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
#2150 - SBML import: Undeclared identifier error when using parameters with initial assignments in observables
Issue -
State: open - Opened by dweindl about 1 year ago
Labels: bug, SBML
#2149 - PEtab SBML import fails when setting an event-assigned parameter via the condition table
Issue -
State: closed - Opened by dweindl about 1 year ago
Labels: PEtab
#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
#2108 - Fix cblas error for models without solver states in combination with forward sensitivities
Pull Request -
State: closed - Opened by dweindl over 1 year ago
- 1 comment
#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
#2090 - Recent sphinxcontrib-matlabdomain (0.19.0) breaks documentation build
Issue -
State: closed - Opened by dweindl over 1 year ago
#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
#2081 - Spline tests: replace hard-coded values by scipy.interpolate.CubicHermiteSpline
Issue -
State: open - Opened by dweindl over 1 year ago
#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