From 244161691fdfec430a62c90ed60abcf8ace3911b Mon Sep 17 00:00:00 2001
From: David Straub <david.straub@tum.de>
Date: Wed, 10 Jan 2018 10:13:34 +0100
Subject: [PATCH] Small fixes after YETI

---
 1 Installation.ipynb        | 24 ++++++++---------
 2 Basic concepts.ipynb      | 51 +++++++++++++++++--------------------
 3 Wilson coefficients.ipynb | 14 +---------
 4 Fits.ipynb                | 18 ++++++++-----
 5 Extending.ipynb           |  2 +-
 requirements.txt            |  2 ++
 6 files changed, 51 insertions(+), 60 deletions(-)

diff --git a/1 Installation.ipynb b/1 Installation.ipynb
index 3cc8cd9..31c94e7 100644
--- a/1 Installation.ipynb	
+++ b/1 Installation.ipynb	
@@ -365,6 +365,17 @@
     "Unit tests play an important role in making the code as reliable as possible and making development easier "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
+    "(If the `nosetests` command doesn't work on your system, try running `python3 -m nose flavio` instead)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -376,7 +387,7 @@
     "### Installing Jupyter & IPython\n",
     "\n",
     "```bash\n",
-    "pip3 install jupyter --user\n",
+    "pip3 install ipython jupyter --user\n",
     "```\n",
     "\n",
     "... and the run it:\n",
@@ -421,17 +432,6 @@
     "4. [Fits](4 Fits.ipynb) (statistical inference)\n",
     "5. [Extending flavio](5 Extending.ipynb) (adding new observables)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "slideshow": {
-     "slide_type": "slide"
-    }
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/2 Basic concepts.ipynb b/2 Basic concepts.ipynb
index 212f9ec..4864b6d 100644
--- a/2 Basic concepts.ipynb	
+++ b/2 Basic concepts.ipynb	
@@ -380,8 +380,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%time flavio.sm_uncertainty('<P5p>(B0->K*mumu)',\n",
-    "                            q2min=1, q2max=6, N=100)"
+    "%%time\n",
+    "flavio.sm_uncertainty('<P5p>(B0->K*mumu)',\n",
+    "                      q2min=1, q2max=6, N=100)"
    ]
   },
   {
@@ -390,8 +391,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%time flavio.sm_uncertainty('<P5p>(B0->K*mumu)',\n",
-    "                            q2min=1, q2max=6, N=100, threads=2)"
+    "%%time\n",
+    "flavio.sm_uncertainty('<P5p>(B0->K*mumu)',\n",
+    "                      q2min=1, q2max=6, N=100, threads=2)"
    ]
   },
   {
@@ -421,11 +423,24 @@
    "cell_type": "markdown",
    "metadata": {
     "slideshow": {
-     "slide_type": "fragment"
+     "slide_type": "subslide"
     }
    },
    "source": [
-    "This can now be visualized:"
+    "This can now be visualized.\n",
+    "\n",
+    "Necessary imports:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import flavio.plots as fpl\n",
+    "%matplotlib inline\n",
+    "%config InlineBackend.figure_format = 'svg'"
    ]
   },
   {
@@ -524,36 +539,18 @@
     "### Things to do with measurements: e.g. plots"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Necessary imports"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import flavio.plots as fpl\n",
-    "import matplotlib.pyplot as plt\n",
-    "%matplotlib inline\n",
-    "%config InlineBackend.figure_format = 'svg'"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "scrolled": true,
+    "scrolled": false,
     "slideshow": {
-     "slide_type": "subslide"
+     "slide_type": ""
     }
    },
    "outputs": [],
    "source": [
+    "import matplotlib.pyplot as plt\n",
     "obs = '<P5p>(B0->K*mumu)';\n",
     "fpl.bin_plot_exp(obs, col_dict={'LHCb': 'C0', 'CMS': 'C1', 'ATLAS': 'C2'});\n",
     "plt.legend()\n",
diff --git a/3 Wilson coefficients.ipynb b/3 Wilson coefficients.ipynb
index c4991aa..d7c2dce 100644
--- a/3 Wilson coefficients.ipynb	
+++ b/3 Wilson coefficients.ipynb	
@@ -404,7 +404,7 @@
    },
    "outputs": [],
    "source": [
-    "! cat 'SPheno.spc.MSSM'"
+    "! cat 'files/SPheno.spc.MSSM'"
    ]
   },
   {
@@ -495,18 +495,6 @@
    "source": [
     "Next: [Fits](4 Fits.ipynb)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "scrolled": true,
-    "slideshow": {
-     "slide_type": "slide"
-    }
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/4 Fits.ipynb b/4 Fits.ipynb
index 65a7221..db12a7d 100644
--- a/4 Fits.ipynb	
+++ b/4 Fits.ipynb	
@@ -804,6 +804,17 @@
     "Plotting the result"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fpl.density_contour_joint(scan.result[:, -2], scan.result[:, -1]);\n",
+    "plt.xlim([-0.07, 0.07]);\n",
+    "plt.ylim([-2, 2]);"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -900,13 +911,6 @@
    "source": [
     "Next: [Extending flavio](5 Extending.ipynb)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/5 Extending.ipynb b/5 Extending.ipynb
index 2d7b27f..d04eb0b 100644
--- a/5 Extending.ipynb	
+++ b/5 Extending.ipynb	
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
+   "execution_count": null,
    "metadata": {
     "slideshow": {
      "slide_type": ""
diff --git a/requirements.txt b/requirements.txt
index cd3023c..53ff708 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,3 +4,5 @@ flavio==0.27
 matplotlib>=2.1
 nose
 RISE
+emcee
+iminuit