From bd745d4704e69643cace2b3b143cace8308c770c Mon Sep 17 00:00:00 2001
From: Bryn Keller <xoltar@xoltar.org>
Date: Wed, 27 Feb 2019 20:41:41 -0800
Subject: [PATCH] Prep for upload

---
 example/RIVET Python API Tour.ipynb | 48 ++++++++++++++---------------
 pyrivet/rivet.py                    |  4 +--
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/example/RIVET Python API Tour.ipynb b/example/RIVET Python API Tour.ipynb
index 05213a6..e481155 100644
--- a/example/RIVET Python API Tour.ipynb	
+++ b/example/RIVET Python API Tour.ipynb	
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 27,
    "metadata": {
     "collapsed": true
    },
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -50,7 +50,7 @@
        " 'points5.txt']"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 28,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -65,7 +65,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [
     {
@@ -74,7 +74,7 @@
        "'../../rivet/data/Test_Point_Clouds/circle_data_60pts_codensity.txt.H1_x20_y20.rivet'"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 29,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -97,7 +97,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
@@ -107,7 +107,7 @@
        " ((45.0, 1.0), Barcode([Bar(5.65685, 5.68564, 1)]))]"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -115,7 +115,7 @@
    "source": [
     "with open(computed_file_path, 'rb') as f:\n",
     "    computed_data = f.read()\n",
-    "\n",
+    "    \n",
     "codes = rivet.barcodes(computed_data, [\n",
     "    (45, 0), # 45 degrees, offset 0\n",
     "    (45, 1), # 45 degrees, offset 1\n",
@@ -132,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -141,7 +141,7 @@
        "Barcode([Bar(6.98695, 7.68564, 1), Bar(5.65685, 6.28825, 1)])"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 31,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -160,7 +160,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 32,
    "metadata": {},
    "outputs": [
     {
@@ -170,7 +170,7 @@
        "       [5.65685, 6.28825, 1.     ]])"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 32,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -188,7 +188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [
     {
@@ -204,7 +204,7 @@
        " [1.]], xi_0=[(0, 0, 5)], xi_1=[(0, 1, 1), (0, 2, 1), (0, 3, 1), (0, 5, 1)], xi_2=[])"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -238,7 +238,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [
     {
@@ -254,7 +254,7 @@
        " [1. 2. 2. 2. 2. 2.]], xi_0=[(0, 0, 1), (1, 0, 2), (2, 0, 1), (3, 0, 1), (4, 0, 1), (5, 0, 1)], xi_1=[(1, 1, 1), (2, 6, 1), (3, 2, 1), (3, 5, 1), (4, 3, 1), (5, 4, 1)], xi_2=[(3, 6, 1)])"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 34,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -292,7 +292,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 35,
    "metadata": {},
    "outputs": [
     {
@@ -328,7 +328,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 36,
    "metadata": {},
    "outputs": [
     {
@@ -360,16 +360,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x1110b09b0>"
+       "<matplotlib.image.AxesImage at 0x1143fa2e8>"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 37,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -404,16 +404,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 38,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x111826e80>"
+       "<matplotlib.image.AxesImage at 0x114cc9908>"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 38,
      "metadata": {},
      "output_type": "execute_result"
     },
diff --git a/pyrivet/rivet.py b/pyrivet/rivet.py
index c90a849..b761989 100644
--- a/pyrivet/rivet.py
+++ b/pyrivet/rivet.py
@@ -231,8 +231,8 @@ def compute_file(input_name, output_name=None, homology=0, x=0, y=0, threads=1):
         cmd = "%s %s %s -H %d -x %d -y %d --redis %s --threads %d" % \
               (rivet_client, input_name, output_name, homology, x, y, server_url, threads)
     else:
-        cmd = "%s %s %s -H %d -x %d -y %d -f msgpack --num_threads %s" % \
-              (rivet_executable, input_name, output_name, homology, x, y, threads)
+        cmd = "%s %s %s -H %d -x %d -y %d -f msgpack" % \
+              (rivet_executable, input_name, output_name, homology, x, y)
     subprocess.check_output(shlex.split(cmd))
     return output_name