doc: cleaned documentation and fixed Siesta link to Gitlab

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

README.md

@@ -145,8 +145,8 @@ Links to external and internal sites.
 [sisl-gitter]: https://gitter.im/sisl-tool/Lobby
 [issue]: https://github.com/zerothi/sisl/issues
 [pr]: https://github.com/zerothi/sisl/pulls
-[siesta]: https://launchpad.net/siesta
-[tbtrans]: https://launchpad.net/siesta
+[siesta]: https://gitlab.com/siesta-project/siesta
+[tbtrans]: https://gitlab.com/siesta-project/siesta
 [workshop]: https://github.com/zerothi/ts-tbt-sisl-tutorial
 [doi]: http://dx.doi.org/10.5281/zenodo.597181
 [lgpl]: http://www.gnu.org/licenses/lgpl.html

docs/epilog.dummy

@@ -25,9 +25,8 @@
 
 .. DFT codes
 .. _Siesta: https://departments.icmab.es/leem/siesta
-.. _TranSiesta: https://launchpad.net/siesta
-.. _TBtrans: https://launchpad.net/siesta
-
+.. _TranSiesta: https://gitlab.com/siesta-project/siesta
+.. _TBtrans: https://gitlab.com/siesta-project/siesta
 .. _BigDFT: http://www.bigdft.org
 .. _OpenMX: http://www.openmx-square.org
 .. _VASP: https://www.vasp.at

docs/tutorials/tutorial_es_1.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from __future__ import print_function, division\n",
     "import numpy as np\n",
     "from sisl import *\n",
     "import matplotlib.pyplot as plt\n",
@@ -521,7 +520,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_es_2.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from __future__ import print_function, division\n",
     "import numpy as np\n",
     "from sisl import *\n",
     "import matplotlib.pyplot as plt\n",
@@ -284,7 +283,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.2"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_siesta_1.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from __future__ import print_function, division\n",
     "import os\n",
     "os.chdir('siesta_1')\n",
     "import numpy as np\n",
@@ -21,9 +20,9 @@
    "source": [
     "# Siesta --- the H2O molecule\n",
     "\n",
-    "This tutorial will describe a complete walk-through of some of the `sisl` functionalities that may be related to the [Siesta code](http://launchpad.net/siesta).\n",
+    "This tutorial will describe a complete walk-through of some of the `sisl` functionalities that may be related to the [Siesta code](https://gitlab.com/siesta-project/siesta).\n",
     "\n",
-    "## Creating the geometry to investigate\n",
+    "## Creating the geometry\n",
     "\n",
     "Our system of interest will be the $\\mathrm H_2\\mathrm O$ system. The first task will be to create the molecule geometry.\n",
     "This is done using lists of atomic coordinates and atomic species. Additionally one needs to define the supercell (or if you prefer: unit-cell) where the molecule resides in. Siesta is a periodic DFT code and thus all directions are periodic. I.e. when simulating molecules it is vital to have a large vacuum gap between periodic images. In this case we use a supercell of side-lengths $10\\mathrm{Ang}$."
@@ -318,7 +317,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_siesta_2.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from __future__ import print_function, division\n",
     "import os\n",
     "os.chdir('siesta_2')\n",
     "import numpy as np\n",
@@ -21,11 +20,11 @@
    "source": [
     "# Siesta ---  graphene\n",
     "\n",
-    "This tutorial will describe a complete walk-through of a large fraction of the `sisl` functionalities that may be related to the [Siesta code](http://launchpad.net/siesta).\n",
+    "This tutorial will describe a complete walk-through of a large fraction of the `sisl` functionalities that may be related to the [Siesta code](https://gitlab.com/siesta-project/siesta).\n",
     "\n",
     "Contrary to the $\\mathrm H_2\\mathrm O$ system this tutorial will emphasize the usefulness of performing bandstructures etc. directly in Python using sisl.\n",
     "\n",
-    "## Creating the geometry to investigate\n",
+    "## Creating the geometry\n",
     "\n",
     "Our system of interest will be the smallest graphene cell. Instead of defining the atomic positions, the carbon atoms and supercell for graphene, we use a default implementation of graphene in `sisl`. There are a small selection of the typical geometries, including graphene."
    ]
@@ -361,7 +360,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,