My changes for this week#8

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hsauro wants to merge 1855 commits into

AndySomogyi:developfrom

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Commits on Dec 1, 2020

Commits on Dec 2, 2020

Fixes to get plugins to work in new configuration.
luciansmith
committed

Commits on Dec 5, 2020

Allow users to pick which Python is being used.
luciansmith
committed

Commits on Dec 9, 2020

Commits on Dec 11, 2020

Commits on Dec 16, 2020

Azure pipelines possible complete for mac, windows and linux + py36/37/38
Ciaran Welsh
committed

Commits on Dec 18, 2020

Attempt to fix readthedocs
Kiri Choi
committed
Drop bibtex extension
Kiri Choi
committed

Commits on Jan 6, 2021

Commits on Jan 11, 2021

Install test models (used by tellurium).
luciansmith
committed

Commits on Jan 19, 2021

Commits on Jan 20, 2021

Add test of ExtendedVersionInformation function
luciansmith
committed

Commits on Jan 21, 2021

Commits on Jan 22, 2021

Remove debug print statements
matthiaskoenig
authored

Commits on Jan 29, 2021

Make documentation link a title
Ciaran Welsh
authored
Update github badge for azure pipelines
Ciaran Welsh
authored

Commits on Feb 5, 2021

Merge pull request #728 from sys-bio/matthiaskoenig-patch-2
luciansmith
authored

Commits on Feb 9, 2021

make error message about missing dependencies less confusing
Ciaran Welsh
committed

Commits on Feb 16, 2021

Merge pull request #731 from sys-bio/fix-err-msg
Ciaran Welsh
authored
make a start on docs
Ciaran Welsh
committed
fixed links in rr docs. The problem was that autosummary does not work when linking to C++ functions. Instead we can use the :cpp:class: r::clsName directive
Ciaran Welsh
committed

Commits on Feb 17, 2021

copied and linked doxygen generated html into the documentation website
Ciaran Welsh
committed
changed location of doxygen styled documentation and fixed link locally. Needs testing remotely
Ciaran Welsh
committed
reformat headers of rrplugins docs so the toctree is right
Ciaran Welsh
committed
clean up some of the sphinx generated warnings
Ciaran Welsh
committed
use of "override" instead of virtual.
Ciaran Welsh
committed
Merge pull request #734 from sys-bio/look-at-docs
Ciaran Welsh
authored
Begin the process of updating sundials. Still at a "work out what needs to be done" stage since sundials has changed a lot since version 2.3. Specifically, they no longer have a CVDense solver. The…
Ciaran Welsh
committed

Commits on Feb 18, 2021

Commits on Feb 19, 2021

Commits on Feb 23, 2021

Add new branch to azure-pipelines.yml
CiaranWelsh
committed
Replaced linear solver with non-linear solver. Now the tests pass locally.
CiaranWelsh
committed
minor refactorings.
CiaranWelsh
committed
delete trigger and pr section from azure-pipelines.yml - when they are omitted, everything gets passed through azure.
CiaranWelsh
committed
added some comments to azure for where to find the pipeline id of dependency package
CiaranWelsh
committed
remove references to sundials arkode package, since we'll not be using differential algebraic equations.
Ciaran Welsh
committed
Fix merge conflict
Ciaran Welsh
committed
Merge pull request #727 from sys-bio/matthiaskoenig-patch-1
CiaranWelsh
authored

Commits on Feb 24, 2021

Commits on Feb 26, 2021

Clean up old files
Ciaran Welsh
committed
Change public to private.
Ciaran Welsh
committed
Remove tests that were dependent on private methods.
Ciaran Welsh
committed

Commits on Mar 3, 2021

Commits on Mar 5, 2021

First pass implementation of NewtonIteration.cpp from sundials suite. Good progress has been made but still work to do cleaning up code, testing, implementing optional features and implementing the…
Ciaran Welsh
committed
refactor Log macro to rrLog
Ciaran Welsh
committed
Refactor Log to rrLog
Ciaran Welsh
committed
Merge branch 'refactor-log' into kinsol
Ciaran Welsh
committed

Commits on Mar 8, 2021

Commits on Mar 9, 2021

Successfully built in presimulation feature
Ciaran Welsh
committed
NewtonIteration integration tests pass
Ciaran Welsh
committed
tests pass (I think)
Ciaran Welsh
committed
Make use of namespace std consistent throughout the source directory
Ciaran Welsh
committed
Implement solver stats
Ciaran Welsh
committed

Commits on Mar 10, 2021

progress with computing rank of arbitrary matrix.
Ciaran Welsh
committed

Commits on Mar 11, 2021

fixed memory leak in SVD. Add third test for SVD
Ciaran Welsh
committed
added rank computation to SVD
Ciaran Welsh
committed
add method to SVD return singularity status of matrix
Ciaran Welsh
committed
tidy up kinsol options
Ciaran Welsh
committed
Moved presimulation option so that it is shared among all ss solvers. Begin jazzing up presimulation
Ciaran Welsh
committed
Add method to update a solvers settings from another dictionary after construction
Ciaran Welsh
committed
Make empty virtual method from top of Solver heirachy pure
Ciaran Welsh
committed
Remove commented out line
Ciaran Welsh
committed
Build errors
Ciaran Welsh
committed

Commits on Mar 12, 2021

Implement SteadyStateSolver.cpp implementation of LoadConfig
Ciaran Welsh
committed
clean up comment
Ciaran Welsh
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Commits on Mar 13, 2021

Presimulation Decorator implemented and tested.
Ciaran Welsh
committed

Commits on Mar 14, 2021

Implemented presimulation feature as decorator for steady state solver.
Ciaran Welsh
committed

Commits on Mar 15, 2021

Bugfix in cmake regarding test name
Ciaran Welsh
committed
Make error handler throw when there is an error, rather than just log to error.
Ciaran Welsh
committed
Bugfix where updateKinsol was being called at the wrong time. Now, it always gets called right before the call to KINSolve, to ensure options provided by users are properly passed to kisnol
Ciaran Welsh
committed
implemented an approximate steady state decorator
Ciaran Welsh
committed
Add test checking that we throw error when NewtonIteration fails to converge to steady state
Ciaran Welsh
committed
Added approximate steady state decorator, which is now fully tested (unit and integration) and operational.
Ciaran Welsh
committed
tidy up comment
Ciaran Welsh
committed
Clean up todo's and FIXME's. Deprecated the steadyStateApprox method with documentation on how to use the replacement. Deleted some commented out code.
Ciaran Welsh
committed
Make rrNLEQ1Interface 1 and 2 depend directly on the Dictionary interface, rather going throught the rrSteadyStateSolver.cpp which has been abandoned some time ago it seems.
Ciaran Welsh
committed
Fix missing include
Ciaran Welsh
committed
return void when updateSettings method has nullptr argument. This broke the c_api_tests but is now fixed.
Ciaran Welsh
committed
remove rrSteadyStateSolver from cmakelists.txt
Ciaran Welsh
committed
Minor bugfix
Ciaran Welsh
committed
Remove KinsolSteadyStateSolverTests.cpp. No longer needed as it'll be tested through subclasses NewtonIteration and FixedPointIteration
Ciaran Welsh
committed
Fix broken test.
Ciaran Welsh
committed
fix some delete[] var vs delete var problems and fix a missing std:: problem
Ciaran Welsh
committed

Commits on Mar 16, 2021

remove cout statement
Ciaran Welsh
committed
fix some std:: namespace issues in swig interface file
Ciaran Welsh
committed
added deprecation warning steadyStateApproximate. Users are informed that they should use the steadyState method instead, along with the relevant arguments to do so
Ciaran Welsh
committed
add py39 to azure
Ciaran Welsh
committed

Commits on Mar 18, 2021

remove shared ptr in favour of raw in tests because it makes swig easier
Ciaran Welsh
committed
add some swig bindings for TestModelFactory to expose test data to Python
Ciaran Welsh
committed

Commits on Mar 19, 2021

Commits on Mar 20, 2021

Commits on Mar 23, 2021

Added new roadrunner Python tests to __main__.py
Ciaran Welsh
committed
Refactor SBMLTestModel to just TestModel to better differentiate it from the SBML test suite
Ciaran Welsh
committed
Refactor SBMLTestModel to just TestModel to better differentiate it from the SBML test suite
Ciaran Welsh
committed
Add new overload of Variant_to_py for Variant pointer types
Ciaran Welsh
committed
Add new steady state solver classes to swig
Ciaran Welsh
committed
Add some typemaps to TestModelFactory.h swig bindings along with some tests.
Ciaran Welsh
committed
Swig bindings for solver.getSettingsMap correctly converts unordered map to Python dict
Ciaran Welsh
committed
Impement new typemap for unordered_map<string, DoublePair> to Python dict
Ciaran Welsh
committed
Add Python tests for NewtonIteration. It behaves the same in Python as it does in C++
Ciaran Welsh
committed
Clear up some memory leaks introduced into swig bindings by using the %newobject directive
Ciaran Welsh
committed
Fix NewtonIterationUnitTests
Ciaran Welsh
committed
modified cmake so that it copies roadrunner.py as well as _roadrunner.so to lib/site-packages in binary tree. CTest uses this package.
Ciaran Welsh
committed
commented out Brown2004 model in NewtonIterationIntegrationTests because gtest on mac seems to think its failed instead of just disabled
Ciaran Welsh
committed

Commits on Mar 24, 2021

Commits on Mar 26, 2021

Played around with fixed point iteration without luck. Refactor newton iteration with parameter strategy into two separate algorithms newton and newton_linesearch
Ciaran Welsh
committed
refactored NewtonITeration into basic and linesearch classes. They are similar but separate algorithms with different options pertaining to each - so this design is better
Ciaran Welsh
committed
tests pass again except for python
Ciaran Welsh
committed
fix bug in nleq where alternative private variable 'model' was being used instead of the class heirachy version 'mModel'
Ciaran Welsh
committed
bug in Brown2004 fixed. NLEQ1 and 2 tests added to steady state solver tests
Ciaran Welsh
committed
Make all tests pass on windows locally
Ciaran Welsh
committed
try update swig version in azure
Ciaran Welsh
committed
typo which breaks linux: sundials --> SUNDIALS
Ciaran Welsh
committed

Commits on Mar 27, 2021

Added presimulation program and experiment with mechanisms of automatically addressing the need for turning on moiety conservation
Ciaran Welsh
committed
removed experimental operation in RoadRunner constructor for computing the need for moiety conservation. Both strategies (svd.isSingular and numConservedMoieties > 0) are very expensive
Ciaran Welsh
committed
do check for auto moiety conservation analysis in steadyState
Ciaran Welsh
committed
fix gtest weirdness that seems to arise from several test classes in one cpp file
Ciaran Welsh
committed
typo in defaults
Ciaran Welsh
committed
Remove extra test output
Ciaran Welsh
committed
bug fix where nleq forgot to implement some of the virtual methods, causing loss of settings. Bug fix where the allow_negtive was not being properly respected and negative values prevented converga…
Ciaran Welsh
committed
tests pass
Ciaran Welsh
committed

Commits on Mar 29, 2021

add to cvode integrator tests. Use full time series matrix instead of single time point for test
Ciaran Welsh
committed

Commits on Mar 30, 2021

Add option to steady state base class which enables automatic conservation analysis
Ciaran Welsh
committed
remove print statement
Ciaran Welsh
committed
add python tests to binary and install tree. Make sure new python tests are run in azure
Ciaran Welsh
committed
Remove strategy parameter from tests. This feature has been refactored into newton and newton-linesearch classes so the option is no longer avaiable
Ciaran Welsh
committed
remove the approximate method - its covered by ApproxDecorator. Comment out swig cache in azure, it seems to be randomly using swig-3.0.0 again
Ciaran Welsh
committed
uncomment out swig cache from azure
Ciaran Welsh
committed
update link for swigwin to 4.0.2
Ciaran Welsh
committed
update swigwin link again on azure.
Ciaran Welsh
committed
swigwin link on azure
Ciaran Welsh
committed

Commits on Apr 8, 2021

add dockerfiles for manylinux, one for a base env and one with roadrunner prebuilt. The base env will be used in azure. Add lib64 subfolder of dependencies to cmake_prefix_path since on centos it s…
Ciaran Welsh
committed
docker base, docker build and azure
Ciaran Welsh
committed
manylinux azure typo
Ciaran Welsh
committed
update swigwin link.
Ciaran Welsh
committed
Download swig using non default user agent as the default one does not follow source forge redirects
Ciaran Welsh
committed
increase time out cmake option
Ciaran Welsh
committed

Commits on Apr 9, 2021

print out variables on azure for debugging azure
Ciaran Welsh
committed
typo
Ciaran Welsh
committed
typo
Ciaran Welsh
committed
azure
Ciaran Welsh
committed
pip install numpy for manylinux on azure
Ciaran Welsh
committed
pip install numpy for manylinux on azure
Ciaran Welsh
committed
install missing dependency on manylinuux build: ncurses
Ciaran Welsh
committed
require root
Ciaran Welsh
committed
add yum install ncurses to base dockerfile
Ciaran Welsh
committed
wrong artifact directory published
Ciaran Welsh
committed

Commits on Apr 20, 2021

Commits on Apr 23, 2021

update docs and test cases to deal with new addSpecies et al methods
penavon
committed
Merge branch 'kinsol' into develop
Ciaran Welsh
committed
Merge pull request #750 from sys-bio/kinsol
Ciaran Welsh
authored
Added new test for regenerate method
penavon
committed

Commits on Apr 26, 2021

Go through recent changes and look for old code that has crept into a later commit by merge. Only a single cmakelists slipped through, but there was also a call to Log rather than rrLog. Furthermor…
Ciaran Welsh
committed
refactor regenerate() to regenerateModel()
Ciaran Welsh
committed
add back in docs for regenerateModel
Ciaran Welsh
committed
add back in the regenerate() method, and deprecated it. Open closed principle
Ciaran Welsh
committed
endl -> std::endl;
Ciaran Welsh
committed
update swig in find_package(SWIG ...
Ciaran Welsh
committed
comment out deprecated annotations. They are not swigable. However even without these swig no longer compiles.
Ciaran Welsh
committed
added [[deprecated]] back in, and swig seems to allow it this time(?). Not sure what happened, keep an eye on it
Ciaran Welsh
committed
Merge branch 'develop' into fix-broken-merge
Ciaran Welsh
committed
remove code added by git wierdness
Ciaran Welsh
committed
removed addSpecies() and regenerate(). addSpecies is not used very often and so changing it to addSpeciesConcentration and addSpeciesAmount will have negligible impact whilst regenerate() was only …
Ciaran Welsh
committed
remove calls to regenerate()
Ciaran Welsh
committed
Add ncurses to mac build. Remove old test ode for debugging sundials
Ciaran Welsh
committed
Merge branch 'fix-broken-merge' of https://github.com/sys-bio/roadrunner into fix-broken-merge
Ciaran Welsh
committed
update python tests to reflect changes in addSpecies
Ciaran Welsh
committed
Merge branch 'fix-broken-merge' of https://github.com/sys-bio/roadrunner into fix-broken-merge
Ciaran Welsh
committed
update python tests to use addSpeciesConcentration
Ciaran Welsh
committed
add find_package(Curses) to linux and mac cmake
Ciaran Welsh
committed
Merge branch 'fix-broken-merge' of https://github.com/sys-bio/roadrunner into fix-broken-merge
Ciaran Welsh
committed
deal with curses and windows
Ciaran Welsh
committed
rejig make include dirs and link libraries to account for ncurses, which is needed on linux and macos but not windows.
Ciaran Welsh
committed
Merge pull request #755 from sys-bio/fix-broken-merge
Ciaran Welsh
authored