simularium/simulariumio issues and pull requests

#190 - use python 3.10 instead of 3.8 for main build

Pull Request - State: closed - Opened by ascibisz 4 months ago

#189 - CI Build Broken for Python 3.8

Issue - State: closed - Opened by ascibisz 4 months ago
Labels: maintenance

#188 - Make centering cytosim fibers optional

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

#187 - ci(dependabot): bump actions/add-to-project from 1.0.1 to 1.0.2

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

#186 - ci(dependabot): bump actions/add-to-project from 1.0.0 to 1.0.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#185 - TrajectoryFileInfo only declares/allows a PerspectiveCameraSpec

Issue - State: open - Opened by toloudis about 1 year ago - 1 comment

#184 - Fix/use display names

Pull Request - State: closed - Opened by blairlyons 7 months ago

#183 - Feature/draw md bonds

Pull Request - State: closed - Opened by advaitathreya 8 months ago - 7 comments

#182 - Version compatibility conflict with cellpack and simularium (local development)

Issue - State: open - Opened by advaitathreya 8 months ago
Labels: bug

#181 - Pin cellpack version to 1.0.3

Pull Request - State: closed - Opened by mogres 8 months ago
Labels: dependencies

#180 - Include option to draw bonds from MD trajectory

Pull Request - State: closed - Opened by advaitathreya 8 months ago - 3 comments

#179 - ci(dependabot): bump actions/add-to-project from 0.5.0 to 1.0.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#178 - WIP: NERDSS Converter

Pull Request - State: open - Opened by ascibisz 8 months ago

#177 - ci(dependabot): bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#176 - ci(dependabot): bump actions/add-to-project from 0.5.0 to 0.6.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 2 comments
Labels: dependencies

#175 - ci(dependabot): bump extractions/setup-just from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#174 - ci(dependabot): bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#173 - Maya plugin

Issue - State: open - Opened by blairlyons 9 months ago

#172 - Convert aLens

Issue - State: open - Opened by blairlyons 9 months ago

#170 - update smoldyn autoconversion templates to match design spec

Pull Request - State: closed - Opened by ascibisz 9 months ago - 1 comment

#169 - subpoints relative to agent position

Pull Request - State: closed - Opened by ascibisz 9 months ago - 3 comments

#168 - Convert VMD data

Issue - State: closed - Opened by blairlyons 9 months ago

#167 - Convert lattice microbes data

Issue - State: closed - Opened by blairlyons 9 months ago - 1 comment

#166 - Convert MEM3DG models

Issue - State: open - Opened by blairlyons 10 months ago

#165 - Convert NERDSS data

Issue - State: open - Opened by blairlyons 9 months ago

#164 - Update README.md

Pull Request - State: closed - Opened by meganrm 12 months ago

#163 - Update file_format.md

Pull Request - State: closed - Opened by meganrm 12 months ago - 2 comments

#162 - ci(dependabot): bump conda-incubator/setup-miniconda from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#161 - Help with MCell

Issue - State: open - Opened by corredD almost 1 year ago

#160 - move things we need in octopus to top level simulariumio package

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

#159 - ci(dependabot): bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#158 - Add update functions to TrajectoryData

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

#157 - Add New Data Types for Simularium Frame Data

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

#156 - Documentation on how to make children(ie states)

Issue - State: open - Opened by meganrm about 1 year ago
Labels: maintenance

#155 - Append multiple agents to TrajectoryData objects

Pull Request - State: closed - Opened by mogres over 1 year ago - 6 comments

#154 - Fix/update examples

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

#153 - Issues with appending agents to TrajectoryData object

Issue - State: open - Opened by mogres over 1 year ago - 2 comments
Labels: bug

#152 - Center position data for smoldyn and medyan

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

#151 - Add New Data Types for Simularium Frame Data

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

#150 - Implement data structures for entire dataset slicing

Issue - State: open - Opened by blairlyons over 1 year ago - 1 comment

#149 - Update example Jupyter notebooks

Issue - State: closed - Opened by blairlyons over 1 year ago
Labels: maintenance

#148 - Feature/auto handle scale factor

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

#147 - Feature/auto handle scale factor

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

#146 - Automatically handle scale factor

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

#145 - Center Smoldyn and MEDYAN data

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

#144 - Fix default display data

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

#143 - Update template to match new design

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

#142 - Feature/progress callback on converters

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

#141 - Feature/input data errors

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

#140 - Jagged list for agent data

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

#139 - ci(dependabot): bump actions/add-to-project from 0.4.0 to 0.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#138 - Feature/binary reader leaves binary spatial data

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

#137 - ci(dependabot): bump actions/add-to-project from 0.3.0 to 0.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#136 - Feature/add more UI templates

Pull Request - State: closed - Opened by ascibisz almost 2 years ago

#135 - Make agent names case insensitive

Pull Request - State: closed - Opened by ascibisz about 2 years ago - 3 comments

#134 - Use TrajectoryData in converter tests

Issue - State: open - Opened by blairlyons about 2 years ago
Labels: maintenance

#133 - add from_dict to SmoldynData

Pull Request - State: closed - Opened by ascibisz about 2 years ago - 2 comments

#132 - Feature/smoldyn-autoconversion

Pull Request - State: closed - Opened by ascibisz about 2 years ago - 1 comment

#131 - Fix ReaDDy conversion for types missing display data

Pull Request - State: closed - Opened by blairlyons about 2 years ago - 1 comment

#130 - fix/pin-flake8-pyprojecttoml-to-fix-lint

Pull Request - State: closed - Opened by evamaxfield about 2 years ago - 2 comments

#129 - Updates to smoldyn UI template

Pull Request - State: closed - Opened by blairlyons about 2 years ago - 2 comments

#128 - Raise consistent error for problems with input files

Issue - State: closed - Opened by blairlyons about 2 years ago - 1 comment
Labels: 11

#127 - Option to fit box size

Issue - State: open - Opened by blairlyons about 2 years ago

#126 - Option to center trajectory

Issue - State: closed - Opened by blairlyons about 2 years ago - 1 comment

#125 - ci(dependabot): bump actions/add-to-project from 8f59162ff6331da7cfb994cdfdea456d39c0c9bf to 0.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#124 - Feature/load open binary data

Pull Request - State: closed - Opened by ascibisz about 2 years ago

#123 - Make agent names case insensitive

Issue - State: closed - Opened by blairlyons about 2 years ago
Labels: current sprint, 10

#122 - Load open binary data

Issue - State: closed - Opened by blairlyons about 2 years ago
Labels: current sprint, 9

#121 - Add missing comma between dependencies

Pull Request - State: closed - Opened by jessicasyu about 2 years ago

#120 - Fix/include jmol colors csv

Pull Request - State: closed - Opened by blairlyons about 2 years ago

#119 - Rewrite Trajectory Converter Tests

Pull Request - State: closed - Opened by ascibisz about 2 years ago - 1 comment

#118 - Progress callback

Issue - State: closed - Opened by blairlyons about 2 years ago
Labels: 11

#117 - import recipeloader from main package

Pull Request - State: closed - Opened by meganrm about 2 years ago

#116 - Bugfix/validate agent id size

Pull Request - State: closed - Opened by ascibisz about 2 years ago

#115 - Update infrastructure and fix docs

Issue - State: closed - Opened by blairlyons about 2 years ago - 1 comment
Labels: maintenance

#114 - admin/update-to-new-cookiecutter

Pull Request - State: closed - Opened by evamaxfield about 2 years ago - 3 comments

#113 - Feature/particle orientations

Pull Request - State: closed - Opened by blairlyons over 2 years ago

#112 - Edge cases for particle orientations

Issue - State: open - Opened by blairlyons over 2 years ago

#111 - Add transform offsets for files in DisplayData

Issue - State: open - Opened by blairlyons over 2 years ago

#110 - Update PhysiCell importer

Pull Request - State: closed - Opened by blairlyons over 2 years ago

#109 - Subpoints relative to agent transform

Issue - State: closed - Opened by blairlyons over 2 years ago

#108 - Handle chunked files

Issue - State: open - Opened by blairlyons over 2 years ago

#107 - consistent API naming for frames or timesteps

Issue - State: open - Opened by toloudis over 2 years ago
Labels: maintenance

#105 - Feature/metaballs

Pull Request - State: closed - Opened by blairlyons over 2 years ago - 4 comments

#104 - Initial UI template

Issue - State: closed - Opened by blairlyons over 2 years ago - 1 comment
Labels: 8

#103 - Metaballs for PhysiCell

Issue - State: open - Opened by blairlyons over 2 years ago

#99 - Feature/Smoldyn templates

Pull Request - State: closed - Opened by blairlyons over 2 years ago - 5 comments

#98 - Rewrite converter tests

Issue - State: closed - Opened by meganrm over 2 years ago
Labels: maintenance

#97 - use VIZ_TYPE constant, always multiply radius by scale_factor, use co…

Pull Request - State: closed - Opened by meganrm over 2 years ago

#96 - Metaballs display type

Issue - State: closed - Opened by blairlyons over 2 years ago - 4 comments
Labels: priority: urgent, 7

#95 - Fix failing tests caused by old numpy version

Pull Request - State: closed - Opened by meganrm over 2 years ago

#94 - Fix/v3 updates

Pull Request - State: closed - Opened by blairlyons almost 3 years ago