Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / AMICI-dev/AMICI issues and pull requests

#2584 - Doc: Add missing python3-dev requirement

Pull Request - State: open - Opened by dweindl 5 days ago - 1 comment

#2583 - Fix `SUNContext` in `ModelStateDerived` copy ctor

Pull Request - State: closed - Opened by dweindl 7 days ago - 1 comment

#2582 - Update steady state solver notebook

Issue - State: open - Opened by dweindl 7 days ago
Labels: documentation, steady state

#2581 - Release 0.28.0

Pull Request - State: closed - Opened by dweindl 7 days ago - 1 comment

#2580 - Update codecov config

Pull Request - State: closed - Opened by dweindl 7 days ago - 1 comment

#2579 - Occassional segfaults in ExampleSplinesSwameye2003.ipynb

Issue - State: closed - Opened by dweindl 7 days ago - 2 comments

#2578 - Optional warning in `fill_in_parameters`

Pull Request - State: closed - Opened by dweindl 7 days ago - 1 comment

#2577 - GHA: require Python3.13 tests to pass

Pull Request - State: closed - Opened by dweindl 8 days ago - 1 comment

#2576 - Fix potentially incorrect disabling of Newton's method

Pull Request - State: closed - Opened by dweindl 8 days ago - 1 comment

#2574 - Change default steady-state method to `integrationOnly`

Pull Request - State: closed - Opened by dweindl 9 days ago - 1 comment

#2573 - Redundant/ambiguous information in amici::Model

Issue - State: open - Opened by dweindl 9 days ago
Labels: refactoring, c++

#2572 - GHA: Workaround for macos segfaults

Pull Request - State: closed - Opened by dweindl 12 days ago - 2 comments

#2571 - Change default steady-state method to integrationOnly?

Issue - State: closed - Opened by dweindl 23 days ago - 1 comment
Labels: steady state

#2570 - Fix problem ID and output in benchmark collection tests

Pull Request - State: closed - Opened by dweindl 24 days ago - 1 comment

#2569 - Refactor benchmark collection tests

Pull Request - State: closed - Opened by dweindl 24 days ago - 2 comments

#2568 - Support for sympy expressions for observables and sigmas

Issue - State: open - Opened by dweindl 24 days ago
Labels: enhancement, python

#2566 - GHA: PYTHONFAULTHANDLER=1

Pull Request - State: closed - Opened by dweindl 24 days ago - 1 comment

#2565 - scripts/run-python-tests.sh: line 22: 7262 Segmentation fault

Issue - State: open - Opened by dweindl 24 days ago - 11 comments
Labels: ci

#2564 - Fix benchmark collection gradient check

Pull Request - State: closed - Opened by dweindl 25 days ago - 1 comment

#2563 - Check for unsupported observable IDs in sigma expressions

Pull Request - State: closed - Opened by dweindl 25 days ago - 1 comment

#2562 - PEtab import: Fix potentially incorrect sensitivities with state-depe…

Pull Request - State: closed - Opened by dweindl 25 days ago - 1 comment

#2560 - Add missing simulation status codes

Pull Request - State: closed - Opened by dweindl 25 days ago - 1 comment

#2559 - Add missing simulation status codes

Issue - State: closed - Opened by dweindl 27 days ago

#2558 - Rate limit for inf/nan warnings

Issue - State: open - Opened by dweindl 29 days ago
Labels: enhancement

#2557 - GHA: Ignore python3.13 failures for now

Pull Request - State: closed - Opened by dweindl 29 days ago - 1 comment

#2556 - Fix dangling pointer in SolverTest.SettersGettersWithSetup

Pull Request - State: closed - Opened by dweindl 29 days ago - 1 comment

#2555 - Fix crashes when errors occur at output timepoints

Pull Request - State: closed - Opened by dweindl 29 days ago - 1 comment

#2554 - Release 0.27.0

Pull Request - State: closed - Opened by dweindl 29 days ago - 2 comments

#2553 - add 3.13 to test matrix

Pull Request - State: closed - Opened by FFroehlich 29 days ago - 5 comments

#2552 - update jax notebook

Pull Request - State: closed - Opened by FFroehlich 29 days ago - 2 comments

#2551 - Fix capturing SUNDIALS warnings after 7.1.1 upgrade

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2550 - Sundials warnings not showing since 7.1.1 upgrade

Issue - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2549 - Fix `_collect_heaviside_roots` for `sympy.Heaviside` arguments

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2548 - Fix pysb branch

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2547 - CMake: Don't attempt to create alias target if target of the same name already exists

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2546 - model name "model" leads to cmake failures

Issue - State: closed - Opened by FFroehlich about 1 month ago - 1 comment
Labels: cmake

#2545 - SBML import: Incorrect processing of piecewise/Heaviside function

Issue - State: closed - Opened by dweindl about 1 month ago - 6 comments
Labels: bug, SBML

#2544 - Add missing command in python_installation.rst

Pull Request - State: closed - Opened by ChocolateCharlie about 1 month ago

#2543 - Optimize includes

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2542 - Fix duplicated log messages

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2541 - Add simulation status AMICI_FIRST_QRHSFUNC_ERR

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2540 - Update CMake export config

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2539 - CMake: Set policies for CMake 3.31

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2538 - Refactor symbolic event processing

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2536 - Fix SBML test IDs

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2535 - Fix AmiVector::nvec_ for size 0

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2534 - SBML test suite fails since sundials upgrade

Issue - State: closed - Opened by dweindl about 1 month ago

#2533 - Refactor: move Model::state_ initalization to ModelState ctor

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2532 - Pin sphinx<8 / update sphinx config for sphinx8

Pull Request - State: closed - Opened by dweindl about 1 month ago - 2 comments

#2531 - Refactor: move Model::state_ initalization to ModelState ctor

Issue - State: closed - Opened by dweindl about 1 month ago
Labels: refactoring, c++

#2530 - Fix initialization of Model::simulation_parameters_::pscale

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2528 - Install `amici[vis]` for binder

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#2527 - Deprecation warnings in `python/examples/example_jax/ExampleJax.ipynb`

Issue - State: closed - Opened by dweindl about 2 months ago - 1 comment
Labels: documentation

#2526 - Install `amici[vis]` for binder

Issue - State: closed - Opened by dweindl about 2 months ago

#2525 - Release 0.26.3

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2524 - CI: Re-enable benchmark model gradient checks / prettify gradient check output

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2523 - Doc: show plotting measurements

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2522 - GHA: Install benchmark collection only where necessary

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2521 - Refactor NewtonSolver

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2520 - Refactor SUNLinSolWrapper

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2519 - Build SuiteSparse as a single extension

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2518 - Update references

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2517 - Get rid of petab DeprecationWarnings

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2516 - CMake: restrict visibility of private headers

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2515 - Everything in debug mode with ENABLE_AMICI_DEBUGGING=TRUE

Pull Request - State: closed - Opened by dweindl about 2 months ago - 2 comments

#2514 - Fix up SuiteSparse upgrade

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2513 - Upgrade SUNDIALS to 7.1.1

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2512 - Benchmark model tests: fix gradients checks

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2511 - Reduce tolerances in benchmark model gradient checks

Issue - State: open - Opened by dweindl about 2 months ago - 2 comments
Labels: ci

#2510 - Refactor benchmark collection tests

Issue - State: closed - Opened by dweindl about 2 months ago
Labels: ci, python

#2509 - Get rid of petab DeprecationWarnings

Issue - State: closed - Opened by dweindl about 2 months ago
Labels: python, PEtab

#2508 - Require CMake>=3.22

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2507 - Refactor ModelDimension and initialization of ModelStateDerived

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2506 - Refactor Model::steadystate_mask_

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2505 - Refactor: Move spl_ from ModelState to ModelStateDerived

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2504 - Refactor Model, ModelState, ModelStateDerived

Issue - State: closed - Opened by dweindl about 2 months ago
Labels: refactoring

#2503 - ReturnData: remove protected data members

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2502 - CI: skip spline tests under valgrind

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2501 - Simplify SuiteSparse installation

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2500 - Update SuiteSparse to 7.8.2

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2499 - Fix sympy float comparison issue in spline code

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2498 - test_multiple_splines fails

Issue - State: closed - Opened by dweindl about 2 months ago
Labels: ci

#2497 - Release 0.26.2

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2496 - GHA: Update sonar scanner

Pull Request - State: closed - Opened by dweindl about 2 months ago - 2 comments

#2495 - pre-commit autoupdate

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2494 - GHA: cache remote test files

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2493 - CMake: AmiciConfig.cmake -> AmiciConfig.cmake.in

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2492 - Set CMake3.30 policies

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#2491 - Assertion error in ForwardProblem::getSimulationStateTimepoint

Issue - State: closed - Opened by dweindl 2 months ago - 1 comment
Labels: bug, c++

#2490 - Test amici with no-GIL Python

Issue - State: open - Opened by dweindl 3 months ago

#2489 - Add tests for installing amici under conda

Issue - State: open - Opened by dweindl 3 months ago
Labels: ci

#2488 - Tests: Fix petab benchmark models paths

Pull Request - State: closed - Opened by dweindl 4 months ago - 1 comment

#2487 - Update references

Pull Request - State: closed - Opened by dweindl 4 months ago - 1 comment

#2486 - Segmentation fault when importing amici on Mac

Issue - State: closed - Opened by anamariemartinez 4 months ago - 10 comments
Labels: new

#2485 - Release 0.26.1

Pull Request - State: closed - Opened by dweindl 4 months ago - 1 comment