Include functionality for rearranging algebraic loops to turn certain DAEs into ODEs - #1400

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agarny wants to merge 177 commits into

cellml:mainfrom

agarny:issue1050

Commits on Dec 12, 2025

Hardcoded installation of symengine and gmp
RLee64
committed
af16cf6
Created basic rearrangement test case
RLee64
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9e2b0b3
Basic implementation of equation rearrangement
RLee64
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dafb56e
Change symEngineRepresentation to symEngineEquation
RLee64
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4331798
Added TODO comments
RLee64
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3953282
Renamed equation to seEquation
RLee64
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2de9098
Defined type aliases for symengine maps
RLee64
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1238673
Updated function parameters to use const and pass by reference
RLee64
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539dbf7
Added support for parsing SymEngine integers to AST
RLee64
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f2cab14
Assign parenthood to recreated ast tree
RLee64
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bdb3bd1
Removed DAE test case and associated files
RLee64
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3b2c5cc
Replaced exception use in symEngineEquation()
RLee64
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060b815
Removed redundant map include
RLee64
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685e1a1
Change SymEngineEquationResult to use tuple instead of pair
RLee64
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81f5766
Added rearrangement test suite
RLee64
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5dc3fcb
Create new test cases for rearrangement
RLee64
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4d4ba97
Remove old rearrangement test case
RLee64
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d9c4d10
Simple Equation Rearrangement.
agarny
authored
3e8456d

Commits on Dec 14, 2025

Make SymEngine -> AST parsing work with 3+ children
RLee64
committed
bd67b0c
Updated unarranged addition cellml file
RLee64
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c8d2bd8
Add/Sub symengine parsing support
RLee64
committed
080d5c3
Fixed unarranged multiplication cellml file
RLee64
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cce543f
Mult/div symengine parsing support
RLee64
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41e85ce
Improved unarranged trig test cases
RLee64
committed
4cbc787

Commits on Dec 15, 2025

Simple trig rearrangement support
RLee64
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a47ce0d
Updated unarranged constants cellml file
RLee64
committed
e157f82
Added support for various numbers and constants
RLee64
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4fdae53
Fix unarranged polynomial test cases
RLee64
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339a003
Added support for rearranging polynomials
RLee64
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5caecad
Update unary +/- parsing
RLee64
committed
5d9cd2f

Commits on Dec 17, 2025

Made explicit types auto
RLee64
committed
3a553be
Deleted unused test cases
RLee64
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9efff06
Renamed symengine cellml test files
RLee64
committed
f8a39f5
Cleaned up symengine trigonometric test case
RLee64
committed
d79d8fc
Fix issue with recreating unary functions for AST
RLee64
committed
aab7d89
Fixed children not setting their parent AST
RLee64
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9c1e0b8
Cleaned symengine test cases
RLee64
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fc1cf1c
Test expected generator equation code
RLee64
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ec0ace2
Made childSeExpression retrieval inline
RLee64
committed
f50049e
Fixed spelling error in symengine test files
RLee64
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5ca91b3
Removed redundant symengine multiplication test case
RLee64
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156bd52

Commits on Dec 18, 2025

Manual simplification of symengine results
RLee64
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ef336d5
Extended rearrangement.
agarny
authored
7c34ff2
Cleaned up symengine parsing to AST
RLee64
committed
1e11ef2
Added support for all trigonometric expressions
RLee64
committed
c79d3fd
Fixed issue with minus operator incorrectly applied
RLee64
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38d35fc
Support for rearranging exponents and logarithms
RLee64
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4854bfe
Analyser: some minor cleaning up.
agarny
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ad7b103
CI: temporarily allow CI tests to be run on PRs to the `staging` branch.
agarny
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b82e75b
Support for rearranging uncommon arithmetic operators
RLee64
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2486b9d

Commits on Dec 19, 2025

Commits on Jan 7, 2026

Rearrangement Restructure
RLee64
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e429b4d
Algebraic loop test case
RLee64
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ea06c14

Commits on Jan 8, 2026

Simple DAE to ODE solver.
RLee64
committed
8945d7e
Bug fixes and clean-up to dae tearing
RLee64
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7d7dfc8
Fixed algebraic loop test case
RLee64
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9c74638
GHA: allow code spelling check outside of cellml/libcellml.
agarny
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f7af1f3
CMake: temporarily disable Python bindings.
agarny
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d891992
CMake: find and use SymEngine.
agarny
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465abfd
Analyser: a SymEngine rational should be converted to a division.
agarny
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4af7d68
CI: temporarily disable our JavaScript job.
agarny
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6938ed9
Generator: temporarily disable some tests.
agarny
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6505b65
Analyser: addressed an MSVC warning (and therefore error).
agarny
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0f563bc
Tests: put the analyser's SymEngine tests in their own category.
agarny
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ef06b52
Analyser: SymEngine behaves slightly differently on different systems.
agarny
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dcbae1d
Analyser: some minor cleaning up.
agarny
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f62218a
Temporary changes to get 100% coverage.
agarny
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bcc01b9
Allow for classification of basic NLA systems
RLee64
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34f8d17
CMake: added support for SymEngine.
agarny
authored
0074611

Commits on Jan 9, 2026

Merge remote-tracking branch 'origin/staging' into full-rearrangement-support
RLee64
committed
e165b85
Further fixes
RLee64
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90f17de
Fixed rearrangement test case issue
RLee64
committed
e1d91b1

Commits on Jan 12, 2026

fix symengine derivative issues
RLee64
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1f019f0
Removed faulty test case
RLee64
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6c784a1
Commend out sine import test
RLee64
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143c887
Revert Mac/Linux test case change
RLee64
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aea0ece
Merge branch 'full-rearrangement-support' into dae-to-ode-v2
RLee64
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d05f827
Assume initialised variables are constants
RLee64
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d49ac38
Assume state variables used outside of DIFF elements as known
RLee64
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581350f
Improved isolated variable detection
RLee64
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86eb807
Cleaned up tearing comments
RLee64
committed
6b8a2e0

Commits on Jan 13, 2026

Handling equivalent variables
RLee64
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fd1812a
Move parsing functions to analyserimpl area
RLee64
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e149393
Ignore VoI when matching relationships
RLee64
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d4b4038

Commits on Jan 14, 2026

Treat should be state variables like state variables
RLee64
committed
987a051

Commits on Jan 15, 2026

Update symengine test cases for changed rearrangement
RLee64
committed
3b18017

Commits on Jan 16, 2026

Updated rearrangement test cases
RLee64
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324326d
Tearing refactor
RLee64
committed
6cde3d4
Fixed DAE to ODE test cases
RLee64
committed
d923a13

Commits on Jan 19, 2026

Improved NLA classification
RLee64
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9dce648
Switching back from dummy to symbol
RLee64
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d6047fc
Added capillary network test case
RLee64
committed
0504355
Fixed test cases (again)
RLee64
committed
fbc1ac0
Fixed computed constant equations being misinterpreted as constants
RLee64
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fbd2eac
Use is_null() instead of SymEngine::null
RLee64
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39e274e

Commits on Jan 20, 2026

Fixed issue with states not being tracked as dependencies
RLee64
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84070e9
Original capillary dae to ode test case fix
RLee64
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08450c9

Commits on Jan 23, 2026

Separated functionality for populating uncausalised
RLee64
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ec66ac9
Equation simplification
RLee64
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2a5e5cf

Commits on Jan 28, 2026

Improved simplification
RLee64
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349b420
Renaming matching and tearing
RLee64
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b957280
Reassigning local variable on matching
RLee64
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f593df7
Stop tracking matched variable as dependency
RLee64
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79db406
Track known variables as dependencies
RLee64
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04e6254

Commits on Jan 29, 2026

Replace AST tree for all equations
RLee64
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ff59bb6
Extra internal equation considerations
RLee64
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f506593

Commits on Jan 30, 2026

Simplified dependency building
RLee64
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bfac9e0
Fixing external variable support
RLee64
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e9558cd
Test case equation sequence rearrangement
RLee64
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33cc309
Bug fix
RLee64
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c129c35
Lower priority of variable-based matching
RLee64
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c58b876
Consider initialising externals
RLee64
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1f14cb6
Sunset original check function
RLee64
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83f6f4d
Update generator test case files
RLee64
committed
fdc0f8d
Fixed error with incorrect population of dependency chain
RLee64
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f9cbd32
Reduced substitution
RLee64
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ca1e9d3
Fixed bug with simplification not working
RLee64
committed
cf9a903

Commits on Feb 4, 2026

Test case fixes
RLee64
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924909c
Block dangerous external variable matching
RLee64
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d3aeecd
Tearing algorithm clean-up
RLee64
committed
26f6580
Fix CI checks
RLee64
committed
86d4965

Commits on Feb 5, 2026

Tearing algorithm clean-up
RLee64
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4ba4937
Re-enable test case
RLee64
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b6c42aa
Merge branch 'dae-to-ode' of https://github.com/RLee64/libcellml into dae-to-ode
RLee64
committed
5a19b93

Commits on Apr 24, 2026

Commits on Apr 27, 2026

Merge branch 'main' into issue1368
agarny
authored
6e53a5b

Commits on May 25, 2026

Merge branch 'main' into issue1368.
agarny
committed
617f531
Some cleaning up following the merging in of Rayen's DAE->ODE's work.
agarny
committed
7b3682b
Removed our original C++20 standard code.
agarny
committed
84fa4c1
Analyser: removed the use of some sets.
agarny
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3ffd4a8
Removed the SHARED keyword from `add_library()` in `tests/CMakeLists.txt`.
agarny
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c807f25
Merge branch 'issue1368' into issue1050
agarny
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07db850
Analyser: removed the use of some sets.
agarny
committed
eb5d08a
Removed the SHARED keyword from `add_library()` in `tests/CMakeLists.txt`.
agarny
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6164f8f
Merge branch 'issue1368' into issue1050
agarny
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e3ce274
Formatting.
agarny
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72fbd7e
Don't redeclare `rearrangedSEExpression`.
agarny
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c0cc876

Commits on Jun 5, 2026

Commits on Jun 9, 2026

Tests: account for differences between Windows/Linux and macOS.
agarny
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0b36ed9
Python: make sure that libCellML's dependencies can be found.
agarny
committed
c071293
Added AnalyserEquationAst::clone() to our bindings.
agarny
committed
4e0c9f6
CI: revised our JavaScript CI test.
agarny
committed
a2cd792
Fixed a memory leak issue.
agarny
committed
fca9945
Addressed a coverage issue in our use of SymEngine in the analyser.
agarny
committed
8a78d90
CMake: fixed an issue with get_runtime_dlls_from_target() on Windows.
agarny
committed
c425b61
Tests: account for differences between Windows, Linux, and macOS.
agarny
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15b17c5
Tests: fixed some expected generated codes.
agarny
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a0674cd
Analyser: fixed a topological NLA dependency order and added an opaque symbol swap condition.
agarny
committed
d846f2d
CI: specify the Intel architecture for our dependencies on Windows and Linux.
agarny
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64075a9
Python: make sure that SymEngine can be found.
agarny
committed
0bcdd43
Merge branch 'cache-equiv-vars' into issue1368
agarny
committed
f0606c5
Don't reserve.
agarny
committed
ead0820
Some minor cleaning up.
agarny
committed
7f008c1
Put back something that got mistakenly deleted during the last merge.
agarny
committed
131a762
Merge branch 'issue1368' into issue1050
agarny
committed
060bdc9
Merge branch 'main' into issue1368
agarny
authored
85e409b
Merge branch 'main' into issue1050
agarny
authored
fc6de54

Commits on Jul 9, 2026

Merge branch 'main' into issue1368
agarny
committed
264c3b3
Some cleaning up as a result of the last merge.
agarny
committed
c67d9c9
Merge branch 'main' into issue1368.
agarny
committed
32b3740
Merge branch 'issue1368' into issue1050
agarny
committed
bd2206c
XmlNode: improved the conversion to a tripped string.
agarny
committed
be89bad
Generator: removed unneeded header file.
agarny
committed
1d642bf
Generator: simplified parenthesis wrapping.
agarny
committed
0829a38
Generator: cache profile lookups.
agarny
committed
4ec16da
Merge branch 'issue1368' into issue1050
agarny
committed
ff6df1b
Generator: some minor cleaning up following the last merge.
agarny
committed
1c21b32