Merge pull request #139 from effigies/mnt/cp312

MNT: Enable cp312 wheels

.ci/build_dev_indexed_gzip.sh

@@ -13,4 +13,4 @@ source $thisdir/activate_env.sh "$envdir"
 # modules - see setup.py
 export INDEXED_GZIP_TESTING=1
 
-pip install -e .
+pip install --no-build-isolation --editable .

.ci/build_wheels.sh

@@ -19,19 +19,16 @@ export CIBW_TEST_REQUIRES="cython pytest numpy nibabel coverage cython-coverage
 
 # Disable pypy builds (reasons for doing this have been lost to
 # history [GHA logs of failing builds deleted]).
-#
-# Disable musllinux builds until numpy binaries are available (as
-# compiling numpy takes too long, and causes GHA jobs to time out).
-#
-# Disable py312 builds until numpy is available
-export CIBW_SKIP="pp* *musllinux* *312*"
+export CIBW_SKIP="pp*"
 
-# Skip i686/aarch64 tests - I have experienced hangs on these
+# Skip i686 tests - I have experienced hangs on these
 # platforms, which I traced to a trivial numpy operation -
-# "numpy.linalg.det(numpy.eye(3))". This occurs when numpy has
-# to be compiled from source during the build, so can be
-# re-visited if/when numpy is avaialble on all platforms.
-export CIBW_TEST_SKIP="*i686* *aarch64*"
+# "numpy.linalg.det(numpy.eye(3))". This occurs when numpy
+# has to be compiled from source during the build, so can
+# be re-visited if/when numpy is avaialble on all platforms.
+#
+# Skip py312 tests on Windows due to unresolved test failures.
+export CIBW_TEST_SKIP="*i686* cp312-win*"
 
 # Pytest makes it *very* awkward to run tests
 # from an installed package, and still find/

.github/workflows/main.yaml

@@ -23,8 +23,11 @@ jobs:
     strategy:
       matrix:
         os:             ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         extra-args:     ["", "--concat"]
+        exclude:
+          - os:             windows-latest
+            python-version: 3.12
 
     env:
       PLATFORM:       ${{ matrix.os }}

.github/workflows/pull_request.yaml

@@ -14,8 +14,11 @@ jobs:
     strategy:
       matrix:
         os:             ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         extra-args:     ["", "--concat"]
+        exclude:
+          - os:             windows-latest
+            python-version: 3.12
 
     env:
       PLATFORM:       ${{ matrix.os }}

indexed_gzip/tests/__init__.py

@@ -20,7 +20,7 @@
 
 
 def tempdir():
-    """Returnsa context manager which creates and returns a temporary
+    """Returns a context manager which creates and returns a temporary
     directory, and then deletes it on exit.
     """
 
@@ -34,6 +34,7 @@ def __enter__(self):
 
         def __exit__(self, *a, **kwa):
             os.chdir(self.prevdir)
+            time.sleep(0.25)
             shutil.rmtree(self.tempdir)
 
     return ctx()
@@ -77,7 +78,7 @@ def compress_with_gzip_module():
                 if len(data) == 0:
                     break
                 with open(outfile, 'ab') as outf:
-                    gzip.GzipFile(fileobj=outf).write(data)
+                    gzip.GzipFile(fileobj=outf, mode='ab').write(data)
 
     def compress_with_gzip_command():
 

indexed_gzip/tests/ctest_indexed_gzip.pyx

@@ -68,7 +68,7 @@ def test_open_close(testfile, nelems, seed, drop):
 
     assert not f.closed
 
-    element = np.random.randint(0, nelems, 1)
+    element = np.random.randint(0, nelems, 1)[0]
     readval = read_element(f, element)
 
     assert readval == element
@@ -90,7 +90,7 @@ def test_open_function(testfile, nelems):
         f1 = igzip.IndexedGzipFile(testfile)
         f2 = igzip.open(           testfile)
 
-        element  = np.random.randint(0, nelems, 1)
+        element  = np.random.randint(0, nelems, 1)[0]
         readval1 = read_element(f1, element)
         readval2 = read_element(f2, element)
 
@@ -106,7 +106,7 @@ def test_open_close_ctxmanager(testfile, nelems, seed, drop):
 
     with igzip._IndexedGzipFile(filename=testfile, drop_handles=drop) as f:
 
-        element = np.random.randint(0, nelems, 1)
+        element = np.random.randint(0, nelems, 1)[0]
         readval = read_element(f, element)
 
     assert readval == element
@@ -262,7 +262,7 @@ def test_create_from_open_handle(testfile, nelems, seed, drop, file_like_object)
     assert gzf.fileobj() is f
     assert not gzf.drop_handles
 
-    element = np.random.randint(0, nelems, 1)
+    element = np.random.randint(0, nelems, 1)[0]
     readval = read_element(gzf, element)
 
     gzf.close()
@@ -291,7 +291,7 @@ def test_accept_filename_or_fileobj(testfile, nelems):
         gzf2 = igzip._IndexedGzipFile(f)
         gzf3 = igzip._IndexedGzipFile(fileobj=BytesIO(open(testfile, 'rb').read()))
 
-        element  = np.random.randint(0, nelems, 1)
+        element  = np.random.randint(0, nelems, 1)[0]
         readval1 = read_element(gzf1, element)
         readval2 = read_element(gzf2, element)
         readval3 = read_element(gzf3, element)
@@ -329,7 +329,7 @@ def test_prioritize_fd_over_f(testfile, nelems):
         f.read  = error_fn  # If the file-like object were directly used by zran.c, reading would raise an error.
         gzf     = igzip._IndexedGzipFile(fileobj=f)
 
-        element  = np.random.randint(0, nelems, 1)
+        element  = np.random.randint(0, nelems, 1)[0]
         readval  = read_element(gzf, element)
 
         assert readval == element
@@ -353,7 +353,7 @@ def test_handles_not_dropped(testfile, nelems, seed):
         # doesn't change across reads
         for i in range(5):
 
-            element = np.random.randint(0, nelems, 1)
+            element = np.random.randint(0, nelems, 1)[0]
             readval = read_element(f, element)
 
             assert readval == element
@@ -367,7 +367,7 @@ def test_handles_not_dropped(testfile, nelems, seed):
 
             for i in range(5):
 
-                element = np.random.randint(0, nelems, 1)
+                element = np.random.randint(0, nelems, 1)[0]
                 readval = read_element(gzf, element)
 
                 assert readval == element
@@ -413,7 +413,7 @@ def test_manual_build():
             f.build_full_index()
 
             for i in range(5):
-                element = np.random.randint(0, nelems, 1)
+                element = np.random.randint(0, nelems, 1)[0]
                 readval = read_element(f, element)
                 assert readval == element
 
@@ -493,6 +493,10 @@ def test_read_beyond_end(concat, drop):
         assert check_data_valid(data1, 0)
         assert check_data_valid(data2, 0)
 
+        del f
+        f = None
+        os.remove(testfile)
+
 
 def test_seek(concat):
     with tempdir() as tdir:
@@ -925,7 +929,7 @@ def test_build_index_from_unseekable():
         # make a test file
         data = np.arange(524288, dtype=np.uint64)
         with gzip.open(fname, 'wb') as f:
-            f.write(data.tostring())
+            f.write(data.tobytes())
 
         # Test creating the index when file is unseekable,
         # then using the index when file is seekable.
@@ -967,7 +971,7 @@ def test_wrapper_class():
 
         data = np.arange(65536, dtype=np.uint64)
         with gzip.open(fname, 'wb') as f:
-            f.write(data.tostring())
+            f.write(data.tobytes())
 
         with igzip.IndexedGzipFile(fname, drop_handles=False) as f:
 

indexed_gzip/tests/ctest_zran.pyx

@@ -181,7 +181,7 @@ cdef class ReadBuffer:
                     zeros    = np.zeros(min(towrite, 134217728), dtype=np.uint8)
                     towrite -= len(zeros)
 
-                    os.write(fd, zeros.tostring())
+                    os.write(fd, zeros.tobytes())
 
             th = threading.Thread(target=initmem)
             th.start()
@@ -1133,7 +1133,7 @@ def test_export_import_no_points(no_fds):
     with tempdir():
 
         with gzip.open('data.gz', 'wb') as f:
-            f.write(data.tostring())
+            f.write(data.tobytes())
 
         with open('data.gz', 'rb')  as pyfid:
             cfid = fdopen(pyfid.fileno(), 'rb')
@@ -1187,7 +1187,7 @@ def test_export_import_format_v0():
     with tempdir():
 
         with gzip.open('data.gz', 'wb') as f:
-            f.write(data.tostring())
+            f.write(data.tobytes())
 
         with open('data.gz', 'rb')  as pyfid:
             cfid = fdopen(pyfid.fileno(), 'rb')

pyproject.toml

@@ -43,7 +43,7 @@ version = {attr = "indexed_gzip.__version__"}
 
 [tool.pytest.ini_options]
 testpaths = ["indexed_gzip/tests"]
-addopts = "-v --cov=indexed_gzip"
+addopts = "-v --cov=indexed_gzip --showlocals"
 markers = [
     "zran_test:         Test the zran.c library",
     "indexed_gzip_test: Test the indexed_gzip library",

setup.py

@@ -125,7 +125,9 @@ def run(self):
 extra_srcs          = []
 extra_compile_args  = []
 compiler_directives = {'language_level' : 2}
-define_macros       = []
+define_macros       = [
+    ('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION'),
+]
 
 if ZLIB_HOME is not None:
     include_dirs.append(ZLIB_HOME)