DamCB/tyssue issues and pull requests

#287 - Pypi

Pull Request - State: closed - Opened by glyg 10 months ago

#286 - use pypi

Pull Request - State: closed - Opened by glyg 10 months ago

#285 - pypi

Pull Request - State: closed - Opened by glyg 10 months ago

#284 - Dev

Pull Request - State: closed - Opened by glyg 10 months ago

#283 - Dev

Pull Request - State: closed - Opened by glyg 10 months ago

#282 - Using T1 Transitions instead of reconnect?

Issue - State: open - Opened by sniffo 10 months ago - 3 comments

#281 - Dev

Pull Request - State: closed - Opened by glyg 11 months ago - 9 comments

#280 - Update history.py

Pull Request - State: closed - Opened by sniffo 11 months ago

#279 - Pyproject

Pull Request - State: closed - Opened by glyg 11 months ago

#278 - Release

Pull Request - State: closed - Opened by glyg 11 months ago

#277 - CI-CD update

Pull Request - State: closed - Opened by glyg 11 months ago

#276 - new release?

Issue - State: open - Opened by Pablo1990 12 months ago - 1 comment

#275 - Improved History recording efficiency - no more exponential run-time increase possibly

Issue - State: closed - Opened by sniffo about 1 year ago - 7 comments

#274 - Update history.py

Pull Request - State: closed - Opened by sniffo about 1 year ago - 5 comments

#273 - History.retrieve() efficiency. Any workarounds?

Issue - State: closed - Opened by sniffo about 1 year ago - 10 comments

#272 - QSsolver find energy min always return success is False

Issue - State: closed - Opened by sophietheis about 1 year ago - 2 comments

#271 - Pandas 2.0 incompatibility - df.append removed

Issue - State: closed - Opened by sniffo about 1 year ago - 4 comments

#270 - Definition of ux, uy

Issue - State: closed - Opened by Lepinja666 over 1 year ago - 2 comments

#269 - Faces become deformed and can overlap

Issue - State: closed - Opened by Lepinja666 over 1 year ago - 3 comments

#268 - Prevent a print when setting up specs

Issue - State: closed - Opened by Lepinja666 over 1 year ago - 5 comments

#267 - tyssue doc site is down

Issue - State: open - Opened by kephale almost 2 years ago - 4 comments

#266 - Cannot scale periodic boundary sheet

Issue - State: closed - Opened by Lepinja666 almost 2 years ago - 4 comments

#265 - Value out of range for T1 transition (ValueError, KeyError) - Periodic sheet

Issue - State: closed - Opened by Lepinja666 almost 2 years ago - 2 comments

#264 - merge from glyg

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

#263 - Solving mesh collision

Pull Request - State: closed - Opened by sophietheis about 2 years ago - 14 comments

#262 - Use collision solver change QS result

Issue - State: closed - Opened by sophietheis about 2 years ago - 9 comments

#261 - Cell division failed for cell at the border

Issue - State: closed - Opened by sophietheis about 2 years ago

#260 - Planar periodic sheet

Issue - State: closed - Opened by Lepinja666 about 2 years ago - 13 comments

#259 - napari integration

Issue - State: open - Opened by kephale about 2 years ago - 13 comments

#258 - `ax` argument not considered in `tyssue.plt_draw.sheet_view`

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

#257 - Rearrangement (T1&T3) with QS Solver

Issue - State: open - Opened by sophietheis over 2 years ago - 6 comments

#256 - Last version of pandas (1.3.5) not working with Tyssue

Issue - State: closed - Opened by sophietheis over 2 years ago - 4 comments

#255 - Create gif

Issue - State: open - Opened by vlachina over 2 years ago - 1 comment

#254 - add geometry calculation to prevent midline crossing

Pull Request - State: closed - Opened by btbest almost 3 years ago - 6 comments

#253 - release v1.0

Issue - State: open - Opened by glyg almost 3 years ago

#252 - Random addition of vertices fails for internal cells

Issue - State: closed - Opened by jonathan-f almost 3 years ago - 6 comments

#251 - Bug encountered while running "sheet_from_cell_centers" function on points generated using from "sheet_from_cell_centers"

Issue - State: closed - Opened by sniffo about 3 years ago - 2 comments

#250 - Neighbour exchanges in delamination

Pull Request - State: closed - Opened by btbest about 3 years ago - 10 comments

#249 - Bug in HistoryHDF5

Issue - State: open - Opened by glyg over 3 years ago

#248 - adds zarr support

Pull Request - State: closed - Opened by glyg over 3 years ago - 1 comment

#247 - Add research notice

Pull Request - State: closed - Opened by yochannah over 3 years ago - 1 comment

#246 - Has anybody successfully implemented constriction with the viscous solver?

Issue - State: closed - Opened by btbest over 3 years ago - 5 comments

#245 - ENH: pass column name to `data_at_opposite`

Issue - State: closed - Opened by glyg over 3 years ago

#244 - Remove html tags, fix citation syntax, minor edits

Pull Request - State: closed - Opened by pdebuyl over 3 years ago - 1 comment

#243 - Fix reference

Pull Request - State: closed - Opened by sophietheis over 3 years ago

#242 - Fix spell issues

Pull Request - State: closed - Opened by sophietheis over 3 years ago - 1 comment

#241 - FIx link to demo notebooks and documentation

Pull Request - State: closed - Opened by sophietheis over 3 years ago

#240 - Fix link to contributors

Pull Request - State: closed - Opened by sophietheis over 3 years ago - 1 comment

#239 - Counting T1 transitions

Issue - State: open - Opened by glyg over 3 years ago - 21 comments

#238 - some bug fixses and numpy 1.20 compat

Pull Request - State: closed - Opened by glyg over 3 years ago - 1 comment

#237 - area_grad does not return unit vectors

Issue - State: closed - Opened by btbest over 3 years ago - 4 comments

#236 - BIUG upcast does not preserve dims if argument is an np.ndarray

Issue - State: closed - Opened by glyg over 3 years ago
Labels: bug

#235 - use precomputed relative positions

Issue - State: closed - Opened by glyg over 3 years ago

#234 - Further corrections to my suggested code, sorry for the multiple PLs

Pull Request - State: closed - Opened by gcourcou over 3 years ago - 7 comments

#233 - Question Regarding Formulation for Area Elasticity, Perimeter Elasticity, and Line Tension

Issue - State: closed - Opened by sniffo over 3 years ago - 3 comments

#232 - Changing parameters over-time in the viscous solver?

Issue - State: closed - Opened by sniffo over 3 years ago - 4 comments

#231 - New pull request, way healthier than last one

Pull Request - State: closed - Opened by gcourcou over 3 years ago - 3 comments

#230 - Jupyter-book based doc

Pull Request - State: closed - Opened by glyg over 3 years ago - 4 comments

#229 - Some issue with ucoords in 0.8.1

Issue - State: closed - Opened by btbest over 3 years ago - 6 comments

#228 - Update bibliography and figures

Pull Request - State: closed - Opened by sophietheis over 3 years ago - 2 comments

#227 - Improve `plot_force` and fix `spec_updater`

Pull Request - State: closed - Opened by sophietheis over 3 years ago - 4 comments

#226 - `spec_updater` does not add new element

Issue - State: closed - Opened by sophietheis over 3 years ago

#225 - Update paper

Pull Request - State: closed - Opened by sophietheis over 3 years ago - 2 comments

#224 - ENH: write mean_srce, mean_trgt etc. functions

Issue - State: closed - Opened by glyg almost 4 years ago

#223 - ENH: array / callable `"visible"` spec

Issue - State: open - Opened by glyg almost 4 years ago

#222 - Chemo.no autoscale constant pressure

Pull Request - State: closed - Opened by gcourcou almost 4 years ago - 1 comment

#221 - ENH: meshio export

Issue - State: closed - Opened by glyg almost 4 years ago - 6 comments

#220 - Introducing holes or removing a patch of cells from within a tissue

Issue - State: open - Opened by sniffo almost 4 years ago - 16 comments

#219 - Functionality to avoid self-intersections and edges intersecting each other?

Issue - State: closed - Opened by sniffo almost 4 years ago - 2 comments

#218 - Problem with link to Bibtex

Issue - State: closed - Opened by BenitoJG almost 4 years ago - 2 comments

#217 - bug fix (opening a config file in r+ mode)

Pull Request - State: closed - Opened by glyg almost 4 years ago - 1 comment

#216 - Manually Setting Coordinates for Vertices

Issue - State: closed - Opened by sniffo almost 4 years ago - 2 comments

#215 - set release to true

Pull Request - State: closed - Opened by glyg almost 4 years ago

#214 - Update paper.md

Pull Request - State: closed - Opened by glyg about 4 years ago - 2 comments

#213 - A lot of stuff

Pull Request - State: closed - Opened by glyg about 4 years ago - 2 comments

#212 - Force inference does not work

Issue - State: open - Opened by sophietheis about 4 years ago

#211 - T1 Transitions and Collision - Quasistatic and Viscous Solvers

Issue - State: closed - Opened by sniffo about 4 years ago - 6 comments

#210 - hard coded values in `relax` action

Issue - State: closed - Opened by glyg about 4 years ago - 3 comments

#209 - ENH: Save all by default in history

Issue - State: closed - Opened by glyg about 4 years ago

#208 - Paper draft

Pull Request - State: closed - Opened by sophietheis about 4 years ago - 3 comments

#207 - Really fixed memory leak

Pull Request - State: closed - Opened by sophietheis about 4 years ago - 1 comment

#206 - Fixed memory leak during history record.

Pull Request - State: closed - Opened by sophietheis about 4 years ago - 1 comment

#205 - New gif possibility and minor changes.

Pull Request - State: closed - Opened by sophietheis about 4 years ago - 2 comments

#204 - Bug fix

Pull Request - State: closed - Opened by glyg over 4 years ago - 1 comment

#203 - HistoryHDF5 can store a time point twice

Issue - State: closed - Opened by glyg over 4 years ago
Labels: bug

#202 - Standardization of dt value

Pull Request - State: closed - Opened by sophietheis over 4 years ago - 1 comment

#201 - Use the same dt parameter in viscous solver and sheet.settings

Issue - State: closed - Opened by sophietheis over 4 years ago - 1 comment

#200 - Cannot reindex from duplicate axis when running extract_bounding_box on sheet from history

Issue - State: closed - Opened by sophietheis over 4 years ago - 3 comments
Labels: bug

#199 - Has anyone else thought of applying viscous/frictional forces in the energy min implementation? We are currently allowing large deformations to occur instantaneously. In the literature, this class of models is termed active vertex models.

Issue - State: closed - Opened by gcourcou over 4 years ago - 10 comments

#198 - Fixed issues and new geometries

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

#197 - Add option so that face_rotations output can have Nf rotations

Issue - State: closed - Opened by glyg over 4 years ago - 2 comments

#196 - Noise in Sheet.planar_sheet_2d creates erratic cell shapes at the tissue boundaries

Issue - State: closed - Opened by sniffo over 4 years ago - 7 comments

#195 - KeyError when running get_opposite on sheet retrieve from history

Issue - State: closed - Opened by sophietheis over 4 years ago - 1 comment
Labels: bug

#194 - Version 0.7.1 on Anaconda? CGAL support for periodic boundary conditions?

Issue - State: closed - Opened by sniffo over 4 years ago - 11 comments

#193 - Euler Solver solve method results in nan and inf in edge_df for Sheet objects (question from email)

Issue - State: closed - Opened by sniffo over 4 years ago - 4 comments

#192 - AssertionError when runing `get_extra_indices()`

Issue - State: closed - Opened by sophietheis over 4 years ago - 1 comment
Labels: bug

#191 - Any built-in methods to add/remove specific vertices, edges and cells and have all datasets updated accordingly?

Issue - State: closed - Opened by sniffo over 4 years ago - 5 comments

#190 - Measure force inference

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

#189 - use zarr as base file format instead of HDF5

Issue - State: open - Opened by glyg over 4 years ago - 1 comment
Labels: question, design

#188 - Use meshio as single import / export interface

Issue - State: closed - Opened by glyg over 4 years ago - 2 comments

GitHub / DamCB/tyssue issues and pull requests