Restructuring TARDIS Documentation (Issue #948)

docs/configuration/index.rst

@@ -13,6 +13,7 @@ and pages provide more details concerning the TARDIS configuration process.
 .. toctree::
   :maxdepth: 2
 
+  integrator
   configuration
   config_validator
   read_configuration

docs/installation.rst

@@ -114,11 +114,11 @@ To compile TARDIS for parallel execution::
 Installation Troubles (FAQ)
 ===========================
 
-We highly encourage with any installation problems to try the recommended install
-method because this often fix problems. Here are some common problems when
+With any installation problems, we highly encourage you to try the recommended 
+installation method because this often fixes problems. Here are some common problems when
 installing and their fixes:
 
-**Problem:** While building tardis via ``python setup.py`` build you
+**Problem:** While building tardis via ``python setup.py build`` you
 may encounter the following error::
 
     error: tardis/montecarlo/montecarlo.c: Could not find C file tardis/montecarlo/montecarlo.c for Cython file tardis/montecarlo/montecarlo.pyx when building extension tardis.montecarlo.montecarlo. Cython must be installed to build from a git checkout.

docs/physics/plasma/plasma.rst

@@ -49,7 +49,7 @@ Here's an example how to instantiate a simple base plasma::
     >>> from tardis.io import atomic
     >>> atom_data = atomic.AtomData.from_hdf()
     >>> my_plasma = plasma.BasePlasma({'Fe':0.5, 'Ni':0.5}, 10000, 1e-13, atom_data)
-    >>> print my_plasma.abundances
+    >>> print(my_plasma.abundances)
     atomic_number abundance_fraction number_density
     ------------- ------------------ --------------
                28                0.5  513016973.936

docs/physics/plasma/plasma_plots/nebular_ionization_balance.py

@@ -90,7 +90,7 @@
 #Plotting the ion fractions
 
 for ion_number in [0, 1, 2, 3]:
-    print "w=0.5"
+    print("w=0.5")
     current_ion_density = ion_number_densities.ix[14, ion_number]
     ax1.plot(current_ion_density.index, current_ion_density.values, '%s--' % ion_colors[ion_number],
              label='Si %s W=0.5' % tardis.util.base.int_to_roman(ion_number + 1).upper())

docs/running/index.rst

@@ -1,6 +1,6 @@
-**************
-Running TARDIS
-**************
+*************************
+TARDIS Configuration File
+*************************
 
 The TARDIS code needs three components to calculate spectra:
 

docs/running/interaction/hdf_writer.ipynb

@@ -15,9 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from tardis.io.util import HDFWriterMixin\n",
@@ -34,9 +32,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -67,9 +63,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "obj.to_hdf(file_path='test.hdf', path='test')\n",
@@ -86,9 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -104,7 +96,7 @@
    "source": [
     "#Read HDF file\n",
     "with pd.HDFStore('test.hdf','r') as data:\n",
-    "    print data\n",
+    "    print(data)\n",
     "    #print data['/test/mock_setup/property1']"
    ]
   },
@@ -157,9 +149,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -176,7 +166,7 @@
    "source": [
     "#Read HDF file\n",
     "with pd.HDFStore('nested_test.hdf','r') as data:\n",
-    "    print data"
+    "    print(data)"
    ]
   },
   {
@@ -231,9 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -249,27 +237,27 @@
     "obj3 = DemoClass('random_string')\n",
     "obj3.to_hdf('demo_class.hdf')\n",
     "with pd.HDFStore('demo_class.hdf','r') as data:\n",
-    "    print data"
+    "    print(data)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.13"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.7"
   }
  },
  "nbformat": 4,

docs/running/interaction/to_hdf.ipynb

@@ -17,9 +17,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -62,9 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -203,9 +199,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -254,7 +248,6 @@
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {
-    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -328,7 +321,7 @@
    "source": [
     "import pandas as pd\n",
     "data = pd.HDFStore('/tmp/full_example.hdf')\n",
-    "print data"
+    "print(data)"
    ]
   },
   {
@@ -341,9 +334,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -375,7 +366,7 @@
     }
    ],
    "source": [
-    "print data['/simulation/model/homologous_density/density_0']"
+    "print(data['/simulation/model/homologous_density/density_0'])"
    ]
   },
   {
@@ -392,9 +383,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -405,7 +394,7 @@
     }
    ],
    "source": [
-    "print data['/simulation/model/scalars']['t_inner']"
+    "print(data['/simulation/model/scalars']['t_inner'])"
    ]
   },
   {
@@ -427,9 +416,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "simulation.plasma.to_hdf('/tmp/plasma_output.hdf', path='parent')"
@@ -439,7 +426,6 @@
    "cell_type": "code",
    "execution_count": 8,
    "metadata": {
-    "collapsed": false,
     "scrolled": true
    },
    "outputs": [
@@ -489,7 +475,7 @@
    "source": [
     "import pandas\n",
     "with pandas.HDFStore('/tmp/plasma_output.hdf') as data:\n",
-    "    print data"
+    "    print(data)"
    ]
   },
   {
@@ -502,9 +488,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from tardis.plasma.properties.base import Input\n",
@@ -514,9 +498,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -535,7 +517,7 @@
    "source": [
     "import pandas\n",
     "with pandas.HDFStore('/tmp/plasma_input_output.hdf') as data:\n",
-    "    print data"
+    "    print(data)"
    ]
   },
   {
@@ -549,9 +531,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "simulation.model.to_hdf('/tmp/model_output.hdf')"
@@ -568,9 +548,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "simulation.runner.to_hdf('/tmp/runner_output.hdf')"
@@ -579,9 +557,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -612,29 +588,29 @@
    "source": [
     "import pandas\n",
     "with pandas.HDFStore('/tmp/runner_output.hdf') as data:\n",
-    "    print data"
+    "    print(data)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.13"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }