Fix bugs, connect to travis CI, pyPI and readthedocs

.gitignore

@@ -1,6 +1,7 @@
 # Python setup folders
 build/
 *.egg-info
+numjuggler/version.py
 
 # Byte-compiled
 *.pyc
@@ -24,3 +25,7 @@ numjuggler.sfood2
 *.log
 .coverage
 htmlcov/
+
+# Travis tests
+travis_tests/*.diff
+travis_tests/*.res

.readthedocs.yml

@@ -0,0 +1,4 @@
+mkdocs:
+    configuration: mkdocs.yml 
+python:
+  version: 2.7

.travis.yml

@@ -0,0 +1,16 @@
+language: python
+
+python:
+    - 2.7
+    - 3.7
+
+before_install:
+    - python --version
+    - pip install -U pip
+
+install:
+    - pip install .
+
+script:
+    ./travis_run_all.sh
+

README.md

@@ -1,16 +1,40 @@
-# WARNING
-The versions starting with 2.23a.17 should be considered as untested. Since
-version 2.22a.17, there were a lot of modifications toward more functionality,
-however, these changes were applied only to a small set of problems and
-therefore should be considered as not tested. If you experience any problems,
-consider fall back to the version 2.22a.17.
+# numjuggler
+Tool to rename cells, surfaces, materials and universes in MCNP input files. See https://numjuggler.readthedocs.io
+
+
+## Current status
+
+[![Build Status](https://travis-ci.org/travleev/numjuggler.svg?branch=master)](https://travis-ci.org/travleev/numjuggler) -- shows status of the tests defined in [travis_tests](travis_tests) folder. 
+
+[![PyPI version](https://badge.fury.io/py/numjuggler.svg)](https://badge.fury.io/py/numjuggler) -- available from PyPI. 
+
+[![Documentation Status](https://readthedocs.org/projects/badge-demo/badge/?version=latest)](https://badge-demo.readthedocs.io/en/latest/?badge=latest) -- documentation
+
 
 Information in the help message, returned by ``numjuggler -h mode`` is
 outdated. Therefore, the best way to see all current modes is to search for
 ``args.mode == `` string in ``main.py``, and read comments in the correspondent
 sections of code.
 
+## Documentation
+
+https://numjuggler.readthedocs.io should be considered as the main source of information. 
+
+There is also a github repo [numjuggler.docs](https://github.com/inr-kit/numjuggler.docs) containing presentations and reports related to numjuggler. 
+
+## Install
+The numjuggler package is available at PyPI: https://pypi.org/project/numjuggler/. The preffered
+way to install it using pip:
+
+    >pip install numjuggler
+
+Alternatively, one can clone from github and install in so-called development mode:
+
+    >git clone [email protected]:travleev/numjuggler.git
+    >cd numjuggler
+    >pip install -e .
 
+<!---
 
 # numjuggler
 Tool to rename cells, surfaces, materials and universes in MCNP input files. See https://numjuggler.readthedocs.io
@@ -54,3 +78,4 @@ instructions:
 
 There is also a github repo, [numjuggler.docs](https://github.com/inr-kit/numjuggler.docs), related to numjuggler documentation.
 
+--->

dev_tests/itab.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# Will tab be printed as tab?
+echo -e -"\t"- > itab.out
+python -c 'print "=\t="' >> itab.out
+
+# --preservetabs flag. The --debug flag turns off the use of dump file (which can also affect the tabs. BTW why?
+numjuggler -s 10 itab_ --debug                > itab_.tabsno
+numjuggler -s 10 itab_ --debug --preservetabs > itab_.tabsyes
+

dev_tests/itab_

@@ -0,0 +1,13 @@
+Input file with tabs
+1 0 -1	imp:n=1	imp:p=1
+2 0  1
+	imp:n=0
+	imp:p=0
+
+c surfaces
+1 so 10
+
+sdef pos 0 0 0
+
+
+

docs/cdens.md

@@ -0,0 +1,35 @@
+# Description
+
+Change cell densities according to the map file. 
+
+In the map file one can specify coefficients to multiply the original input
+file densities. The coefficients can be specified for particular cells and/or
+materials (or their ranges -- see descritpion of the map file format). 
+
+## Rationale
+
+One of the approaches to get the first guess for the 
+weight-window mesh through the model geometry is to decrease
+material densities for all cells between the source and tally region by several orders of magnitude and 
+perform particle transport to generate the weight-window mesh. Experience shows that the obtained weight-window mesh
+applied to the original (i.e. with nominal densities) model allready helps to improve statistics. 
+
+
+## Invocation example
+
+in the following example, the map file is `densities.txt`, the original input
+file is `input.orig` and the new input file is written to `input.new`:
+
+```bash
+>numjuggler --mode cdens --map densities.txt input.orig > input.new
+```
+
+The content of `densities.txt`:
+
+    c 1 -- 10: 0.01  # In cells 1 to 10 multiply density by 0.01
+    c 12: 0.1        # Multiply cell 12 density by 0.1
+
+    m 5: 1e-3        # For all cells filled with material 5 multiply density by 1e-3
+
+
+

docs/forjekyll/_data/navigation.yml

@@ -0,0 +1,5 @@
+- name: Home
+  link: /
+
+- name: About
+  link: /about.html

docs/forjekyll/_includes/navigation.html

@@ -0,0 +1,8 @@
+<nav>
+    {% for item in site.data.navigation %}
+    <a href="{{item.link}}" {% if page.url == item.link %}class="current"{% endif %}>
+        {{item.name}}
+    </a>
+    {% endfor %}
+</nav>
+

docs/forjekyll/_layouts/default.html

@@ -0,0 +1,13 @@
+<!doctype html>
+<html>
+    <head>
+        <meta charset="utf-8">
+        <title> {{ page.title }} </title>
+        <link rel="stylesheet" href="assets/css/styles.css">
+    </head>
+
+    <body>
+        {% include navigation.html %}
+        {{content}}
+    </body>
+</html>

docs/forjekyll/_sass/main.scss

@@ -0,0 +1,3 @@
+.current {
+    color: green;
+}

docs/forjekyll/_site/about.html

@@ -0,0 +1,28 @@
+<!doctype html>
+<html>
+    <head>
+        <meta charset="utf-8">
+        <title> About </title>
+        <link rel="stylesheet" href="assets/css/styles.css">
+    </head>
+
+    <body>
+        <nav>
+
+    <a href="/" >
+        Home
+    </a>
+
+    <a href="/about.html" class="current">
+        About
+    </a>
+
+</nav>
+
+
+        <h1 id="about-page">About page</h1>
+<p>Numjuggler is a command line tool to perform specific tasks on the MCNP input files.</p>
+
+
+    </body>
+</html>

docs/forjekyll/_site/index.html

@@ -0,0 +1,26 @@
+<!doctype html>
+<html>
+    <head>
+        <meta charset="utf-8">
+        <title> Numjuggler documentation </title>
+        <link rel="stylesheet" href="assets/css/styles.css">
+    </head>
+
+    <body>
+        <nav>
+
+    <a href="/" class="current">
+        Home
+    </a>
+
+    <a href="/about.html" >
+        About
+    </a>
+
+</nav>
+
+
+        <h1>Hello World 2!</h1>
+
+    </body>
+</html>

docs/forjekyll/_site/index.md

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+# Numjuggler documentation
+
+## Available execution modes
+

docs/forjekyll/_site/note.rst

@@ -0,0 +1,53 @@
+Organisation of documentation
+==================================
+
+Approach: put the source of documentation in md, and get text messages for
+interactive help by converting md to txt. The md can be directly published with
+the help of gh-pages.  Usage statistics can be collected with e.g. google
+analytics. 
+
+Task: Organize minimal structure with md files that can be used for publishing
+and where information is read for interactive help. 
+
+
+How the command line arguments of numjugller should look like?
+=====================================================================================================
+
+I want that each mode has its own set of command line options. General help
+should provide the general form of the command line args. And there should be
+a way to get particular info about each execution mode. For example::
+
+   >numjuggler
+   >numjuggler -h
+   >numjuggler --help
+
+   # General info, 
+   # general commad line form,
+   # the list of available modes,
+   # how to get additional info
+
+
+   >numjuggler -h <mode> 
+   >numjuggler -h <mode> -i
+
+   # Synopsis of the <mode>: short description and the list of available 
+   # command line options. How to get additional info.
+
+
+   >numjuggler -h <mode> -e
+   # Examples for <mode>. 
+
+
+   >numjuggler -h <mode> -a
+   # Detailed description of the arguments
+
+   >numjuggler -h <mode> -iea
+   # Complete information about <mode>. The order of information does not
+   # depend on the order of command line options, only itspresence. 
+
+Usual invocation of numjuggler assumes particular execution mode. Previously,
+there was the default mode, assumed if no ``--mode`` was given. This behaviour
+should be preserved and one should understand how to distinguish between
+the actual execution and asking for help. In the above examples, the command
+line arguments always start with the ``-h`` or ``--help`` flag. 
+

docs/forjekyll/about.md

@@ -0,0 +1,8 @@
+---
+layout: default
+title: About
+---
+
+# About page
+Numjuggler is a command line tool to perform specific tasks on the MCNP input files. 
+

docs/forjekyll/assets/css/styles.scss

@@ -0,0 +1,4 @@
+---
+---
+@import "main";
+

docs/forjekyll/index.html

@@ -0,0 +1,7 @@
+---
+layout: default
+title: Numjuggler documentation
+---
+
+
+<h1>Hello World 2!</h1>

docs/forjekyll/index.md

@@ -0,0 +1,4 @@
+# Numjuggler documentation
+
+## Available execution modes
+