Release 0.4.4 #297
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Release 0.4.4 #297
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dweindl
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Oct 13, 2020
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dweindl
commented
- AMICI-related
- Update to AMICI v0.11.2 (Update to AMICI v0.11.2 (featuring adjoint preequilibration) #295)
- adjoint preequilibration
- reduced memory requirements
- Make proper use of amici::RDataReporting to avoid computing costly disregarded results (Make proper use of amici::RDataReporting to avoid computing costly disregarded results #296)
- Add script / cmake target to update amici (Closes add script / cmake target to update amici #288)
- Handle AMICI failures more gracefully
- Fix misc/rebuild_amici.sh in case of changed AMICI SWIG interface
- Fix: HierarchicalOptimizationWrapper: Return full parameters and full gradient even if nothing computed analytically
- Fix C++17 in CMakeLists template
- Fix: Use absolute path in misc/setup_amici_model.sh
- Fix PEtab import issues
- Fix icpc option overriding warning (Closes Fix warning icpc: command line warning #10121: overriding '-xHOST' with '-march=native' #220)
- Update example notebooks and run on github actions (Update example notebooks and run on github actions #294)
- Add CLI option to simulator to run simulations with nominal parameters (Add CLI option to simulator to run simulations with nominal parameters #293)
- Various cleanup
- Various cleanup #287, Misc cleanup #285, Misc cleanup #271, Cleanup #270, Cleanup #268, Cleanup #267, and others
- Remove obsolete parpeamici/steadystateSimulator.cpp
- Remove outdated amiciHelper.py module for parsing AMICI source files
- Remove all uses of std::tmpnam
- Handle IpOpt reporting obj_value 0.0 in case of non-finite fval or gradient (Verify optimal values reported by ipopt #221)
- Base image ubuntu:19.10 (EOL ubuntu:19.04)
- adapt dataprovider and simulatio to df to third column in simulation condition table (adapt dataprovider and simulatio to df to third column in simulation … #272)
- Update gsllite (Update gsllite #269)
- Fix petab import when online some measurements have preequilibrationCondition set
- Add basic contribution guide
- Fix race conditions in steadystate example (Fix race conditions in steadystate example #265)
- Cache sonar files on github actions
- CI: No shallow clone for running sonarscanner
- Remove obsolete and unreliabe functions parpe::launchedWithMpi and parpe::initMpiIfNeeded -- using MPI must be specified via CLI now
…rpe::initMpiIfNeeded
* Include thread ID in log messages * Fix race conditions in steadystate example Don't try deleting old result file in workers. This may hit the already newly created file from master. Should fix random CI failures. * Verbose pytest * cleanup * Simulator: Avoid reopening files. Lock HDF5 mutex for closing to avoid race conditions.
* Don't shadow members * Don't shadow members * Don't shadow members * Don't shadow members * Replace call to the non reentrant function 'localtime' by a call to 'localtime_r'. * Don't shadow members * Make swap noexcept * Replace strcpy by strncpy * Don't shadow members * Don't shadow members * Don't shadow members * Explicit ctr for HDF5Exception * define to constexpr
* Cleanup misc/venv.sh, handle blanks in filenames, readability * Cleanup misc/setup_amici_model.sh, handle blanks in filenames, readability * Remove obsolete runExamples.sh * Python coverage? * Fixup: unbound variable * env bash * constexpr * Explicit * Explicit * Remove using namespace from header file
* Update gsl-lite * Throw on contract violation instead of terminate to get more meaningful message * RELEASE_ASSERT to Expects/Ensures
* Update gsl-lite * Throw on contract violation instead of terminate to get more meaningful message * RELEASE_ASSERT to Expects/Ensures * clang-format; add expectation * clang-format * Extract hierarchicalOptimizationAnalyticalParameterProvider from hierarchicalOptimization * Explicit; unused function; doc * clang-format * Replace asserts by RELEASE_ASSERT and Expects * Replace asserts by RELEASE_ASSERT and Expects * doc * Update .gitignore * Add MultiConditionDataProviderHDF5::setModel * cleanup * cleanup * MultiConditionDataProviderHDF5: make date members private
* Remove useless ctor * doc * clang-format * explicit * Explicitly capture variables for lambda * ref
…condition table (#272)
subrepo: subdir: "deps/AMICI" merged: "ef52e1ca" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "5df19a8d" git-subrepo: version: "0.4.1" origin: "???" commit: "???"
subrepo: subdir: "deps/AMICI" merged: "8af86315" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "8ffe3cf4" git-subrepo: version: "0.4.1" origin: "???" commit: "???"
update Amici in parPE to hotfix version, which prunes out constant species from x_solver, allowing to have full rank Jacobian despite constant species. This enables steady state sensitivity computation in preequilibration via solving the lienar system of the Jacobian
subrepo: subdir: "deps/AMICI" merged: "dd2bff10" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "3515d4e1" git-subrepo: version: "0.4.1" origin: "???" commit: "???"
update back to develop branch. As I had to resolve a merge conflict in Amici, I don't want to squash this merge, in order to not mess up history of the Amici subrepo.
* git subrepo clone --branch=develop --force [email protected]:ICB-DCM/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "6313a226" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "6313a226" git-subrepo: version: "0.4.1" origin: "https://github.com/ingydotnet/git-subrepo" commit: "a04d8c2" * Replace removed AMICI function calls: ReturnData::invalidate* * Update test to newly introduced amici::RDataReporting
* update to amici v0.11
AMICI should always return ReturnData. Apparently this is not the case. Therefore, check it behaves as expected, otherwise use NAN for all (not) computed quantities.
* git subrepo clone --branch=develop --force [email protected]:ICB-DCM/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "71b2b001" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "71b2b001" git-subrepo: version: "0.4.1" origin: "https://github.com/ingydotnet/git-subrepo" commit: "a04d8c2" * Update to new amici namespaces * raise amici req * more namespace
* doc * Use C++17 standard * explicit fallthrough * virtual function calls in ctor * cleanup * model_ private * Don't hardcode OpenMP flags, use cmake instead * Use CMake for finding CERES * Cleanup optimizer cmake code * member private * find_package OpenMP
* cast * remove unused * cleanup * HierarchicalOptimizationWrapper: make wrapped function private and use non-owning pointer to fix issues with double delete
* update to AMICI develop 11.1, after merge of #1132
…CI.git deps/AMICI (#291) subrepo: subdir: "deps/AMICI" merged: "ed333d2c" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "ed333d2c" git-subrepo: version: "0.4.1" origin: "https://github.com/ingydotnet/git-subrepo" commit: "a04d8c2"
#293) * Add CLI option to simulator to run simulations with nominal parameters Closes #292 Breaking change: Simulator CLI now *always* requires condition file *and* parameter file (although they may be identical * Move getOuterParameters to hierarchicalOptimization.cpp * Add parameter IDs to cost function; select explicitly whether to compute inner parameter for simulation * Add hdf5GroupExists(const H5::H5File &file, const std::string &groupName) * Fix deadlock, fix saving states * Handle case of AMICI-computed sigmas not recomputed in hierarchical optimization
* Update notebook parpeExampleSteadystateBasic.ipynb * Add misc/run_notebook.sh * Run notebook on github actions * Update .gitignore * Update notebook parpeExampleSteadystateHierarchical.ipynb * Run notebook on github actions * Update notebook parpeExampleSteadystateMinibatch.ipynb * mpiexec --allow-run-as-root * Run all notebooks * --oversubscribe * create minibatch example input file * skip minibatch example
* defaults were not handled correctly for observableTransformation and noiseDistribution * mixed preequilibration and non-preequilibration were not handled correctly
* add sensi_meth_preeq to parPE generated h5 files * adapt unittest to new rdata * Fix PEtab import issues * defaults were not handled correctly for observableTransformation and noiseDistribution * mixed preequilibration and non-preequilibration were not handled correctly * git subrepo clone (merge) --branch=develop --force [email protected]:ICB-DCM/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "d220128f" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "develop" commit: "d220128f" git-subrepo: version: "0.4.1" origin: "https://github.com/ingydotnet/git-subrepo" commit: "a04d8c2" * Extend checking of test results * Set mpiexec options from test runs as PARPE_TESTS_MPIEXEC env var
… gradient even if nothing computed analytically ... led to parameters not being saved
Fixes > TypeError: add_source_parser() takes 2 positional arguments but 3 were given
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