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

#2175 - Use proper labels for plotting if IDs are available in ReturnData

Issue - State: open - Opened by dweindl about 1 year ago
Labels: enhancement, good first issue, python

#2174 - Doc: Rename 'steadystate example'

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

#2173 - Doc: Add installation instructions for Arch Linux

Pull Request - State: closed - Opened by stephanmg about 1 year ago - 2 comments

#2172 - Doc: Update reference list

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

#2171 - Fix pre-commit configuration

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

#2170 - Change `ReturnDataView` attributes to `xarray.DataArray`?

Issue - State: open - Opened by dweindl about 1 year ago - 1 comment
Labels: question

#2169 - setup.py build_ext alternatives?

Issue - State: open - Opened by dweindl about 1 year ago
Labels: python

#2168 - Fix unused pysb2amici / sbml2amici / DEExporter `compiler` argument

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

#2167 - CI: Update sonar-scanner

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

#2166 - CI: Update to jdk 17 to meet changed sonarcloud requirements

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

#2165 - Fix lib/ vs lib64/ issue with SUNDIALS config

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

#2164 - Release 0.19.0

Pull Request - State: closed - Opened by dweindl about 1 year ago - 4 comments

#2163 - CMake: fix scope for -DHAS_BOOST_CHRONO

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

#2162 - Set CMake policies for cmake 3.27

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

#2161 - Only build required SuiteSparse function

Issue - State: open - Opened by dweindl about 1 year ago
Labels: performance

#2160 - Remove complex / complex long KLU functions

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

#2159 - Combine code for sparse model functions and their index files

Pull Request - State: closed - Opened by dweindl about 1 year ago - 3 comments

#2158 - cmake 3.27 & CMP0144

Issue - State: closed - Opened by dweindl about 1 year ago
Labels: cmake

#2157 - libsbml.CompFlatteningConverter memory leak

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

#2156 - Fix SBML import for event-assigned parameters with non-float initial assignments

Pull Request - State: closed - Opened by dweindl about 1 year ago - 3 comments

#2155 - Editable installation fails on Windows?

Issue - State: open - Opened by dweindl about 1 year ago
Labels: python

#2154 - Cleanup includes in hdf5.cpp

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

#2153 - Doc: Update Windows installation instructions

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

#2152 - Evaluate and plot symbolic expressions based on simulation results

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

#2151 - AMICI installation on Windows

Issue - State: closed - Opened by anavalinhas about 1 year ago - 15 comments

#2148 - Add AMICI_TRY_ENABLE_HDF5 env var

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

#2147 - Update reference list

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

#2146 - Refactor SBML sympification

Issue - State: open - Opened by dweindl about 1 year ago - 1 comment
Labels: refactoring, python, SBML

#2145 - Fix SBML import for events with trigger functions depending on parame…

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

#2144 - Error with ninja when running with amici version 0.18.1 vs 0.16.0

Issue - State: closed - Opened by ahjanee about 1 year ago - 23 comments

#2143 - lib/ vs lib64/ is not properly handled

Issue - State: closed - Opened by dweindl about 1 year ago
Labels: bug

#2142 - Simplify / document antimony import

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

#2141 - Amici installation with hdf5 support in conda env

Issue - State: closed - Opened by shoepfl about 1 year ago - 4 comments
Labels: new

#2140 - sbml2amici / DEExporter `compiler` argument doesn't do anything

Issue - State: closed - Opened by dweindl about 1 year ago
Labels: bug

#2139 - Doc: update sbml2amici

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

#2138 - Doc: Update reference list

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

#2137 - prevent the second run of newton's method in case simulation was turn…

Pull Request - State: closed - Opened by plakrisenko about 1 year ago - 1 comment

#2136 - Increase maxSteps for ExampleSplinesSwameye2003.ipynb

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

#2135 - Fix steadystate sensitivity mode for performance test

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

#2134 - SBML import: Allow hardcoding of numerical values

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2133 - Release 0.18.1

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2132 - Reduce flakiness of benchmark model tests

Pull Request - State: closed - Opened by dweindl over 1 year ago - 2 comments

#2131 - Fix sympy DeprecationWarning

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2130 - CI: Fail on warnings

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2129 - Add min version for pandas

Pull Request - State: closed - Opened by dilpath over 1 year ago - 1 comment

#2128 - GHA: Update sonar scanner

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2127 - GHA pypa/gh-action-pypi-publish@master -> @release/v1

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2126 - Logging typo in SBML import

Pull Request - State: closed - Opened by dilpath over 1 year ago - 1 comment

#2125 - Readme: containers

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2124 - Fix sp.Matrix errors with numpy==1.25

Pull Request - State: closed - Opened by dweindl over 1 year ago - 4 comments

#2123 - Update valgrind suppression

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2122 - Fix PEtab deprecation warning

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2121 - Import breaks for Benchmark Model

Issue - State: closed - Opened by jvanhoefer over 1 year ago - 4 comments

#2120 - SBML import: Support for rateOf

Pull Request - State: closed - Opened by dweindl over 1 year ago - 4 comments

#2119 - Single-file models

Issue - State: open - Opened by dweindl over 1 year ago
Labels: enhancement, python, performance

#2118 - [petab] fix pysb pattern matching

Pull Request - State: closed - Opened by FFroehlich over 1 year ago - 1 comment

#2117 - Fix DeprecationWarnings

Issue - State: closed - Opened by dweindl over 1 year ago - 1 comment
Labels: python

#2116 - GHA: Skip spline tests under valgrind

Pull Request - State: closed - Opened by dweindl over 1 year ago

#2115 - Release 0.18.0

Pull Request - State: closed - Opened by dweindl over 1 year ago - 3 comments

#2114 - Pin nbsphinx

Pull Request - State: closed - Opened by dweindl over 1 year ago

#2113 - CI: Increase number of starts in ExampleSplinesSwameye2003.ipynb

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2112 - Fix import error for models with events and 0 states

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2111 - Fix compilation error for models with events and xdot=0

Pull Request - State: closed - Opened by dweindl over 1 year ago - 2 comments

#2110 - Compilation error during import of SBML semantic case 01355

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: bug, python

#2109 - ShapeError: Matrix size mismatch during import of SBML semantic case 01240

Issue - State: closed - Opened by dweindl over 1 year ago - 4 comments
Labels: bug, python

#2107 - Simulation with forward sensitivities crashes for model with 0 states

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

#2106 - sympy.matrices.common.ShapeError when importing SBML models with AlgebraicRule and Event

Issue - State: open - Opened by dweindl over 1 year ago - 2 comments
Labels: bug, SBML, DAE, events

#2105 - Fix unquoted filename

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2104 - CMake: Try FindBLAS if no other information was provided

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2103 - 0.17.1 install fails

Issue - State: closed - Opened by Mjvolk3 over 1 year ago - 2 comments

#2102 - Requesting sensitivities for algebraic equations breaks simulation

Issue - State: open - Opened by dilpath over 1 year ago - 1 comment
Labels: bug

#2101 - Sensitivities for AlgebraicRule models

Pull Request - State: open - Opened by dweindl over 1 year ago - 1 comment
Labels: help wanted

#2100 - CMake: Fix choosing SWIG via env variable

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2099 - Update Doxygen

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2098 - update swig ignores

Pull Request - State: closed - Opened by FFroehlich over 1 year ago - 1 comment

#2097 - Warn if ASA is used in combination with events

Pull Request - State: closed - Opened by dweindl over 1 year ago - 3 comments

#2096 - Cleanup time symbols

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2095 - SBML import: cleanup _gather_base_locals

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2094 - SBML import - faster _get_list_of_species_references

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2093 - Add gradient checks for SBML test suite

Pull Request - State: open - Opened by dilpath over 1 year ago - 2 comments

#2092 - Add test for events with state-dependent `ddeltaxd{t,p,x}`

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2091 - Update documentation stack / require sphinxcontrib-matlabdomain<0.19.0

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2089 - Add tests for models with events with state-dependent `ddeltaxd{t,p,x}`

Issue - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2088 - Model import: Don't create spl.h and sspl.h for models without splines

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2087 - Model import: Don't create spl.h and sspl.h for models without splines

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: python

#2086 - Incorrect forward sensitivities in model with events

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: bug, python

#2085 - pre-commit: sort imports / update contrib doc

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2084 - Fix sensitivities for models with events / extend and cleanup event tests

Pull Request - State: closed - Opened by dweindl over 1 year ago - 4 comments

#2083 - Run clang-format / cmake-format

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2082 - Run pre-commit run --all-files

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2080 - State sensitivities computation at steady state

Issue - State: open - Opened by plakrisenko over 1 year ago - 3 comments
Labels: enhancement, new

#2079 - Fix AttributeError in petab_import_pysb with petab==0.2.0

Pull Request - State: closed - Opened by dweindl over 1 year ago - 3 comments

#2078 - AttributeError in petab_import_pysb with petab==0.2.0

Issue - State: closed - Opened by dweindl over 1 year ago

#2077 - Release 0.17.1

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment

#2076 - CMake: Find static suitesparse on mac

Pull Request - State: closed - Opened by dweindl over 1 year ago - 1 comment