Control: tags 955456 + pending
Dear maintainer,
_g.
I've prepared an NMU for bitshuffle (versioned as 0.3.5-3.1) and
uploaded it to DELAYED/2. Please feel free to tell me if I
should delay it longer.
Regards.
diff -Nru bitshuffle-0.3.5/debian/changelog bitshuffle-0.3.5/debian/changelog
--- bitshuffle-0.3.5/debian/changelog 2019-12-01 19:03:38.000000000 +0100
+++ bitshuffle-0.3.5/debian/changelog 2020-04-07 20:50:47.000000000 +0200
@@ -1,3 +1,21 @@
+bitshuffle (0.3.5-3.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+
+ [ Drew Parsons <dpars...@debian.org>, Gilles Filippini <p...@debian.org> ]
+ * Closes: #955456
+ - fix-deprecated.patch: fix test_h5filter.py and test_h5plugin.py
+ to open files with flag 'w' when required
+ - Build-Depends: python3-h5py-mpi to force using the mpi flavour
+ of h5py
+ - override_dh_auto_test:
+ - Run the tests via mpirun so that h5py knows it has to invoke its
+ mpi implementation
+ - Launch the tests for each python version separately to permit MPI
+ initialization at each run
+
+ -- Gilles Filippini <p...@debian.org> Tue, 07 Apr 2020 20:50:47 +0200
+
bitshuffle (0.3.5-3) unstable; urgency=medium
* don't use -march=native when building the package
diff -Nru bitshuffle-0.3.5/debian/control bitshuffle-0.3.5/debian/control
--- bitshuffle-0.3.5/debian/control 2019-12-01 19:03:38.000000000 +0100
+++ bitshuffle-0.3.5/debian/control 2020-04-06 14:46:51.000000000 +0200
@@ -11,7 +11,7 @@
# , libopenmpi-dev
, openmpi-bin
, python3-setuptools
- , python3-h5py
+ , python3-h5py-mpi
, quilt
, cmake
, pkg-config
diff -Nru bitshuffle-0.3.5/debian/patches/fix-deprecated.patch
bitshuffle-0.3.5/debian/patches/fix-deprecated.patch
--- bitshuffle-0.3.5/debian/patches/fix-deprecated.patch 1970-01-01
01:00:00.000000000 +0100
+++ bitshuffle-0.3.5/debian/patches/fix-deprecated.patch 2020-04-06
14:46:44.000000000 +0200
@@ -0,0 +1,53 @@
+Index: bitshuffle-0.3.5/bitshuffle/tests/test_h5filter.py
+===================================================================
+--- bitshuffle-0.3.5.orig/bitshuffle/tests/test_h5filter.py
++++ bitshuffle-0.3.5/bitshuffle/tests/test_h5filter.py
+@@ -23,7 +23,7 @@ class TestFilter(unittest.TestCase):
+ dtype = np.int64
+ data = np.arange(shape[0])
+ fname = "tmp_test_filters.h5"
+- f = h5py.File(fname)
++ f = h5py.File(fname, 'w')
+ h5.create_dataset(f, b"range", shape, dtype, chunks,
+ filter_pipeline=(32008, 32000),
+ filter_flags=(h5z.FLAG_MANDATORY, h5z.FLAG_MANDATORY),
+@@ -43,7 +43,7 @@ class TestFilter(unittest.TestCase):
+ dtype = np.int64
+ data = np.arange(shape[0])
+ fname = "tmp_test_filters.h5"
+- f = h5py.File(fname)
++ f = h5py.File(fname, 'w')
+ h5.create_dataset(f, b"range", shape, dtype, chunks,
+ filter_pipeline=(32008, 32000),
+ filter_flags=(h5z.FLAG_MANDATORY, h5z.FLAG_MANDATORY),
+@@ -65,7 +65,7 @@ class TestFilter(unittest.TestCase):
+ dtype = np.int64
+ data = np.arange(shape[0])
+ fname = "tmp_test_filters.h5"
+- f = h5py.File(fname)
++ f = h5py.File(fname, 'w')
+ h5.create_dataset(f, b"range", shape, dtype, chunks,
+ filter_pipeline=(32008,),
+ filter_flags=(h5z.FLAG_MANDATORY,),
+Index: bitshuffle-0.3.5/bitshuffle/tests/test_h5plugin.py
+===================================================================
+--- bitshuffle-0.3.5.orig/bitshuffle/tests/test_h5plugin.py
++++ bitshuffle-0.3.5/bitshuffle/tests/test_h5plugin.py
+@@ -34,7 +34,7 @@ class TestFilterPlugins(unittest.TestCas
+ dtype = np.int64
+ data = np.arange(shape[0])
+ fname = "tmp_test_filters.h5"
+- f = h5py.File(fname)
++ f = h5py.File(fname, 'w')
+ tid = h5t.py_create(dtype, logical=1)
+ sid = h5s.create_simple(shape, shape)
+ #
+@@ -72,7 +72,7 @@ class TestFilterPlugins(unittest.TestCas
+ # return
+ # # Does not appear to be supported by h5py.
+ # fname = "tmp_test_h5py_hl.h5"
+- # f = h5py.File(fname)
++ # f = h5py.File(fname, 'w')
+ # f.create_dataset("range", np.arange(1024, dtype=np.int64),
+ # compression=32008)
+
diff -Nru bitshuffle-0.3.5/debian/patches/series
bitshuffle-0.3.5/debian/patches/series
--- bitshuffle-0.3.5/debian/patches/series 2019-12-01 19:03:38.000000000
+0100
+++ bitshuffle-0.3.5/debian/patches/series 2020-04-06 14:46:44.000000000
+0200
@@ -1,2 +1,3 @@
hdf5-old-api.patch
change-build-flags.patch
+fix-deprecated.patch
diff -Nru bitshuffle-0.3.5/debian/rules bitshuffle-0.3.5/debian/rules
--- bitshuffle-0.3.5/debian/rules 2019-08-20 19:29:38.000000000 +0200
+++ bitshuffle-0.3.5/debian/rules 2020-04-06 14:46:58.000000000 +0200
@@ -24,5 +24,11 @@
%:
dh $@ --with python3 --buildsystem=pybuild
+override_dh_auto_test:
+ set -e; \
+ for py in `py3versions -s -v`; do \
+ mpirun -n 1 pybuild --test -i python{version} -p $$py; \
+ done
+
#override_dh_auto_clean:
# dh_auto_clean
