Merge 99fe85e into f944a45

.travis.yml

@@ -22,7 +22,7 @@ branches:
   except: gh-pages
 
 before_install:
-  - git clone https://github.com/njoy/NJOY2016.git && (cd NJOY2016 && mkdir build && cd build && cmake .. && make) # install NJOY
+  - git clone https://github.com/njoy/NJOY2016.git && (cd NJOY2016 && mkdir build && cd build && cmake -DPython3_EXECUTABLE=$(which python3) .. && make) # install NJOY
   - rm -rf NJOY2016/tests
   - pip install sphinx sphinx_rtd_theme codecov numpydoc coveralls pytest-cov
   - pip install -r requirements.txt
@@ -31,8 +31,7 @@ install:
   - python setup.py install
 
 script:
-  - pytest --cov=sandy/
-  -pytest --nbval notebooks/fy_notebook.ipynb
+  - pytest --cov=sandy sandy
 
 after_success:
   - coveralls

INSTALL.md

@@ -0,0 +1,108 @@
+# Installation
+
+## Download
+
+The SANDY source code is available as a git repository.
+The recommended way to get SANDY is by cloning the source package using your 
+local git distribution 
+(*click [here](https://git-scm.com/downloads) to download it!*).
+
+```sh
+git clone https://github.com/luca-fiorito-11/sandy.git
+cd sandy
+```
+
+If a `SSL Certificate problem` appears when pushing or pulling with git, 
+one can tell git to not perform the validation of the certificate using the 
+global option:
+
+```git
+git config --global http.sslVerify false
+```
+
+## Installation using Anaconda
+
+### Downloading Anaconda
+The recommended way to install the SANDY requirements (especially on Windows) 
+is with the Anaconda distribution, which already includes several python 
+packages and few other cool tools.
+The installer for the most recent Anaconda distributions can be found 
+[here](https://www.anaconda.com/products/individual).
+For the Anaconda installation documentation, click 
+[here](https://docs.anaconda.com/anaconda/install/).
+
+### Getting started with Anaconda
+The user guide to get yourself acquainted with Anaconda is available 
+[here](https://docs.anaconda.com/anaconda/user-guide/).
+On a Windows machine we recommend that you use the Anaconda Prompt terminal.
+
+### Installing SANDY
+
+We advise to install the SANDY dependences in a python environment that was 
+not previously altered.
+You can do so from a terminal/Anaconda Prompt using the package/environment 
+management system `conda` included in Anaconda, as
+```sh
+conda update --name base conda
+conda create -y --name sandy-devel -c conda-forge python=3.7 jupyterlab jupyter_nbextensions_configurator
+```
+I like to include jupyterlab to my environment!
+
+Then, dependences are installed from the requirement file,
+```sh
+conda install --force-reinstall -y --name sandy-devel -c conda-forge --file requirements_conda.txt
+```
+Make sure you are in the folder `sandy` that you cloned with git and where 
+file `requirement.txt` is located.
+
+From now on, every time you want to use SANDY in your python distribution 
+you need to activate the correct environemt.
+```sh
+conda activate sandy-devel
+...
+conda deactivate
+```
+To manage your python environments read the 
+[conda cheatsheet](https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf).
+Do not forget to add the `sandy` folder to your `PYTHONPATH`, or else you 
+won't be able to use SANDY when you change folder.
+You can do the following
+
+**in Linux**
+```sh
+export PYTHONPATH="/path/to/sandy:${PYTHONPATH}"
+```
+Add the previous command to your `${HOME}/.bashrc` or `${HOME}/.bash_profile` 
+file to make your changes permanent.
+
+**in Windows**
+```dos
+set PYTHONPATH=%PYTHONPATH%;C:\path\to\sandy
+```
+or, if you want the changes to be permanent,
+```dos
+setx PYTHONPATH=%PYTHONPATH%;C:\path\to\sandy
+```
+
+## Running python
+1. Open a terminal/Anaconda Prompt
+2. Switch to the correct python environment
+3. Type `python` or `ipython` to open up a python/ipython session,
+4. Then type,
+```python
+import sandy
+```
+
+Now, if `sandy` is available you are ready to roll!
+
+## Running SANDY in a Jupyter notebook
+
+For combatibility issues we recommend installing a python kernel specific 
+for the `sandy-devel` environment.
+For that, you can run the following after making sure that `ipykernel` is 
+installed in the virtual environment.
+
+```sh
+conda activate sandy-devel
+python -m ipykernel install --user --name sandy-devel --display-name "Python3 (sandy-devel)"
+```

conftest.py

@@ -1 +1,12 @@
+import pandas as pd
+import pytest
+
+
 collect_ignore = ["setup.py"]
+
+
+@pytest.fixture(autouse=True, scope='session')
+def pandas_terminal_width():
+    pd.options.display.float_format = '{:.5e}'.format
+    pd.set_option('display.max_columns', 1000)
+    pd.set_option('display.width', 1000)

notebooks/decay_notebook.ipynb

@@ -20,13 +20,26 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sandy\n",
+    "import os\n",
+    "\n",
     "import yaml\n",
     "\n",
     "from IPython.core.interactiveshell import InteractiveShell\n",
     "InteractiveShell.ast_node_interactivity = \"all\""
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sandy\n",
+    "\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -43,11 +56,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "tape = sandy.read_formatted_file(\"dec-027_Co_060.endf\")"
+    "tape = sandy.Endf6.from_file(\"dec-027_Co_060.endf\")"
    ]
   },
   {
@@ -60,7 +73,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -89,15 +102,15 @@
        "  'spin': 2.0,\n",
        "  'parity': 1.0,\n",
        "  'decay_energy': {'beta': 56430.24,\n",
-       "   'gamma': 6614.704,\n",
+       "   'gamma': 6614.704000000001,\n",
        "   'alpha': 0.0,\n",
        "   'total': 63044.943999999996},\n",
        "  'decay_energy_uncertainties': {'beta': 8461.567,\n",
        "   'gamma': 425.0476,\n",
        "   'alpha': 0.0}}}"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -116,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -148,7 +161,7 @@
       "  decay_energy:\n",
       "    alpha: 0.0\n",
       "    beta: 56430.24\n",
-      "    gamma: 6614.704\n",
+      "    gamma: 6614.704000000001\n",
       "    total: 63044.943999999996\n",
       "  decay_energy_uncertainties:\n",
       "    alpha: 0.0\n",
@@ -226,7 +239,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -265,7 +278,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -350,7 +363,7 @@
        "3  270601    280600    1.0  0.0024  1.103702e-03"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -369,7 +382,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -424,7 +437,7 @@
        "270601       0.0     0.0"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -443,7 +456,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -498,7 +511,7 @@
        "270601    1.110223e-16     1.0"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -518,9 +531,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:  NumExpr defaulting to 4 threads.\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -573,7 +593,7 @@
        "270601    0.000000e+00 -0.001104"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -600,9 +620,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "dumping decay data for ZAM=270600...\n",
+      "dumping decay data for ZAM=270601...\n"
+     ]
+    }
+   ],
    "source": [
     "h5filename = \"decay.hdf5\"\n",
     "libname = \"endfb_71\"\n",
@@ -611,13 +640,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
     "rdd2 = sandy.DecayData.from_hdf5(h5filename, libname)\n",
     "assert rdd2.get_decay_chains().equals(chains)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "os.remove(h5filename)"
+   ]
   }
  ],
  "metadata": {
@@ -636,7 +674,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.1"
   }
  },
  "nbformat": 4,