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Analyser/Generator: support systems of non-linear algebraic equations #942

Merged
merged 161 commits into from
May 23, 2023
Merged

Analyser/Generator: support systems of non-linear algebraic equations #942

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0af2aaa
Generator: added a test for a model with one algebraic equation with …
agarny Jul 20, 2021
d0f31cd
Merge branch 'main' into issue882
agarny Jul 26, 2021
ad2ad79
Merge branch 'main' into issue882.
agarny Dec 1, 2022
ed13665
Merge branch 'main' into issue882
agarny Dec 1, 2022
0c6e7b4
Merge branch 'main' into issue882
agarny Dec 2, 2022
5de37f5
Merge branch 'main' into issue882.
agarny Dec 4, 2022
bc8f17c
Merge branch 'issue1070' into issue882.
agarny Dec 5, 2022
b03c34f
Merge branch 'issue1070' into issue882.
agarny Dec 5, 2022
793c0b5
Tests: some minor cleaning up.
agarny Dec 5, 2022
062370c
Merge branch 'main' into issue882.
agarny Dec 5, 2022
228b83e
Tests: some minor cleaning up.
agarny Dec 6, 2022
2e1fc3d
Generator: added the NLA type of model.
agarny Dec 7, 2022
b956602
Added a test for an algebraic system with three linked unknowns.
agarny Dec 7, 2022
3aad22f
Analyser: some minor cleaning up.
agarny Dec 7, 2022
e0867e3
Analyser: some minor cleaning up.
agarny Dec 7, 2022
b89fc7f
Analyser: distinguish between different types of initialised variables.
agarny Dec 9, 2022
84e88c7
Merge branch 'issue882' of https://github.com/agarny/libcellml into i…
agarny Dec 9, 2022
81b6c5a
Revert "Merge branch 'issue882' of https://github.com/agarny/libcellm…
agarny Dec 9, 2022
7912056
Analyser: distinguish between different types of initialised variables.
agarny Dec 9, 2022
ca1085c
Merge branch 'issue1074' into issue882.
agarny Dec 22, 2022
a4f7666
Updated our API documentation.
agarny Dec 22, 2022
c3fc8d0
Some minor cleaning up.
agarny Dec 22, 2022
faac4b1
Analyser: allow an algebraic variable to be initialised.
agarny Dec 22, 2022
d653301
Analyser: improved branch coverage.
agarny Jan 4, 2023
7145e12
Check calls to std::weak_ptr<T>::lock().
agarny Jan 5, 2023
fb13118
Merge branch 'issue1082' into issue882.
agarny Jan 26, 2023
0b24ec5
Merge branch 'issue1079' into issue1082.
agarny Jan 26, 2023
8f6494e
Merge branch 'issue1082' into issue882.
agarny Jan 26, 2023
71a4f7b
Fixed various things following commit fb13118b.
agarny Jan 26, 2023
79a84ca
Some minor cleaning up.
agarny Jan 26, 2023
f9cd90f
Don't sort our internal variables or equations.
agarny Jan 26, 2023
3b52ccd
Merge branch 'issue1082' into issue882.
agarny Jan 26, 2023
dfbf849
Some minor cleaning up.
agarny Jan 30, 2023
efcd8f3
Merge branch 'issue1089' into issue882
agarny Jan 30, 2023
ffef96b
Merge branch 'issue1089' into issue882.
agarny Jan 31, 2023
425f928
Some minor cleaning up following a previous merge.
agarny Jan 31, 2023
523028e
Merge branch 'issue1089' into issue882.
agarny Jan 31, 2023
254029c
Some minor cleaning up following a previous merge.
agarny Jan 31, 2023
988474a
Merge branch 'issue1089' into issue882.
agarny Jan 31, 2023
f5cb55a
Some minor cleaning up following a previous merge.
agarny Jan 31, 2023
102e0c6
Analyser: replace RATE with ODE.
agarny Feb 1, 2023
c49eed7
Some minor cleaning up.
agarny Feb 1, 2023
13c256f
Fixed the algebraicEqnWithOneNonIsolatedUnknown test.
agarny Feb 1, 2023
93cd002
Analyser: some work on detecting a variable computed through one NLA …
agarny Feb 2, 2023
896f0bc
Generator profile: some work on supporting code for a variable comput…
agarny Feb 2, 2023
8d06412
Generator: some work on generating code for a variable computed throu…
agarny Feb 2, 2023
694165b
Merge branch 'issue1089' into issue882.
agarny Feb 5, 2023
e461d66
Merge branch 'issue1089' into issue882.
agarny Feb 7, 2023
60045b0
Merge branch 'issue1089' into issue882.
agarny Feb 7, 2023
5d61cdb
Merge branch 'issue1089' into issue882.
agarny Feb 7, 2023
b9c180a
Some minor cleaning up.
agarny Feb 8, 2023
2a6db1e
NLA-related tests: roots are always computed in computeVariables().
agarny Feb 13, 2023
83665d1
Analyser: handle the case where an equation is used to compute one or…
agarny Feb 8, 2023
2bdf680
Merge branch 'issue1089' into issue882.
agarny Feb 14, 2023
767c596
Analyser: handle the case where an equation is used to compute one or…
agarny Feb 14, 2023
e6a9182
Merge branch 'issue1089' into issue882.
agarny Feb 14, 2023
e52edd4
Merge branch 'issue1089' into issue882.
agarny Feb 14, 2023
74039b1
Analyser: renamed ASSIGNMENT to EQUALITY.
agarny Feb 14, 2023
aeaf428
Analyser: make sure that equations are equality statements.
agarny Feb 14, 2023
f3e3b9e
Analyser: properly define the type of a model and of an equation.
agarny Feb 14, 2023
37f0534
Analyser: handle the case where an equation is used to compute one or…
agarny Feb 14, 2023
0285bc0
qwe
agarny Feb 16, 2023
fe14bc0
qwe
agarny Feb 16, 2023
d72f68e
qwe
agarny Feb 17, 2023
8e86236
qwe
agarny Feb 17, 2023
4a6cbdc
qwe
agarny Feb 17, 2023
fc1afa7
TEMP
agarny Feb 20, 2023
1613e6f
Analyser: handle the case where an equation is used to compute one or…
agarny Feb 14, 2023
2312e4c
Merge branch 'issue882' of https://github.com/agarny/libcellml into i…
agarny Feb 22, 2023
b876e01
Merge branch 'issue446' into issue882.
agarny Mar 2, 2023
9bd1a96
Fixed some merging issues.
agarny Mar 2, 2023
cc78c75
Merge branch 'issue1130' into issue882.
agarny Mar 2, 2023
3f61f13
Some minor cleaning up.
agarny Mar 2, 2023
6062d27
Merge branch 'issue1134' into issue882.
agarny Mar 2, 2023
104d106
Merge branch 'issue1134' into issue882.
agarny Mar 2, 2023
5a96cf5
Analyser: more consistent with the rest of our codebase.
agarny Mar 2, 2023
9731db3
Some minor cleaning up.
agarny Mar 3, 2023
54b3e1c
Generator: genearte a-(-b) rather than a--b.
agarny Mar 8, 2023
aa4060c
Analyser: handle the case where an equation is used to compute one or…
agarny Mar 7, 2023
8038775
Some minor cleaning up.
agarny Mar 13, 2023
03bd6dc
Analyser/Generator: added some more tests.
agarny Mar 13, 2023
07e7186
Debug: have `printAst()` use the `Debug` class.
agarny Mar 13, 2023
b6aa87e
Generator: added a static `equationCode()` method.
agarny Mar 14, 2023
e18ecf5
Generator: some minor cleaning up.
agarny Mar 14, 2023
7c77b44
Debug: added a couple of methods to list variables and equations of a…
agarny Mar 14, 2023
f54e55a
Analyser: make sure that external variables are properly handled in a…
agarny Mar 15, 2023
3b4b2df
Analyser: added a test for an overconstrained NLA system.
agarny Mar 16, 2023
7e15594
Some minor cleaning up.
agarny Mar 16, 2023
0680980
Analyser: added a test for an algebraic system with various dependenc…
agarny Mar 17, 2023
269e62a
Analyser: added a non-ordered version of the test for an algebraic sy…
agarny Mar 17, 2023
9e0a62b
Some minor cleaning up.
agarny Mar 17, 2023
e982f34
Added the ODE and DAE versions of the Robertson model.
agarny Mar 20, 2023
c7a1458
Generator: make sure that we can generate code for something like dx/dt.
agarny Mar 20, 2023
b985141
Generator tests: temporarily disable some tests.
agarny Mar 20, 2023
f00e363
Merge branch 'issue1137' into issue882.
agarny Mar 21, 2023
5a3509c
Analyser: handle the case where an equation is used to compute one or…
agarny Mar 21, 2023
287ff10
Analyser: removed some tests as a result of supporting NLA systems.
agarny Mar 22, 2023
4fc61f6
Generator: refined our algebraicSystemWithVariousDependenciesOrdered …
agarny Mar 22, 2023
8b878bc
Analyser: handle the case where an equation is used to compute one or…
agarny Mar 22, 2023
13d5e5c
Merge branch 'issue1082' into issue882.
agarny Mar 23, 2023
876e1d7
Generator: fixed a merging issue.
agarny Mar 23, 2023
fe71b98
Tests: updated the algebraic_system_with_various_dependencies test.
agarny Mar 24, 2023
a0981e0
Debug utilities: make sure that `astAsCode()` can handle a nullptr AST.
agarny Mar 27, 2023
b546b2f
Generator: fixed some tests.
agarny Mar 27, 2023
7af6496
Analyser/generator: fixed various issues.
agarny Mar 27, 2023
ba0d0d8
Merge branch 'main' into issue882
agarny Mar 28, 2023
1059cf0
Fixed a merging issue.
agarny Mar 28, 2023
fa2da51
Fixed the generated code for the hodgkinHuxleySquidAxonModel1952Nla t…
agarny Mar 29, 2023
633a79a
Some consistency-related changes.
agarny Mar 29, 2023
43c93fb
Merge branch 'main' into issue882.
agarny Mar 30, 2023
698b191
Analyser: don't allow rates to be computed using an NLA equation.
agarny Mar 30, 2023
78889c0
Coverage: make sure that we generate parentheses for the RHS of a `mi…
agarny Mar 30, 2023
dcfec77
Analyser/generator: replaced some `if...else if...` statements with s…
agarny Mar 31, 2023
fc6ff5e
Generator: added a research-based DAE model test.
agarny Apr 4, 2023
057492a
Robertson model tests: mimic MATLAB's output.
agarny Apr 4, 2023
b163cd3
Merge branch 'main' into issue882
agarny Apr 5, 2023
5b4e206
Merge branch 'main' into issue882
agarny Apr 5, 2023
d748d6a
Merge branch 'issue1144' into issue882.
agarny Apr 5, 2023
2d8e4ef
Fixed merging issue.
agarny Apr 5, 2023
7da189b
Merge branch 'issue1148' into issue882.
agarny Apr 6, 2023
cf388ae
Windows: make it possible to build a release version of libCellML.
agarny Apr 6, 2023
6ff5cd6
Merge branch 'main' into issue882.
agarny Apr 12, 2023
41cd46c
Merge branch 'ubuntu22.04' into issue882.
agarny Apr 12, 2023
4b4178b
Merge branch 'issue446' into issue882.
agarny Apr 17, 2023
8b68828
Merge branch 'issue1144' into issue882.
agarny Apr 17, 2023
c565374
Merge branch 'main' into issue882
agarny Apr 25, 2023
6dc1a48
Merge branch 'main' into issue882
agarny Apr 25, 2023
9d2aa8b
Merge branch 'main' into issue882.
agarny Apr 25, 2023
4f9896b
Merge branch 'main' into issue882.
agarny Apr 25, 2023
884b153
Merge branch 'issue446' into issue882.
agarny Apr 26, 2023
ccbe8d1
Merge branch 'main' into issue882.
agarny Apr 26, 2023
1d7aab7
Debug: some minor re-ordering.
agarny Apr 26, 2023
40c846e
Merge branch 'main' into issue882.
agarny Apr 26, 2023
d9f9df4
Debug: fixed a merging issue.
agarny Apr 26, 2023
dd15127
Simplified the undefinition of some constants.
agarny Apr 27, 2023
f87deb9
Updated the documentation for AnalyserModel::Type.
agarny Apr 27, 2023
451bd0b
Generator: improved our documentation for equationCode().
agarny Apr 27, 2023
d3ea8b9
Slight improvements to the API documentation.
agarny Apr 27, 2023
879039b
Updated the documentation for AnalyserEquation::Type.
agarny Apr 27, 2023
55b770a
Updated the documentation for Generator::equationCode().
agarny Apr 27, 2023
9d93591
GeneratorProfile: improved the API documentation.
agarny Apr 27, 2023
fee74ad
Minor comment clarifications.
agarny Apr 27, 2023
2c66a58
Analyser/generator tests: removed/moved some tests.
agarny May 2, 2023
2c11d7d
Analyser: clarified an error message.
agarny May 2, 2023
92405cf
Generator profile: slight improvement to our API documentation.
agarny May 3, 2023
d4973c3
Renamed undefine.h to undefines.h.
agarny May 3, 2023
d565555
undefines.h: some notes about this special header file.
agarny May 3, 2023
a291966
JavaScript bindings: renamed some generator-related methods.
agarny May 3, 2023
740b478
Generator: changed the version of the generator from 0.3.2 to 0.4.0.
agarny May 3, 2023
fd85f4f
Merge branch 'main' into issue882.
agarny May 3, 2023
aa9a96d
Merge branch 'main' into issue882.
agarny May 4, 2023
ef180f2
Analyser: simplified our code a bit.
agarny May 4, 2023
3688aaf
Python generator: import the nla_solve() method.
agarny May 12, 2023
cd2e3d6
Addressed a branch coverage issue as a result of commit 3688aaf0.
agarny May 14, 2023
958413b
Analyser: removed some extraneous comments.
agarny May 14, 2023
efff78d
Generator: improved/fixed our Python-generated code.
agarny May 15, 2023
39beada
Generator: initialise arrays with NaNs.
agarny May 16, 2023
87dbf2c
Generator: initialise variables that need to be computed using an NLA…
agarny May 16, 2023
43b7db1
JavaScript tests: account for our recent changes.
agarny May 17, 2023
da751a3
Tests: updated our DAE version of the HH52 model.
agarny May 17, 2023
842346d
Analyser/generator: allow rates to be computed using an NLA equation.
agarny May 17, 2023
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2 changes: 2 additions & 0 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ set(GIT_API_HEADER_FILES
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/reset.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/strict.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/types.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/undefines.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/units.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/validator.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/variable.h
Expand Down Expand Up @@ -233,6 +234,7 @@ target_include_directories(cellml_debug_utilities
set_target_properties(cellml_debug_utilities PROPERTIES
CXX_VISIBILITY_PRESET hidden
DEBUG_POSTFIX d
POSITION_INDEPENDENT_CODE 1
VISIBILITY_INLINES_HIDDEN 1
)

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