Rewrote README, added License, styles

.gitignore

@@ -8,4 +8,5 @@ NM
 builds/build
 builds/*
 !builds/make.py
-!builds/README.md
\ No newline at end of file
+!builds/README.md
+requirements.txt
\ No newline at end of file

README.md

+# CORNish PASDy -- COsmic-Ray Neutron flavored Processing and Analysis of Sensor Data in pYthon
 
-# Cornish Pasdy -- COsmic-Ray Neutron flavored Pasdy
-# Pasdy -- Processing and Analysis of Sensor Data in pYthon
+This is a project developed by Martin Schrön, Jannis Jakobi, Mandy Kasner, Rafael Rosolem,
+in order to make Cosmic Ray Neutron Sensing Data Analysis accessible for everyone!
+Please ask us about coauthorship if you use our code for a publication.
 
-## Install
+*Note:* This version of PASDy is specific for Cosmic-Ray Neutron Sensing (CRNS). A more general version of PASDy features are to be developed in the far future.
+
+## Contribution
+
+- Did you find a bug or are you missing a feature? Please report your experience in the [project issues](https://git.ufz.de/CRNS/cornish_pasdy/issues).
+- Have you resolved errors or added new features? Please push your contributions back to GitLab such that the whole community can benefit from your work. Contact [Martin](mailto:martin.schroen@ufz.de) to receive write permission.
+
+## Usage
 
-### Install Python 3.*
+The CORNish PASDy package aims to allow various ways of usage depending on the level of detail and interaction required by individual users. It can be used in the following ways:
 
-e.g. from here: <https://www.python.org/downloads/>
+- **Mouse click** on the file `instantPASDy.py` processes the sensor data instantly. It requires a file `config.cfg` to be present locally. Use this option if you have only one type of sensor for which the exact same analysis needs to be performed over and over again.
+- In the **console**, type
     
+        python instantPASDy.py path/to/your/configfile.cfg
     
-### Install Jupyter
+    Use this option if you don't like GUIs or you apply batch scripting. Add the parameter `--nonstop` to avoid the final input prompt at the end of the script.
+- **Execute** `instantPASDy-GUI.py` where the config file can be selected and ammended directly through the interface.
+- Work on your own scripts (e.g., using Jupyter notebooks) and **import** the required snippets from the PASDy package.  
+    *(This option is currently under development)*
+   
 
-Is it already installed? Try typing `jupyter notebook`. Otherwise install:
+## Install
 
-      pip3 install jupyter
-      pip3 install jupyterlab
-      
-      
-### Configure Jupyter
-
-Install more packages:
-
-- Check https://github.com/matplotlib/jupyter-matplotlib
-- Apply `pip3 install` on:
-
-		qgrid
-		utm
-		tzlocal
-		pympler
-		os
-		sys
-		inspect
-		math
-		numpy
-		matplotlib
-		datetime
-		rasterio
-		IPython.display
-		pandas
-		warnings
-		re
-		cartopy
-		netCDF4
-		requests
-		configparser
-		utm
-		copy
-		itertools
-		
-	If some modules fail, try out downloading and installing the corresponding wheel file form <https://www.lfd.uci.edu/~gohlke/pythonlibs/>.
-    
-Activate Widgets:
+### Python 3.*
 
-    jupyter nbextension enable --py --sys-prefix widgetsnbextension
-    
-Apply visual styles:
+Get Python from here: <https://www.python.org/downloads/>
 
-1. copy the file `install/custom.css` into your home folder to `~/.jupyter/custom/`
-2. copy the file `install/pasdy.mplstyle` into your home folder to `~/.matplotlib/stylelib/`
-3. Install the `Handlee` font family: <https://fonts.google.com/specimen/Handlee?selection.family=Handlee>
+### Packages
+
+Find out what packages you need to install or update:
 
+    pip install pipreqs
+    pipreqs ./
     
-### Run Jupyter
+The list of required packages is saved in `requirements.txt`. Install all of them using:
 
-Type
+    pip install -r requirements.txt
 
-    jupyter notebook
-    
-or
+Examples for important packages used by PASDy are:  qgrid, utm, tzlocal, pympler, os, sys, inspect, math, numpy, matplotlib, datetime, rasterio, IPython.display, pandas, warnings, re, cartopy, netCDF4, requests, configparser, utm, copy, itertools.
+
+If the installation of some modules fails, try out downloading and installing the corresponding wheel file directly from <https://www.lfd.uci.edu/~gohlke/pythonlibs/>.
+
+
+### Jupyter Lab
+
+Jupyter notebooks are a great way to play with python, here is a short instruction of installation:
+
+    pip install jupyter
+    pip install jupyterlab
+    jupyter nbextension enable --py --sys-prefix widgetsnbextension
+    jupyter labextension install @jupyterlab/git
+    pip install --upgrade jupyterlab-git
+    jupyter serverextension enable --py jupyterlab_git
+      
+Apply beautiful styles:
+
+1. copy the file `docs/custom.css` into your home folder to `~/.jupyter/custom/`
+2. copy the file `docs/pasdy.mplstyle` into your home folder to `~/.matplotlib/stylelib/`
+3. Install the `Handlee` font family: <https://fonts.google.com/specimen/Handlee?selection.family=Handlee>
+
+Run Jupyter Lab:
 
     jupyter lab
-    
-And it will open in the browser.
-    
-    
\ No newline at end of file
+

docs/custom.css

+/* Motivating and distraction-free design for `Jupyter`*/
+/************************************ by Martin Schrön */
+
+/*
+Body
+*/
+    html, body, .notebook_app > #header, body > #header {
+        background-color: #eff9e0; }
+    
+    body {
+        font-family: Handlee, "Helvetica Neue", Helvetica, Arial, sans-serif; }
+/*
+File name
+*/
+    span.save_widget span.filename {
+        color: #00aa00;
+        font-weight: bold; }
+
+    span.save_widget span.filename:hover {
+        background-color: white; }
+/*
+File status
+*/
+    span.checkpoint_status, span.autosave_status {
+        color: #aaccaa; }
+/*
+Logos
+*/
+    #ipython_notebook img, #kernel_logo_widget .current_kernel_logo {
+        opacity: 0.1; }
+/*
+Header
+*/
+    body > #header .header-bar {
+        height: 0px;
+        background: #dfe9d0; }
+        
+    #kernel_indicator {
+        color: #bfc9b0; }      
+/*
+Menu bar
+*/
+    .navbar-default {
+        background-color: #dfe9d0;
+        border-color: #cfd9c0;
+        border: 0; }
+
+    .navbar-default .navbar-nav > .open > a, .navbar-default .navbar-nav > .open > a:hover, .navbar-default .navbar-nav > .open > a:focus {
+        background-color: #cfd9c0; }
+/*
+Tabs
+*/
+    .navbar-default,
+    .nav-tabs > li.active > a, .nav-tabs > li.active > a:hover, .nav-tabs > li.active > a:focus,
+    .nav > li > a:hover, .nav > li > a:focus {
+        background-color: #dfe9d0;
+        border-color: #cfd9c0; }
+
+    .nav-tabs {
+        border-color: #cfd9c0; }        
+        
+    .nav-tabs > li > a {
+        outline: none; }
+/*
+GUI Table
+*/
+    .list_header  {
+        background-color: #dfe9d0;
+        border-color: #cfd9c0; }
+        
+    .list_container, .list_container > div {
+        border-color: #cfd9c0; }
+        
+    .list_header > div .item_link, .list_item > div .item_link {
+        font-family: Consolas, monospace;
+        color: #00aa00;  }
+/*
+Cell
+*/
+    div.cell.selected {
+        background: linear-gradient(to right, #eeeeee -40px, #eeeeee 5px, transparent 5px, transparent 100%);
+        /*background: linear-gradient(to right, #cfd9c0 -40px, #cfd9c0 5px, transparent 5px, transparent 100%);*/
+        /*background: linear-gradient(to right, #00aa00 -40px, #00aa00 5px, #eff9e0 5px, transparent 100%);*/
+        /*background: linear-gradient(to right, #00aa00 -40px, #00aa00 5px, #eff9e0 5px, #eff9e0 100%)*/
+        border: 0; }
+
+    div.input_prompt, div.output_prompt {
+        font-family: Consolas, monospace;
+        color: #cfd9c0; }
+/*
+Markdown text 
+*/   
+    div.text_cell_render {
+        color: #666666;
+        font-size: 120%; }
+/*
+Input
+*/
+    div.input_area {
+        border: 1px solid #e0f0ff;
+        background: #eef5ff; /*#eff9e0*/ }
+/*
+Code
+*/
+    .CodeMirror, code, kbd, pre, samp {
+        font-family: Consolas, monospace; }
+/*
+Output
+*/
+    div.output_area pre, div.output_area p, div.output_text {
+        font-family: Consolas, monospace;
+        color: #0077ff; /*#00aa00;*/ }
+/*
+Output Table
+*/
+    div.output_area .rendered_html table {
+        font-family: Consolas, monospace;
+        font-size: 70%;
+        line-height: 10px;
+        border: 1px solid #aaaaaa;
+        border-collapse: initial;
+        border-radius: 3px;
+        border: 3px solid #eeeeee; }
+        
+    table.dataframe tr th:first-child {
+        background-color: #eeeeee;
+        color: #666666;
+        font-weight: normal }
+
+    table.dataframe thead th {
+        background-color: #eeeeee;
+        color: #000000; }
+        
+    .rendered_html tr, .rendered_html th, .rendered_html td {
+        border: 1px solid #cccccc;
+        border-width: 1px 0 0 1px;
+        border-collapse: initial; }
+/*
+Widget
+*/
+    .ui-widget-header {
+        border: 0;
+        background: transparent;
+    
\ No newline at end of file