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draft Model to MTK.___System conversion. #40

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draft Model to MTK.___System conversion. #40

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cfe431e
draft Model to MTK.___System conversion.
paulflang Apr 14, 2021
fd6ad63
add kwargs to constructors of MTK types (to support @named)
paulflang Apr 22, 2021
32f5e4d
throw error when model contains reversible reactions
paulflang Apr 22, 2021
5f94736
add initialConcentration to species
paulflang Apr 22, 2021
d188def
convert initial_concentrations to initial_amounts
paulflang Apr 22, 2021
402acbc
draft to_extensive_math function
paulflang Apr 22, 2021
6558506
add test case for `to_initial_amounts`
paulflang Apr 23, 2021
de7d16b
add test for mtk_reaktion() and -getsubstitution()
paulflang Apr 23, 2021
bf6b080
untrack Manifest.toml
paulflang Apr 23, 2021
f837186
add test case for u0map
paulflang Apr 23, 2021
f9221d1
add test for get_paramap()
paulflang Apr 23, 2021
09a7228
add tests for creating ReactionSystem
paulflang Apr 23, 2021
8e6a03c
add tests for ODESystem and ODEProblem constructors
paulflang Apr 24, 2021
7e58ca6
add conversion_options argument to readSBML()
paulflang May 3, 2021
4c7e8dd
make OrdinaryDiffEq a test dependency
paulflang May 3, 2021
2c483c0
add test cases for promoting localParameters
paulflang May 3, 2021
3347462
add test case to expandFunctionDefinitions
paulflang May 3, 2021
b235622
add SBML level and version converter
paulflang May 10, 2021
4da59f3
add SBML.Math to Symbolics conversion
paulflang May 28, 2021
f7af82d
resolve merge conflicts from upstream master
paulflang May 29, 2021
6b64f41
resolve merge conflicts from upstream master
paulflang May 29, 2021
fb84639
fix test cases after last merge
paulflang May 29, 2021
a3dce09
impement hOSU handling
paulflang May 30, 2021
570bc7c
add test for `make_extensive()`
paulflang May 30, 2021
beda38e
update test cases
paulflang May 30, 2021
ec1fa52
add test cases
paulflang May 30, 2021
6ee8876
fix failing test cases
paulflang May 30, 2021
bfe4170
centralize imports to src/SBML.jl
paulflang May 31, 2021
40b1d98
add `reversible` field to Reaction
paulflang May 31, 2021
ce4f03b
add checksupport function
paulflang May 31, 2021
537296b
simplify isequal(x, nothing) to isnothing(x)
paulflang May 31, 2021
5455600
clean up comments and file endings
paulflang May 31, 2021
e686e91
allow SBML models with unset SubstanceUnits
paulflang May 31, 2021
6913135
overload Base.convert instead of writing an sbml2symbolics converter …
paulflang May 31, 2021
a1af25a
change type of Model.gene_products and Model.function_definitions
paulflang May 31, 2021
1ffe96a
clean loaddynamimodels
paulflang May 31, 2021
dce53c3
update test/loaddynamicmodels.jl
paulflang Jun 1, 2021
44d88f5
fix failing tests in test/reactionsystem.jl; put variables in testset…
paulflang Jun 1, 2021
69fa2ff
move sbml files to test/data
paulflang Jun 1, 2021
3d0e09f
move variables in test/sbml2symbolics to testset scope
paulflang Jun 1, 2021
667240f
include all test files
paulflang Jun 1, 2021
2d98356
add power as valid SBML function
paulflang Jun 3, 2021
42fcd07
add multiply as valid SBML function
paulflang Jun 3, 2021
d56ab94
add factorial as valid SBML function
paulflang Jun 3, 2021
b7d9abb
add `checksupport` function
paulflang Jun 3, 2021
f528a2f
support hOSU species in compartments without size but raise warning
paulflang Jun 3, 2021
1909a19
add support for bidirectional kineticLaws
paulflang Jun 3, 2021
3da6440
fix conversion to unidirectional reactions
paulflang Jun 4, 2021
1202b30
add ceiling and factorial as valid SBML functions
paulflang Jun 4, 2021
a9a19af
add `piecewise` parsing
paulflang Jun 5, 2021
f23b0c1
use IfElse to evaluate `piecewise`
paulflang Jun 6, 2021
77a5743
report unsupported math elements by name
paulflang Jun 6, 2021
e51201d
remove `println` statements that caused errors bu returning tuple of …
paulflang Jun 6, 2021
778ba4a
add tests for conversion of ReactionSystem to ODESystem and ODESystem…
paulflang Jun 6, 2021
48db58b
remove compartments with no size from parameters
paulflang Jun 6, 2021
3600346
fix simulation for with `ceil` or `factorial` in kineticLaw
paulflang Jun 6, 2021
9932b3b
parse SBML Booleans to SBML.MathVal{Bool} instead of SBML.MathVal{Str…
paulflang Jun 6, 2021
7e11c2e
add `floor` as supported SBML function.
paulflang Jun 6, 2021
d714fb5
use `initial_concentration` as `initial_amount` when Compartment.size…
paulflang Jun 6, 2021
ea55421
throw error when attempting to convert a model without reactions to a…
paulflang Jun 6, 2021
b11f448
set version to 0.4.1
paulflang Jun 7, 2021
4169c47
add independent variable to the states
paulflang Jun 8, 2021
87766de
make all species function of time to get structural_simplify working
paulflang Jun 13, 2021
f460328
add tests for structural_simplify
paulflang Jun 13, 2021
59fd135
raise warning when species are `boundaryCondition` or `constant` and …
paulflang Jun 13, 2021
f726cdb
fix handling of hOSU species
paulflang Jun 14, 2021
3c9d313
sync with upstream master
paulflang Jun 15, 2021
67a8f84
sync upstream master
paulflang Jun 15, 2021
bbe19eb
fix initialConcentration parsing
paulflang Jun 15, 2021
4ae0332
fix hOSU handling
paulflang Jun 15, 2021
1070601
fix tests after merging upstream master
paulflang Jun 16, 2021
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