CI-CD update #277
Merged
CI-CD update #277
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
glyg
added a commit
that referenced
this pull request
Dec 27, 2023
* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * dependency (#277) * bug fixes --------- Co-authored-by: Guillaume Gay <[email protected]>
glyg
added a commit
that referenced
this pull request
Jan 10, 2024
* dependency * Update history.py > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * Solving mesh collision (#263) * Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * dependency (#277) * bug fixes --------- Co-authored-by: Guillaume Gay <[email protected]> * tests pass * fixes unknown namz --------- Co-authored-by: sniffo <[email protected]> Co-authored-by: Sophie THEIS <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
[ANN] Working on a 1.0 release
Dear tyssue user or prospective user, I come with good bearings.
This commit to the **new default branch
mainis the official start of the 1.0 release. It is long overdue and there is a lot of house keeping.Short term