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float64_t support removed #43

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12 changes: 6 additions & 6 deletions seqlearn/_decode/bestfirst.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -6,16 +6,16 @@ import numpy as np

np.import_array()

cdef np.float64_t NEGINF = -np.inf
cdef np.float64 NEGINF = -np.inf


@cython.boundscheck(False)
@cython.wraparound(False)
def bestfirst(np.ndarray[ndim=2, dtype=np.float64_t] score,
def bestfirst(np.ndarray[ndim=2, dtype=np.float64] score,
trans_score,
np.ndarray[ndim=2, dtype=np.float64_t] trans,
np.ndarray[ndim=1, dtype=np.float64_t, mode="c"] init,
np.ndarray[ndim=1, dtype=np.float64_t, mode="c"] final):
np.ndarray[ndim=2, dtype=np.float64] trans,
np.ndarray[ndim=1, dtype=np.float64, mode="c"] init,
np.ndarray[ndim=1, dtype=np.float64, mode="c"] final):
"""First-order heuristic best-first decoder.

See viterbi for the arguments. score may be overwritten.
Expand All @@ -24,7 +24,7 @@ def bestfirst(np.ndarray[ndim=2, dtype=np.float64_t] score,

cdef:
np.ndarray[ndim=1, dtype=np.npy_intp, mode="c"] path
np.float64_t candidate, maxval
np.float64 candidate, maxval
np.npy_intp i, j, maxind, n_samples, n_states

if trans_score is not None:
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14 changes: 7 additions & 7 deletions seqlearn/_decode/viterbi.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,16 @@ import numpy as np

np.import_array()

cdef np.float64_t NEGINF = -np.inf
cdef np.float64 NEGINF = -np.inf


@cython.boundscheck(False)
@cython.wraparound(False)
def viterbi(np.ndarray[ndim=2, dtype=np.float64_t] score,
np.ndarray[ndim=3, dtype=np.float64_t] trans_score,
np.ndarray[ndim=2, dtype=np.float64_t] b_trans,
np.ndarray[ndim=1, dtype=np.float64_t] init,
np.ndarray[ndim=1, dtype=np.float64_t] final):
def viterbi(np.ndarray[ndim=2, dtype=np.float64] score,
np.ndarray[ndim=3, dtype=np.float64] trans_score,
np.ndarray[ndim=2, dtype=np.float64] b_trans,
np.ndarray[ndim=1, dtype=np.float64] init,
np.ndarray[ndim=1, dtype=np.float64] final):
"""First-order Viterbi algorithm.

Parameters
Expand All @@ -41,7 +41,7 @@ def viterbi(np.ndarray[ndim=2, dtype=np.float64_t] score,

cdef np.ndarray[ndim=2, dtype=np.npy_intp, mode='c'] backp
cdef np.ndarray[ndim=1, dtype=np.npy_intp, mode='c'] path
cdef np.float64_t candidate, maxval
cdef np.float64 candidate, maxval
cdef np.npy_intp i, j, k, n_samples, n_states

n_samples, n_states = score.shape[0], score.shape[1]
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4 changes: 2 additions & 2 deletions seqlearn/_utils/safeadd.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ np.import_array()

@cython.boundscheck(False)
@cython.wraparound(False)
def safe_add(np.ndarray[ndim=2, dtype=np.float64_t] A, B):
def safe_add(np.ndarray[ndim=2, dtype=np.float] A, B):
"""A += B where B is a sparse (CSR or CSC) matrix.

__rsub__ on a sparse matrix densifies prior to subtracting, making it
Expand All @@ -20,7 +20,7 @@ def safe_add(np.ndarray[ndim=2, dtype=np.float64_t] A, B):
"""

cdef:
np.ndarray[ndim=1, dtype=np.float64_t, mode="c"] data
np.ndarray[ndim=1, dtype=np.float, mode="c"] data
np.ndarray[ndim=1, dtype=int, mode="c"] indices
np.ndarray[ndim=1, dtype=int, mode="c"] indptr

Expand Down