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SBML import: conservation laws for non-constant species #1669

Merged
merged 234 commits into from
Feb 17, 2022
Merged

SBML import: conservation laws for non-constant species #1669

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2c1a127
Switch the default steady-state sensitivity method to simulationFSA.
stephanmg Jul 27, 2021
4d5f8f9
Adding stub for non-const conservation laws.
stephanmg Aug 4, 2021
8ab2393
Implementing method stub for non-const CLs.
stephanmg Aug 5, 2021
f113d2b
Update installation notes for non-venv users.
stephanmg Aug 5, 2021
f2a6be3
Adding scipy dependency.
stephanmg Aug 5, 2021
7734529
Documentation fix.
stephanmg Aug 5, 2021
b26f83e
Switching back default steady-state sensitivity method.
stephanmg Aug 16, 2021
eff972e
Merge remote-tracking branch 'upstream/develop' into develop
stephanmg Aug 16, 2021
4ed4c9c
Adding part a) of algorithm (De Martino 2014)
stephanmg Aug 18, 2021
5db345d
Removing superfluous code in sbml_import.py
stephanmg Aug 18, 2021
2a8d4dc
Additions to the algorithmic part a)
stephanmg Aug 19, 2021
1d1d7b7
Implementing LinearDependence.
stephanmg Aug 20, 2021
6f1227f
Implementing Reduce
stephanmg Aug 20, 2021
7a96b08
Implemented MonteCarlo simulated annealing
stephanmg Aug 23, 2021
7262ffd
Adding Relaxation
stephanmg Aug 23, 2021
60e322f
Adding additional relaxation parameter.
stephanmg Aug 23, 2021
928959a
Finalizing draft for conserved moeities, see TODOs.
stephanmg Aug 23, 2021
d50a770
WIP: Debugging.
stephanmg Aug 24, 2021
1012520
More debugging.
stephanmg Aug 24, 2021
1dfc0f0
Reduce method needs more debugging.
stephanmg Aug 24, 2021
6684af8
Adding TODOs, output details of moeities, debugging.
stephanmg Aug 24, 2021
d574f6c
DeMartino case working. Double-check!
stephanmg Aug 24, 2021
abd8dd5
Adding important implementation notes.
stephanmg Aug 24, 2021
64227c5
Beginning benchmarking and optimization.
stephanmg Aug 24, 2021
51a9c54
Corrections of mis-translated code blocks.
stephanmg Aug 26, 2021
d182f6e
Begin of proper documentation.
stephanmg Aug 26, 2021
7c58fe0
Adding unit test for conserved moeities.
stephanmg Sep 3, 2021
86b5802
Refactoring to logger.
stephanmg Sep 3, 2021
903a97b
Preparation to adapt conservation law during SBML iport.
stephanmg Sep 17, 2021
19a000b
Adding non-const species conservation laws.
stephanmg Sep 22, 2021
071a6f1
Renaming variables for consistency.
stephanmg Sep 22, 2021
d65c7ab
Adding conserved_moeities as module
stephanmg Nov 12, 2021
10cb2a3
Adding implementation of conserved moieties.
stephanmg Nov 12, 2021
d5f320e
Fix typo.
stephanmg Nov 12, 2021
bd63f15
Fix another typo.
stephanmg Nov 12, 2021
466e1a3
Adding integration test for conserved moieties with Blasi model.
stephanmg Nov 15, 2021
c76f2a5
Preparation for PR to develop, see TODO notes.
stephanmg Jan 19, 2022
0d3f4cc
Merged.
stephanmg Feb 8, 2022
55154dc
Correcting setup.cfg.
stephanmg Feb 8, 2022
f32fd3e
Fixing test_conserved_moieties.py
stephanmg Feb 8, 2022
0f82e26
Correcting reduction of conserved moieties when there are none to red…
stephanmg Feb 8, 2022
fc26eff
Identified sloc breaking sbml tests.
stephanmg Feb 8, 2022
1b09501
Merge remote-tracking branch 'origin/develop' into conserved_moieties
stephanmg Feb 8, 2022
12a3965
Retrieving also stochiometric matrix from remote.
stephanmg Feb 8, 2022
01a54c4
fix conservation laws
dweindl Feb 10, 2022
d03a1c4
Merge branch 'develop' into conserved_moieties
dweindl Feb 10, 2022
10bd164
remove unrelated files
dweindl Feb 10, 2022
1559b3e
unused imports
dweindl Feb 10, 2022
6a901b7
stray dbg
dweindl Feb 10, 2022
9cbccfa
formatting, unused imports
dweindl Feb 10, 2022
4c56941
formatting, unused imports
dweindl Feb 10, 2022
9198073
formatting, unused imports
dweindl Feb 10, 2022
13ee279
unused imports; revert unrelated changes
dweindl Feb 10, 2022
777641e
fix local file reference
dweindl Feb 10, 2022
8e57d2b
fix typos, formatting
dweindl Feb 10, 2022
aa3e1ed
Move test code to tests
dweindl Feb 10, 2022
3db00fa
formatting, simplify, typos
dweindl Feb 10, 2022
27f9b92
handle parametertrized S
dweindl Feb 11, 2022
0db1e09
relax runtime check
dweindl Feb 11, 2022
a368998
remove test_conserved_moieties_integration.py; implicitly tested else…
dweindl Feb 11, 2022
6aaf58d
remove duplicated/obsolete test
dweindl Feb 11, 2022
67e11bd
cleanup test; remove obsolete functions
dweindl Feb 11, 2022
48b3aab
Improving documentation.
stephanmg Feb 11, 2022
03357ed
Reduce test verbosity
dweindl Feb 11, 2022
1f63f83
relax timelimit on GHA
dweindl Feb 11, 2022
a4f99cf
simplify
dweindl Feb 11, 2022
50b1abb
Merge branch 'develop' into conserved_moieties
dweindl Feb 11, 2022
b0410b3
fix assertion
dweindl Feb 11, 2022
fa08ec6
simplify
dweindl Feb 11, 2022
742f1d0
Merged.
stephanmg Feb 11, 2022
92c1e3b
Documentation update.
stephanmg Feb 11, 2022
9532345
formatting
dweindl Feb 11, 2022
96e9598
refactor
dweindl Feb 11, 2022
ac2e3ba
fixup import; renaming
dweindl Feb 11, 2022
4e1ff11
Fix bug in while-loop.
stephanmg Feb 11, 2022
69c87dd
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 11, 2022
bdeffbd
Removing un-used variable.
stephanmg Feb 11, 2022
f5f0f3e
rename; typehints
dweindl Feb 11, 2022
fd73ceb
fill(): remove redundant parameter matched_size
dweindl Feb 11, 2022
dfb2922
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 11, 2022
f53ff2d
typehints, rename
dweindl Feb 11, 2022
1cc6b3b
doc
dweindl Feb 11, 2022
44d917c
Adding return values description (pydoc).
stephanmg Feb 11, 2022
b153405
Merged.
stephanmg Feb 11, 2022
57c2000
typehints, naming
dweindl Feb 11, 2022
02af6c2
Type annotations.
stephanmg Feb 11, 2022
ec7f8b8
Merged.
stephanmg Feb 11, 2022
9155687
Math notation for stoichiometric matrix S.
stephanmg Feb 11, 2022
f6f3ee4
typehints
dweindl Feb 11, 2022
5c0b230
rename
dweindl Feb 11, 2022
59c6c6f
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 11, 2022
af11bc1
fixup names; refactor
dweindl Feb 11, 2022
27b87fb
refactor
dweindl Feb 11, 2022
4dcb0f1
refactor
dweindl Feb 11, 2022
48a0d94
simplify
dweindl Feb 11, 2022
b8c96f2
simplify
dweindl Feb 11, 2022
423d65f
rename; simplify
dweindl Feb 11, 2022
e719715
cleanup
dweindl Feb 11, 2022
c032fe7
simplify
dweindl Feb 11, 2022
eea4383
private
dweindl Feb 11, 2022
9fa1b18
fix CLs?!
dweindl Feb 11, 2022
ed4eaca
simplify
dweindl Feb 11, 2022
fd39fa5
cleanup
dweindl Feb 11, 2022
62b2b35
use full algorithm, not just kernel()
dweindl Feb 11, 2022
e41f627
doh
dweindl Feb 11, 2022
aa008c1
..
dweindl Feb 11, 2022
820d470
cleanup
dweindl Feb 11, 2022
57b2b81
replace states from previous CLs
dweindl Feb 12, 2022
61301dd
no assert
dweindl Feb 12, 2022
b67033f
T
dweindl Feb 12, 2022
7e7c403
fix interdependent CLs
dweindl Feb 12, 2022
cc0f918
Merge branch 'develop' into conserved_moieties
dweindl Feb 12, 2022
52a04ab
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
bcb2c4c
Corrections?
stephanmg Feb 14, 2022
016744d
Possible more corrections...
stephanmg Feb 14, 2022
f4795d5
not a bug. simplify.
dweindl Feb 14, 2022
a13737d
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
ef5c877
revert range change; simplify
dweindl Feb 14, 2022
ffbbfc3
obiwan
dweindl Feb 14, 2022
d4103e8
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
75fbcf2
obiwan; simplify
dweindl Feb 14, 2022
570d404
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
84cc1f6
Removing superfluous function call (without side-effects).
stephanmg Feb 14, 2022
387c8ce
Commenting an if-else statement
stephanmg Feb 14, 2022
2cc25be
fix true/false
dweindl Feb 14, 2022
c64c6c6
undo bad assert
dweindl Feb 14, 2022
01b8834
fix fill
dweindl Feb 14, 2022
0607774
fixup max
dweindl Feb 14, 2022
aeed67f
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
d7e5858
simplify
dweindl Feb 14, 2022
3aa769f
Fix various issues in relax()
dweindl Feb 14, 2022
b0115dc
simplify
dweindl Feb 14, 2022
6770b38
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
7e781d0
simplify
dweindl Feb 14, 2022
2582e15
Don't return inputs
dweindl Feb 14, 2022
61ca370
fix obiwan
dweindl Feb 14, 2022
8606c41
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
7cbe4fb
Simplify
dweindl Feb 14, 2022
16fdb77
min is not a good variable name
dweindl Feb 14, 2022
dd98ee6
simplify
dweindl Feb 14, 2022
02009bc
Fix indexing error
dweindl Feb 14, 2022
9152737
fill() only if needed
dweindl Feb 14, 2022
ec52bd5
simplify, fix doc
dweindl Feb 14, 2022
b35c930
rename
dweindl Feb 14, 2022
805b056
Update test
dweindl Feb 14, 2022
864441a
fix error in MC
dweindl Feb 14, 2022
efc492f
fix reused loop variable in reduce()
dweindl Feb 14, 2022
bc5eccc
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
c108bb1
cleanup, fix typehints
dweindl Feb 14, 2022
b6fa21b
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 14, 2022
c6f1549
Removing non-relevant asserts.
stephanmg Feb 14, 2022
00dcc74
Small refactoring.
stephanmg Feb 14, 2022
61490b0
fixup //
dweindl Feb 14, 2022
51f2e2b
fixup //
dweindl Feb 14, 2022
e335e54
fix indexing error
dweindl Feb 14, 2022
e69cee5
fix indexing error
dweindl Feb 14, 2022
674be35
Fix yet another indexing error
dweindl Feb 14, 2022
14a5b99
simplify
dweindl Feb 14, 2022
2b4885a
Fix abundance
dweindl Feb 15, 2022
03894f8
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 15, 2022
3d420ae
Fix abs error
dweindl Feb 15, 2022
79439f7
Cleanup
dweindl Feb 15, 2022
176a453
Cleanup
dweindl Feb 15, 2022
dbd4d23
Fix state substitution in CLs
dweindl Feb 15, 2022
fbe5b6a
handle interdependent state expressions
dweindl Feb 15, 2022
3115e6d
fix loop
dweindl Feb 15, 2022
a0e5983
Add simpler test case
dweindl Feb 15, 2022
39b8985
relax test time limit
dweindl Feb 15, 2022
24ab231
catch circular dependencies
dweindl Feb 15, 2022
46309b5
no rate rules for now
dweindl Feb 15, 2022
fdad815
doh
dweindl Feb 15, 2022
75cb81c
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 15, 2022
cf9667c
handle suboptimal solution in test
dweindl Feb 15, 2022
89b4538
simplify kernel()
dweindl Feb 15, 2022
000af06
fixup 24ab231cf03d766e3ae23b0970aedcc0951c1041
dweindl Feb 15, 2022
1a3225c
no heavisides yet
dweindl Feb 15, 2022
2358320
handle compartment sizes
dweindl Feb 15, 2022
aeddb39
cleanup
dweindl Feb 15, 2022
3e42aae
skip parameter-dependent compartments; cleanup
dweindl Feb 15, 2022
9851e1d
fixup compartment substitution, cleanup
dweindl Feb 15, 2022
55cef0c
fixup
dweindl Feb 15, 2022
e646d49
fix loop condition in relax()
dweindl Feb 15, 2022
eb236d9
int
dweindl Feb 15, 2022
ea47bbb
fix test after changed output
dweindl Feb 16, 2022
c467315
increase number of MC steps from 10 to 20, increasing probability of …
dweindl Feb 16, 2022
e1cc9a0
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
f016a15
cleanup
dweindl Feb 16, 2022
2aae1c7
Documentation.
stephanmg Feb 16, 2022
4320a26
Merged.
stephanmg Feb 16, 2022
981d004
cleanup
dweindl Feb 16, 2022
cf91610
Adding test for J, J2, fields after fill(...) call.
stephanmg Feb 16, 2022
6332a49
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
6e28c52
cleanup/simplify
dweindl Feb 16, 2022
9ea4662
cleanup mc
dweindl Feb 16, 2022
7655788
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
b2ce28e
cleanup
dweindl Feb 16, 2022
87e1680
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
3eb578f
simplify
dweindl Feb 16, 2022
4fa158e
test: increase max_tries
dweindl Feb 16, 2022
0791ca4
adjust tolerance
dweindl Feb 16, 2022
697d82a
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
84e1752
Formatting.
stephanmg Feb 16, 2022
46aa8e6
private; formatting; cleanup
dweindl Feb 16, 2022
917d632
Merged.
stephanmg Feb 16, 2022
3650a23
de-duplicate
dweindl Feb 16, 2022
73fa520
Some documentation for _monte_carlo(...).
stephanmg Feb 16, 2022
2d2ee0a
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
c2d486c
modularize tests; de-duplicate
dweindl Feb 16, 2022
a75c4a7
cleanup
dweindl Feb 16, 2022
2ee9656
Cleanup
dweindl Feb 16, 2022
e19ab4b
cleanup
dweindl Feb 16, 2022
dd2ea89
formatting
dweindl Feb 16, 2022
3fefd27
Merge branch 'conserved_moieties' of github.com:AMICI-dev/AMICI into …
stephanmg Feb 16, 2022
4698d99
Refactoring: Rename variables
stephanmg Feb 16, 2022
d0a29a4
Refactoring: Rename variables
stephanmg Feb 16, 2022
a934098
relax timeout for remote file retrieval
dweindl Feb 16, 2022
2623d32
Refactoring: Extract Method.
stephanmg Feb 16, 2022
637366f
Fix.
stephanmg Feb 16, 2022
b074261
Removing unused import.
stephanmg Feb 16, 2022
106e219
Refactoring: Rename function.
stephanmg Feb 16, 2022
bedb763
Revert "Refactoring: Rename function."
stephanmg Feb 16, 2022
77a119a
Revert "Removing unused import."
stephanmg Feb 16, 2022
e621e3d
Revert "Fix."
stephanmg Feb 16, 2022
34e9def
Revert "Refactoring: Extract Method."
stephanmg Feb 16, 2022
6e3f647
Update python/amici/sbml_import.py
dweindl Feb 16, 2022
450f0da
globalize MIN/MAX
dweindl Feb 16, 2022
d25c949
rng seed
dweindl Feb 16, 2022
cd5dc5a
refactor state choice
dweindl Feb 16, 2022
a46175d
fixup
dweindl Feb 16, 2022
632be8c
fixup
dweindl Feb 16, 2022
7e5eac8
seed 1->32
dweindl Feb 16, 2022
2fcd723
cleanup
dweindl Feb 16, 2022
8066258
Make optional / default=off / env: AMICI_EXPERIMENTAL_SBML_NONCONST_CLS
dweindl Feb 16, 2022
8862b1c
doc experimental
dweindl Feb 17, 2022
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -192,6 +192,6 @@ tests/performance/CS_Signalling_ERBB_RAS_AKT/
tests/performance/CS_Signalling_ERBB_RAS_AKT_petab/*
coverage_SBMLSuite.xml
Benchmark-Models-PEtab/

/test_bmc/

CS_Signalling_ERBB_RAS_AKT/
1 change: 1 addition & 0 deletions documentation/python_modules.rst
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Expand Up @@ -21,3 +21,4 @@ AMICI Python API
amici.logging
amici.gradient_check
amici.parameter_mapping
amici.conserved_moieties
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