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news.yml
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page_title: News
news:
- date: 2025-01-29
title: Version 1.8.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.8.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>improved mesh visualizations <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/1021">#1021</a>
<li>more 3d example models <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/1015">#1015</a>
<li>more documentation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/1020">#1020</a>
</ul>
- date: 2024-10-30
title: Version 1.7.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.7.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>Python 3.13 wheels <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/1002">#1002</a>
<li>colours in the geometry image can now be changed <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/960">#960</a>
<li>voxels can be selected in the 3d rendering of the geometry image <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/979">#979</a>
</ul>
<h6 id="added">Fixed</h6>
<ul>
<li>parameter optimization error with 3d models <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/1007">#1007</a>
</ul>
- date: 2024-04-09
title: Version 1.6.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.6.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>support for using the DuneCopasi simulator with 3d models <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/937">#937</a>
<li>3d volume rendering for voxel visualization <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/926">#926</a>
<li>visualization of 3d model geometry meshes <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/882">#882</a>
<li>import of geometry image files by drag and drop onto the GUI <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/933">#933</a>
</ul>
- date: 2023-12-01
title: Version 1.5.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.5.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>support for dune-copasi 2 <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/908">#908</a>
<li>Python 3.12 wheels <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/897">#897</a>
<li>Apple Silicon wheels and binaries <a href="https://github.com/ssciwr/sme-osx-arm64">ssciwr/sme-osx-arm64</a>
</ul>
- date: 2023-09-23
title: Version 1.4.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.4.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>initial support for 3d spatial models <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/850">#850</a>
<li>support for anisotropic voxels <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/879">#879</a>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>disable OK button while selecting geometry image colours <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/878">#878</a>
<li>image arrays in sme (Python interface) now include a z dimension <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/850">#850</a>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>lack of geometry image could cause a crash in some cases <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/872">#872</a>
</ul>
- date: 2023-05-23
title: Version 1.3.6 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.6
description: >
<h6 id="added">Added</h6>
<ul>
<li>support for importing RGBA TIFF image files <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/862">#862</a></li>
</ul>
- date: 2023-03-02
title: Version 1.3.5 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.5
description: >
<h6 id="fixed">Fixed</h6>
<ul>
<li>incorrect function evaluations in some cases <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/855">#855</a>, <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/856">#856</a>, <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/857">#857</a></li>
</ul>
- date: 2023-02-23
title: Version 1.3.4 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.4
description: >
<h6 id="fixed">Fixed</h6>
<ul>
<li>incorrect initial concentrations with DUNE simulator for some models <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/852">#852</a></li>
</ul>
- date: 2022-12-05
title: Version 1.3.3 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.3
description: >
<h6 id="changed">Changed</h6>
<ul>
<li>export format of Image Sampled Field from colors to indices <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/710">#710</a> and <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/830">#830</a>.</li>
</ul>
- date: 2022-10-13
title: Version 1.3.2 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.2
description: >
<h6 id="added">Added</h6>
<ul>
<li>support for importing Combine archives <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/828">#828</a></li>
</ul>
- date: 2022-08-10
title: Version 1.3.1 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.1
description: >
<h6 id="changed">Changed</h6>
<ul>
<li>offer to use alternative simulator if simulation setup fails <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/814">#814</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>crash caused by analytic initial species concentrations involving dividing by zero <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/805">#805</a></li>
<li>disappearing simulation progress bar dialog <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/752">#752</a></li>
</ul>
- date: 2022-06-10
title: Version 1.3.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.3.1
description: >
<h6 id="added">Added</h6>
<ul>
<li><a href="https://spatial-model-editor.readthedocs.io/en/stable/reference/parameter-fitting.html">parameter fitting</a> functionality to GUI <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/757">#757</a></li>
<li>support for reading SBML files compressed with bzip2 <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/246">#246</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>GUI no longer writes logging output to console <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/771">#771</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>analytic initial species concentrations were not updated when a parameter value was modified <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/776">#776</a></li>
</ul>
- date: 2022-04-28
title: Version 1.2.2 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.2.2
description: >
<h6 id="added">Added</h6>
<ul>
<li>support for reading compressed sampledFields <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/709">#709</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>TBB is now used everywhere for multithreading (previously linux Python wheels used OpenMP) <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/732">#732</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>improved multi-threading performance <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/742">#742</a></li>
<li>spurious simulation times are no longer appended upon simulation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/751">#751</a></li>
</ul>
- date: 2021-09-30
title: Version 1.2.1 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.2.1
description: >
<h6 id="added">Added</h6>
<ul>
<li>topology-preserving line simplification option <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/328">#328</a></li>
<li>python interface: <code>ctrl+c</code> now cancels a currently running simulation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/665">#665</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>model reactions with invalid locations can now be seen and removed or relocated <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/615">#615</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>functions with zero arguments are now fully supported <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/674">#674</a></li>
<li>python interface: setting <code>n_threads=1</code> for simulate takes precedence over <code>n_threads</code> value in model <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/672">#672</a></li>
<li>bug where membrane reactions could disappear when geometry was changed <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/679">#679</a></li>
<li>bug where removing a compartment could result in an invalid model or a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/685">#685</a></li>
<li>SBML export includes any ModifierSpecies in reactions <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/133">#133</a></li>
</ul>
<h6 id="removed">Removed</h6>
<ul>
<li>incomplete Parametric geometry sbml export support <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/599">#599</a></li>
</ul>
- date: 2021-09-13
title: Version 1.2.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.2.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>non-spatial model guided import with automatic reaction rate rescaling <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/607">#607</a></li>
<li>python interface: optional multithreading (via OpenMP) for Pixel simulations on linux <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/662">#662</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug where loading a model with simulation data and changing model units could cause a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/666">#666</a></li>
<li>show warning message before dune simulation of model with non-spatial species <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/664">#664</a></li>
<li>minimum supported version of MacOS is now 10.14 instead of 10.15 <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/669">#669</a></li>
</ul>
- date: 2021-09-01
title: Version 1.1.5 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.5
description: >
<h6 id="added">Added</h6>
<ul>
<li>python interface: access to all built-in example models <a href="https://github.com/spatial-model-editor/spatial-model-editor/pull/637">#637</a></li>
<li>python interface: view and edit uniform/analytic/image species initial concentrations <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/644">#644</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>compartment colour assignments are now preserved when the geometry image is resized <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/587">#587</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>python interface: bug where compartment geometry mask was not updated after geometry image changed <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/630">#630</a></li>
<li>slow loading of models with large geometry images <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/632">#632</a></li>
<li>avoid constructing mesh twice on model load <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/597">#597</a></li>
<li>crash when importing geometry image after importing non-spatial model <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/651">#651</a></li>
</ul>
- date: 2021-08-17
title: Version 1.1.4 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.4
description: >
<h6 id="added">Added</h6>
<ul>
<li>python interface: <code>Model.simulation_results()</code> provides access to existing model simulation data <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/622">#622</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>python interface: simulation results now provided in <a href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html">numpy.ndarray</a> format <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/610">#610</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug where opening a corrupted sme file caused a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/618">#618</a></li>
</ul>
- date: 2021-08-10
title: Version 1.1.3 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.3
description: >
<h6 id="added">Added</h6>
<ul>
<li>python interface: add option to simulate without returning the results to reduce RAM usage <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/610">#610</a></li>
<li>more detailed error message when a model cannot be loaded <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/449">#449</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug where invalid reaction rate expression caused simulation to crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/609">#609</a></li>
</ul>
- date: 2021-07-13
title: Version 1.1.2 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.2
description: >
<h6 id="added">Added</h6>
<ul>
<li>autocomplete when editing maths <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/559">#559</a></li>
<li>support for all L3 sbml math in reaction rates (with Pixel simulator) <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/569">#569</a></li>
<li>option to invert y-axis of images <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/568">#568</a></li>
<li>option to set size of geometry image in third dimension <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/582">#582</a></li>
<li><code>umol</code> unit of amount added to built-in units <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/600">#600</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>simulation length/intervals only loaded from model on 'reset' click or new model load <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/565">#565</a></li>
<li>models exported as 3d SBML models (to be consistent with our 3d units for species concentrations and volumes) <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/588">#588</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug when clicking on simulation results plot selected wrong timepoint <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/570">#570</a></li>
<li>reaction rates involving species from unrelated compartments now displays an error, instead of only giving an error on simulation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/552">#552</a></li>
<li>simulation crash when species is changed to constant & simulation data are re-loaded <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/561">#561</a></li>
<li>inaccuracy when re-starting a simulation that was stopped early <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/388">#388</a></li>
<li>bug where compartment sizes were not updated when compartment image resolution was altered <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/583">#583</a></li>
<li>bug where invalid mesh could cause a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/585">#585</a></li>
<li>bug where simulating after changing geometry image size could cause a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/591">#591</a></li>
<li>incorrect units used for compartment volumes when referenced in reaction rates <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/584">#584</a></li>
<li>bug where membrane area could be incorrect on model load <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/595">#595</a></li>
</ul>
- date: 2021-05-30
title: Version 1.1.1 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.1
description: >
<h6 id="added">Added</h6>
<ul>
<li>COPASI cps file import support (if COPASI is installed and on path) <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/492">#492</a></li>
<li>shift + mouse scroll to zoom in and out of images <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/532">#532</a></li>
<li>support for spatial models with reactions whose compartment is not specified <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/481">#481</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>mouse scroll no longer changes species stoichiometry in reactions <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/549">#549</a></li>
<li>membrane reaction rates automatically rescaled by membrane area on non-spatial model import <a href="https://github.com/spatial-model-editor/spatial-model-editor/pull/557">#557</a></li>
<li>reactions moved between compartments and membranes rescaled by ratio of area to volume <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/558">#558</a></li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug loading simulation settings depending on system locale setting <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/535">#535</a></li>
<li>slow loading of simulation data <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/504">#504</a></li>
<li>bug where simulation doesn't run again after being stopped <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/545">#545</a></li>
<li>bug where selected reaction sometimes changes when reaction location is changed <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/548">#548</a></li>
<li>ensure species involved in a reaction are valid when reaction location is changed <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/551">#551</a></li>
<li>bug where loading existing simulation uses initial concentrations instead of latest simulation concentrations <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/541">#541</a></li>
</ul>
- date: 2021-05-04
title: Version 1.1.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.1.0
description: >
<h6 id="added">Added</h6>
<ul>
<li>sme file format, contains model, simulation settings and simulation results <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/482">#482</a></li>
<li>support multiple simulation lengths as comma delimited lists <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/464">#464</a></li>
<li>support for simulating models with empty compartments with the Dune-Copasi simulator <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/435">#435</a></li>
<li>option to resize the number of pixels in the geometry image <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/462">#462</a></li>
<li>option to reduce the number of colours in the geometry image <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/280">#280</a></li>
<li>support for non-integer stoichiometries in reactions <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/495">#495</a></li>
<li>optional grid and scale to geometry image <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/497">#497</a></li>
<li>python interface: DUNE simulator can now be used <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/276">#276</a></li>
<li>python interface: existing simulations can be continued <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/514">#514</a></li>
<li>zoom option to geometry image <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/516">#516</a></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>use v1.1.0 of Dune-Copasi simulator</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>python interface: revert change in default simulate() behaviour when doing a second simulation of a model <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/475">#475</a></li>
<li>multiple event related simulation bugs <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/484">#484</a>, <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/485">#485</a>, <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/486">#486</a></li>
<li>incorrect compartment name displayed in simulate display options <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/487">#487</a></li>
<li>simulation image intervals changing length of simulation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/492">#492</a></li>
<li>bug where removing compartment could cause a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/506">#506</a></li>
<li>artefacts in import of species concentrations into simulation <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/508">#508</a></li>
<li>DUNE maximum iteraction count simulation error <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/490">#490</a></li>
</ul>
- date: 2021-04-06
title: Version 1.0.9 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.9
description: >
<h6 id="added">Added</h6>
<ul>
<li>open/save as <code>.sme</code> filetype: contains both the model and the simulation results <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/461">#461</a></li>
<li>support for time-based events: parameters and species concentrations can be set at specified times in the simulation</li>
<li>diagnostic info & image when a simulation fails <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/432">#432</a></li>
<li>zoom option for Boundary and Mesh images in the Geometry Tab</li>
<li>new option in Simulation Tab to export concentrations to model as initial concentrations</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>simulation is no longer reset when the Simulate tab is left in the GUI</li>
<li>simulations can be continued using a different simulator</li>
<li>use v1.0.0 of Dune-Copasi simulator</li>
<li>GUI warns before closing a model with unsaved changes <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/346">#346</a></li>
<li>Membrane names can now be edited in the GUI and in the python interface</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>diffusion constant bug in the Pixel simulator <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/468">#468</a></li>
<li>bug in dune-copasi mesh generation that could cause a crash <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/434">#434</a></li>
<li>bug where unused diffusion constant parameter was sometimes not removed from sbml document</li>
<li>data race in generating simulation concentration images <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/434">#434</a></li>
</ul>
<h6 id="removed">Removed</h6>
<ul>
<li>incomplete Parametric geometry sbml import support <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/452">#452</a></li>
</ul>
- date: 2021-02-10
title: Version 1.0.8 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.8
description: >
<h6 id="added">Added</h6>
<ul>
<li>python library can now import a new geometry image using <code>sme.Model.import_geometry_from_image()</code></li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>mesh generation is now done using the CGAL library</li>
</ul>
<h6 id="removed">Removed</h6>
<ul>
<li>dependence on Triangle mesh library removed due to its non-free license</li>
</ul>
- date: 2021-02-07
title: Version 1.0.7 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.7
description: >
<h6 id="fixed">Fixed</h6>
<ul>
<li>illegal instruction crash on old CPUs <a href="https://github.com/spatial-model-editor/spatial-model-editor/issues/422">#422</a></li>
</ul>
- date: 2021-01-29
title: Version 1.0.6 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.6
description: >
<h6 id="added">Added</h6>
<ul>
<li>python library <code>sme.Model.simulate</code>:<ul>
<li>simulation results now also contain rate of change of concentrations</li>
<li>option to return partial results instead of throwing on simulation timeout</li>
</ul>
</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>more accurate initial concentration interpolation for dune-copasi simulations<ul>
<li>applies to both GUI simulations and exported TIFF files for stand-alone dune-copasi simulation</li>
</ul>
</li>
<li>improved performance of interior point determination in mesh construction</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>meshing bug where invalid 2-point boundary line could cause crash</li>
</ul>
- date: 2021-01-02
title: Version 1.0.5 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.5
description: >
<h6 id="added">Added</h6>
<ul>
<li>user can edit dune-copasi Newton solver parameters</li>
<li>Pixel simulator supports reactions that explicitly depend on t, x, y</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>dune-copasi simulations now support membrane flux terms<ul>
<li>rectangular membrane compartments no longer required</li>
<li>simpler mesh generation</li>
<li>faster and more accurate simulations</li>
</ul>
</li>
<li>improved boundary construction<ul>
<li>use pixel edges as boundary edges instead of pixels</li>
<li>shared boundaries and their end points now unambiguously determined</li>
</ul>
</li>
<li>improved line simplification</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>bug in scaling of membrane reactions in Pixel simulations<ul>
<li>added missing <code>1/a</code> factor, where <code>a</code> is the width of a pixel in model units</li>
</ul>
</li>
</ul>
<h6 id="removed">Removed</h6>
<ul>
<li>inconsistent <code>RateRule</code> support in SBML import</li>
</ul>
- date: 2020-10-22
title: Version 1.0.4 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.4
description: >
<h6 id="added">Added</h6>
<ul>
<li>simulation display options are now saved</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>python library API<ul>
<li>lists now have name-based look-up, old name-based look-up functions removed</li>
<li>examples of old -> new change required in user code:<ul>
<li><code>model.compartment("name")</code> -> <code>model.compartments["name"]</code></li>
<li><code>model.specie("name")</code> -> <code>model.species["name"]</code></li>
</ul>
</li>
</ul>
</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>species removal bug</li>
</ul>
- date: 2020-10-19
title: Version 1.0.3 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.3
description: >
<h6 id="added">Added</h6>
<ul>
<li>python library example notebooks</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>python library performance improvements</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>python library segfault / missing data issue on some linux platforms</li>
</ul>
- date: 2020-10-16
title: Version 1.0.2 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.2
description: >
<h6 id="added">Added</h6>
<ul>
<li>python library documentation and example notebooks</li>
<li>support for import of geometry image with alpha channel / transparency</li>
<li>display compartment size and membrane length</li>
</ul>
<h6 id="changed">Changed</h6>
<ul>
<li>python library performance improvements</li>
</ul>
<h6 id="fixed">Fixed</h6>
<ul>
<li>normalisation of simulation concentration images</li>
<li>geometry imported from another model not saved bug</li>
<li>python library segfault / missing data issue on linux</li>
<li>reaction removal bug</li>
</ul>
- date: 2020-10-5
title: Version 1.0.1 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.1
description: >
<h6 id="added">Added</h6>
<ul>
<li>membranes to python library</li>
<li>compartment pixel mask to python library</li>
<li>timeout parameter to simulate function in python library</li>
</ul>
- date: 2020-10-2
title: Version 1.0.0 released
url: https://github.com/spatial-model-editor/spatial-model-editor/releases/tag/1.0.0
description: >
<p>First official release.</p>