debian/changelog

+python-hdf4 (0.9.2-1) unstable; urgency=medium
+
+  * New upstream release.
+  * debian/patches
+    - drop 0001-Use-hdf4-alt.patch: no longer necessary
+    - drop 0002-Do-not-pass-empty-arguments-to-setup.patch:
+      no longer necessary
+
+ -- Antonio Valentino <antonio.valentino@tiscali.it>  Wed, 20 Feb 2019 07:04:19 +0000
+
 python-hdf4 (0.9.1-1) unstable; urgency=medium
 
   * Initial version (Closes: #917254)

debian/patches/0001-Use-hdf4-alt.patch

-From: Antonio Valentino <antonio.valentino@tiscali.it>
-Date: Mon, 24 Dec 2018 19:02:31 +0000
-Subject: Use hdf4-alt
-
----
- setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index 77987e4..e847a51 100644
---- a/setup.py
-+++ b/setup.py
-@@ -125,7 +125,7 @@ if sys.platform == 'win32':
- if sys.platform == 'win32':
-     libraries = ["hm423m", "hd423m", "xdr_for_dll" ]
- else:
--    libraries = ["mfhdf", "df"]
-+    libraries = ["mfhdfalt", "dfalt"]
- 
- if szip_installed:
-     extra_compile_args = []

debian/patches/0002-Do-not-pass-empty-arguments-to-setup.patch

-From: Antonio Valentino <antonio.valentino@tiscali.it>
-Date: Sun, 30 Dec 2018 16:37:26 +0000
-Subject: Do not pass empty arguments to setup
-
----
- setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index e847a51..d8d2570 100644
---- a/setup.py
-+++ b/setup.py
-@@ -148,7 +148,7 @@ _hdfext = Extension('pyhdf._hdfext',
-                     include_dirs = include_dirs,
-                     extra_compile_args = extra_compile_args,
-                     library_dirs = library_dirs,
--                    extra_link_args=[extra_link_args],
-+                    extra_link_args=[extra_link_args] if extra_link_args else [],
-                     libraries = libraries,
-                     )
- 

debian/patches/series

-0001-Use-hdf4-alt.patch
-0002-Do-not-pass-empty-arguments-to-setup.patch

doc/install.rst

@@ -30,9 +30,9 @@ The following packages are required to build and install Python-HDF4:
 - `libjpeg <http://www.ijg.org/>`_ 
 
 On Debian and Debian-based Linux distributions (e.g. Ubuntu), you can install
-all the requirements using this command::
+all the requirements for Python 3 using this command::
 
-    apt-get install python-dev python-numpy libhdf4-dev -y
+    apt-get install build-essential python3-dev python3-numpy libhdf4-dev -y
 
 OS X users can obtain jpeg libraries `here
 <http://ethan.tira-thompson.com/Mac%20OS%20X%20Ports.html>`_. 

pyhdf/SD.py

@@ -1304,21 +1304,7 @@ class SDAttr(object):
             buf = _C.array_byte(n_values)
 
         elif data_type == SDC.INT8:
-            # SWIG refuses negative values here. We found that if we
-            # pass them as byte values, it will work.
             buf = _C.array_int8(n_values)
-            values = list(values)
-            for n in range(n_values):
-                v = values[n]
-                if v >= 0:
-                    v &= 0x7f
-                else:
-                    v = abs(v) & 0x7f
-                    if v:
-                        v = 256 - v
-                    else:
-                        v = 128         # -128 in 2s complement
-                values[n] = v
 
         elif data_type == SDC.INT16:
             buf = _C.array_int16(n_values)
@@ -2538,17 +2524,7 @@ class SDS(object):
             buf = _C.array_byte(n_values)
 
         elif data_type == SDC.INT8:
-            # SWIG refuses negative values here. We found that if we
-            # pass them as byte values, it will work.
             buf = _C.array_int8(n_values)
-            if fill_val >= 0:
-                fill_val &= 0x7f
-            else:
-                fill_val = abs(fill_val) & 0x7f
-                if fill_val:
-                    fill_val = 256 - fill_val
-                else:
-                    fill_val = 128    # -128 in 2's complement
 
         elif data_type == SDC.INT16:
             buf = _C.array_int16(n_values)
@@ -2617,30 +2593,8 @@ class SDS(object):
             buf2 = _C.array_byte(n_values)
 
         elif data_type == SDC.INT8:
-            # SWIG refuses negative values here. We found that if we
-            # pass them as byte values, it will work.
             buf1 = _C.array_int8(n_values)
             buf2 = _C.array_int8(n_values)
-            v = min
-            if v >= 0:
-                v &= 0x7f
-            else:
-                v = abs(v) & 0x7f
-                if v:
-                    v = 256 - v
-                else:
-                    v = 128    # -128 in 2's complement
-            min = v
-            v = max
-            if v >= 0:
-                v &= 0x7f
-            else:
-                v = abs(v) & 0x7f
-                if v:
-                    v = 256 - v
-                else:
-                    v = 128    # -128 in 2's complement
-            max = v
 
         elif data_type == SDC.INT16:
             buf1 = _C.array_int16(n_values)
@@ -3113,21 +3067,7 @@ class SDim(object):
             buf = _C.array_byte(n_values)
 
         elif data_type == SDC.INT8:
-            # SWIG refuses negative values here. We found that if we
-            # pass them as byte values, it will work.
             buf = _C.array_int8(n_values)
-            scale = list(scale)
-            for n in range(n_values):
-                v = scale[n]
-                if v >= 0:
-                    v &= 0x7f
-                else:
-                    v = abs(v) & 0x7f
-                    if v:
-                        v = 256 - v
-                    else:
-                        v = 128         # -128 in 2's complement
-                scale[n] = v
 
         elif data_type == SDC.INT16:
             buf = _C.array_int16(n_values)

pyhdf/test_SD.py

@@ -5,6 +5,7 @@ import os
 import pyhdf.SD
 import tempfile
 from nose.tools import eq_
+from numpy.testing import assert_array_equal
 from pyhdf.SD import SDC
 
 def test_long_varname():
@@ -28,3 +29,31 @@ def test_long_varname():
         eq_(sds_name, name)
     finally:
         os.unlink(path)
+
+def test_negative_int8():
+    _, path = tempfile.mkstemp(suffix='.hdf', prefix='pyhdf_')
+    try:
+        sd = pyhdf.SD.SD(path, SDC.WRITE|SDC.CREATE|SDC.TRUNC)
+        data = np.zeros(shape=(20,20), dtype=np.int8)
+        sds = sd.create("testsds", SDC.INT8, data.shape)
+        sds.setfillvalue(-1)
+        eq_(sds.getfillvalue(), -1)
+
+        sds.setrange(-50, -30)
+        min, max = sds.getrange()
+        eq_(min, -50)
+        eq_(max, -30)
+
+        attr = sds.attr("testattr")
+        attr.set(SDC.INT8, -1)
+        eq_(attr.get(), -1)
+
+        dim = sds.dim(0)
+        scale = [-1]*20
+        dim.setscale(SDC.INT8, scale)
+        assert_array_equal(dim.getscale(), scale)
+
+        sds[:,:] = -40
+        sd.end()
+    finally:
+        os.unlink(path)

setup.py

@@ -27,6 +27,7 @@ from numpy.distutils.core import setup, Extension
 import sys
 import os
 import os.path as path
+import shlex
 
 CLASSIFIERS = """\
 Development Status :: 5 - Production/Stable
@@ -57,11 +58,29 @@ def _find_args(pat, env):
         pass
     return val
 
+# A Debian based linux distribution might be using libhdf4 (contains netcdf
+# routines) or libhdf4-alt (does not contain netcdf routines). This function
+# tries to detect if the alt version should be used.
+def _use_hdf4alt(libdirs):
+    if not sys.platform.startswith("linux"):
+        return False
+    libdirs.extend(os.environ.get("LD_LIBRARY_PATH", "").split(os.pathsep))
+    libdirs.append("/usr/lib")
+    libdirs.append("/usr/local/lib")
+    libdirs.append("/lib")
+    for d in libdirs:
+        if os.path.exists(os.path.join(d, "libdfalt.so")) and \
+           os.path.exists(os.path.join(d, "libmfhdfalt.so")):
+            return True
+    return False
+
 include_dirs = _find_args('-i', 'INCLUDE_DIRS')
 library_dirs = _find_args('-l', 'LIBRARY_DIRS')
 szip_installed = 'SZIP' in os.environ
 compress = 'NO_COMPRESS' not in os.environ
-extra_link_args = os.environ.get('LINK_ARGS', '')
+extra_link_args = None
+if "LINK_ARGS" in os.environ:
+    extra_link_args = shlex.split(os.environ["LINK_ARGS"])
 
 
 msg = 'Cannot proceed without the HDF4 library.  Please ' \
@@ -124,6 +143,8 @@ if sys.platform == 'win32':
 
 if sys.platform == 'win32':
     libraries = ["hm423m", "hd423m", "xdr_for_dll" ]
+elif _use_hdf4alt(library_dirs):
+    libraries = ["mfhdfalt", "dfalt"]
 else:
     libraries = ["mfhdf", "df"]
 
@@ -148,7 +169,7 @@ _hdfext = Extension('pyhdf._hdfext',
                     include_dirs = include_dirs,
                     extra_compile_args = extra_compile_args,
                     library_dirs = library_dirs,
-                    extra_link_args=[extra_link_args],
+                    extra_link_args=extra_link_args,
                     libraries = libraries,
                     )
 
@@ -166,7 +187,7 @@ setup(name         = 'python-hdf4',
       license      = 'MIT',
       long_description = "\n".join(DOCLINES[2:]),
       url          = 'https://github.com/fhs/python-hdf4',
-      version      = '0.9.1',
+      version      = '0.9.2',
       packages     = ['pyhdf'],
       ext_modules  = [_hdfext],
       data_files   = data_files,