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

#2503 - ReturnData: remove protected data members

Pull Request - State: open - Opened by dweindl 4 days ago - 1 comment

#2502 - CI: skip spline tests under valgrind

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

#2501 - Simplify SuiteSparse installation

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

#2500 - Update SuiteSparse to 7.8.2

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

#2499 - Fix sympy float comparison issue in spline code

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

#2498 - test_multiple_splines fails

Issue - State: closed - Opened by dweindl 5 days ago
Labels: ci

#2497 - Release 0.26.2

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

#2496 - GHA: Update sonar scanner

Pull Request - State: closed - Opened by dweindl 5 days ago - 2 comments

#2495 - pre-commit autoupdate

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

#2494 - GHA: cache remote test files

Pull Request - State: closed - Opened by dweindl 6 days ago - 1 comment

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

Pull Request - State: closed - Opened by dweindl 6 days ago - 1 comment

#2492 - Set CMake3.30 policies

Pull Request - State: closed - Opened by dweindl 6 days ago - 1 comment

#2490 - Test amici with no-GIL Python

Issue - State: open - Opened by dweindl 28 days ago

#2489 - Add tests for installing amici under conda

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

#2488 - Tests: Fix petab benchmark models paths

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

#2487 - Update references

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

#2486 - Segmentation fault when importing amici on Mac

Issue - State: open - Opened by anamariemartinez 2 months ago - 9 comments
Labels: new

#2485 - Release 0.26.1

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2484 - Fix uncaught C++ exceptions crashing Python

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2483 - Handle reserved names during code-printing

Pull Request - State: open - Opened by dweindl 3 months ago - 1 comment

#2482 - Update gcc minimum required version warning

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2481 - GHA: -Werror only for amici repo

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2480 - CMake: Set CMP0167

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2479 - Wrong conservation laws for pysb models

Issue - State: open - Opened by FFroehlich 3 months ago
Labels: bug, PySB

#2478 - Uncaught C exceptions

Issue - State: closed - Opened by FFroehlich 3 months ago - 7 comments
Labels: bug, c++

#2477 - GHA: -Werror only for amici repo

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

#2476 - Set CMP0167 for CMake 3.30

Issue - State: closed - Opened by dweindl 3 months ago
Labels: cmake

#2475 - Survey: MATLAB users / continuation of AMICI's MATLAB interface

Issue - State: open - Opened by dweindl 3 months ago
Labels: question, matlab

#2474 - Doc: Update installation under conda

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2473 - Release 0.26.0

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2472 - Update reference list

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2471 - Use `petab.v1`

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2470 - Doc: fix formatting

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2469 - Illegal value in CVodeGetDky

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

#2468 - CMake: Set SUNDIALS_ROOT

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2467 - CMake Error during AMICI installation on WSL

Issue - State: closed - Opened by LarkinIt 3 months ago - 4 comments
Labels: bug, cmake

#2466 - Doc: Update AMICI papers

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2465 - Add deprecation policy

Pull Request - State: closed - Opened by dweindl 3 months ago - 2 comments

#2464 - Deprecate passing individual tables to `amici_import_petab`

Pull Request - State: closed - Opened by dweindl 3 months ago - 2 comments

#2463 - 'reduce' is not a member of 'std' std::reduce(idlist.begin(), idlist.end())

Issue - State: closed - Opened by derleanfv 3 months ago - 2 comments
Labels: windows, c++, matlab

#2462 - Require sympy>=1.12.1 for numpy>=2.0 compatibility

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#2461 - Handle reserved names in PEtab parameter mapping

Issue - State: open - Opened by dweindl 3 months ago - 3 comments
Labels: bug, PEtab

#2457 - Release 0.25.2

Pull Request - State: closed - Opened by dweindl 4 months ago - 2 comments

#2456 - PEtab: Fix estimated initial conditions specified via the conditions table

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

#2454 - Piecewise function

Issue - State: closed - Opened by aidinbii 4 months ago - 1 comment

#2453 - Update doxygen to 1.11.0

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

#2452 - Timeseries

Pull Request - State: open - Opened by FFroehlich 4 months ago

#2451 - Release 0.25.1

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2450 - TimeCourse Implementation

Issue - State: open - Opened by FFroehlich 5 months ago

#2449 - PEtab: fix missing parameters in fill_in_parameters

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2448 - pytest: ignore log(0) warnings

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2447 - cmake: replace explicit checks for CMAKE_BUILD_TYPE

Issue - State: closed - Opened by dweindl 5 months ago
Labels: cmake

#2446 - Pin cmake_build_extension==0.5.1

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2445 - Specify cmake build types and require cmake-build-extension==0.6.0

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2444 - `Benchmark Collection` workflow fails for Lang_PLOSComputBiol2024

Issue - State: closed - Opened by dweindl 5 months ago - 2 comments
Labels: PEtab

#2443 - CMake: Fix MKL detection when not using environment modules

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2442 - IMPORTED_LOCATION not set for imported target "Upstream::amici"

Issue - State: closed - Opened by dweindl 5 months ago - 1 comment
Labels: bug, cmake

#2441 - Compilation fails with Intel OneApi MKL 2024.1

Issue - State: closed - Opened by kaiserls 5 months ago - 2 comments
Labels: cmake

#2440 - Avoid symbol clashes in plot_expressions

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2439 - Bump matlab-actions/setup-matlab from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#2438 - Bump matlab-actions/run-command from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#2437 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#2436 - Bump matlab-actions/setup-matlab from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#2435 - Bump matlab-actions/run-command from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 2 comments
Labels: dependencies, github_actions

#2434 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#2433 - Release 0.25.0

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2432 - Not installing on Mac M1

Issue - State: closed - Opened by MadNietzsche 5 months ago - 4 comments

#2431 - Fix execution of multiple event assignments from the same event

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2430 - Execution of multiple event assignments from the same event

Issue - State: closed - Opened by dweindl 5 months ago - 3 comments
Labels: SBML, events

#2429 - SBML import: handle `useValuesFromTriggerTime` attribute on events

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2428 - Fix handling of event assignments to compartments

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2427 - SBML import ignores `useValuesFromTriggerTime` attribute on events

Issue - State: closed - Opened by dweindl 5 months ago
Labels: bug, SBML, events

#2426 - Incorrect handling of event assignments to compartments

Issue - State: closed - Opened by dweindl 5 months ago
Labels: bug, SBML, events

#2425 - Support event-assignments to compartments that aren't rate rule targets

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2424 - Support event-assignments to compartments

Issue - State: closed - Opened by dweindl 5 months ago
Labels: enhancement, python, SBML, events

#2423 - Remove wurlitzer dependency

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2422 - np.Inf -> np.inf for numpy 2.0 compatibility

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2421 - Add stacklevel to warnings

Pull Request - State: closed - Opened by dweindl 5 months ago - 5 comments

#2420 - Remove setup.cfg

Pull Request - State: closed - Opened by dweindl 5 months ago

#2419 - Increase test tolerances

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2418 - InitialAssignment issue

Issue - State: open - Opened by aidinbii 5 months ago - 6 comments
Labels: bug, PEtab, SBML

#2416 - GHA: Let dependabot update actions

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2415 - macos-latest tests failing since last night

Issue - State: closed - Opened by dweindl 5 months ago - 1 comment

#2414 - Update reference list

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2413 - Deploy releases to Docker Hub

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2412 - zip(... , strict=True)

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2411 - pyupgrade, pre-commit autoupdate

Pull Request - State: closed - Opened by dweindl 5 months ago - 1 comment

#2410 - zip(... , strict=True)

Issue - State: closed - Opened by dweindl 5 months ago
Labels: python

#2409 - Remove wurlitzer dependency

Issue - State: closed - Opened by dweindl 5 months ago
Labels: c++, python

#2408 - setup.cfg -> pyproject.toml

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2406 - Release 0.24.0

Pull Request - State: closed - Opened by dweindl 5 months ago - 2 comments

#2402 - Fix to conda installation.

Pull Request - State: closed - Opened by BartoszBartmanski 6 months ago - 4 comments

#2396 - Get rid of amici.swig_wrappers.ExpData

Pull Request - State: closed - Opened by dweindl 6 months ago - 1 comment

#2394 - cmake: set sundials path hint for python package

Issue - State: closed - Opened by dweindl 6 months ago
Labels: cmake