
     """
     if sys.version_info[0] < 3:
         # We can't set the .read attribute in Python 2
@@ -521,15 +522,15 @@ def test_read_exception(testfile, nelems):
     gzf  = None
 
     MY_ERROR = "This error should be preserved"
-    # We'll use a weakref to check that we are handling reference counting correctly,
-    # and you cannot weakref an Exception, so we need a subclass.
+
+    # We'll use a weakref to check that we are handling reference counting
+    # correctly, and you cannot weakref an Exception, so we need a subclass.
     class MyException(Exception):
         pass
-    my_err_weak = None
+    my_err_weak = [None]
     def my_error_fn(*args, **kwargs):
         err = MyException(MY_ERROR)
-        nonlocal my_err_weak
-        my_err_weak = weakref.ref(err)
+        my_err_weak[0] = weakref.ref(err)
         raise err
 
     try:
@@ -540,15 +541,20 @@ def my_error_fn(*args, **kwargs):
         try:
             gzf.read(1)
         except Exception as e:
-            assert MY_ERROR in str(e) or MY_ERROR in str(e.__cause__), f"Exception was not preserved; got {e}"
+            assert (MY_ERROR in str(e) or MY_ERROR in str(e.__cause__),
+                    "Exception was not preserved; got {}".format(e))
+            del e
         else:
             assert False, "Expected an exception to be raised"
+
+
     finally:
         if gzf is not None: gzf.close()
         if f   is not None: f  .close()
         del f
         del gzf
-    assert my_err_weak is None or my_err_weak() is None, "Exception was not garbage collected"
+    assert (my_err_weak[0] is None or my_err_weak[0]() is None,
+            "Exception was not garbage collected")
 
 
 def test_seek(concat):