SBML Spatial To Finite Volume Input

Add an endpoint which allows for SBML spatial files to be uploaded, and then converted into Finite Volume Input files.

Faster CLI BioSim logging upgrade

7.7.0.13

pass in duration_s as double to BiosimulationLog

Java-based BioSim-logging in CLI

Merge pull request #1396 from virtualcell/biosim-log-pure-java

write Biosimulation log file directly from Java

try to return to vcell after login/logout

use Java's Desktop to request forground for vcell client after login and logout. this works in development mode, but may not work in production on all platforms. releasing to deploy and test on various platforms.

Patch for VCell CLI logging regression and KiSAO update

Merge pull request #1393 from virtualcell/Ontology-update

Updated KiSAO OBO and added parsing for KiSAO_694

omex execution improvements

• hdf5 library porting to test on macos M3
• Spring SaLaD improvements
• improved handling and observability into OMEX import and execution

sbml import of NaN and Infinity

sbml import of NaN and Infinity

Bugfix release for new CLI container

7.7.0.7

Replacing deprecated "apt-get" with "apt"

removed legacy ncsa.jhdf5 native lib from hdf5 exporter

use pure-java io.jhdf library for nonspatial HDF5 file writing while executing omex archives.
use cisc.jhdf5 for spatial HDF5 file exporting, also used in omex archive execution.
use io.jhdf for reading multi-trial stochastic data.

sbml import fixes

1. import of reactions from SBML with vcell reserved symbols for 'id'.
2. support for proper expression infix names for compartment sizes in the model namespace.