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@@ -0,0 +1,8 @@
+
+.PHONY: clean
+
+
+clean:
+ -rm -rf build/ saga.egg-info/ temp/ MANIFEST dist/ *.egg-info
+ make -C docs clean
+ find . -name \*.pyc -exec rm -f {} \;
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@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b01a59cbadba2a2e69b70132a1b242d3
-tags: fbb0d17656682115ca4d033fb2f83ba1
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@@ -1,70 +0,0 @@
-Armstrong Sphinx Theme
-======================
-Sphinx theme for Armstrong documentation
-
-
-Usage
------
-Symlink this repository into your documentation at ``docs/_themes/armstrong``
-then add the following two settings to your Sphinx ``conf.py`` file::
-
- html_theme = "armstrong"
- html_theme_path = ["_themes", ]
-
-You can also change colors and such by adjusting the ``html_theme_options``
-dictionary. For a list of all settings, see ``theme.conf``.
-
-
-Defaults
---------
-This repository has been customized for Armstrong documentation, but you can
-use the original default color scheme on your project by copying the
-``rtd-theme.conf`` over the existing ``theme.conf``.
-
-
-Contributing
-------------
-
-* Create something awesome -- make the code better, add some functionality,
- whatever (this is the hardest part).
-* `Fork it`_
-* Create a topic branch to house your changes
-* Get all of your commits in the new topic branch
-* Submit a `pull request`_
-
-.. _Fork it: http://help.github.com/forking/
-.. _pull request: http://help.github.com/pull-requests/
-
-
-State of Project
-----------------
-Armstrong is an open-source news platform that is freely available to any
-organization. It is the result of a collaboration between the `Texas Tribune`_
-and `Bay Citizen`_, and a grant from the `John S. and James L. Knight
-Foundation`_. The first stable release is scheduled for September, 2011.
-
-To follow development, be sure to join the `Google Group`_.
-
-``armstrong_sphinx`` is part of the `Armstrong`_ project. Unless you're
-looking for a Sphinx theme, you're probably looking for the main project.
-
-.. _Armstrong: http://www.armstrongcms.org/
-.. _Bay Citizen: http://www.baycitizen.org/
-.. _John S. and James L. Knight Foundation: http://www.knightfoundation.org/
-.. _Texas Tribune: http://www.texastribune.org/
-.. _Google Group: http://groups.google.com/group/armstrongcms
-
-
-Credit
-------
-This theme is based on the the excellent `Read the Docs`_ theme. The original
-can be found in the `readthedocs.org`_ repository on GitHub.
-
-.. _Read the Docs: http://readthedocs.org/
-.. _readthedocs.org: https://github.com/rtfd/readthedocs.org
-
-
-License
--------
-Like the original RTD code, this code is licensed under a BSD. See the
-associated ``LICENSE`` file for more information.
@@ -1,3 +0,0 @@
-##############
-BigJob Architecture
-##############
@@ -1,37 +0,0 @@
-.. BigJob documentation master file, created by
- sphinx-quickstart on Mon Dec 3 21:55:42 2012.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-##############################
-BigJob |version| User Manual
-##############################
-
-BigJob is a light-weight Python package that provides a Pilot-based Job and Data Management system. BigJob aims to be as flexible and extensible as possible - it installs where you want it (requiring no root access to the target machine). Unlike many other Pilot-Job systems, BigJob natively supports MPI jobs and, because of its integration with saga-python_, works on a variety of backend systems (such as SGE, PBS, SLURM, etc.). BigJob has been shown to work on grids, clouds, and clusters, as well as locally on your personal computer.
-
-More information can be found at the BigJob_ website.
-
-.. _BigJob: https://github.com/saga-project/BigJob/
-.. _saga-python: ttps://github.com/saga-project/saga-python/
-
-
-Contents
---------
-
-.. toctree::
- :numbered:
- :maxdepth: 2
-
- intro/index.rst
- install/index.rst
- usage/index.rst
- patterns/index.rst
- library/index.rst
- tutorial/index.rst
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`search`
-
@@ -1,54 +0,0 @@
-#############
-Configuration
-#############
-
-.. note::
-
- SAGA has been designed as a zero-configuration library. Unless you are
- experiencing problems with one of the default configuration settings, there's
- really no need to create a configuration file for SAGA.
-
-SAGA and its individual middleware adaptors provide various optional
-:ref:`conf_options`. While SAGA tries to provide sensible default values for
-the majority of these options (zero-conf), it can sometimes be necessary to
-modify or extend SAGA's configuration. SAGA provides two ways to access and
-modify its configuration: via :ref:`conf_file` (recommended) and via the
-:ref:`conf_api` (for advanced use-cases).
-
-.. _conf_file:
-
-Configuration Files
--------------------
-
-If you need to make persistent changes to any of SAGA's :ref:`conf_options`, the
-simplest option is to create a configuration file. During startup, SAGA checks
-in two different locations for the existence of a configuration file:
-
-- ``/etc/saga.conf`` - for a system-wide configuration
-- ``$HOME/.saga.conf`` - for a user-specific configuration (Note that it start with a '.')
-
-If a configuration file is found, it is parsed by SAGA's configuration system.
-If files are present in both locations, SAGA will try to merge both, with the
-user-level configuration (``$HOME/.saga.conf``) always having precedence over
-the system-wide configuration (``$HOME/.saga.conf``). SAGA configuration files
-use a structure that looks like this::
-
- [saga.core]
- option = value
-
- [saga.logging]
- option = value
-
- [saga.adaptor.name]
- option = value
-
-
-.. _conf_options:
-
-Configuration Options
----------------------
-
-.. warning:: This should be generated automatically!
-
-
-
@@ -1,17 +0,0 @@
-.. _using-index:
-
-############
-Installation
-############
-
-
-This part of the documentation is devoted to general information on the setup
-and configuration of BigJob and things that make working with BigJob easier.
-
-
-.. toctree::
-
- install.rst
- redis.rst
- xsede.rst
- trouble.rst
@@ -1,154 +0,0 @@
-
-#################
-Installing BigJob
-#################
-
-=================
-Environment Setup
-=================
-
-This section will explain how to set up your environment and install BigJob.
-
------------------
-Prerequisites
------------------
-* Python 2.6 or higher. Python 2.7.x is recommended.
-* Redis Server
-* SAGA-Python Installation (automatically installed when installing BigJob following this guide)
-
------------------
-Bootstrap your Local Python Environment
------------------
-
-Assuming you don't want to mess with your system Python installation, you need a place where you can install BigJob locally. A small tool called `virtualenv <http://pypi.python.org/pypi/virtualenv/>`_ allows you to create a local Python software repository that behaves exactly like the global Python repository, with the only difference that you have write access to it. This is referred to as a 'virtual environment.'
-
-To create your local Python environment run the following command (you can install virtualenv on most systems via apt-get or yum, etc.)::
-
- virtualenv $HOME/.bigjob/python
-
-If you don't have virtualenv installed and you don't have root access to your machine, you can use the following script instead::
-
- curl --insecure -s https://raw.github.com/pypa/virtualenv/master/virtualenv.py | python - $HOME/.bigjob/python
-
------------------
-Activate your Local Python Environment
------------------
-
-You need to *activate* your Python environment in order to make it work. Run the command below. It will temporarily modify your :code:`PYTHONPATH` so that it points to :code:`$HOME/.bigjob/python/lib/python2.7/site-packages/` instead of the the system site-package directory::
-
- source $HOME/.bigjob/python/bin/activate
-
-Activating the virtualenv is *very* important. If you don't activate your virtual Python environment, the rest of this tutorial **will not work.** You can usually tell that your environment is activated properly if your bash command-line prompt starts with :code:`(python)`.
-
-The last step in this process is to add your newly created virtualenv to your :code:`.bashrc` so that any batch jobs that you submit have the same Python environment as you have on your submitting resource. Add the following line at the end of your :code:`$HOME/.bashrc` file::
-
- source $HOME/.bigjob/python/bin/activate
-
-=================
-Install BigJob
-=================
-
-After your virtual environment is active, you are ready to install BigJob. BigJob is available via PyPi and can be installed using easy_install as follows::
-
- easy_install BigJob
-
-You can change the default installation directory by calling::
-
- easy_install --prefix=<target-dir> BigJob
-
-To make sure that your installation works, run the following command to check if the BigJob module can be imported by the python interpreter::
-
- python -c "import pilot; print pilot.version"
-
-=================
-Execution Setup
-=================
-
-There are two requirements for proper BigJob execution:
-
-#. Agent Directory
-#. SSH Password-Less Login
-
------------------
-Create your Agent Directory
------------------
-
-BigJob needs a working directory in which to store all of its output, run information, and any errors that may occur. This directory can be named anything you choose, but for any examples in this manual, we will call the directory 'agent' (default). You should create this directory in the same location you run your scripts from, i.e. usually :code:`$SCRATCH` or :code:`$WORK`. You can create this directory by typing::
-
- mkdir agent
-
------------------
-SSH Password-Less Login
------------------
-
-If you are planning to submit from one resource to another, you must have SSH password-less login enabled to the submitting resource. This is achieved by placing your public key on one resource in the authorized_keys file on the target machine.
-
-Examples of when you would need password-less login:
-
-#. You want to submit from your local machine to an XSEDE resource
-#. You want to submit from one XSEDE resource to another
-#. You want to submit from your local cluster to external clusters, etc. etc.
-
-^^^^^^^^^^^^^^^^^
-Prerequisites
-^^^^^^^^^^^^^^^^^
-
-* :code:`openssh-server` (if you're running on your own system)
-* If running on XSEDE or FutureGrid systems, you do not have prerequisites.
-
-^^^^^^^^^^^^^^^^^
-Key Generation and Installation
-^^^^^^^^^^^^^^^^^
-
-1. **Generate Public/Private Key Pair**
-
-First, you have to generate a key. You do this as follows:
-
-* Step 1: Use the command :code:`ssh-keygen -t rsa -C <your-e-mail>` to generate the key.
-* Step 2: Specify the KeyPair location and name. We recommend that you use the default location if you do not yet have another key there, e.g. :code:`/home/username/.ssh/id_rsa`
-* Step 3: Type user defined passphrase when asking passphrase for the key.
-
-Example::
-
- ssh-keygen -t rsa -C johndoe@email.edu
-
- Generating public/private rsa key pair.
- Enter file in which to save the key (/home/johndoe/.ssh/id_rsa):
- Enter passphrase (empty for no passphrase):
- Enter same passphrase again:
- Your identification has been saved in /home/johndoe/.ssh/id_rsa.
- Your public key has been saved in /home/johndoe/.ssh/id_rsa.pub.
- The key fingerprint is: 34:87:67:ea:c2:49:ee:c2:81:d2:10:84:b1:3e:05:59 johndoe@email.edu
-
-2. **List the Result**
-
-You can find your key under the key location. As we used the .ssh directory, it will be located there.::
-
- cd /home/username/.ssh
- ls
-
-Verify that you have created the files :code:`id_rsa` and :code:`id_rsa.pub`.
-
-3. **Capture the Public Key for Target Machine**
-
-Use a text editor to open the :code:`id_rsa.pub` file. Copy the **entire** contents of this file.
-
-The contents of this file needs to be appended to the target machine's :code:`.ssh/authorized_keys` file. If the authorized_keys file is not accessible, then just create a :code:`.ssh/authorized_keys2` file and paste the key.
-
-Now the target machine is ready to accept your ssh key.
-
-4. **Test your Key Installation**
-
-The ssh-add command tells the machine which keys to use. For a test, type::
-
- ssh-agent sh -c 'ssh-add < /dev/null && bash'
-
-This will start the ssh-agent, add your default identity (prompting you for your passphrase), and spawn a bash shell.
-
-From this new shell, you should be able to :code:`ssh target_machine`. This should let you in without typing a password or passphrase.
-
-Test whether you have a password-less login to the target machine by executing the simple command::
-
- ssh <hostname> /bin/date
-
-This command should execute without password input.
@@ -1,28 +0,0 @@
-
-#########################
-Setting Up a Redis Server
-#########################
-
-BigJob uses a Redis server for coordination and task management. Redis is the most stable and fastest backend (requires Python >2.5) and the recommended way of using BigJob. BigJob will **not** work without a coordination backend.
-
-Redis can easily be run in user space. For additional information about redis, please visit the website, `redis.io<http://www.redis.io>`_. To install your own redis server, please take the following steps::
-
- wget http://download.redis.io/redis-stable.tar.gz
- tar xvzf redis-stable.tar.gz
- cd redis-stable
- make
-
-Once you have downloaded and installed it, start a Redis server on the machine of your choice as follows::
-
- $ cd redis-stable
- $ ./src/redis-server
- [489] 13 Sep 10:11:28 # Warning: no config file specified, using the default config. In order to specify a config file use 'redis-server /path/to/redis.conf'
- [489] 13 Sep 10:11:28 * Server started, Redis version 2.2.12
- [489] 13 Sep 10:11:28 * The server is now ready to accept connections on port 6379
- [489] 13 Sep 10:11:28 - 0 clients connected (0 slaves), 922160 bytes in use
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-You can install redis on a persistent server and use this server as your dedicated coordination server.
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