--- Begin Message ---
Source: h5py
Version: 2.2.1-1
Severity: important
Tags: patch
User: [email protected]
Usertags: HDF5-transition
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Hi,
The hdf5 1.8.13 package in experimental features a new layout for
headers and libraries, so that all the binary packages are now
co-installable.
Moreover the 1.8.13 upstream release has the mpiposix API removed.
Please find attached a patch proposal to support both the current
and the new layouts, and acknowledge the mpiposix API removal. Using
codesearch.debian.net I've checked that none of the h5py build-rdeps
uses the mpiposix API.
Because this bug is in the way of the hdf5 transition I intend to NMU
in a few days. I apologize for the urge, and I hope this approach won't
offend you. Please tell me otherwise.
Kind regards,
_g.
- -- System Information:
Debian Release: jessie/sid
APT prefers testing
APT policy: (500, 'testing'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 3.14-1-486
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
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diff -Nru h5py-2.2.1/debian/changelog h5py-2.2.1/debian/changelog
--- h5py-2.2.1/debian/changelog 2014-01-04 23:20:59.000000000 +0100
+++ h5py-2.2.1/debian/changelog 2014-07-31 09:52:25.000000000 +0200
@@ -1,3 +1,12 @@
+h5py (2.2.1-1.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Support hdf5 1.8.13 new packaging path layout.
+ * Patch drop-mpiposix.patch: MPIPOSIX interface was dropped in
+ hdf5 1.8.13
+
+ -- Gilles Filippini <[email protected]> Sat, 12 Jul 2014 11:56:28 +0200
+
h5py (2.2.1-1) unstable; urgency=low
* New upstream version
diff -Nru h5py-2.2.1/debian/patches/drop-mpiposix.patch h5py-2.2.1/debian/patches/drop-mpiposix.patch
--- h5py-2.2.1/debian/patches/drop-mpiposix.patch 1970-01-01 01:00:00.000000000 +0100
+++ h5py-2.2.1/debian/patches/drop-mpiposix.patch 2014-07-31 09:51:41.000000000 +0200
@@ -0,0 +1,112 @@
+Index: h5py-2.2.1/h5py/h5fd.pyx
+===================================================================
+--- h5py-2.2.1.orig/h5py/h5fd.pyx
++++ h5py-2.2.1/h5py/h5fd.pyx
+@@ -31,7 +31,6 @@ CORE = H5FD_CORE
+ FAMILY = H5FD_FAMILY
+ LOG = H5FD_LOG
+ MPIO = H5FD_MPIO
+-MPIPOSIX = H5FD_MPIPOSIX
+ MULTI = H5FD_MULTI
+ SEC2 = H5FD_SEC2
+ STDIO = H5FD_STDIO
+Index: h5py-2.2.1/h5py/_hl/files.py
+===================================================================
+--- h5py-2.2.1.orig/h5py/_hl/files.py
++++ h5py-2.2.1/h5py/_hl/files.py
+@@ -130,8 +130,7 @@ class File(Group):
+ """Low-level HDF5 file driver used to open file"""
+ drivers = {h5fd.SEC2: 'sec2', h5fd.STDIO: 'stdio',
+ h5fd.CORE: 'core', h5fd.FAMILY: 'family',
+- h5fd.WINDOWS: 'windows', h5fd.MPIO: 'mpio',
+- h5fd.MPIPOSIX: 'mpiposix'}
++ h5fd.WINDOWS: 'windows', h5fd.MPIO: 'mpio'}
+ return drivers.get(self.fid.get_access_plist().get_driver(), 'unknown')
+
+ @property
+Index: h5py-2.2.1/h5py/h5fd.pxd
+===================================================================
+--- h5py-2.2.1.orig/h5py/h5fd.pxd
++++ h5py-2.2.1/h5py/h5fd.pxd
+@@ -33,7 +33,6 @@ cdef extern from "hdf5.h":
+ # hid_t H5FD_GASS not in 1.8.X
+ hid_t H5FD_LOG
+ hid_t H5FD_MPIO
+- hid_t H5FD_MPIPOSIX
+ hid_t H5FD_MULTI
+ hid_t H5FD_SEC2
+ hid_t H5FD_STDIO
+Index: h5py-2.2.1/h5py/h5fd.c
+===================================================================
+--- h5py-2.2.1.orig/h5py/h5fd.c
++++ h5py-2.2.1/h5py/h5fd.c
+@@ -474,7 +474,6 @@ static char __pyx_k__LOG_ALL[] = "LOG_AL
+ static char __pyx_k__WINDOWS[] = "WINDOWS";
+ static char __pyx_k__MEM_DRAW[] = "MEM_DRAW";
+ static char __pyx_k__MEM_OHDR[] = "MEM_OHDR";
+-static char __pyx_k__MPIPOSIX[] = "MPIPOSIX";
+ static char __pyx_k____main__[] = "__main__";
+ static char __pyx_k____test__[] = "__test__";
+ static char __pyx_k__LOG_ALLOC[] = "LOG_ALLOC";
+@@ -534,7 +533,6 @@ static PyObject *__pyx_n_s__MEM_NTYPES;
+ static PyObject *__pyx_n_s__MEM_OHDR;
+ static PyObject *__pyx_n_s__MEM_SUPER;
+ static PyObject *__pyx_n_s__MPIO;
+-static PyObject *__pyx_n_s__MPIPOSIX;
+ static PyObject *__pyx_n_s__MULTI;
+ static PyObject *__pyx_n_s__SEC2;
+ static PyObject *__pyx_n_s__STDIO;
+@@ -598,7 +596,6 @@ static __Pyx_StringTabEntry __pyx_string
+ {&__pyx_n_s__MEM_OHDR, __pyx_k__MEM_OHDR, sizeof(__pyx_k__MEM_OHDR), 0, 0, 1, 1},
+ {&__pyx_n_s__MEM_SUPER, __pyx_k__MEM_SUPER, sizeof(__pyx_k__MEM_SUPER), 0, 0, 1, 1},
+ {&__pyx_n_s__MPIO, __pyx_k__MPIO, sizeof(__pyx_k__MPIO), 0, 0, 1, 1},
+- {&__pyx_n_s__MPIPOSIX, __pyx_k__MPIPOSIX, sizeof(__pyx_k__MPIPOSIX), 0, 0, 1, 1},
+ {&__pyx_n_s__MULTI, __pyx_k__MULTI, sizeof(__pyx_k__MULTI), 0, 0, 1, 1},
+ {&__pyx_n_s__SEC2, __pyx_k__SEC2, sizeof(__pyx_k__SEC2), 0, 0, 1, 1},
+ {&__pyx_n_s__STDIO, __pyx_k__STDIO, sizeof(__pyx_k__STDIO), 0, 0, 1, 1},
+@@ -828,7 +825,6 @@ PyMODINIT_FUNC PyInit_h5fd(void)
+ * FAMILY = H5FD_FAMILY
+ * LOG = H5FD_LOG # <<<<<<<<<<<<<<
+ * MPIO = H5FD_MPIO
+- * MPIPOSIX = H5FD_MPIPOSIX
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_LOG); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+@@ -839,7 +835,6 @@ PyMODINIT_FUNC PyInit_h5fd(void)
+ * FAMILY = H5FD_FAMILY
+ * LOG = H5FD_LOG
+ * MPIO = H5FD_MPIO # <<<<<<<<<<<<<<
+- * MPIPOSIX = H5FD_MPIPOSIX
+ * MULTI = H5FD_MULTI
+ */
+ __pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIO); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+@@ -847,21 +842,8 @@ PyMODINIT_FUNC PyInit_h5fd(void)
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__MPIO, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+- /* "h5py/h5fd.pyx":34
+- * LOG = H5FD_LOG
+- * MPIO = H5FD_MPIO
+- * MPIPOSIX = H5FD_MPIPOSIX # <<<<<<<<<<<<<<
+- * MULTI = H5FD_MULTI
+- * SEC2 = H5FD_SEC2
+- */
+- __pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIPOSIX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+- __Pyx_GOTREF(__pyx_t_1);
+- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__MPIPOSIX, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+-
+ /* "h5py/h5fd.pyx":35
+ * MPIO = H5FD_MPIO
+- * MPIPOSIX = H5FD_MPIPOSIX
+ * MULTI = H5FD_MULTI # <<<<<<<<<<<<<<
+ * SEC2 = H5FD_SEC2
+ * STDIO = H5FD_STDIO
+@@ -872,7 +854,6 @@ PyMODINIT_FUNC PyInit_h5fd(void)
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "h5py/h5fd.pyx":36
+- * MPIPOSIX = H5FD_MPIPOSIX
+ * MULTI = H5FD_MULTI
+ * SEC2 = H5FD_SEC2 # <<<<<<<<<<<<<<
+ * STDIO = H5FD_STDIO
diff -Nru h5py-2.2.1/debian/patches/series h5py-2.2.1/debian/patches/series
--- h5py-2.2.1/debian/patches/series 1970-01-01 01:00:00.000000000 +0100
+++ h5py-2.2.1/debian/patches/series 2014-07-31 09:51:41.000000000 +0200
@@ -0,0 +1 @@
+drop-mpiposix.patch
diff -Nru h5py-2.2.1/debian/rules h5py-2.2.1/debian/rules
--- h5py-2.2.1/debian/rules 2013-11-16 17:46:56.000000000 +0100
+++ h5py-2.2.1/debian/rules 2014-07-31 10:08:38.000000000 +0200
@@ -2,6 +2,11 @@
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/python-distutils.mk
+ifneq ($(wildcard /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial/libhdf5.so),)
+ export CPPFLAGS=-I/usr/include/hdf5/serial
+ export LDFLAGS=-Wl,-L/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
+endif
+
binary-install/python-h5py::
dh_python2
dh_python3
--- End Message ---
