From 8ff627109af7c3e041720ee391e8d0ef06a803f6 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Tue, 20 Jul 2021 16:26:03 -0400
Subject: [PATCH] fix: fix the breaking change in hmmlearn (#1239)

---
 reacnetgenerator/_detect.py    | 2 +-
 reacnetgenerator/_hmmfilter.py | 3 ++-
 reacnetgenerator/_matrix.py    | 4 ++--
 reacnetgenerator/utils_np.pyx  | 4 ++--
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/reacnetgenerator/_detect.py b/reacnetgenerator/_detect.py
index d2a4db5e8..88dc50935 100644
--- a/reacnetgenerator/_detect.py
+++ b/reacnetgenerator/_detect.py
@@ -165,7 +165,7 @@ def _readNfunc(self, f):
                         iscompleted = True
                         stepaindex = index
                     N = [int(s) for s in line.split() if s.isdigit()][0]
-                    atomtype = np.zeros(N, dtype=np.int)
+                    atomtype = np.zeros(N, dtype=int)
             else:
                 s = line.split()
                 atomtype[int(s[0])-1] = int(s[1])-1
diff --git a/reacnetgenerator/_hmmfilter.py b/reacnetgenerator/_hmmfilter.py
index 7fb41ef85..641d51096 100644
--- a/reacnetgenerator/_hmmfilter.py
+++ b/reacnetgenerator/_hmmfilter.py
@@ -21,6 +21,7 @@
 import tempfile
 from contextlib import ExitStack
 
+import numpy as np
 from hmmlearn import hmm
 
 from .utils import WriteBuffer, appendIfNotNone, bytestolist, listtobytes, run_mp, SharedRNGData
@@ -60,7 +61,7 @@ def _getoriginandhmm(self, item):
             origin) if self.getoriginfile else None
         hmmbytes = None
         if self.runHMM:
-            hmmsignal = self._model.predict(origin)
+            hmmsignal = self._model.predict(origin).astype(np.int8)
             if check_zero_signal(hmmsignal) or self.printfiltersignal:
                 hmmbytes = listtobytes(hmmsignal)
         return originbytes, hmmbytes, line_c
diff --git a/reacnetgenerator/_matrix.py b/reacnetgenerator/_matrix.py
index 7a1b7e69a..33b5c7291 100644
--- a/reacnetgenerator/_matrix.py
+++ b/reacnetgenerator/_matrix.py
@@ -71,8 +71,8 @@ def _printtable(self, allroute, timeaxis=None):
                     newreactions.append(reac)
             sortedreactions = newreactions
 
-        table = np.zeros((maxsize, maxsize), dtype=np.int)
-        reactionnumber = np.zeros((2), dtype=np.int)
+        table = np.zeros((maxsize, maxsize), dtype=int)
+        reactionnumber = np.zeros((2), dtype=int)
         with open(self.reactionfilename if timeaxis is None else f"{self.reactionfilename}.{timeaxis}", 'w') as f:
             for reaction, n_reaction in sortedreactions:
                 f.write(f"{n_reaction} {'->'.join(reaction)}\n")
diff --git a/reacnetgenerator/utils_np.pyx b/reacnetgenerator/utils_np.pyx
index bad4d0034..4bfc41b23 100644
--- a/reacnetgenerator/utils_np.pyx
+++ b/reacnetgenerator/utils_np.pyx
@@ -7,7 +7,7 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
-DTYPE = np.int
+DTYPE = int
 ctypedef np.int_t DTYPE_t
 DTYPE8 = np.int8
 ctypedef np.int8_t DTYPE8_t
@@ -31,7 +31,7 @@ cpdef idx_to_signal(DTYPE_t[:] idx, int step):
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cpdef check_zero_signal(DTYPE_t[:] signal):
+cpdef check_zero_signal(DTYPE8_t[:] signal):
     """Benchmark for 1,000,000 loops (1000/2000):
     Cython: 1.45 s
     Python: 3.67 s