[fixes 23878281] initial setup

Add usefull Gem:
- facets

development
- rspec
- yard
- yard-rspec (doesn't work on my machine )

developper confort
- guard (doesn't work on my machine)

Setup ruby version to 1.9.3
for whatever reason Jruby didn't like facets.
Maybe a wrong version of JDK.
Merge pull request #1 from maxigit/development

[fixes 23878281] initial setup
[fixes #23883331] Create README
[fixes #23720871] Create a Laboratory domain skeleton.

Can load and save a Flowcell using the Sequel gem.

Squashed commit of the following:

commit df44bff5d778d45923e70b24d488f6a32406addb
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 18:59:16 2012 +0000

    Move join on aliquot into Lane class.

commit d6b6f2c7be813f70f01f562f9850699661b0bba7
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 18:17:20 2012 +0000

    Rename Labware to Laboratory

commit 82545c91ccf2fd93995df4985a05ed42f06fb7ca
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 17:46:46 2012 +0000

    Remove Quota.

commit 58fa474a4d9f49a29066f45a47dba60d3c646e26
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 17:25:05 2012 +0000

    Replace should by must in spec when applicable.

commit 70bb5e8fcb31fcc015275df276ef89f5f7dcbb72
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 17:04:22 2012 +0000

    ensure in_session=false

commit 0229055741b2991f23aba107f50332d6e915f50d
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 16:13:13 2012 +0000

    Replace == [] by be_empty on spec.

commit 6d921780b96d69e455bd4ab7512e151e894ba4ae
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Mar 20 11:15:22 2012 +0000

    Move Lane into Flowcell

    All test passes except from spec/labware/plate_spec.rb

commit 1bf2447e7608721a3bd7afa798dc16a6b422bc6a
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Mon Mar 19 16:49:51 2012 +0000

    Fix spec

    plate are still failing as not implemented.

commit c7e9267b2f50038d8f95ffae849d2693bb1f30ec
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Mar 2 16:14:08 2012 +0000

    Update doc.

commit c90f235d02b95ecc855de366289eb6cda9b0a374
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Mar 2 15:33:18 2012 +0000

    Implement basic update of Flowcell.

commit 900d84755df2e5cfd05da25720eb90d73502f6df
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Mar 1 17:39:37 2012 +0000

    Complete identity_map specs.

commit 1ccff294fac4c3bb80b677bc21de5f3b7d6de6d2
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Mar 1 17:26:24 2012 +0000

    Add identity map and specs. new tests passes.

commit 53c1d2d757620ea5906a2c2e1f42a6f8086e1716
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Mar 1 12:27:38 2012 +0000

    Remove flowcell from Lane

commit 99696fef22f279ae19cbc3e458867ec16ec0d29e
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Mar 1 10:15:48 2012 +0000

    Write update flowcell test.

commit da3c0f14fefbd51490b3431d16326f5ffe797af4
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 29 14:59:42 2012 +0000

    Rewrite test

commit 7b08105a805e06d965b3590bc826e4b6666492e0
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 29 14:31:56 2012 +0000

    Save and load of a new flowcell works

commit 9869fd3fc1d70da1f758029229f7b8b07f212e6b
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 29 11:28:51 2012 +0000

    Compare flowcells in specs. test fails

    Needs a proper == operator

commit be2b908a367de4a0bb355b384ad58d9989634f83
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 28 13:46:07 2012 +0000

    Saving flowcell should be alright.

    Loading is not implemented, therefore tests fail.

commit b0bc90e83478193f671fb401f4d40ce3af8bd204
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Mon Feb 27 19:44:56 2012 +0000

    [f] Add Aliquot and Lane in Persistance::Sequel

    test doesn't pass

commit 93627650e19cd62c229bf539aa4def66756496ad
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Mon Feb 27 16:29:37 2012 +0000

    Adding resource

commit 6d58587c97de2f4727f7dd6f8749b8c8707580b9
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Mon Feb 27 11:42:59 2012 +0000

    Add Sequel::* classes necessary to save/load a Flowcell.

    Test compile but not pass.

commit 4449ec1a75d354dd5ae6f3a6dac2065041ac1f33
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 24 11:33:58 2012 +0000

    Add sequel_store spec. pass

commit 14e5b3e4078c90f5628455c3da4ddd3f90d5ad3e
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 16 17:31:14 2012 +0000

    Backup

commit 25bada2051c9ff10c52e5df64122b3d76e3b5062
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 16 11:18:21 2012 +0000

    Fix [] bug on receptacle

commit 8064a1186366fd2a7594f4d36a63b690564a4115
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 16 11:18:07 2012 +0000

    Add flowcell attribute to Lane

    And fix [] bug

commit 403e775e402f14f3b16c7a058655c6a8a4a42887
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 15 16:28:02 2012 +0000

    Fix local vimrc

commit e782f0658424b002f7c4c86e07bb13e657da9309
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 15 15:05:16 2012 +0000

    Add lanes to flowcell (with specs). needs refactoring

    Lane has been added to flowcell directly.
    Things (code and test) will probably be needed to be moved
    to  Container.

commit ad48bc02ed04deaed85bf1bb29ab0a4b6bb7bbdb
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 15 10:37:48 2012 +0000

    Add autotest

    And make failing test pending.

commit f40bc1deaa8d238e3e7772ed9e4ada3b4a52d57f
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 15 10:05:25 2012 +0000

    Configure rdebug

commit 0753bf52698792514d36aeda91e1419f313f4ecc
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 15 10:01:22 2012 +0000

    Make quantity required pending in specs.

commit 84ba0087808c60004e51bf14b0ec7bac7a2c2e34
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 17:01:11 2012 +0000

    Refactor receptacle_examples.

commit 7c88cf3c1da22690fef54e47d0719b056687f90e
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 16:23:52 2012 +0000

    Update receptacle spec

commit 98bdfe7a626d86f8d1c5251b333ad64085688823
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 16:21:28 2012 +0000

    Skip wip tagged spec

commit 356b5d254364e87cfbb1b6d4562c56896c148374
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 15:11:32 2012 +0000

    Add rspec in vimrc

commit 3634b38851c15e80aa9ded52502f63c359b3527d
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 15:10:23 2012 +0000

    Add Receptacle#take , code and test

commit 3bb2f446d1a1012be884cce437662011a686f0fe
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 14 09:34:12 2012 +0000

    Add Virtus and Aequitas

    Add some specs to check Aequitas work.

commit b86819f077c3833dc7456a6e8b24b39d50016843
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Mon Feb 13 13:19:21 2012 +0000

    Add labellable to Tube

commit 51e9742355f294c7988886db358651c5d897cfe0
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 9 15:25:33 2012 +0000

    Change Chemical to Labware in tag.

commit 3dafd615d9cac3264ef97fe28e7c7024efb5a766
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 17:28:45 2012 +0000

    [fixes #24630005] Fix doc

commit 7d208ee22bb2954f70683d05faa2a32a4ca3866a
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 17:20:30 2012 +0000

    [#24630005] Group Actions

    Rename Action to Actions

commit c3ab812b113c189ca3ec50a77e8e2804e443fcdb
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 16:29:02 2012 +0000

    [#24630005] Group Organization.

    Group DataRelease, Funding, Ordering into Organization module.

commit 9beb30e0f8e94899ab6e5aa78cc16a651ff773ef
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 14:48:10 2012 +0000

    [#24630005] Group Labware.

    Group Labware and Chemical into Labware.

commit 60a81d4f6abb0a2ef0a432c5c2288ffc84d8c5c8
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 11:46:42 2012 +0000

    Add user.

commit 63c615d2b431a19e80b63977f28591d72c385a71
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 11:30:48 2012 +0000

    Add quota

commit 518e28ad3bb2c9267347d7480affa8b1222ad69b
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 7 18:00:42 2012 +0000

    Add flowcell and lane.

commit 71645336fe0172f0176886c5bfdd1c44ce58a443
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 8 10:22:49 2012 +0000

    Add local vimrc

commit 35d20c9d03bdeaf2c8b354d30c3e5a5272abcb8d
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 7 18:00:26 2012 +0000

    Add releasable.

commit af2541241560fb3aa0f63a10ca1dd457ef924f9f
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Feb 7 16:39:11 2012 +0000

    Fix modeline

commit 1215e0970fabcaf49d40b35e6c42037a8b55d948
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 17:14:07 2012 +0000

    Require main classes in each modules files.

commit 3c36fa38b593be0655429927ecad5849a6ca7d28
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 17:03:43 2012 +0000

    Add Ordering.

commit fef5a338bdb0cdd6a39260ff8ca580076e27d09f
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 17:03:16 2012 +0000

    Add funding.

commit 1bf97ffd0572591df350fd0c6a4a07fe9125bea1
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 16:33:21 2012 +0000

    Add DataRelease

commit 0d38a5875b23d751820c5808dc75c5a3fc2fb16b
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 14:24:42 2012 +0000

    Add spec to yardoc generation.

commit 6230c75f25a7b9ae655e531454f1e5f2cfbbf78e
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 10:51:26 2012 +0000

    Add Chemical

commit fa458181874f50e4a3d3aa92632373ec9171c0c3
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Fri Feb 3 09:52:38 2012 +0000

    Add actions

commit 3828d40e49728c2e9b9de5ccdcc30630ad360eaa
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 2 11:57:04 2012 +0000

    Add default require to  labware

commit 6686c08c3d7cd3372cd3155e5468e9236640a00b
Merge: 6dc51fe cc0a5bb
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 2 11:10:52 2012 +0000

    Merge branch 'to_rebase' into development

commit cc0a5bbcf64b77db0325d9a9c87917518db6350f
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 1 16:49:28 2012 +0000

    Add flowcell and lanes

commit 9049debb2946abd6814128a92915e387cc094797
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 1 15:28:00 2012 +0000

    Add labellables

commit 9c444242149879fc3efa02fdc9b6612e78535f14
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Thu Feb 2 11:08:25 2012 +0000

    Adding miscellaneous modules and shared example

commit 6dc51fefcde153c04165ab1aefff6217d566ffb1
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 1 16:49:28 2012 +0000

    Add flowcell and lanes

commit 3d7425738df5b4a2c3ca25144a9c8fd4d01bda61
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 1 15:28:00 2012 +0000

    Add labellables

commit 66cf3d3fbac1ff51646a37c13f9bbd6c19dd4bb6
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Feb 1 14:36:30 2012 +0000

    Fix rspec not working

    fix require

commit c9cb05191d0338610a7dbc1b703ed6a9fafe804d
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Jan 25 15:59:14 2012 +0000

    Update doc

    Add a common.rb as initializer

commit bb76846d04e448b610861cf6f5cc9dcdf4a43709
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Wed Jan 25 15:00:11 2012 +0000

    Adding miscellaneous modules and shared example

commit 99cd985482ffae119a3f3344c3fe5511e19252b6
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Jan 24 17:09:08 2012 +0000

    add Lims::Core module overwiew (Doc).

commit 0543b97dfcfcf20a7246321715ee05b9fcb76062
Author: Maxime Bourget <bmx007@gmail.com>
Date:   Tue Jan 24 17:08:14 2012 +0000

    [fixes #23883331] Create README
Merge pull request #2 from maxigit/development

Development
[fixes #26791113 p] Plate added.

All tests pass.
Merge pull request #3 from maxigit/development

[fixes #26791113 p] Plate added.
[fixes #26914781] require container shared examples
[fixes #26791177 p] Add plate persistance.

All tests pass.
Code needs to be mutualize between Flowcell and Plate.
Merge pull request #4 from maxigit/development

Add plate persistance.
Remove breakpoint
create_plate spec pass and those expected to fail fail.

Those expecting to fail are related to plate creation, as it's not
implemented yet.
[fixes #27002077] implementes CreatePlate action
Merge pull request #5 from maxigit/27002077_design_action_implement_create_plate_action_example

27002077 design action implement create plate action example
[ fixes #27391077 ] Rename Persistance to Persistence.
Merge pull request #6 from maxigit/27391077_rename_persistance_to_persistence

[ fixes #27391077 ] Rename Persistance to Persistence.
[fixes #27009433] create plate transfer action

Corresponding specs passes. Needs now to find a way to
load plates in the same session as the action.
Merge pull request #7 from maxigit/27009433_create_plate_transfer_action

[fixes #27009433] create plate transfer action
[fixes #28076359] Add Persistence::Logger
[fixes #28291495] Refactor persistence

Add Logger::Store and Session.
Refactor as well the normal persistence by adding a Persistor class.
This is needed to dry up the code between the Sequel and the Logger
persistor.
Merge pull request #8 from maxigit/28076359_create_logger_store

[fixes #28076359] Add Persistence::Logger