use JIT compiled functions with fastmath flag where possible

Author: NimaSarajpoor

docs/Tutorial_DAMP.ipynb

@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "c9564cff",
    "metadata": {},
    "outputs": [],
@@ -55,6 +55,7 @@
     "import matplotlib.pyplot as plt\n",
     "import stumpy\n",
     "\n",
+    "from numba import njit\n",
     "from stumpy import core\n",
     "from scipy.io import loadmat"
    ]
@@ -69,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 3,
    "id": "409dad09",
    "metadata": {},
    "outputs": [],
@@ -128,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "c21c4587",
    "metadata": {},
    "outputs": [],
@@ -152,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 5,
    "id": "dd1f7b3d",
    "metadata": {},
    "outputs": [],
@@ -222,7 +223,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 6,
    "id": "5e45d72c",
    "metadata": {},
    "outputs": [
@@ -235,7 +236,7 @@
        "       [  0,  56]])"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -256,11 +257,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "id": "79663447",
    "metadata": {},
    "outputs": [],
    "source": [
+    "@njit(fastmath={\"nnan\", \"nsz\", \"arcp\", \"contract\", \"afn\", \"reassoc\"})\n",
     "def _backward_process(\n",
     "    T, \n",
     "    m, \n",
@@ -318,7 +320,7 @@
     "    \"\"\"\n",
     "    nn_distance = np.inf\n",
     "    for (start, stop) in chunks_range:\n",
-    "        QT = core.sliding_dot_product(\n",
+    "        QT = core._sliding_dot_product(\n",
     "            T[query_idx : query_idx + m], \n",
     "            T[start : stop],\n",
     "        )\n",
@@ -345,11 +347,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 8,
    "id": "c76317b5",
    "metadata": {},
    "outputs": [],
    "source": [
+    "@njit(fastmath={\"nnan\", \"nsz\", \"arcp\", \"contract\", \"afn\", \"reassoc\"})\n",
     "def _foreward_process(\n",
     "    T, \n",
     "    m,  \n",
@@ -404,7 +407,7 @@
     "    stop = min(start + lookahead, len(T))\n",
     "    \n",
     "    if stop - start >= m:\n",
-    "        QT = core.sliding_dot_product(T[query_idx : query_idx + m], T[start : stop])\n",
+    "        QT = core._sliding_dot_product(T[query_idx : query_idx + m], T[start : stop])\n",
     "        D = core._mass(\n",
     "            T[query_idx : query_idx + m],\n",
     "            T[start : stop],\n",
@@ -424,7 +427,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 9,
    "id": "769bddad",
    "metadata": {},
    "outputs": [],
@@ -512,7 +515,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 10,
    "id": "2cfbc771",
    "metadata": {},
    "outputs": [],
@@ -527,7 +530,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 11,
    "id": "a935f31f",
    "metadata": {},
    "outputs": [
@@ -537,7 +540,7 @@
      "text": [
       "discord_dist:  8.500883427933504\n",
       "discord_index:  209\n",
-      "running time [sec]:  4.881464958190918\n"
+      "running time [sec]:  4.886792898178101\n"
      ]
     }
    ],
@@ -557,7 +560,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 12,
    "id": "2b461592",
    "metadata": {},
    "outputs": [
@@ -567,7 +570,7 @@
      "text": [
       "discord_dist:  8.500883427933504\n",
       "discord_index:  209\n",
-      "running time [sec]:  2.2210960388183594\n"
+      "running time [sec]:  0.4022231101989746\n"
      ]
     }
    ],
@@ -596,7 +599,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 13,
    "id": "d8e9fa63",
    "metadata": {},
    "outputs": [],
@@ -611,7 +614,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 14,
    "id": "263bca9c",
    "metadata": {},
    "outputs": [
@@ -621,7 +624,7 @@
      "text": [
       "discord_dist:  7.606279752022369\n",
       "discord_index:  8109\n",
-      "running time [sec]:  4.996989965438843\n"
+      "running time [sec]:  5.08968710899353\n"
      ]
     }
    ],
@@ -642,7 +645,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 15,
    "id": "78d09bda",
    "metadata": {},
    "outputs": [
@@ -652,7 +655,7 @@
      "text": [
       "discord_dist:  7.606279752022363\n",
       "discord_index:  8109\n",
-      "running time [sec]:  6.67956805229187\n"
+      "running time [sec]:  2.9500508308410645\n"
      ]
     }
    ],
@@ -681,7 +684,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 16,
    "id": "6d64f488",
    "metadata": {},
    "outputs": [],
@@ -696,7 +699,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 17,
    "id": "159e03dc",
    "metadata": {},
    "outputs": [
@@ -706,7 +709,7 @@
      "text": [
       "discord_dist:  29.42331306408431\n",
       "discord_index:  6110\n",
-      "running time [sec]:  5.483174085617065\n"
+      "running time [sec]:  5.911180019378662\n"
      ]
     }
    ],
@@ -727,7 +730,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 18,
    "id": "9ef28e10",
    "metadata": {},
    "outputs": [
@@ -737,7 +740,7 @@
      "text": [
       "discord_dist:  29.423313064084333\n",
       "discord_index:  6110\n",
-      "running time [sec]:  55.60335397720337\n"
+      "running time [sec]:  34.58638381958008\n"
      ]
     }
    ],