{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":32533164,"defaultBranch":"main","name":"tyssue","ownerLogin":"DamCB","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-03-19T16:27:24.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/7861101?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1707985220.0","currentOid":""},"activityList":{"items":[{"before":"833ba9d11626d806d2521962e4e8935c96df91be","after":"c15063e0ae3ee29e178180f157d7113723a7b247","ref":"refs/heads/main","pushedAt":"2024-02-15T08:01:53.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Vispy bug (#288)\n\n* use pypi\r\n\r\n* split actions\r\n\r\n* no double\r\n\r\n* merge jobs\r\n\r\n* fix yml?\r\n\r\n* try to fix cmake\r\n\r\n* try to fix cmake\r\n\r\n* try to fix cmake\r\n\r\n* revert commending out Development.Embed in cmakelist\r\n\r\n* don't build wheels through pypi\r\n\r\n* revert changes in CMakelists\r\n\r\n* remove spurious action\r\n\r\n* don't fail on vispy import","shortMessageHtmlLink":"Vispy bug (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2135861307\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/288\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/288/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/288\">#288</a>)"}},{"before":"998eac331cc8b8973e9c5c62f5498463016ca91e","after":"d4a45184b81b6ac9d9281ef1d637526bd57f75e4","ref":"refs/heads/vispy_bug","pushedAt":"2024-02-15T07:53:19.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Merge branch 'main' into vispy_bug","shortMessageHtmlLink":"Merge branch 'main' into vispy_bug"}},{"before":"ffb160358da791507252165ec7010b5ccd0de8eb","after":"998eac331cc8b8973e9c5c62f5498463016ca91e","ref":"refs/heads/vispy_bug","pushedAt":"2024-02-14T15:20:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"don't fail on vispy import","shortMessageHtmlLink":"don't fail on vispy import"}},{"before":null,"after":"ffb160358da791507252165ec7010b5ccd0de8eb","ref":"refs/heads/vispy_bug","pushedAt":"2024-02-14T15:18:27.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"remove spurious action","shortMessageHtmlLink":"remove spurious action"}},{"before":"9117f96aa8e354071087e8a5fe8a7d93051d6d5f","after":"833ba9d11626d806d2521962e4e8935c96df91be","ref":"refs/heads/main","pushedAt":"2024-02-14T13:58:29.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Pypi (#287)\n\n* use pypi\r\n\r\n* split actions\r\n\r\n* no double\r\n\r\n* merge jobs\r\n\r\n* fix yml?\r\n\r\n* try to fix cmake\r\n\r\n* try to fix cmake\r\n\r\n* try to fix cmake\r\n\r\n* revert commending out Development.Embed in cmakelist\r\n\r\n* don't build wheels through pypi\r\n\r\n* revert changes in CMakelists\r\n\r\n* remove spurious action","shortMessageHtmlLink":"Pypi (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2133813766\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/287\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/287/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/287\">#287</a>)"}},{"before":"6d0d287ee50e5de40ce5ce3970596332fb014eae","after":"ffb160358da791507252165ec7010b5ccd0de8eb","ref":"refs/heads/pypi","pushedAt":"2024-02-14T10:44:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"remove spurious action","shortMessageHtmlLink":"remove spurious action"}},{"before":"7c3e7e8e298c09551003054acce845eba2d6fb4d","after":"6d0d287ee50e5de40ce5ce3970596332fb014eae","ref":"refs/heads/pypi","pushedAt":"2024-02-14T10:21:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"revert changes in CMakelists","shortMessageHtmlLink":"revert changes in CMakelists"}},{"before":"ffff23e7a2be0598b656a4854591e08a919bd538","after":"7c3e7e8e298c09551003054acce845eba2d6fb4d","ref":"refs/heads/pypi","pushedAt":"2024-02-14T10:05:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"don't build wheels through pypi","shortMessageHtmlLink":"don't build wheels through pypi"}},{"before":"1d309c0caae37821ff294373d2f6aa4943f9c795","after":"ffff23e7a2be0598b656a4854591e08a919bd538","ref":"refs/heads/pypi","pushedAt":"2024-02-14T09:59:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"revert commending out Development.Embed in cmakelist","shortMessageHtmlLink":"revert commending out Development.Embed in cmakelist"}},{"before":"e00dd2515c24924a8818c530ca06b3dadf6eacff","after":"1d309c0caae37821ff294373d2f6aa4943f9c795","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:55:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"try to fix cmake","shortMessageHtmlLink":"try to fix cmake"}},{"before":"215c56bf1d3d737d959fc105c52f24a9e56d591e","after":"e00dd2515c24924a8818c530ca06b3dadf6eacff","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:47:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"try to fix cmake","shortMessageHtmlLink":"try to fix cmake"}},{"before":"580fd5a411057c052ff7514d0c050fc783f200f9","after":"215c56bf1d3d737d959fc105c52f24a9e56d591e","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:44:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"try to fix cmake","shortMessageHtmlLink":"try to fix cmake"}},{"before":"31898aa3dbcc4fa2b0c500a6851fc9b5c7c6b26a","after":"580fd5a411057c052ff7514d0c050fc783f200f9","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:36:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"fix yml?","shortMessageHtmlLink":"fix yml?"}},{"before":"d8bab931065b033f98a2a31392c457f82eeaa3a9","after":"31898aa3dbcc4fa2b0c500a6851fc9b5c7c6b26a","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:35:01.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Merge branch 'main' into pypi","shortMessageHtmlLink":"Merge branch 'main' into pypi"}},{"before":null,"after":"d8bab931065b033f98a2a31392c457f82eeaa3a9","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:33:02.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"merge jobs","shortMessageHtmlLink":"merge jobs"}},{"before":"c6d2c73dd463c3b55409523a392d32833b228059","after":null,"ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:11:13.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"}},{"before":"af9d8a0ace24ada90a404f4c80da8e6281bc84cc","after":"9117f96aa8e354071087e8a5fe8a7d93051d6d5f","ref":"refs/heads/main","pushedAt":"2024-02-14T08:11:10.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"use pypi (#286)\n\n* use pypi\r\n\r\n* split actions\r\n\r\n* no double","shortMessageHtmlLink":"use pypi (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2133759087\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/286\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/286/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/286\">#286</a>)"}},{"before":"7d46c6409dd6fd641676185911a9ac5a97fabf5c","after":"c6d2c73dd463c3b55409523a392d32833b228059","ref":"refs/heads/pypi","pushedAt":"2024-02-14T08:00:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"no double","shortMessageHtmlLink":"no double"}},{"before":"7f4ffbcf199e19722f6b44d52d6d1c8cdf18b4b0","after":"7d46c6409dd6fd641676185911a9ac5a97fabf5c","ref":"refs/heads/pypi","pushedAt":"2024-02-14T07:59:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"split actions","shortMessageHtmlLink":"split actions"}},{"before":"af9d8a0ace24ada90a404f4c80da8e6281bc84cc","after":"7f4ffbcf199e19722f6b44d52d6d1c8cdf18b4b0","ref":"refs/heads/pypi","pushedAt":"2024-02-14T07:55:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"use pypi","shortMessageHtmlLink":"use pypi"}},{"before":null,"after":"af9d8a0ace24ada90a404f4c80da8e6281bc84cc","ref":"refs/heads/pypi","pushedAt":"2024-02-14T07:55:14.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Dev (#284)\n\n* Fix for Issues #261 - cell division failed at the border\r\n\r\n* Fix Mesh creation\r\n\r\nSurface mesh create wasn't create all faces. Now it is fixed. \r\nAlso : -add two methods to Mesh to list faces and vertices. \r\n           -generalised coordinates\r\n           -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder\r\n\r\n* Add 2D collision solver\r\n\r\nAdd class to solve collision in 2D or in 3D. \r\n3D collision solver need to be fixed\r\n\r\n* Update README.md\r\n\r\nAdd `How to cite` section\r\nAdd `Geometry` section\r\nAdd `Publications` section\r\nUpdate bibliography link\r\n\r\n* Generalised wich vertex penetrate face\r\n\r\n* Attempt to set out particular cases\r\n\r\n* Detect and fix self-crossing face\r\n\r\nUnable to make this algo works... https://europepmc.org/article/PMC/3660981\r\nUse ordered vertices and their angle position.\r\n     -> uncrossed face : angles are monotonically increasing\r\n     -> crossed face : angles are not monotonically increasing\r\n\r\n* Use `.apply()` \r\n\r\nNeed to recalculate angle_e for twisted face\r\nOne fix which is only suitable for 2D lateral sheet...\r\n\r\n* ENH: write `mean_XX` method in `Epithelium` class (Issue #224)\r\n\r\n* Fix according to comments\r\n\r\n* Fix Issue #258 ax argument not considered in `plt_draw.sheet_view`\r\n\r\n* ENH: pass column name to `data_at_opposite` issue (#245)\r\n\r\n* Add publication and remove bibtex reference\r\n\r\n* Add check face convexity\r\n\r\n* Use reset_index and code simplification\r\n\r\n* yAdd to_mesh function (issue #221) and some test\r\n\r\n* Remove the use of reset_index in face_self_intersect\r\n\r\n* use ipv_draw with 2D data\r\n\r\n* Fix solution after detection point inside polygon\r\n\r\n* Remove solving collision for 2 same face...\r\n\r\n* Abord vertex displacement if it creates twisted face\r\n\r\n* New way to calculate the position of \"penetrate\" vertices\r\n\r\nFor 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.\r\n\r\n* WIP - use force field to fix collision\r\n\r\n* Small fix\r\n\r\n* Remove function duplication due to circular import\r\n\r\n* Calculate \"repulsion\" gradient in the effector method. Remove loop\r\n\r\n* Fix tests\r\n\r\nRemove collisions tests\r\nFix method call in meshes test\r\nComment \"update_repulstion\" method in planar geometry\r\n\r\n* Add lateralsheet shapes + test\r\n\r\n* Update publication + add collapse texte\r\n\r\n* Add test for Repulsion effector\r\n\r\n* Add test update repulsion\r\n\r\n* Remove unused import\r\n\r\n* Add `drop_face` to allow hole (issues #220 and #141) (associate #221)\r\n\r\n* Update readme.md\r\n\r\n* Update publications in README.md\r\n\r\n* Add `lineage` attribute to `Epithelium`\r\n\r\nIn order to keep track of cell lineage\r\n\r\n* Remove memory oscillation\r\n\r\n* builds with pip\r\n\r\nadds pyproject.toml\r\nbuild command:\r\npip install --no-build-isolation --config-settings=editable.rebuild=true -ve.\r\n\r\n* debugging, still no build apparently\r\n\r\n* build and tests\r\n\r\n* update nb submodule\r\n\r\n* fix pyproject\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* adds scikit-build dep\r\n\r\n* python version\r\n\r\n* python version specifier\r\n\r\n* remove strang flags\r\n\r\n* adds _version.py\r\n\r\n* setuptools_scm dep\r\n\r\n* simplified I guess\r\n\r\n* zdds setuptools-scm to env, MakeFilelist shenanigans\r\n\r\n* restricting to 3.10\r\n\r\n* install dev\r\n\r\n* pyhon version coherence\r\n\r\n* install cmd\r\n\r\n* trying to move to modern sckit-build (it's painful)\r\n\r\n* WIP change build\r\n\r\n* getting closer I hope\r\n\r\n* make_spherical test pasess \\o/\r\n\r\n* tests passing, warnings still to be treated\r\n\r\n* don't install editable version in gh action\r\n\r\n* remove diff chars\r\n\r\n* tagging again to avoid metadata mismatch\r\n\r\n* Uncomment 2D repulsion + tests\r\n\r\nFix pandas issue\r\n\r\n* Add comments in effectors.py\r\n\r\n* rmeove _version.py and ignore in git\r\n\r\n* Update history.py (#274)\r\n\r\n> 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\r\n> Edited self.time_stamps() method to return self._time_stamps\r\n> Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded.\r\n\r\n* skip 2 tests\r\n\r\n* fix non existing hdf5\r\n\r\n* submodules\r\n\r\n* adds notebooks submodule\r\n\r\n* should fix history bug\r\n\r\n* adds submodules again\r\n\r\n* minoor fix, notebooks\r\n\r\n* updates readme and rtd\r\n\r\n* fixing pyproject\r\n\r\n---------\r\n\r\nCo-authored-by: Sophie T <sophiets13@gmail.com>\r\nCo-authored-by: sniffo <tasnif.rahman@gmail.com>","shortMessageHtmlLink":"Dev (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2132930296\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/284\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/284/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/284\">#284</a>)"}},{"before":"af73bb46dd51aef4c6850d23e55733a01ede65b3","after":"3f3a2e1f62eb86f5291e9f14ce89173d3a778c67","ref":"refs/heads/dev","pushedAt":"2024-02-14T07:49:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"builds for PyPi in github action","shortMessageHtmlLink":"builds for PyPi in github action"}},{"before":"8eb034f2d6cc18b56c8189560209c27dc2561aaa","after":"af9d8a0ace24ada90a404f4c80da8e6281bc84cc","ref":"refs/heads/main","pushedAt":"2024-02-13T18:45:33.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Dev (#284)\n\n* Fix for Issues #261 - cell division failed at the border\r\n\r\n* Fix Mesh creation\r\n\r\nSurface mesh create wasn't create all faces. Now it is fixed. \r\nAlso : -add two methods to Mesh to list faces and vertices. \r\n           -generalised coordinates\r\n           -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder\r\n\r\n* Add 2D collision solver\r\n\r\nAdd class to solve collision in 2D or in 3D. \r\n3D collision solver need to be fixed\r\n\r\n* Update README.md\r\n\r\nAdd `How to cite` section\r\nAdd `Geometry` section\r\nAdd `Publications` section\r\nUpdate bibliography link\r\n\r\n* Generalised wich vertex penetrate face\r\n\r\n* Attempt to set out particular cases\r\n\r\n* Detect and fix self-crossing face\r\n\r\nUnable to make this algo works... https://europepmc.org/article/PMC/3660981\r\nUse ordered vertices and their angle position.\r\n     -> uncrossed face : angles are monotonically increasing\r\n     -> crossed face : angles are not monotonically increasing\r\n\r\n* Use `.apply()` \r\n\r\nNeed to recalculate angle_e for twisted face\r\nOne fix which is only suitable for 2D lateral sheet...\r\n\r\n* ENH: write `mean_XX` method in `Epithelium` class (Issue #224)\r\n\r\n* Fix according to comments\r\n\r\n* Fix Issue #258 ax argument not considered in `plt_draw.sheet_view`\r\n\r\n* ENH: pass column name to `data_at_opposite` issue (#245)\r\n\r\n* Add publication and remove bibtex reference\r\n\r\n* Add check face convexity\r\n\r\n* Use reset_index and code simplification\r\n\r\n* yAdd to_mesh function (issue #221) and some test\r\n\r\n* Remove the use of reset_index in face_self_intersect\r\n\r\n* use ipv_draw with 2D data\r\n\r\n* Fix solution after detection point inside polygon\r\n\r\n* Remove solving collision for 2 same face...\r\n\r\n* Abord vertex displacement if it creates twisted face\r\n\r\n* New way to calculate the position of \"penetrate\" vertices\r\n\r\nFor 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.\r\n\r\n* WIP - use force field to fix collision\r\n\r\n* Small fix\r\n\r\n* Remove function duplication due to circular import\r\n\r\n* Calculate \"repulsion\" gradient in the effector method. Remove loop\r\n\r\n* Fix tests\r\n\r\nRemove collisions tests\r\nFix method call in meshes test\r\nComment \"update_repulstion\" method in planar geometry\r\n\r\n* Add lateralsheet shapes + test\r\n\r\n* Update publication + add collapse texte\r\n\r\n* Add test for Repulsion effector\r\n\r\n* Add test update repulsion\r\n\r\n* Remove unused import\r\n\r\n* Add `drop_face` to allow hole (issues #220 and #141) (associate #221)\r\n\r\n* Update readme.md\r\n\r\n* Update publications in README.md\r\n\r\n* Add `lineage` attribute to `Epithelium`\r\n\r\nIn order to keep track of cell lineage\r\n\r\n* Remove memory oscillation\r\n\r\n* builds with pip\r\n\r\nadds pyproject.toml\r\nbuild command:\r\npip install --no-build-isolation --config-settings=editable.rebuild=true -ve.\r\n\r\n* debugging, still no build apparently\r\n\r\n* build and tests\r\n\r\n* update nb submodule\r\n\r\n* fix pyproject\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* adds scikit-build dep\r\n\r\n* python version\r\n\r\n* python version specifier\r\n\r\n* remove strang flags\r\n\r\n* adds _version.py\r\n\r\n* setuptools_scm dep\r\n\r\n* simplified I guess\r\n\r\n* zdds setuptools-scm to env, MakeFilelist shenanigans\r\n\r\n* restricting to 3.10\r\n\r\n* install dev\r\n\r\n* pyhon version coherence\r\n\r\n* install cmd\r\n\r\n* trying to move to modern sckit-build (it's painful)\r\n\r\n* WIP change build\r\n\r\n* getting closer I hope\r\n\r\n* make_spherical test pasess \\o/\r\n\r\n* tests passing, warnings still to be treated\r\n\r\n* don't install editable version in gh action\r\n\r\n* remove diff chars\r\n\r\n* tagging again to avoid metadata mismatch\r\n\r\n* Uncomment 2D repulsion + tests\r\n\r\nFix pandas issue\r\n\r\n* Add comments in effectors.py\r\n\r\n* rmeove _version.py and ignore in git\r\n\r\n* Update history.py (#274)\r\n\r\n> 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\r\n> Edited self.time_stamps() method to return self._time_stamps\r\n> Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded.\r\n\r\n* skip 2 tests\r\n\r\n* fix non existing hdf5\r\n\r\n* submodules\r\n\r\n* adds notebooks submodule\r\n\r\n* should fix history bug\r\n\r\n* adds submodules again\r\n\r\n* minoor fix, notebooks\r\n\r\n* updates readme and rtd\r\n\r\n* fixing pyproject\r\n\r\n---------\r\n\r\nCo-authored-by: Sophie T <sophiets13@gmail.com>\r\nCo-authored-by: sniffo <tasnif.rahman@gmail.com>","shortMessageHtmlLink":"Dev (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2132930296\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/284\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/284/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/284\">#284</a>)"}},{"before":"e2581d30840e1d3e78ea095ff35872910939b281","after":"af73bb46dd51aef4c6850d23e55733a01ede65b3","ref":"refs/heads/dev","pushedAt":"2024-02-13T18:37:57.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Merge branch 'main' into dev","shortMessageHtmlLink":"Merge branch 'main' into dev"}},{"before":"3682df2daf1f585bf22b785397c91aecdb403876","after":"e2581d30840e1d3e78ea095ff35872910939b281","ref":"refs/heads/dev","pushedAt":"2024-02-13T18:35:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"fixing pyproject","shortMessageHtmlLink":"fixing pyproject"}},{"before":"2c8de87520fcb6de319e8d778d5e6577bf7cd8a3","after":"8eb034f2d6cc18b56c8189560209c27dc2561aaa","ref":"refs/heads/main","pushedAt":"2024-02-13T18:27:48.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Dev (#283)\n\n* Fix for Issues #261 - cell division failed at the border\r\n\r\n* Fix Mesh creation\r\n\r\nSurface mesh create wasn't create all faces. Now it is fixed. \r\nAlso : -add two methods to Mesh to list faces and vertices. \r\n           -generalised coordinates\r\n           -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder\r\n\r\n* Add 2D collision solver\r\n\r\nAdd class to solve collision in 2D or in 3D. \r\n3D collision solver need to be fixed\r\n\r\n* Update README.md\r\n\r\nAdd `How to cite` section\r\nAdd `Geometry` section\r\nAdd `Publications` section\r\nUpdate bibliography link\r\n\r\n* Generalised wich vertex penetrate face\r\n\r\n* Attempt to set out particular cases\r\n\r\n* Detect and fix self-crossing face\r\n\r\nUnable to make this algo works... https://europepmc.org/article/PMC/3660981\r\nUse ordered vertices and their angle position.\r\n     -> uncrossed face : angles are monotonically increasing\r\n     -> crossed face : angles are not monotonically increasing\r\n\r\n* Use `.apply()` \r\n\r\nNeed to recalculate angle_e for twisted face\r\nOne fix which is only suitable for 2D lateral sheet...\r\n\r\n* ENH: write `mean_XX` method in `Epithelium` class (Issue #224)\r\n\r\n* Fix according to comments\r\n\r\n* Fix Issue #258 ax argument not considered in `plt_draw.sheet_view`\r\n\r\n* ENH: pass column name to `data_at_opposite` issue (#245)\r\n\r\n* Add publication and remove bibtex reference\r\n\r\n* Add check face convexity\r\n\r\n* Use reset_index and code simplification\r\n\r\n* yAdd to_mesh function (issue #221) and some test\r\n\r\n* Remove the use of reset_index in face_self_intersect\r\n\r\n* use ipv_draw with 2D data\r\n\r\n* Fix solution after detection point inside polygon\r\n\r\n* Remove solving collision for 2 same face...\r\n\r\n* Abord vertex displacement if it creates twisted face\r\n\r\n* New way to calculate the position of \"penetrate\" vertices\r\n\r\nFor 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.\r\n\r\n* WIP - use force field to fix collision\r\n\r\n* Small fix\r\n\r\n* Remove function duplication due to circular import\r\n\r\n* Calculate \"repulsion\" gradient in the effector method. Remove loop\r\n\r\n* Fix tests\r\n\r\nRemove collisions tests\r\nFix method call in meshes test\r\nComment \"update_repulstion\" method in planar geometry\r\n\r\n* Add lateralsheet shapes + test\r\n\r\n* Update publication + add collapse texte\r\n\r\n* Add test for Repulsion effector\r\n\r\n* Add test update repulsion\r\n\r\n* Remove unused import\r\n\r\n* Add `drop_face` to allow hole (issues #220 and #141) (associate #221)\r\n\r\n* Update readme.md\r\n\r\n* Update publications in README.md\r\n\r\n* Add `lineage` attribute to `Epithelium`\r\n\r\nIn order to keep track of cell lineage\r\n\r\n* Remove memory oscillation\r\n\r\n* builds with pip\r\n\r\nadds pyproject.toml\r\nbuild command:\r\npip install --no-build-isolation --config-settings=editable.rebuild=true -ve.\r\n\r\n* debugging, still no build apparently\r\n\r\n* build and tests\r\n\r\n* update nb submodule\r\n\r\n* fix pyproject\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* adds scikit-build dep\r\n\r\n* python version\r\n\r\n* python version specifier\r\n\r\n* remove strang flags\r\n\r\n* adds _version.py\r\n\r\n* setuptools_scm dep\r\n\r\n* simplified I guess\r\n\r\n* zdds setuptools-scm to env, MakeFilelist shenanigans\r\n\r\n* restricting to 3.10\r\n\r\n* install dev\r\n\r\n* pyhon version coherence\r\n\r\n* install cmd\r\n\r\n* trying to move to modern sckit-build (it's painful)\r\n\r\n* WIP change build\r\n\r\n* getting closer I hope\r\n\r\n* make_spherical test pasess \\o/\r\n\r\n* tests passing, warnings still to be treated\r\n\r\n* don't install editable version in gh action\r\n\r\n* remove diff chars\r\n\r\n* tagging again to avoid metadata mismatch\r\n\r\n* Uncomment 2D repulsion + tests\r\n\r\nFix pandas issue\r\n\r\n* Add comments in effectors.py\r\n\r\n* rmeove _version.py and ignore in git\r\n\r\n* Update history.py (#274)\r\n\r\n> 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\r\n> Edited self.time_stamps() method to return self._time_stamps\r\n> Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded.\r\n\r\n* skip 2 tests\r\n\r\n* fix non existing hdf5\r\n\r\n* submodules\r\n\r\n* adds notebooks submodule\r\n\r\n* should fix history bug\r\n\r\n* adds submodules again\r\n\r\n* minoor fix, notebooks\r\n\r\n* updates readme and rtd\r\n\r\n---------\r\n\r\nCo-authored-by: Sophie T <sophiets13@gmail.com>\r\nCo-authored-by: sniffo <tasnif.rahman@gmail.com>","shortMessageHtmlLink":"Dev (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2132914360\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/283\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/283/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/283\">#283</a>)"}},{"before":"2d13cb2806763771658a2a62be4dcbf641674850","after":"3682df2daf1f585bf22b785397c91aecdb403876","ref":"refs/heads/dev","pushedAt":"2024-02-13T18:27:17.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Merge branch 'main' into dev","shortMessageHtmlLink":"Merge branch 'main' into dev"}},{"before":"d13a07808c49d30ffbc8db604ac2373afad47447","after":"2d13cb2806763771658a2a62be4dcbf641674850","ref":"refs/heads/dev","pushedAt":"2024-02-13T18:25:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"updates readme and rtd","shortMessageHtmlLink":"updates readme and rtd"}},{"before":"ba9abce1af9f5002ccd36da502400a266e8c9871","after":"d13a07808c49d30ffbc8db604ac2373afad47447","ref":"refs/heads/dev","pushedAt":"2024-02-13T09:38:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"minoor fix, notebooks","shortMessageHtmlLink":"minoor fix, notebooks"}},{"before":"556b8541f3ef1805c6f79e15bd8ece6599804e73","after":"2c8de87520fcb6de319e8d778d5e6577bf7cd8a3","ref":"refs/heads/main","pushedAt":"2024-02-13T08:36:40.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"glyg","name":"Guillaume Gay","path":"/glyg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1426279?s=80&v=4"},"commit":{"message":"Dev (#281)\n\n* Fix for Issues #261 - cell division failed at the border\r\n\r\n* Fix Mesh creation\r\n\r\nSurface mesh create wasn't create all faces. Now it is fixed. \r\nAlso : -add two methods to Mesh to list faces and vertices. \r\n           -generalised coordinates\r\n           -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder\r\n\r\n* Add 2D collision solver\r\n\r\nAdd class to solve collision in 2D or in 3D. \r\n3D collision solver need to be fixed\r\n\r\n* Update README.md\r\n\r\nAdd `How to cite` section\r\nAdd `Geometry` section\r\nAdd `Publications` section\r\nUpdate bibliography link\r\n\r\n* Generalised wich vertex penetrate face\r\n\r\n* Attempt to set out particular cases\r\n\r\n* Detect and fix self-crossing face\r\n\r\nUnable to make this algo works... https://europepmc.org/article/PMC/3660981\r\nUse ordered vertices and their angle position.\r\n     -> uncrossed face : angles are monotonically increasing\r\n     -> crossed face : angles are not monotonically increasing\r\n\r\n* Use `.apply()` \r\n\r\nNeed to recalculate angle_e for twisted face\r\nOne fix which is only suitable for 2D lateral sheet...\r\n\r\n* ENH: write `mean_XX` method in `Epithelium` class (Issue #224)\r\n\r\n* Fix according to comments\r\n\r\n* Fix Issue #258 ax argument not considered in `plt_draw.sheet_view`\r\n\r\n* ENH: pass column name to `data_at_opposite` issue (#245)\r\n\r\n* Add publication and remove bibtex reference\r\n\r\n* Add check face convexity\r\n\r\n* Use reset_index and code simplification\r\n\r\n* yAdd to_mesh function (issue #221) and some test\r\n\r\n* Remove the use of reset_index in face_self_intersect\r\n\r\n* use ipv_draw with 2D data\r\n\r\n* Fix solution after detection point inside polygon\r\n\r\n* Remove solving collision for 2 same face...\r\n\r\n* Abord vertex displacement if it creates twisted face\r\n\r\n* New way to calculate the position of \"penetrate\" vertices\r\n\r\nFor 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.\r\n\r\n* WIP - use force field to fix collision\r\n\r\n* Small fix\r\n\r\n* Remove function duplication due to circular import\r\n\r\n* Calculate \"repulsion\" gradient in the effector method. Remove loop\r\n\r\n* Fix tests\r\n\r\nRemove collisions tests\r\nFix method call in meshes test\r\nComment \"update_repulstion\" method in planar geometry\r\n\r\n* Add lateralsheet shapes + test\r\n\r\n* Update publication + add collapse texte\r\n\r\n* Add test for Repulsion effector\r\n\r\n* Add test update repulsion\r\n\r\n* Remove unused import\r\n\r\n* Add `drop_face` to allow hole (issues #220 and #141) (associate #221)\r\n\r\n* Update readme.md\r\n\r\n* Update publications in README.md\r\n\r\n* Add `lineage` attribute to `Epithelium`\r\n\r\nIn order to keep track of cell lineage\r\n\r\n* Remove memory oscillation\r\n\r\n* builds with pip\r\n\r\nadds pyproject.toml\r\nbuild command:\r\npip install --no-build-isolation --config-settings=editable.rebuild=true -ve.\r\n\r\n* debugging, still no build apparently\r\n\r\n* build and tests\r\n\r\n* update nb submodule\r\n\r\n* fix pyproject\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* install with pip in CI\r\n\r\n* adds scikit-build dep\r\n\r\n* python version\r\n\r\n* python version specifier\r\n\r\n* remove strang flags\r\n\r\n* adds _version.py\r\n\r\n* setuptools_scm dep\r\n\r\n* simplified I guess\r\n\r\n* zdds setuptools-scm to env, MakeFilelist shenanigans\r\n\r\n* restricting to 3.10\r\n\r\n* install dev\r\n\r\n* pyhon version coherence\r\n\r\n* install cmd\r\n\r\n* trying to move to modern sckit-build (it's painful)\r\n\r\n* WIP change build\r\n\r\n* getting closer I hope\r\n\r\n* make_spherical test pasess \\o/\r\n\r\n* tests passing, warnings still to be treated\r\n\r\n* don't install editable version in gh action\r\n\r\n* remove diff chars\r\n\r\n* tagging again to avoid metadata mismatch\r\n\r\n* Uncomment 2D repulsion + tests\r\n\r\nFix pandas issue\r\n\r\n* Add comments in effectors.py\r\n\r\n* rmeove _version.py and ignore in git\r\n\r\n* Update history.py (#274)\r\n\r\n> 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\r\n> Edited self.time_stamps() method to return self._time_stamps\r\n> Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded.\r\n\r\n* skip 2 tests\r\n\r\n* fix non existing hdf5\r\n\r\n* submodules\r\n\r\n* adds notebooks submodule\r\n\r\n* should fix history bug\r\n\r\n* adds submodules again\r\n\r\n---------\r\n\r\nCo-authored-by: Sophie T <sophiets13@gmail.com>\r\nCo-authored-by: sniffo <tasnif.rahman@gmail.com>","shortMessageHtmlLink":"Dev (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2074278620\" data-permission-text=\"Title is private\" data-url=\"https://github.com/DamCB/tyssue/issues/281\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/DamCB/tyssue/pull/281/hovercard\" href=\"https://github.com/DamCB/tyssue/pull/281\">#281</a>)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAD-08OqwA","startCursor":null,"endCursor":null}},"title":"Activity · DamCB/tyssue"}