diff --git a/docs/release.rst b/docs/release.rst index 5ce6bcdd..e82dac06 100644 --- a/docs/release.rst +++ b/docs/release.rst @@ -29,6 +29,9 @@ Release notes * Add codec :class:`numcodecs.gzip.GZip` to replace ``gzip`` alias for ``zlib``, which was incorrect (by :user:`Jan Funke `; :issue:`87`). +* Corrects handling of ``NaT`` in ``datetime64`` and ``timedelta64`` in various + compressors (by :user:`John Kirkham `; :issue:`127`). + .. _release_0.5.5: 0.5.5 diff --git a/fixture/blosc/array.09.npy b/fixture/blosc/array.09.npy new file mode 100644 index 00000000..097aac9a Binary files /dev/null and b/fixture/blosc/array.09.npy differ diff --git a/fixture/blosc/array.10.npy b/fixture/blosc/array.10.npy new file mode 100644 index 00000000..43dfce29 Binary files /dev/null and b/fixture/blosc/array.10.npy differ diff --git a/fixture/blosc/array.11.npy b/fixture/blosc/array.11.npy new file mode 100644 index 00000000..32cdcf08 Binary files /dev/null and b/fixture/blosc/array.11.npy differ diff 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00000000..24f52e5e Binary files /dev/null and b/fixture/zstd/codec.06/encoded.09.dat differ diff --git a/fixture/zstd/codec.06/encoded.10.dat b/fixture/zstd/codec.06/encoded.10.dat new file mode 100644 index 00000000..782b7459 Binary files /dev/null and b/fixture/zstd/codec.06/encoded.10.dat differ diff --git a/fixture/zstd/codec.06/encoded.11.dat b/fixture/zstd/codec.06/encoded.11.dat new file mode 100644 index 00000000..83198897 Binary files /dev/null and b/fixture/zstd/codec.06/encoded.11.dat differ diff --git a/fixture/zstd/codec.06/encoded.12.dat b/fixture/zstd/codec.06/encoded.12.dat new file mode 100644 index 00000000..795cf890 Binary files /dev/null and b/fixture/zstd/codec.06/encoded.12.dat differ diff --git a/numcodecs/compat.py b/numcodecs/compat.py index f3b6e95c..cd749a32 100644 --- a/numcodecs/compat.py +++ b/numcodecs/compat.py @@ -102,5 +102,5 @@ def ensure_text(l, encoding='utf-8'): def handle_datetime(buf): if hasattr(buf, 'dtype') and buf.dtype.kind in 'Mm': - return buf.view('u8') + return buf.view('i8') return buf diff --git a/numcodecs/compat_ext.c b/numcodecs/compat_ext.c index 3e7df9df..b0ef4a45 100644 --- a/numcodecs/compat_ext.c +++ b/numcodecs/compat_ext.c @@ -1451,7 +1451,7 @@ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_MemoryError; static const char __pyx_k_O[] = "O"; static const char __pyx_k_Mm[] = "Mm"; -static const char __pyx_k_u8[] = "u8"; +static const char __pyx_k_i8[] = "i8"; static const char __pyx_k_PY2[] = "PY2"; static const char __pyx_k_obj[] = "obj"; static const char __pyx_k_sys[] = "sys"; @@ -1496,6 +1496,7 @@ static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_flags; static PyObject *__pyx_n_s_getstate; +static PyObject *__pyx_n_s_i8; static PyObject *__pyx_n_s_import; static PyObject *__pyx_n_s_itemsize; static PyObject *__pyx_n_s_kind; @@ -1512,7 +1513,6 @@ static PyObject *__pyx_n_s_setstate; static PyObject *__pyx_n_s_setstate_cython; static PyObject *__pyx_n_s_sys; static PyObject *__pyx_n_s_test; -static PyObject *__pyx_n_s_u8; static PyObject *__pyx_n_s_version_info; static PyObject *__pyx_n_s_view; static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9numcodecs_10compat_ext_Buffer *__pyx_v_self, PyObject *__pyx_v_obj, PyObject *__pyx_v_flags); /* proto */ @@ -1628,7 +1628,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 * self.released = False * if hasattr(obj, 'dtype'): # <<<<<<<<<<<<<< * if obj.dtype.kind in 'Mm': - * obj = obj.view('u8') + * obj = obj.view('i8') */ __pyx_t_1 = __Pyx_HasAttr(__pyx_v_obj, __pyx_n_s_dtype); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 22, __pyx_L1_error) __pyx_t_2 = (__pyx_t_1 != 0); @@ -1638,7 +1638,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 * self.released = False * if hasattr(obj, 'dtype'): * if obj.dtype.kind in 'Mm': # <<<<<<<<<<<<<< - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': */ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_obj, __pyx_n_s_dtype); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 23, __pyx_L1_error) @@ -1654,7 +1654,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 /* "numcodecs/compat_ext.pyx":24 * if hasattr(obj, 'dtype'): * if obj.dtype.kind in 'Mm': - * obj = obj.view('u8') # <<<<<<<<<<<<<< + * obj = obj.view('i8') # <<<<<<<<<<<<<< * elif obj.dtype.kind == 'O': * raise ValueError('cannot obtain buffer from object array') */ @@ -1670,7 +1670,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 __Pyx_DECREF_SET(__pyx_t_3, function); } } - __pyx_t_4 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_5, __pyx_n_s_u8) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_n_s_u8); + __pyx_t_4 = (__pyx_t_5) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_5, __pyx_n_s_i8) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_n_s_i8); __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 24, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); @@ -1682,7 +1682,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 * self.released = False * if hasattr(obj, 'dtype'): * if obj.dtype.kind in 'Mm': # <<<<<<<<<<<<<< - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': */ goto __pyx_L4; @@ -1690,7 +1690,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 /* "numcodecs/compat_ext.pyx":25 * if obj.dtype.kind in 'Mm': - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': # <<<<<<<<<<<<<< * raise ValueError('cannot obtain buffer from object array') * if PY2 and isinstance(obj, array.array): @@ -1705,7 +1705,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 if (unlikely(__pyx_t_1)) { /* "numcodecs/compat_ext.pyx":26 - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': * raise ValueError('cannot obtain buffer from object array') # <<<<<<<<<<<<<< * if PY2 and isinstance(obj, array.array): @@ -1719,7 +1719,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 /* "numcodecs/compat_ext.pyx":25 * if obj.dtype.kind in 'Mm': - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': # <<<<<<<<<<<<<< * raise ValueError('cannot obtain buffer from object array') * if PY2 and isinstance(obj, array.array): @@ -1732,7 +1732,7 @@ static int __pyx_pf_9numcodecs_10compat_ext_6Buffer___cinit__(struct __pyx_obj_9 * self.released = False * if hasattr(obj, 'dtype'): # <<<<<<<<<<<<<< * if obj.dtype.kind in 'Mm': - * obj = obj.view('u8') + * obj = obj.view('i8') */ } @@ -3080,6 +3080,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, {&__pyx_n_s_flags, __pyx_k_flags, sizeof(__pyx_k_flags), 0, 0, 1, 1}, {&__pyx_n_s_getstate, __pyx_k_getstate, sizeof(__pyx_k_getstate), 0, 0, 1, 1}, + {&__pyx_n_s_i8, __pyx_k_i8, sizeof(__pyx_k_i8), 0, 0, 1, 1}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, {&__pyx_n_s_itemsize, __pyx_k_itemsize, sizeof(__pyx_k_itemsize), 0, 0, 1, 1}, {&__pyx_n_s_kind, __pyx_k_kind, sizeof(__pyx_k_kind), 0, 0, 1, 1}, @@ -3096,7 +3097,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, {&__pyx_n_s_sys, __pyx_k_sys, sizeof(__pyx_k_sys), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, - {&__pyx_n_s_u8, __pyx_k_u8, sizeof(__pyx_k_u8), 0, 0, 1, 1}, {&__pyx_n_s_version_info, __pyx_k_version_info, sizeof(__pyx_k_version_info), 0, 0, 1, 1}, {&__pyx_n_s_view, __pyx_k_view, sizeof(__pyx_k_view), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} @@ -3115,7 +3115,7 @@ static CYTHON_SMALL_CODE int __Pyx_InitCachedConstants(void) { __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); /* "numcodecs/compat_ext.pyx":26 - * obj = obj.view('u8') + * obj = obj.view('i8') * elif obj.dtype.kind == 'O': * raise ValueError('cannot obtain buffer from object array') # <<<<<<<<<<<<<< * if PY2 and isinstance(obj, array.array): diff --git a/numcodecs/compat_ext.pyx b/numcodecs/compat_ext.pyx index 6cd3f710..c17b8648 100644 --- a/numcodecs/compat_ext.pyx +++ b/numcodecs/compat_ext.pyx @@ -21,7 +21,7 @@ cdef class Buffer: self.released = False if hasattr(obj, 'dtype'): if obj.dtype.kind in 'Mm': - obj = obj.view('u8') + obj = obj.view('i8') elif obj.dtype.kind == 'O': raise ValueError('cannot obtain buffer from object array') if PY2 and isinstance(obj, array.array): diff --git a/numcodecs/tests/test_blosc.py b/numcodecs/tests/test_blosc.py index b72ae09d..4af485e5 100644 --- a/numcodecs/tests/test_blosc.py +++ b/numcodecs/tests/test_blosc.py @@ -47,6 +47,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_bz2.py b/numcodecs/tests/test_bz2.py index 984bdced..db48ecf0 100644 --- a/numcodecs/tests/test_bz2.py +++ b/numcodecs/tests/test_bz2.py @@ -34,6 +34,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_gzip.py b/numcodecs/tests/test_gzip.py index bba2bcf7..593cfafc 100644 --- a/numcodecs/tests/test_gzip.py +++ b/numcodecs/tests/test_gzip.py @@ -36,6 +36,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_lz4.py b/numcodecs/tests/test_lz4.py index 72c420af..1b4ceabd 100644 --- a/numcodecs/tests/test_lz4.py +++ b/numcodecs/tests/test_lz4.py @@ -37,6 +37,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_lzma.py b/numcodecs/tests/test_lzma.py index 67fef7be..59c462fe 100644 --- a/numcodecs/tests/test_lzma.py +++ b/numcodecs/tests/test_lzma.py @@ -42,6 +42,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_zlib.py b/numcodecs/tests/test_zlib.py index 3ad4381c..b2749246 100644 --- a/numcodecs/tests/test_zlib.py +++ b/numcodecs/tests/test_zlib.py @@ -36,6 +36,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ] diff --git a/numcodecs/tests/test_zstd.py b/numcodecs/tests/test_zstd.py index 7edcd6af..7336aea6 100644 --- a/numcodecs/tests/test_zstd.py +++ b/numcodecs/tests/test_zstd.py @@ -37,6 +37,10 @@ np.random.randint(0, 2**60, size=1000, dtype='u8').view('m8[ns]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('M8[m]'), np.random.randint(0, 2**25, size=1000, dtype='u8').view('m8[m]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('M8[ns]'), + (-np.random.randint(-2**30, 2**30, size=1000, dtype='i8')).view('m8[ns]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('M8[m]'), + (-np.random.randint(-2**12, 2**13, size=1000, dtype='i8')).view('m8[m]'), ]