Parsing improvements - merge `improve-parsing` into `master`#114

Merged

xtrojak merged 116 commits intomasterfrom improve-parsing

May 9, 2024

+2,480-1,472

Commits on May 17, 2023

Added tests for insert_atomic_to_complex case
xtrojak
committed

Commits on May 23, 2023

Merge pull request #74 from xtrojak/72-write-tests
xtrojak
authored

Commits on Jun 1, 2023

parsing tests refactoring
Marketa Opichalova
committed

Commits on Jun 2, 2023

extracting parsing tests
Marketa Opichalova
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parsing tests relocated
Marketa Opichalova
committed
unnecessary parsing models deleted
Marketa Opichalova
committed
Merge pull request #78 from mopichalova/75-separate-test-folders
xtrojak
authored

Commits on Nov 7, 2023

parsing test - atomic
Marketa Opichalova
committed
parsing test - struct
Marketa Opichalova
committed
parsing test - complex
Marketa Opichalova
committed
add parsing test objects
Marketa Opichalova
committed

Commits on Nov 14, 2023

parsing - test side
Marketa Opichalova
committed
parsing - test objects
Marketa Opichalova
committed
test parsing - rate
Marketa Opichalova
committed

Commits on Dec 5, 2023

parsing rate - negative cases added
Marketa Opichalova
committed
parsing rate - negative cases added
Marketa Opichalova
committed
parsing atomic - negative cases added
Marketa Opichalova
committed
parsing complex - negative cases added
Marketa Opichalova
committed

Commits on Dec 7, 2023

parsing - negative cases added
Marketa Opichalova
committed
Add build section to .readthedocs.yaml configuration
xtrojak
authored
Update .readthedocs.yaml
xtrojak
authored

Commits on Dec 11, 2023

Update test_rate.py
mopichalova
authored

Commits on Dec 17, 2023

Merge pull request #85 from mopichalova/79-core-tests
xtrojak
authored

Commits on Jan 3, 2024

testing objects reorganization
Marketa Opichalova
committed
refactor parsing tests and update object references
Marketa Opichalova
committed

Commits on Jan 4, 2024

object creation clean up
Marketa Opichalova
committed
move txt models to dedicated files
Marketa Opichalova
committed

Commits on Jan 8, 2024

rate test correction
Marketa Opichalova
committed
test_vector_model objects creation cleanup
Marketa Opichalova
committed
object testing remove duplicities
Marketa Opichalova
committed

Commits on Jan 9, 2024

Merge pull request #90 from mopichalova/80-testing-objects
xtrojak
authored

Commits on Jan 24, 2024

fix insert parsing logic
Marketa Opichalova
committed

Commits on Jan 29, 2024

comments and docstrings added
Marketa Opichalova
committed

Commits on Jan 30, 2024

Merge pull request #91 from mopichalova/72-improve-insert-handling
xtrojak
authored

Commits on Jan 31, 2024

enable direct usage of complexes
Marketa Opichalova
committed

Commits on Feb 7, 2024

newline enforcement and ban
Marketa Opichalova
committed

Commits on Feb 8, 2024

sections order is arbitrary
Marketa Opichalova
committed
newlines removed after loading lines from file
Marketa Opichalova
committed
regulations ending
Marketa Opichalova
committed

Commits on Feb 12, 2024

arbitrary order of sections - permutations loaded from txt file
Marketa Opichalova
committed
arbitrary order of sections enabled
Marketa Opichalova
committed
remove txt file loading
Marketa Opichalova
committed

Commits on Feb 13, 2024

zooming inserting
Marketa Opichalova
committed
test cases for complexes in abstract sequence
Marketa Opichalova
committed

Commits on Feb 19, 2024

Merge branch 'improve-parsing' into 89-complexes-in-abstr-seq
mopichalova
authored

Commits on Feb 21, 2024

test rule object correction
Marketa Opichalova
committed
test correction - wrong parser for comparing complex objects
Marketa Opichalova
committed

Commits on Feb 22, 2024

refactor model processing to aggregate section's data instead of overwriting
Marketa Opichalova
committed
correction - allow only one regulation
Marketa Opichalova
committed

Commits on Feb 26, 2024

Commits on Feb 27, 2024

tests for bidirectional rules
Marketa Opichalova
committed
bidirectional rules enabled
Marketa Opichalova
committed
bidirectional rules extended
Marketa Opichalova
committed
bidirectional rules with two rates allowed
Marketa Opichalova
committed

Commits on Mar 4, 2024

disallow one rate for bidirectional rules
Marketa Opichalova
committed

Commits on Mar 5, 2024

check if regular label is valid regex and labels in regulation exist
Marketa Opichalova
committed

Commits on Mar 6, 2024

check all possible permutations of the labels in the regex
Marketa Opichalova
committed
new error class for regulation errors
Marketa Opichalova
committed

Commits on Mar 11, 2024

Commits on Mar 12, 2024

merged define rule correction
Marketa Opichalova
committed
rate tests extended
Marketa Opichalova
committed
allow nested fractions
Marketa Opichalova
committed

Commits on Mar 13, 2024

Commits on Mar 14, 2024

Merge pull request #99 from mopichalova/98-zooming-syntax
xtrojak
authored

Commits on Mar 15, 2024

regex pattern to subpattern correction
Marketa Opichalova
committed
regex grammar extended
Marketa Opichalova
committed
Merge branch 'improve-parsing' into 88-regex-labels
mopichalova
authored

Commits on Mar 17, 2024

Merge pull request #100 from mopichalova/87-robust-rate-expr
xtrojak
authored

Commits on Mar 18, 2024

remove tree_to_string duplicity by moving tree_to_string to utils.py
Marketa Opichalova
committed
Merge branch '88-regex-labels' of github.com:makikeo/eBCSgen into 88-regex-labels
Marketa Opichalova
committed

Commits on Mar 20, 2024

Merge pull request #97 from mopichalova/88-regex-labels
xtrojak
authored
implement only unique name atomics in struct
Marketa Opichalova
committed

Commits on Mar 21, 2024

test correction - non-unique atomics
Marketa Opichalova
committed
raise ComplexParsingError when the alias is not defined
Marketa Opichalova
committed
test extended - (non)unique atomics in struct
Marketa Opichalova
committed

Commits on Mar 26, 2024

Commits on Apr 15, 2024

replication rule tests
Marketa Opichalova
committed
replication rules added
Marketa Opichalova
committed

Commits on Apr 16, 2024

tests for observables
Marketa Opichalova
committed
observable grammar added
Marketa Opichalova
committed
observable tests extended
Marketa Opichalova
committed

Commits on Apr 23, 2024

observables extended and scaling implemented
Marketa Opichalova
committed
rule arrows simplified
Marketa Opichalova
committed
test replication rule objects
Marketa Opichalova
committed
scaling complexes with compartments corrected
Marketa Opichalova
committed

Commits on Apr 24, 2024

observables - remove modifiers, quantifiers and stoichiometry
Marketa Opichalova
committed
Merge pull request #107 from mopichalova/106-replication-rules
xtrojak
authored

Commits on Apr 26, 2024

Merge pull request #109 from mopichalova/108-observables
xtrojak
authored