Complete syntax parsing rework to preserve user formatting. - [merged]

[MicahGale]

Merges 48-add-support-for-keeping-comments -> alpha-test

Tests to add:

1. [ ] test tab expansion.
2. [ ] Test SC and FC tally comments
3. [ ] Ensure comments get placed with following object.
4. [ ] Clear out all TODO comments.
5. [ ] Clean up code and refactor.
6. [ ] Update all documentation.
7. [ ] Can I delete allowed_keywords?

[MicahGale]

added 2 commits

• dc707783 - Refactored Syntax class names
• 17e28cee - Removed Card from all class names for semantic layer

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[MicahGale]

added 1 commit

• 7e237289 - Named token classes

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[MicahGale]

added 2 commits

• dfd58129 - Started refactoring data_card file names
• 636fc9ce - Finished cleaning up data_card refactor

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[MicahGale]

added 2 commits

• c499f51b - Refactored problem.data_cards
• d22ebe99 - Removed Card from MCNP_Problem

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[MicahGale]

added 5 commits

• b1c799e5 - Removed Card from MCNPInput and most children
• 2a269e8f - Update data_input in materials docs
• 9cd2f8d4 - Removed input from errors
• 3771e90e - Removed Card from cells
• d87d3cca - Removed card from cell object

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[MicahGale]

added 6 commits

• 99979196 - Removed Card from CellModifierInput
• b6827e5c - Removed Card from surfaces
• 5b6c6ded - Removed Card from input parsing
• 708f6bc3 - Removed Card from data_inputs
• 18adfea5 - Removed card from MCNP_Input
• a4214bcf - Updated tests to not look for CARD

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[MicahGale]

added 2 commits

• 6ebf8184 - Fixed header error
• 0e1eda8c - Fleshed out parser recursive data structure

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[MicahGale]

added 2 commits

• 1571fd36 - Made Input iterable over every single character
• b1de3361 - Started testing possible tokenizer design

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[MicahGale]

added 3 commits

• 5bd6d444 - Completed tokenization and parsing
• ccedd1b1 - Added new lines back to the lines in iteration
• 0b9e6aa8 - Made toy tester more thurough

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[MicahGale]

added 1 commit

• b8cba08b - Reved development number

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[MicahGale]

added 2 commits

• cb693040 - Switched to fixturing a cell parser
• 1dfff5d6 - Worked on Node parser logic.

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[MicahGale]

added 2 commits

• d79d17b1 - Made tokens able to go to subclass
• 6db789f3 - Worked on node parsing logic

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[MicahGale]

added 4 commits

• abb976e3 - Made comments barely parseable
• 099b8d90 - Allowed literals to handle negative numbers
• e9e38578 - Made recursive linear parsing work
• 1ba3f07f - Updated test to be more accurate.

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[MicahGale]

added 1 commit

• a2ccf534 - Started fleshing out a semantic tree

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[MicahGale]

added 5 commits

• e3ce8109 - Fixed class typo with semantic nodes
• dd7f9d97 - Made it so that tokens could be printed in object tree
• d4fa34e4 - Made result namedTuple
• 29c9ddf8 - Moved to returning a tuple and making parser stateless
• ae8a86dc - Worked on fixing recursive logic with independent parsed objects

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[MicahGale]

added 1 commit

• 7acfaa1e - Removed debug statements and added todo for further work

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[MicahGale]

added 3 commits

• b5297055 - Added a space token
• 186b94c2 - Tried to work on getting node parser to work with spaces and comments properly
• e018e904 - Started logic to find last full node

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[MicahGale]

added 1 commit

• 5197e343 - Fixed bug so spaces and comments can be handled after end of tape

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[MicahGale]

added 2 commits

• 170d575e - Made method to find the last leaf parent node
• 0371cfef - Made implicit tokens pop up to the last populated leaf parent

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[MicahGale]

added 1 commit

• 841c498c - Fixed comment double adding

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[MicahGale]

added 1 commit

• e0b1470d - Made token generator a deque

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[MicahGale]

added 1 commit

• 2d1d671f - Updated node parser docs

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[MicahGale]

added 1 commit

• 91b7cb7d - Updated test to use branches for material information

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[MicahGale]

added 1 commit

• abb79450 - Worked on branching logic; caused infinite loop.

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[MicahGale]

added 2 commits

• 55df9af9 - Simplified and fixed bug with allowed values check
• 910e0922 - Did test to do different material branch parsing

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[MicahGale]

added 1 commit

• e74bc012 - Implemented parser clear function

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[MicahGale]

added 3 commits

• 1e41559a - Reformatted
• 4025c76e - Handled case of token children not returning last
• 9c0d0a84 - Ensured that token parser returned failed token

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[MicahGale]

added 1 commit

• 382f2af6 - Fixed double handling comments in branches

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[MicahGale]

added 1 commit

• acbe7bdc - Made generic validator function for token parsing

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[MicahGale]

added 3 commits

• be14d8ec - Fixed token parsing of single parentheses
• 8866bb6a - Made very sketchy test of surface parsing
• 094b7aaf - Tried to avoid infinite branching loops

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[MicahGale]

added 2 commits

• 02693a83 - Added support for class children that are not instantiated
• 99821b66 - Fixed issues with infinite hang.

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[MicahGale]

added 3 commits

• 902ef0f4 - Made recursive branching work with pass_through concept
• 7dbedff7 - Made printing less confusing when data includes parantheses
• f665f7c5 - Removed unnecessary node from surface parsing

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[MicahGale]

added 2 commits

• 9862d826 - Really stressed the recursion out.
• c0c453b9 - Added debug print statements

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[MicahGale]

added 1 commit

• 3b1114b9 - Fixed branching recursion to allow 'nonfailure' branch rewinds

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[MicahGale]

added 2 commits

• c4b98990 - Added surface anding
• 75c49a0a - Allowed supressing implicit spaces

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[MicahGale]

added 2 commits

• b016f4f8 - Simplified anding test
• bc569937 - Tried to avoid infinite recursion on init

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[MicahGale]

added 49 commits

• e762c6fa - Removed old imports
• 8bc347ee - Tried switching over to SLY for tokenizing
• 6e3e2c5c - Switched to simple tokenizing test case
• 8da59e69 - Added more edge case tokens
• 481ff1f3 - Made input text property for tokenizing
• 573c427e - Started writing a cell input parser
• d6870f4c - Made null token and tweaked number parsing priority
• 13499b42 - Prototyped system for parser subclassing
• 9da22247 - Implemented improper geometry parser
• f6eaa4b2 - Tried to make surface logic precedence work.
• fdc52f0b - Tested more complex geometry precedence
• 762df008 - Changed tokens to case insensitive
• f043b1b3 - Moved back to move complex geometry
• 9d8774d8 - Added new level of geometry precedence for negation
• 55f2a008 - Made geometry definition allow spaces and comments
• 57bd45dc - Made particle designation tokens
• 250f2552 - Simplified how NULL tokens are generated
• 0bad9f0d - Got a single parameter working
• de0f04fc - Wrote test for multiple parameters
• a4c872bf - Deleted extra debugging print statement
• 259e2dea - Fixed typo in parameters
• 13810774 - Debugging parser with error supression
• 72ffb91f - Fixed multi-parameter parsing
• 417ef8ee - Changed int and float to number
• a546c8d7 - Ignored more files
• ecb1568c - Moved base to new file
• 66762f3b - Moved cell parser to own file
• 69fe8f38 - Made surface parser shell
• 41df8b19 - Made new system to identify keywords
• 8b74e18b - Added literals for surfaces.
• 3d33a5be - Made number sequence for surfaces
• 92f8bb2e - Tested surface parser
• 7d6f9d18 - Fixed surface parser by adding padding
• 4fa04c4f - Allowed number phrase to end in number
• b8e117f5 - Made surface parser handle transforms, and modifier literals
• bc72014c - Alphabetized tokens
• c95dfdb3 - Added a ZAID token
• 176d2546 - Added keywords for materials
• b709dc29 - Added base material parser
• edfa385e - Wrote material testing
• 1e6e01f3 - Moved parameter to base, and generalized parameter spacer
• 16b69771 - Moved parameters to base parser
• 08e5329c - Added material paremeters parsing
• 45f614f8 - Added text_phrase
• 1c4a85c1 - Fixed ambiguous parameter ending for material
• d7abca4f - Allowed text base parameters
• 562f6270 - Wrote parser for READ
• f61ecd91 - Made Input tokenized
• c98a7763 - Merge branch 'sly_parser' into 48-add-support-for-keeping-comments

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[MicahGale]

added 6 commits

• fff8bed0 - Set python requirements
• 9ac92612 - Made harder read
• b2e5a09d - Removed words and cleaned up input for SLY
• ab47f3a7 - Started making semantic nodes generate with parsing
• 02eba8b1 - Updated ReadInput to use parser objects
• f69e19a5 - Removed useless seen action

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[MicahGale]

added 2 commits

• d15529f0 - Started removing comment logic from chunker
• 10cdebe2 - Started making semantic node with dict tree

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[MicahGale]

added 4 commits

• b0b11b24 - Fixed input tokenizer
• 20186ab2 - Made Semantic node dict actually work
• abab9a8e - Made test for the read input
• 826ea761 - Updated read input and parsing to work with dictionary system

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[MicahGale]

added 3 commits

• 33f11aa6 - Made sure tokens don't discard number formatting
• 9e44b9a4 - Made semantic node for list of values
• e026493b - Made parameters node consistent with base class

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[MicahGale]

added 6 commits

• 0d3b74ee - Made it easy to get a leaf value quickly
• 24c03e84 - Trimmed some hand parsing from MCNP_Input
• e464c8cd - Made cell parser return semantic nodes
• 228a1b18 - Started using syntax tree to init cell
• a51f7d33 - Got rid of _cell_number to be idiomatic
• 2d237c7d - Fixed loading the wrong material variables

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[MicahGale]

added 7 commits

• 093acc6d - Rolled back test to work on geometry syntax tree
• 1e829021 - Added geometry syntax tree node
• 9621cf69 - Updated type for leaf node
• 80c576f3 - Made padding for values settable
• 224c360d - Fixed super bug
• 07e67410 - Made parameters node handle particle designator
• 0102e4f7 - Generated geometry tree node

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[MicahGale]

added 16 commits

• 0102e4f7...9f857496 - 14 commits from branch develop
• 8c619eff - Made way to get the object numbers from the geometry logic
• 2c91cd2a - Merge branch 'develop' into 48-add-support-for-keeping-comments

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[MicahGale]

added 1 commit

• 3d1e940b - Expanded tabs to resolve #79

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[MicahGale]

added 3 commits

• 62b192dc - Raised the right error again
• 3b2558a7 - Raise error with like but formats
• defd8c41 - Tried to get fill parameter sequence working

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[MicahGale]

added 4 commits

• ca18eac3 - Fixed bug with mcnp_input repr
• 5640edd5 - Fixed value node to have nodes
• e9981ed4 - Fixed bugs in geometry parsing
• 8f163f4c - Fixed single surface geometry by adding a shift operator

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[MicahGale]

added 5 commits

• bba5a24a - Fixed parameters that use = space
• 556fa9ca - Fixed geometry having ValueNode leaves by recursion
• 8b23ec0f - Updated test to use simpler parameter
• 97e6899b - Automatically grabbed parameters branch
• de6163cc - Made lists print a value

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[MicahGale]

added 3 commits

• 756b3d5c - Made it possible to get simple value from complex structures
• c022263f - simplified parameters test to not get confused by complex data structures
• 835ed090 - Allowed number sequences to include 0.

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[MicahGale]

added 3 commits

• d36ec5a4 - Time to move onto using test suites
• 547549e4 - updated paramerters test for new value
• cebab065 - Removed cell geometry logic strings

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