Merge version 3.2 - #176

Merged

luciansmith merged 168 commits into

Aug 28, 2026

Commits on Apr 4, 2026

Update the Escher style, with help from libsbmlnetwork.
luciansmith
committed
11d32f3
Merge pull request #148 from sys-bio/update-escher
luciansmith
authored
226e7ac

Commits on Jul 9, 2026

Add a 'getVersionStr' function to the API.
luciansmith
committed
3976195
Fix include directories.
luciansmith
committed
51871e9
More includes for the moved .h file.
luciansmith
committed
a1aa128
Update createAntimonyLib to point at the new file.
luciansmith
committed
793d67d
Fix warnings.
luciansmith
committed
901413c
Merge pull request #150 from sys-bio/add-get-version
luciansmith
authored
b328dd1
Clean up source and build system.
luciansmith
committed
24439ad
Ensure that the comp package is on, instead of asking if it's on.
luciansmith
committed
8ebadb1

Commits on Jul 10, 2026

Clean up CMake/docs references to NSBML.
luciansmith
committed
fb7c83c
Remove WITH_STATIC_SBML.
luciansmith
committed
ec124a6
Convert tests from libcheck to google test.
luciansmith
committed
c3d33d3
Add CI that runs things through valgrind.
luciansmith
committed
ebfbcc6
Update to C++14.
luciansmith
committed
a46bf2a
Add valgrind.supp
luciansmith
committed
b79cef6
Move automatic runs to the release branch, so it'll run faster.
luciansmith
committed
0704e91
Split valgrind-debug into a separate YML file.
luciansmith
committed
2083742
Print valgrind problems as we go.
luciansmith
committed
2e65efb
More messages; split up valgrind-debug run.
luciansmith
committed
5050911
Fix memory leak of test directory by changing it to a string.
luciansmith
committed
d0f697b

Commits on Jul 11, 2026

Fix addDirectory call.
luciansmith
committed
9e972ab
Fix memory leaks in annotations.
luciansmith
committed
e60c200
Fix memory leak in test itself.
luciansmith
committed
39298d7
Fix formatting error.
luciansmith
committed
52af0fd
Fix incorrect malloc/free.
luciansmith
committed
4f90812
Fix memory leak; missed 'delete astn'.
luciansmith
committed
73ecf65
Fix another missed astn deletion.
luciansmith
committed
1e64a5b

Commits on Jul 12, 2026

Update to latest libroadrunner-dev.
luciansmith
committed
42ec86a

Commits on Jul 13, 2026

Commits on Jul 14, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 17, 2026

Give error message windows the Antimony icon as well.
luciansmith
committed
cb86450

Commits on Jul 18, 2026

Commits on Jul 20, 2026

A species can be a floating species controlled by a rule.
luciansmith
committed
8be8f1e
Fix a unit definition used as a port.
luciansmith
committed
5ec8bcc

Commits on Jul 21, 2026

Commits on Jul 22, 2026

Commits on Jul 23, 2026

Update documentation.
luciansmith
committed
eb7d0a2
Simplify comment.
luciansmith
committed
15b4909
More updates
luciansmith
committed
d28c090

Commits on Jul 24, 2026

Fix bug from Tutorial.xxd on mac/intel and Ubuntu.
luciansmith
committed
1933de0
Merge pull request #161 from sys-bio/update-docs
luciansmith
authored
026385d
Merge pull request #151 from sys-bio/general-cleanup
luciansmith
authored
0daebb6
Re-activate the Inno installer of QTAntimony on windows.
luciansmith
committed
4a59475
Fix directory formatting.
luciansmith
committed
f443104
Fix inno command.
luciansmith
committed
31dc860
More adjustments.
luciansmith
committed
e406819

Commits on Jul 28, 2026

Fix potential race condition in CMake/GTest.
luciansmith
committed
9bf0605
Update version number.
luciansmith
committed
894aadd

Commits on Jul 30, 2026

Commits on Jul 31, 2026

Commits on Aug 1, 2026

Merge pull request #165 from sys-bio/supplement-api
luciansmith
authored
7a5e014

Commits on Aug 4, 2026

Add capabilities that the test suite revealed:
luciansmith
committed
8e41a02
Add species conversion factors.
luciansmith
committed
8ab0801
Add test files.
luciansmith
committed
9341625
add a debug line for CI/CD
adelhpour
committed
038a9a5
Merge branch 'develop' into update-ci-cd-workflow
adelhpour
authored
6ec718a
fix the issue with CI/CD unzipping the deps
adelhpour
committed
29f7354
fix mistakenly changed lines of CI/CD
adelhpour
committed
eb45fed
fix mistakenly changed lines of CI/CD
adelhpour
committed
64fa4cb
Add model conversion factor.
luciansmith
committed
908b8d5
Add test for correctly flattening function definitions.
luciansmith
committed
071c3fb
Handle SBML Level 1 'denominator' attribute on speciesRef.
luciansmith
committed
d42bc01
Update libsbml, which should fix functionDefinition bug.
luciansmith
committed
3362638
Add new test CI that roundtrips test suite models and checks results with roadrunner.
luciansmith
committed
501180d
Update main.yml
luciansmith
committed
6324b30
Merge pull request #166 from sys-bio/cover-test-suite-gaps
luciansmith
authored
b52def9
Test the roundtrip CI; fix bugs.
luciansmith
committed
a9ea7ec
Fix downloading test cases.
luciansmith
committed
ecdbcef
Find test cases.
luciansmith
committed
df78696
Fix rule: we can fail original and roundtripped if we get the same error both times.
luciansmith
committed
1ca00b1

Commits on Aug 5, 2026

Fix a harness issue and a real issue.
luciansmith
committed
1278252
No longer error out when a modifier species doesn't appear in a kinetic law.
luciansmith
committed
7e65a42
Don't error out on error categories, instead of string-matched errors.
luciansmith
committed
b51005d
Allow fast reactions to fail original, pass roundtrip.
luciansmith
committed
6c1cc8e
Fix comp lookup errors by giving roadrunner comp version of SBML.
luciansmith
committed
bf9f5f9
Better error diagnostics.
luciansmith
committed
74bb676
Fix parameter names for hierarchical models.
luciansmith
committed
075e264
Fix import of empty constraints.
luciansmith
committed
049c7a6
fix mistakenly changed lines of CI/CD
adelhpour
committed
9c09a4a
Merge branch 'develop' into update-ci-cd-workflow
adelhpour
authored
5cc8291
Fix messages.
luciansmith
committed
b7bad6b
Merge pull request #163 from sys-bio/update-ci-cd-workflow
adelhpour
authored
f02405b
Fix names for identical stoichiometry names on same reaction.
luciansmith
committed
0bdf9eb
Add missing functions to API, and then to createAntimonyLib.py
luciansmith
committed
944ab9c
Workaround for comp models in roadrunner.
luciansmith
committed
6f00ecc
Skip and warn for tests where Antimony renames a variable.
luciansmith
committed
d83690c
If 'fast' is present, don't worry about roundtripped version.
luciansmith
committed
312067b
Fix Antimony writing out hierarchical versions of files with conversion factors.
luciansmith
committed
254d859
Fix 'time' requests to convert to 'time_'.
luciansmith
committed
4069b0f

Commits on Aug 6, 2026

Commits on Aug 7, 2026

added build from source instructions to the README.md
adelhpour
committed
268b914

Commits on Aug 11, 2026

Add test for deleted rate rule with a new value.
luciansmith
committed
1c86219

Commits on Aug 14, 2026

Promote imported events with deleted bits.
luciansmith
committed
1520a6f
Add missing test files.
luciansmith
committed
8aec954
Allow 'sub1_t1' to substitute for 'sub1__t1'.
luciansmith
committed
bef53bc
When parts of reactions are deleted, promote and replace.
luciansmith
committed
0ac3f41
Fix init overrides when replacing multiple submodel elements at once.
luciansmith
committed
1acd20d
Allow booleans anywhere, including priorities.
luciansmith
committed
6c2f741
Add new test53 files.
luciansmith
committed
d3fe761
Move the SBML Test Suite tests into the main CI; run on macos14.
luciansmith
committed
ff62b8a
Merge pull request #170 from sys-bio/test-roundtrip-test-suite-v2
luciansmith
authored
05a3b8a
Update README, and remove more dead configure code.
luciansmith
committed
40df40e

Commits on Aug 15, 2026

Add newer funding.
luciansmith
committed
bed2e3c
More fiddly updates.
luciansmith
committed
a5454b5
Merge pull request #169 from sys-bio/build-instructions
adelhpour
authored
3baebaf

Commits on Aug 22, 2026

Commits on Aug 24, 2026

Commits on Aug 25, 2026

Update README file to not mention CellML.
luciansmith
committed
faa58cd
Merge pull request #162 from sys-bio/build-win-qt-installer
luciansmith
authored
ca0d2a3
Also roundtrip biomodels through Antimony.
luciansmith
committed
43edd2e

Commits on Aug 26, 2026

added runtime evaluation test
adelhpour
committed
26e7f1d
Fix a couple Antimony bugs:
luciansmith
committed
45d40a8
Add new test files.
luciansmith
committed
dc7e237

Commits on Aug 27, 2026

Allow other default compartment names.
luciansmith
committed
c1b7597
Add test for multiple default compartments being removed.
luciansmith
committed
0217768
Merge pull request #173 from sys-bio/roundtrip-biomodels
luciansmith
authored
cc6ae51
Update docs; implement support for readthedocs.
luciansmith
committed
04ffa14
Update docs.
luciansmith
committed
9791a60
Move runtime_evaluation/ to test folder.
luciansmith
committed
ae13ac5
Actually add new examples.
luciansmith
committed
006dc1d
Merge pull request #175 from sys-bio/update-docs
luciansmith
authored
5a492c1

Commits on Aug 28, 2026

Merge pull request #174 from sys-bio/add-runtime-evaluation
luciansmith
authored
0ad0b64