log.txt

* a803195 (HEAD, origin/develop, develop) Adds coffeedoc for undocumented methods in cell
* 581a4cc Fixes coffeedoc @returns error
* 9aa229b Coffeedoc love update
* ee10310 Cleanup and coffeedoc love
* 7d20ede Added classnames for dummy modules
* 49d7110 Coffeedoc love
* 7429eb2 Goodbye PDFTest
*   cc122c5 Merge branch 'feature/routes' into develop
|\  
| * 759ea43 (origin/feature/routes, feature/routes) Annotations
| * 8cf02d4 Lowercase model name
| * a3712e1 Report is now deleted if cell is deleted
| * 13abfd5 Add plural report files and update show/create/delete
| * 2257509 Get rid of all singular report files
|/  
* 9837774 Removes wrong comments
* 07cbafd Fix them tests
* 3c8e84b Cleanup play view
*   5ccd07e Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\  
| *   eed47f6 Merge branch 'develop' of https://github.com/Derkje-J/programming-life into develop
| |\  
| * \   cdbb77b Merge branch 'develop' of https://github.com/Derkje-J/programming-life into develop
| |\ \  
| * | | 2ad9523 Edited ead
* | | |   fd3b170 Merge branch 'feature/undo/refactor' into develop
|\ \ \ \  
| * | | | 27f8d4e Fixed redo bug
* | | | |   398f770 Merge branch 'feature/undo/refactor' into develop
|\ \ \ \ \  
| |_|_|_|/  
|/| | | |   
| * | | | feaf5fb Fixed redo bug
| |/ / /  
* | | |   1f05ff7 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\ \ \ \  
| | |_|/  
| |/| |   
| * | |   d2b89b8 Merge branch 'feature/serialize' into develop
| |\ \ \  
| | |/ /  
| |/| |   
| | * | bf79f54 (origin/feature/serialize, feature/serialize) Update Gemfile.lock for Gemfile
| | * | a0dfb35 Update seeds for migrations
| | * | 467ae99 Fix load/save cell/module
| | * | c668534 Transparent metabolite as module adding
| | * |   5a2e857 Merge branch 'develop' into feature/serialize
| | |\ \  
| | | |/  
| | * | 8c7da0b Fixed reversal migrations
| | * | 2301f13 Added name to module instance
* | | | eb39d6d Fixed redo bug
|/ / /  
* | | 55eb75f Update tree view to current develop
* | | df6d570 Updated Gemlock and implemented tests for module undo/redo
* | |   0725ad5 Merge branch 'develop' into feature/undo/refactor
|\ \ \  
| | |/  
| |/|   
| * | efafe3c Fix them spec tests
| * | b0b4994 Unignores Gemfile.lock
| * | 25b1947 Fixes spelling and equations
| * | 879aa98 Safe seed values
| * | 94fd516 Pack and unpack those metabolites
| * |   aacdd76 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \  
| | * | 73d3249 Update cododoc
| | * | 320276b Fix for @steffansluis merge stuff
| | * | be1af55 Some hover and selected love
| * | | 90621fe Graphs now render in container
| |/ /  
| * | 68f9844 Metabolite fix
| * |   7753f1d Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \  
| | * \   f6180d4 Merge branch 'feature/equations' into develop
| | |\ \  
| | | * | aa09631 (origin/feature/equations, feature/equations) Views update accordingly
| | | * | 76b8a9f Cell update and compliant new spec/modules
| | | * | a2a7052 Update Transporter module
| | | * | d446eb0 Update Transporter spec
| | | * | 89c7203 Update cell spec again
| | | * | 9c9717e Update DNA spec again
| | | * | 3ab0dcd Update Metabolite module
| | | * | 1e46348 Update Metabolite spec
| | | * | 65872d2 Update Protein module
| | | * | 3cf0bf9 Update Protein spec
| | | * | 22adca0 Update Metabolism module
| | | * | 9c464ad Update Metabolism spec
| | | * | f0132ea Update Lipid module
| | | * | 7c4c1f0 Update Lipid spec
| | | * | 0e0bd5b Update ensure method of Base Module
| | | * | 43bfffc Update DNA module
| | | * | 25cb5a5 Update DNA spec
| | | * | 750e628 Update Cell Growth module
| | | * | 93160c2 Update cell growth spec
| | | * | cc7ee71 Updated cell spec for new code
| | | * | dffd495 Enable test to accept arrays, add ensure
| | |/ /  
| * | | b35bf43 Removed depracated tests
| * | |   2f09f5a Merge branch 'develop' into feature/simulation/control
| |\ \ \  
| | |/ /  
| | * | 5e33efd Refactor and cleanup (dummy) module view
| | * |   85d5727 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| | |\ \  
| | | * | 5295268 Refactor module a bit more
| | * | | 36c859e Removed nonsensical 'last updated' column
| | * | | 84a0d0a Fixed tests
| | |/ /  
| | * |   8b3d9d5 Fixed conflict db/schema.rb
| | |\ \  
| | | * \   286b0d0 Conflict solved
| | | |\ \  
| | | | * | f5ebe22 Wicked pdf implemented
| | | * | | d366fb3 Paremeters of modules in report
| | | * | | 6451759 Added report destroy method
| | | * | | c82077c Basic HTML report
| | | * | | 8af31fe Initial MCV setup for report
| | | * | | 9072821 Wicked pdf implemented
| * | | | | 01ec6c2 Fixed red lines
| * | | | | 9bc22d4 Fixed bug in play
| * | | | | 25fdf3c Graph uses Raphael now
| * | | | | d27b7fc Separated cell and visualize
| * | | | | e2e8ef2 Separated main and cell
| |/ / / /  
| * | | |   78b7271 Merge branch 'feature/serialize' into develop
| |\ \ \ \  
| | | |_|/  
| | |/| |   
| | * | | f36f99d Load the module
| | * | | ccf6e0b Load the cell
| | * | | fe119a3 Auto back to number
| | * | | a2ddaa8 Database cleanup
| * | | |   7b37984 Merge branch 'feature/serialize' into develop
| |\ \ \ \  
| | |/ / /  
| | | / /   
| | |/ /    
| |/| |     
| | * | 1949a73 Link reshuffles
| | * | 5005cc0 Fixed cell count display
| * | |   154b18f Merge branch 'feature/serialize' into develop
| |\ \ \  
| | |/ /  
| | * | 9d23fee Can't test on arrays anymore. Todo.
| | * | 7deb005 Correct pagination
| * | | e1ff587 Blank value should display missing data
| * | |   948e30a Merge branch 'feature/serialize' into develop
| |\ \ \  
| | |/ /  
| | * | c8727d2 Fixed failing test
| | * | 84cd5f5 Fixed Module type deserialization
| * | |   fe1a6a7 Merge branch 'feature/serialize' into develop
| |\ \ \  
| | |/ /  
| | * | 411d476 Match other show views
| | * | d2e91db Enables cell saving
| | * | dccf04e Fix for errored fields
| | * | 098aca6 Form fixes
| | * |   f5b76f6 Merge branch 'develop' into feature/serialize
| | |\ \  
| | |/ /  
| |/| |   
| * | | ed13026 Fixes export gone wrong
| * | | 4f96dc1 Fixed TypeError in Chart.js
| * | | 200226e Start cleaning up of GUI code
| | * | 3c71558 Started on save code
| | * | 2654cad Ugly way to set parameters <= instance
| | * | e630350 Migration and rewrote seeds
| | * | 6ffef70 Updated instance and template model
| | * | b04e909 Models have urls
| | * | 4c898ce Better property retainment
| | * | a29f472 Enable given id and creation
* | | |   e23f048 Merge branch 'feature/undo/refactor' of github.com:Derkje-J/programming-life into feature/undo/refactor
|\ \ \ \  
| * | | | 1770f7b Arrow move with drag
* | | | | eea4f0d Arrow move with drag
|/ / / /  
* | | | 96735dc Added dragging
* | | | 3de6fbf Added kind of hacked click action
* | | |   673fc35 Merge branch 'feature/undo/refactor' of github.com:Derkje-J/programming-life into feature/undo/refactor
|\ \ \ \  
| * | | | 47a77ca Revert "Started view for undotree"
| * | | |   e7d7da1 Merge branch 'feature/undo/refactor' of github.com:Derkje-J/programming-life into feature/undo/refactor
| |\ \ \ \  
| | * \ \ \   cd55abc Merge branch 'feature/undo/refactor' of github.com:Derkje-J/programming-life into feature/undo/refactor
| | |\ \ \ \  
| | | * | | | 7a669c8 Started view for undotree
| | | * | | | 44d15ed Namespaced Undo
| | * | | | | 20608ac Basic tree visualisation
| | * | | | | 20a0b4e Fixed broken test
| | * | | | | 9298d71 Added iterators
| | * | | | | e1b8c9b Namespaced Undo
| | | |_|_|/  
| | |/| | |   
| * | | | | 8b72f40 Added arrows
| * | | | | 788c9b7 Basic tree visualisation
| * | | | | 21ae26d Fixed broken test
| * | | | | 7650d20 Added iterators
| * | | | | a9d1af1 Started view for undotree
| * | | | | 6985407 Namespaced Undo
| |/ / / /  
* | | | | 9cdfc3f Added arrows
* | | | | 1d37331 Namespaced Undo
* | | | | 75d0157 Basic tree visualisation
* | | | | 4fa701c Fixed broken test
* | | | | 07754ae Added iterators
* | | | | 29d0902 Namespaced Undo
| |_|/ /  
|/| | |   
* | | |   6984d8c Merge branch 'feature/serialize' into develop
|\ \ \ \  
| | |_|/  
| |/| |   
| * | | 710b510 Test reflect updated serialization
| * | | af027a7 Added function serialization
| * | | c18bb8c Fixture data into contoller test
| * | | 9d53d16 Helper tests
| * | | c8abd01 Ignore journal files
* | | |   61f34af Merge
|\ \ \ \  
| * | | | 6845d98 Added bundle install without sudo. Also fixed server permissions so www-data can execute git
| * | | | 2521db2 Namespaced graph
| * | | |   89cf1f5 Merge branch 'feature/serialize' into develop
| |\ \ \ \  
| | |/ / /  
| | * | | 71d017c xit for unimplemented tests
| | * | | 9a75c37 Added more serialization spectests
| | * | | c4dd8e0 Added serialization spec tests
| | * | | 71499a4 Added json2 pollyfil
| | * | |   357c2fe Merge branch 'develop' into feature/serialize
| | |\ \ \  
| | |/ / /  
| |/| | |   
| * | | | cd43226 Serialize and deserialize cell/module
| * | | |   9a04e16 Merge branch 'feature/serialize' into develop
| |\ \ \ \  
| | |/ / /  
| | * | | 808609e Fixed tests
| | * | | 3a43199 A lot of form changes
| | * | | b8fd102 Nested form jquery
| | * | | a7e5dec Nested form attributes
| | * | | 47909c5 Nested forms gem
| | * | | ff165cd Added file migration
| | * | | 6d019de Added step field
| | * | | 785b287 Template joins
| | * | | efe5133 Instance joins and hash left join
| | * | | afe003a Fixed html escaped links
| | * | | 4cb47c4 Added dependencies
| | * | | 94ee83f Fix for main view (container)
| | * | | f1980ac Link icons for module instances
| | * | | 5047eaa Changed show to add updated time
| | * | | df230ec Migrated
| | * | | 8135b44 Migration for value to be a string
| | * | | 3ac81fa Added main view for container fix
| | * | | d862a7e Updated instance show
| | * | | 67ea75e Updated listings
| | * | | ad53ff1 Added filter and link_to_self helpers
| | * | | 06b5da3 Refined filters
| | * | | 029de98 Cross model controller data
| | * | | 33297d5 Added listify helper method
| | * | | 53dbb90 Removed scaffold link css
| | * | | 7c51c9d Added accesibility for joins
| | * | | cede555 Added pagination gem
| | * | | 04e6e9c Migrated Database
| | * | | 3a06c92 Foreign key migrations
| | * | | aace3f4 Annotated schemes
| | * | | c244156 Various changes
| | * | | 5d3ed77 Schema update
| | * | | e18212f Updated some visuals for templates and cells
| | * | | 937917d Added glyphicons
| | * | | 197130f Removed redundant scaffolds
| | * | | 64971bf Name migration
| | * | | a931c1c Removed validations
| | * | | e432640 Updated schema
| | * | | 8593ec4 Migrations
| | * | | aaa6b52 Relations and associations
| | * | | 083708f Added module_values
| | * | | b79f905 Added module_parameter
| | * | | 124bf80 Added module_instance scaffold
| | * | | 1303f28 Added module_teamplte scaffold
| | * | | 5044dff Id uneditable
| | * | | d2defb2 Added cell scaffold
| | |/ /  
| * | | 124ea5c Add onmouseover to module views
| |/ /  
| * | 1fed981 (origin/feature/module/refbyid, feature/module/refbyid) Re-added raphael
| * | 7839bcb Removed raphael
| * | a0dfc25 Fetch tags on hook
| * | 569ea38 Added Big/Bigdecimal
| * |   9bc5b8e Merge branch 'release/v1.1.0' into develop
| |\ \  
| | * | 77f3c4f (origin/release/v1.1.0) Fixed spec
| | * | 910ea3c Added run action
| | * | 6bf746c Updated graph labels
| | * | 5332059 Added view for actions (buttons)
| | * | 4446a18 Better placement
| | * | e4ecf7a Added dummy interaction
| | * | 7472005 Changed event to be confirm with add module
| | * | dafe27d Naming for transporters and enzymes
| | * | 73bcac9 Added visible property
| | * | aac6fb3 Dummy modules
| | * | 7fa92f7 Fixed inactive css
| | * | df6225a Added unique client_id
| | * | 233f5c9 Renamed views
| | * | b2fb52a Removable modules
| |/ /  
* | | c898e40 Gezeik met git
* | | 0d4b154 Feedback EAD verwerkt
|/ /  
* | 6976671 Raphael update
* | 3007595 Updated messages for hook
* | 5557343 Updated hook route and exec
* | 26cfa21 Removed hook via get
* | 483e3cb Fixed spec tests
* | 5465013 Invoke controller
* | f3ac26a Namespace and mvc fixes
* | fcd5e58 Added javascript controller to ruby
* | f9f3705 Updated vendor libs
* |   27c24c9 Merge branch 'feature/events' into develop
|\ \  
| * | f0b0f81 Minor fixes
| * | 51ab72a Event manager sealed
| * | 2c51f36 Fixed events for module
| * | 45d2a45 Add basic cell visualization
| * |   bac0c15 Merge branch 'develop' into feature/events
| |\ \  
| * | | 441cf88 Event testing
| * | | 6b0d5da More module events
| * | | 9ffdc2a Added events to modules
| * | | 1acfd0d Added events to cells
| * | | 730c225 Event Manager
| | |/  
| |/|   
* | | 1224e44 Updated raphael with master branch version
* | | e7a4ea0 Added raphael uncompressed
| |/  
|/|   
* | a027298 Added raphael uncompressed
* | 4cb7cda Added coverals for serverside
* | 7575831 Trying coveralls
* | 63c29b9 Updated doc for SIG
* | 2a775e8 Removed hacked pane
* | e3f820a Removed console.log
* | 28fb477 Reordered for readability
* | e3a7f3f Updated specs for placment
* | 5a3ec2d Added numeric helpers
* | 254594e Removed substrate function in module
* | 036cc91 Refactored cell function names
* | c701749 Added raphael uncompressed
* |   3507881 Merge branch 'feature/tests' into develop
|\ \  
| |/  
|/|   
| * b071ab8 Improved Cell spec
| *   64da117 Merge branch 'feature/tests' of https://github.com/Derkje-J/programming-life into feature/tests
| |\  
| | * ae923f8 Node fixed and fully tested
| * | d8a6317 Added spectests to substrate
| |/  
| * dbb8483 Added spec tests for CellGrowth and Substrate
| *   7617448 Merge branch 'feature/tests' of github.com:Derkje-J/programming-life into feature/tests
| |\  
| | * bfb3127 Added tests for CellGrowth
| * | 3c6a8cc Fixed date checking test
| |/  
| * 5c905a1 Fixed typo
| * eed4345 Date checking tested
|/  
*   b275338 Merge branch 'release/v1.0.0' into develop
|\  
| * 6d38447 (origin/release/v1.0.0) Cross to close
| *   888f5b8 Merge branch 'release/v1.0.0' of https://github.com/Derkje-J/programming-life into release/v1.0.0
| |\  
| | * 5f9ed20 Added click to text and disabled button if inactive
| * | 7b82681 Resolved conflicts
| * | afc6dd4 Random parameters and show last graph
| * | 4aed6fd Graph dataset limit
| |/  
| * 98a8b40 Fixes and so forth
| *   9334ad0 Merge branch 'release/v1.0.0' of https://github.com/Derkje-J/programming-life into release/v1.0.0
| |\  
| | * bb47a76 Fixed resizing bug
| * | dbcc819 More actions!
| |/  
| *   376a6d2 Merge branch 'release/v1.0.0' of https://github.com/Derkje-J/programming-life into release/v1.0.0
| |\  
| | *   608e1b5 Merge branch 'release/v1.0.0' of github.com:Derkje-J/programming-life into release/v1.0.0
| | |\  
| | * | 99b94a9 Added cowboyhacked pane
| * | | b618505 Minor fixes
| | |/  
| |/|   
* | |   c506e30 Merge branch 'release/v1.0.0' into develop
|\ \ \  
| |/ /  
| * | 8cf3e3b Draws properties
| * | 0fe958a Draw component in module and protein/enzym
| |/  
| * 438ec90 Added placement for products
| * d9d00ed Temp md5 for string to color
| * b3e5c25 Added md5 for quick string to color
|/  
*   9476da4 Merge branch 'feature/draw' into develop
|\  
| * c6f0d03 (origin/feature/draw, feature/draw) Colors for substrate name instead of module name
| * 6972c1d Added substrate drawing
| * 6566713 Removed fill colour so it can be overriden
| * f3eafcf Added substrate color based on name
| * 38fe9b3 Added comments and Transporter subs name
| * 0724090 Fixed substrate drawing and refactored location
| * 205ab34 Add basic cell visualisation
|/  
*   ac23fee Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\  
| * 430e1a7 Changed a bit. Not done yet.
* | 2d7e4f7 Modified the product vision
|/  
*   01329ab Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\  
| * 13ea98e Removed Downloads from Develop
| * 4242649 Added schema migration file
| * e748641 Removed hook.php
| *   7da0ac5 Merge branch 'feature/doc' into develop
| |\  
* | \   193cefd Merge branch 'feature/doc' into develop
|\ \ \  
| * \ \   517d9fe (origin/feature/doc, feature/doc) Merge branch 'feature/doc' of github.com:Derkje-J/programming-life into feature/doc
| |\ \ \  
| | | |/  
| | |/|   
| | * | 2d6ef6d Updated documentation
| | * | 3fbd690 Fixed documentation
| | * | 5e3d682 Fixed documentation
| | * | a60b00f Documentation fixes
| | * |   f5c161c Merge branch 'develop' into feature/doc
| | |\ \  
| | | |/  
| | | * f243f8c Fixed documentation modules
| | | * 8bc5974 Fixed documentation for graph
| | | * 71df4ac Fixed documentation for cell
| | | * 4de0be1 Fixed amount of substrate in cell
| | | * 4496b9b Fixed specs
| | | *   5fd2758 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| | | |\  
| | | | *   7f4e280 Merge branch 'feature/module/substrate' into develop
| | | | |\  
| | | | | * f21b311 Substrates as modules
| | | | | * f09d914 Fixed formulas
| | | | | * 925af31 Fixed spec tests for corrections in formulas
| | | | | * 2e0fc0f Substrate module
| | | * | | 9c76cf9 Refactored hook
| | | * | | 27ad68e Added layout for hook
| | | * | | f0b01d3 Fixed hook controller
| | | * | | 2b79ab9 Added ruby webhook
| | | |/ /  
| | | * |   1e701a0 Merge branch 'feature/cell/visualize' of github.com:Derkje-J/programming-life into feature/cell/visualize
| | | |\ \  
| | | | * \   dc005dc Merge branch 'feature/cell/visualize' of github.com:Derkje-J/programming-life into feature/cell/visualize
| | | | |\ \  
| | | | | * | b77be81 Completed visualize functionality. Fixed minor bug in graph
| | | | | * |   103be41 Merge branch 'develop' of github.com:Derkje-J/programming-life into feature/cell/visualize
| | | | | |\ \  
| | | | | * | | 2df796c Added basic visualize function.
| | | * | | | | e2c048f Removed stub for minimize. Functionality deemed unneccesary
| | | * | | | |   34da7e7 Merge branch 'feature/undo/rebase' of github.com:Derkje-J/programming-life into feature/undo/rebase
| | | |\ \ \ \ \  
| | | | * \ \ \ \   f228358 Merge branch 'feature/undo/rebase' of github.com:Derkje-J/programming-life into feature/undo/rebase
| | | | |\ \ \ \ \  
| | | | | * | | | | 4d448b3 Added stub for minimize
| | | | | * | | | | 7778069 Added node/branch rebasing by reference
| | | | * | | | | | 02f9aca Added stub for minimize
| | | | * | | | | | f5bef16 Added node/branch rebasing by reference
| |_|_|/ / / / / /  
|/| | | | | | | |   
| | | * | | | | | e84a815 Added stub for minimize
| | | * | | | | | 1b1b09d Added node/branch rebasing by reference
| | | * | | | | | 741dd70 Added stub for minimize
| | | * | | | | | b8069d5 Added node/branch rebasing by reference
| |_|/ / / / / /  
|/| | | | | | |   
* | | | | | | | 7d398a7 Added Build status
* | | | | | | | 50c57f4 Create RAILS.md
* | | | | | | | b5feea9 Rails readme removed
| |_|_|_|_|_|/  
|/| | | | | |   
* | | | | | | 373e5d5 Attempt 3 for headless testing
* | | | | | | fb58bb5 Attempt 2 for headless testing
* | | | | | | a5be0c6 Added headless browser for Travis!
* | | | | | | b0c11d5 Goodbye invalid YAML
* | | | | | | a6f69f5 Testing Travis!
| |_|/ / / /  
|/| | | | |   
* | | | | | 1b8a7d9 Refactored a bit and added tests for branching undo
* | | | | | 3bcdf9e Refactored undo functionality to actually be called undo and added codo
* | | | | | cef13fd Dopri testing
* | | | | | 2e9ff01 Rounding is no longer needed
* | | | | |   06ac973 Merge branch 'feature/module/refactored' into develop
|\ \ \ \ \ \  
| * | | | | | 58f7e4a Transporter spec tests for helper functions
| * | | | | | c96fe79 Module Protein spec test changes
| * | | | | | e82fda5 Transporter fixes
| * | | | | | 51f28c1 Module Transporter spec test
| * | | | | | 0bfdc86 Module Protein spec test
| * | | | | | db7a9f3 Metabolism spec
| * | | | | | 9597f09 Added missing test for dna module
| * | | | | | f49d8d0 Rename to indicate base class
| * | | | | | 8a03fca Module Lipid spec test
| * | | | | | b2a7dc3 Module DNA spec test
| * | | | | | 4579451 Spec files for modules
* | | | | | | 74234d1 Fix for missing Model in Controller
| | * | | | | f8e6d74 Converted the product vision to LaTeX and updated it
| | * | | | | 0f3c39b Document with questions to SA added
| | |/ / / /  
| | * | | |   1b070b0 Merge branch 'develop' into feature/doc
| | |\ \ \ \  
| |_|/ / / /  
|/| | | | |   
* | | | | | 347068c Code update!
* | | | | | f4f5f63 Codo update!
* | | | | |   1b664e1 Merge branch 'feature/module/refactored' into develop
|\ \ \ \ \ \  
| |/ / / / /  
| * | | | | bbba311 Extraced mu. Transporter update...
| * | | | | 3dca70a Second attempt
| * | | | | 425bca5 Tried extracting the mu
| * | | | |   57c29b8 Merge branch 'develop' into feature/module/refactored
| |\ \ \ \ \  
| |/ / / / /  
|/| | | | |   
* | | | | | 85bc69c Fixed Coffeedoc
* | | | | | 2666a17 Reordered arguments
* | | | | | 3838861 Added transporter direction
* | | | | | fe3941a Various fixes
* | | | | | 5f0246c Reimplemented undo with tree
* | | | | | ac9875e Added tree and node classes
* | | | | | c203fcf Fixes for the modules
* | | | | | db48a09 Fixed metabolism step function
* | | | | |   00b3fca Merge branch 'feature/module/refactored' into develop
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| |/ / / / /  
| * | | | | 3a7a8b1 Namespacing sweetsticks
| * | | | | 3402870 Fixed cell spec
| * | | | | c5617f4 Added CellGrowth module
| * | | | | 4157099 Renamed files for require tree
| * | | | | 2cd3ac1 Cell has to have at least one sub to grow
| * | | | | bf1f18d Auto add substrates on run. Default cell module
| * | | | | cae0f25 Added Protein module
| * | | | | ab1f95a Added Metabolism module
| * | | | | 90e3aa2 Generator functions for transporter int and ext
| * | | | | e443d21 Added Transporter module
| * | | | | 808bba7 Test only succeeds if non negative
| * | | | | 002646f Added DNA module
| * | | | | 5852cc5 Amended substrates config to lipid
| * | | | | d01482b Added substrates to modules
| * | | | | 1e7be91 Optimized test function and added doc
| * | | | | 57b9d8e Add test functionality for available substrates
| * | | | | 8430fb7 Added references in application
| * | | | | b1b6c47 Added blanks
| * | | | | 08d4d1c Add Lipid refactored
|/ / / / /  
| * | | | a18a96b Finalised draft EAD
| * | | | 5541d97 Modified LaTeX template, adding headshots of team members
| * | | | 127454b Fixed typo title & proofchecked EAD
|/ / / /  
* | | | dbe6f46 Added graph options
* | | | 35e996b Options for graph send through from cell
* | | | 5f1f91b Removed overflow hidden from body
* | | |   cb58612 Merge branch 'feature/module/generator' into develop
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| * | | | 079fe64 Added some sort of cell generator
| * | | |   0e12c4f Merge branch 'develop' into feature/module/generator
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* | | | | | 3dd6071 Lower bounds the substrates
* | | | | | c15fa1e Removed backbone
| |/ / / /  
|/| | | |   
* | | | | d8d9711 Fixed generators
* | | | |   b3ddf8b Merge branch 'feature/module/generator' into develop
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| |/ / / /  
| * | | | b55a38a Default generators
| * | | | 040ec87 Generator file
* | | | |   7046faf Merge branch 'feature/graph' into develop
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| * | | | | ee1eff9 Updated tests
* | | | | |   4817da7 Merge branch 'feature/graph' into develop
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| |/ / / / /  
| * | | | | 07e4804 Options for visualise
| * | | | | 0e77b81 Larger default width
| * | | | | 48bfabf Graph styling
| * | | | | 3e4833f Added size and title
| * | | | | ad8275e Corrected labels and display for graph
| * | | | |   3086908 Merge branch 'develop' into feature/graph
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| |/ / / / /  
|/| | | | |   
* | | | | | 83e3fcf Fixed fence problems
* | | | | | 5140ea8 Fix for labels
* | | | | | f73e40d Coding standards for graph
* | | | | | 7e58492 Interpolate fixed timestep
* | | | | | 3cf3b79 Maximum number of labels
* | | | | | d2be885 Updated visualize some more
* | | | | |   373bd80 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\ \ \ \ \ \  
| * \ \ \ \ \   c23c8ad Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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* | \ \ \ \ \ \   6f70c36 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| |/ / / / / / /  
|/| / / / / / /   
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| * | | | | | 01b7321 Fixed naming convention private functions
| * | | | | | 7967112 Added coverage to ignore
* | | | | | | 2ea1614 Updated visualize and added a basic test
|/ / / / / /  
* | | | | |   f4233b4 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| * | | | | | 343bd92 Updated tests conform updated cell
| * | | | | |   d325eae Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| | * | | | | | d5e2567 Updated cell conform coding standards
| * | | | | | | bc36145 Removed default db from version control
| |/ / / / / /  
| * | | | | | 12546be My bad?
| * | | | | | 47bbb0b Added integration tests
| * | | | | |   21aef4a Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| | | |_|/ / /  
| | |/| | | |   
| | * | | | | f227797 Completed visualize functionality. Fixed minor bug in graph
| | | |/ / /  
| | |/| | |   
| * | | | | f83ebf7 Completed visualize functionality. Fixed minor bug in graph
| |/ / / /  
| * | | | aff3a65 Updated graph tests to BDD
| * | | | b77ee4a Updated module tests to BDD
| * | | | d673d97 Added tests for integrated code in module
| * | | | 0a0d4a8 Fixed failing test
| * | | |   568a176 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \  
| | * | | | 7df1867 Integration of cell for modules
| | * | | | eb570fd Remove Cell.js.coffee (note the capital C)
| * | | | |   c902a7b Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| | |/ / / /  
| | * | | |   c18ac7b Merge branch 'feature/cell-class' into develop
| | |\ \ \ \  
| | | * | | | e426477 Added the ODE
| | | * | | | 380efd6 All equations added (commented)
| | | * | | | 1934420 Testing set for equations
| | | * | | | 8226df3 Fixed numeric asset
| | | * | | | 2cb97de Removed step function
| | | * | | | 92c2f1c Added numeric lib
| | | * | | | a683973 Fixed terminology substance <> substrate
| | * | | | | 395b98d Added cell class
| | * | | | | 0776cd8 Added numeric lib
| | * | | | | f191dd5 Cell tests
| * | | | | |   b7b8a44 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| | |/ / / / /  
| | * | | | | 6cfe7c6 Add raphael.js to assist with vector image manipulation.
| * | | | | |   89c5db3 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| | |/ / / / /  
| * | | | | |   539c558 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| * \ \ \ \ \ \   ed3dc00 (tag: v0.1.0) Merge branch 'develop'
| |\ \ \ \ \ \ \  
| * \ \ \ \ \ \ \   6001419 Merge branch 'develop'
| |\ \ \ \ \ \ \ \  
* | \ \ \ \ \ \ \ \   e5975f8 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| | |_|_|_|/ / / / /  
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| * | | | | | | | | 23e3321 Add raphael.js to assist with vector image manipulation.
| | |_|_|/ / / / /  
| |/| | | | | | |   
| * | | | | | | | 8afa83e Change tests for module to implement new interface
| * | | | | | | | 2eeca25 Test for if history or future is present before undo / redo.
* | | | | | | | | 9f7f84b Removed old test and default database from version tracking
|/ / / / / / / /  
* | | | | | | | 242fdd0 Add basic undo and redo functionality
* | | | | | | | 131370c Fixed failing graph tests
* | | | | | | |   966e35d Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
|\ \ \ \ \ \ \ \  
| * | | | | | | | 19d9ae6 Added teabag for testing
* | | | | | | | | 620ea93 Added teabag for testing
|/ / / / / / / /  
* | | | | | | | e9aec53 Reorganizing
* | | | | | | | bb2a720 Added log, aux, out, pdf and synctex.gz to gitignore
* | | | | | | | ac376cb Structuring directory layout
* | | | | | | | 7217171 Conclusion added
* | | | | | | | 175518b Add introduction to seminar report
* | | | | | | | 458ece3 Remove a newline to fix building tex on linux
* | | | | | | | 38c3ae1 Abstract to toc
* | | | | | | |   cf2ec95 Merge branch 'develop' of https://github.com/Derkje-J/programming-life into develop
|\ \ \ \ \ \ \ \  
| * | | | | | | | 666e6bd Fixed spelling
| * | | | | | | | 6fd0f8b Abstract
* | | | | | | | | a4b0014 Added Vision on product need and utility to conext seminar report
|/ / / / / / / /  
* | | | | | | | c85ff1d Added bioinformatics vision
* | | | | | | | 95cca36 Cleanup.
* | | | | | | | 11d8712 Added conclusion and ToC to seminar report
* | | | | | | | 7393435 Small changes to context seminar report
* | | | | | | | 6325b8c Added Context Seminar source to deliverables, including photos
* | | | | | | |   b460922 Merge branch 'feature/skeleton' into develop
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| |_|_|_|_|_|_|/  
|/| | | | | | |   
| * | | | | | | c9c8b81 Add stub for main class
| * | | | | | | e5d6ae1 Skeleton: add stub skeleton with two graph rows at the bottom
|/ / / / / / /  
* | | | | | | 95965f2 Add bootstrap to the project
* | | | | | | 08b1274 graph.js: add graph and its dependencies to application.js
| |_|_|_|_|/  
|/| | | | |   
* | | | | | 6e367de graph.js: fix an issue where a certain global variable is not yet defined
* | | | | | 1959912 Made the document compileable and changed section depth for the table of contents.
* | | | | | 4fc5ff5 graph.js: introducing interface changes
* | | | | | 0d5743e graph.js: add a method to change the dimensions of a graph
* | | | | | c782aa9 graph.js: fix an issue where the labels would not show up
* | | | | | d9cec53 Fixed double clientbackends.
* | | | | | 30e8452 Added technologies and extra design goals.
* | | | | | afc91ae Added new EAD image
* | | | | |   7d30ca6 Merge branch 'feature/module' into develop
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| * | | | | | 23506a8 Added default modules with arbitrary equation values
* | | | | | | cba4208 Create samenvatting.txt
|/ / / / / /  
* | | | | |   a0775c9 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| * | | | | | c12f65f Removed jasmine examples code
| * | | | | | 92c4836 Removed the temp graph file
| * | | | | |   82f07c6 Merge branch 'feature/cell-class' into develop
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| | | |_|_|/ /  
| | |/| | | |   
| | * | | | | 2295882 Added Codo documentation
| | * | | | | 8ebcc21 Returns the cell in the callback
| | * | | | | a6e0548 In Coffeescript use @ for this
| | * | | | | 8d72c79 Added run logic
| | * | | | | b89a744 SpecTest for Cell class
| | * | | | | 22cd33b Fixed has function
| | * | | | | ebbc680 Some interfaced functions
| | * | | | | 5efcf78 Basic cell class
| * | | | | |   24ab69e Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \ \ \ \  
| * \ \ \ \ \ \   c2eb1bd Merge branch 'feature/graph' into develop
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| | | |_|_|_|_|/  
| | |/| | | | |   
| | * | | | | | 07b3e7e Graph: Add codo for clear() method
| | * | | | | | 0d44df5 Refactor Graph and create unit tests
| | * | | | | | e42ebb7 Add Graph class
* | | | | | | |   bac2d8c Merge branch 'feature/moduleClass' into develop
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| |_|_|/ / / / /  
|/| | | | | | |   
| * | | | | | | 9a8d01a Setter fixed and comments Codo-ized
| * | | | | | | b56f617 Module documentated and cleaned it up
| * | | | | | | 0028b87 Module equation, getters and setters added
* | | | | | | | 941d7af Server Ruby Documentation
* | | | | | | | c532e05 Client Coffeescript Documentation
* | | | | | | | 2e634a5 Removed old documentation
|/ / / / / / /  
* | | | | | | f329e6a Type of the module implemented and tested
| |/ / / / /  
|/| | | | |   
* | | | | | 069ddcf Added backbone and underscore to default js
* | | | | | 804c1b2 Added backbone + dependencies
* | | | | | 595beef Updated EAD to comply with project guidelines and incorporate feedback
* | | | | | 2304b76 Processed feedback and made a LaTex template
| |/ / / /  
|/| | | |   
* | | | |   04bfe49 Started document structure for EAD.
|\ \ \ \ \  
| * | | | | 7688cca (tag: v0.1.1) Added Jasmine examples
* | | | | |   91a5fd2 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| |/ / / / /  
| * | | | | 6a0db9d Installed jasmine
| * | | | | 32ed035 Added jasmine to gemfile
* | | | | |   b0b9397 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| |/ / / / /  
| * | | | | 205ed06 Added all default ignores
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| |/| | |   
| * | | | 2ebe8c3 Added main index template
| * | | | 5bee6b6 Added hook and default routes
| * | | | bf5d23a Added index action for main controller
| * | | | 42434c5 Removed greetings
| * | | | 5e4eb58 Added main controller
| * | | | 96f00f6 Added hook controller
| |/ / /  
| * | | 78b0067 Ignore updated for deliverables
| * | | ea3fe9a Added product vision deliverable
| * | | 814acb4 Added Glossary and definition of done
| * | | 8773262 Initial product vision update
| * | | c2289a7 Added pv
| * | | 71c1f96 Removed compiled samenvatting (added to gh-pages)
| * | | 72c62ea Remove redundant readme
| * | | b8ae808 Formatting
| * | | 5a7c81b Formatting
| * | | a0a65b0 Update README.md
| * | | e68f619 Update README.md
| * | |   fd91c48 Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
| |\ \ \  
* | \ \ \   0733ddc Merge branch 'develop' of github.com:Derkje-J/programming-life into develop
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| |/ / / /  
|/| / / /   
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| * | | 02a95a7 Update docs/planning samenvatten.txt
* | | | 0b0cbaf Removed tracked log files from tracking
|/ / /  
* | | 7a71a4a Corrected spelling mistake
* | | 7bbc837 Moved some stuff around and added samenvattingen
* | | d0e5ab5 Added deliverables
* | | 126d25b Added file extension
| |/  
|/|   
* | 209fd8c Removed development log
* | 2ba1fb9 Show some routing and basic page handling
* | ff76f9c Coffeescript removal
* | 951dbee Generated default greetings controller
* | 6c1f941 Updated site to rails 3.2
* | 134782e Special ignore file for ROR
|/  
* 2dbfaee Line normalisation
* f943c1b Added ignore
*   b18c70c Merge branch 'master' of github.com:Derkje-J/programming-life
|\  
| * 3f5ea59 Added CSS formatter.
* | 22006db Added CSS formatter.
|/  
* e752799 Added formatting script for Ruby on Rails code
* 6b2246f Added the 2 assignments for programming life
* 0b8be9c Fixed markup for planning
* d997dfa Add docs folder, add planning for text summaries
* 17319fe Initial commit