First derivative - #151

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sjanssen2 wants to merge 78 commits into

outside_looporderfrom

first_derivative

Commits on Oct 21, 2022

Commits on Oct 22, 2022

let the AST know that the user requested code generation for derivatives
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fc73e8b
enable adding another argument to the front
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19458b7
injecting first statements in inside code
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5d388d2

Commits on Oct 25, 2022

adding first derivatives test
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60c364c
add functions to generate getter and setter for derivatives
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b35e257
report derivatives instead of outside results
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50b95aa
pass calling-NT to alt code generation
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eb7ed8b
moved additional functionallity from generated *.hh to here
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4084123
make OUTSIDE_NT_PREFIX more visible in grammar.hh
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6afe046
record user provided axiom, since it will be changes in outside generation
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087fabc
pass ast to init_ret_stmts
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60d2e7c
add "candidates" list in NT generation to record use of sub-solutions
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44677b5
define functions for derivative reporting function generation
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69cfed9
inject and init new traces Vector in Table Declartion; define DERIVATIVES; generate method to print derivatives
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ecef00b
pass calling-NT to alt code generation; for outside-NTs: retrieve pre-recorded trace weights as backward pass;
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58f7af2
adding scoring algebra for derivative testing
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402a382
use proper return variable name
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8f600a0
move execution of statements to a) enable debugging and b) use same "code" for both getters
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40b4a23
moving functionality into own function, since it need to be called in moving boundary and single split context
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4da7e91
alts might be parameterized Terminals. Don't inject in these cases
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ad1c566
activating two more tests: needleman wunsch derivatives
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e01e058

Commits on Oct 26, 2022

adding Gotoh grammar for further testing
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2f9cdc2
in order to add statements for tracing within the IF condition for pushing a valid candidate to the answer list, we create a new list::statement "derivative_statements" onto which these code lines …
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4af9441
codestyle
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edc2495
switch order of grammar definitions to pass mod tests
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1255074
add check for untabulated results
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2ccb881
adding a todo
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73cfab3
use correct alt table, also consider direct link to other non-terminal as in A -> InsX
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d9cf41d
adding Gotoh test
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e61d6d8
codestyle
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84c23e7
add missing condition
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2cafbbe
per definition outside_axiom table returns a list, i.e. cannot be reduced to a single value
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69d3d50
proper newline for 1D NTs
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3af1850

Commits on Nov 4, 2022

Commits on Dec 2, 2022

adding branch that shall execute tests
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402fd8b

Commits on Dec 5, 2022

rename "first derivatives" into "1. derivatives"
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2fe5793

Commits on Dec 7, 2022

Commits on Dec 9, 2022

Commits on Dec 16, 2022

set recursion base to 1.0 for first derivative computation
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23b388f
add Sonne-Regen test
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c9cf750
add probabilistically proper Sonne Regen HMM
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2de7319

Commits on Dec 20, 2022

log space requires re-transformation here
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d9fcd54
replace h with sum
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1ace193
add function to replace h with sum in outside rules for derivative generation
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6e59960

Commits on Dec 21, 2022

fixing type optimization for derivative versions of choice functions
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e7eb90f
remove tab
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c6a3cd0

Commits on Dec 23, 2022

adding normalize_derivative functions
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99962ec
pass the user prodived normalization function as another argument
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30a1b90
lint & typo
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0623602
new semantic check that tests for presense of normalization function for derivatives
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77c0f39
make special normalization "static"
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acbef3a
run check for derivative function
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75f306f
use passed user function to normalize a trace VS partition function, i.e. all weights combined
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2131890
when searching for answer type, skip choice functions
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c7979c5
revert stupid error: type inference independent on actual check
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76d87dd

Commits on Jan 13, 2023

Merge pull request #164 from jlab/hSUM
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7a1656a
Merge branch 'master' of github.com:jlab/gapc into hSUM
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fa97cd9
Merge pull request #169 from jlab/hSUM
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68ab4f0

Commits on Jan 16, 2023

Merge branch 'outside_looporder' into first_derivative
sjanssen2
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ac5fa8f