Rearangments refactoring (#148)

* re-implements type1 transition based on Finegan et al 2019

* removes rank computation in collapse edge

* More functional  rearangements

* bumps version number

* add nbval to travis

* moves connectivity module to utils and ads an  update_rank method

* adds test for update_rank, removes test with old T1 solving

* update notebooks

* adds a bounds argument to viscous and fixes a bug in remove_two_sided_faces

.travis.yml

@@ -14,13 +14,14 @@ before_install:
   - conda env create -q -f environment.yml
   - source activate tyssue
   - conda install pytest pytest-cov
-  - pip install coveralls
+  - pip install coveralls nbval
 
 install:
   - python setup.py install
 
 script:
   - make coverage
+  - make nbtest
 
 after_success:
   - coveralls

Makefile

@@ -11,3 +11,6 @@ coverage:
 
 nbtest:
 	cd doc/notebooks && pytest --nbval-lax && cd ../..
+
+pdbtest:
+	cd tests && pytest --pdb . && cd ..

changelog.md

@@ -1,3 +1,29 @@
+
+# What's new in 0.5
+
+## Major rewrite of the rearangements
+
+We now allow for rosettes to form, and split type1 transition in two steps: merging of edges bellow the critical length and spliting more than rank 3 vertices (or more than rank 4 in 3D). The splitting frequency is governed by two settings `p_4` and `p5p`.This follows Finegan et al 2019. See  doc/notebooks/Rosettes.ipynb for a demo.
+
+A look a the diffs in `sheet_topology` and `bulk_topology` should convince the reader that this should result in a major increase in stability.
+
+Automated reconnection is now treated as an event (treated by an `EventManager` instance), see `tyssue.behavior.base_events.reconnect`.
+
+In EulerSolver, this avoids raising `TopologyChangeError` at least in explicit Euler. Topology changes in IVPSolver are not supported for now.
+
+
+## Viscous solver
+
+- added a `bounds` attribute to EulerSolver. This simply clips the displacement to avoid runaway conditions.
+
+
+## Core and topology
+
+- A new `update_rank` method allows to compute the rank of a vertex (as the number of _flat_ edges connected to it). This required to move the `connectivity` module to utils to avoid circular imports.
+
+- We explicitly allow two sided faces to be created by `collapse_edge` or `remove_face`, they are directly eliminated.
+
+
 # What's new in 0.4
 
 ##  Time dependant solvers

doc/bibliography/tyssue.bib

@@ -1913,7 +1913,6 @@ @article{MunozStressdependentmorphogenesiscontinuum2010a
   pages = {451-467},
   keywords = {Time Factors,Models; Biological,Myosins,Drosophila melanogaster,Animals,Biomechanical Phenomena,Epithelium,Stress; Mechanical,Actins,Embryo; Nonmammalian,Morphogenesis},
   author = {Mu\~noz, Jos\'e J. and Conte, Vito and Miodownik, Mark},
-  file = {/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/QAQZNIAW/Munoz2009.pdf},
   eprinttype = {pmid},
   eprint = {20069442}
 }
@@ -3509,5 +3508,19 @@ @article{GraciaMechanicalimpactepithelial2019
   file = {/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/TFHZNG4S/Gracia et al. - 2019 - Mechanical impact of epithelial−mesenchymal transi.pdf;/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/4H5NARIY/s41467-019-10720-0.html}
 }
 
+@article{Finegantricellularvertexspecificadhesion2019,
+  langid = {english},
+  title = {The Tricellular Vertex-Specific Adhesion Molecule {{Sidekick}} Facilitates Polarised Cell Intercalation during {{Drosophila}} Axis Extension},
+  url = {https://www.biorxiv.org/content/10.1101/704932v1},
+  doi = {10.1101/704932},
+  abstract = {{$<$}p{$>$}In epithelia, tricellular vertices are emerging as important sites for the regulation of epithelial integrity and function. Compared to bicellular contacts, however, much less knowledge is available. In particular, resident proteins at tricellular vertices were identified only at occluding junctions, with none known at adherens junctions. In a previous study, we discovered that in Drosophila embryos, the adhesion molecule Sidekick (Sdk), well known in invertebrates and vertebrates for its role in the visual system, localises at tricellular vertices at the level of adherens junctions. Here, we survey a wide range of Drosophila epithelia and establish that Sdk is a resident protein at tricellular adherens junctions, the first of its kind. Clonal analysis suggests that pair-wise homophilic adhesion is necessary and sufficient for Sdk tricellular vertex localisation. Super-resolution imaging using structured illumination reveals that Sdk proteins form string-like structures at vertices. Postulating that Sdk may have a role in epithelia where adherens junctions are actively remodelled, we analysed the phenotype of sdk null mutant embryos during Drosophila axis extension, using quantitative methods. We find that apical cell shapes are strikingly abnormal in sdk mutants. Moreover, adhesion at apical vertices is compromised in rearranging cells, with holes forming and persisting throughout axis extension. Finally, we show that polarized cell intercalation is decreased and abnormal in sdk mutants. Mathematical modeling of the cell behaviours supports the conclusion that the T1 transitions of polarized cell intercalation are delayed in sdk mutants. We propose that this delay, in combination with a change in the mechanical properties of the converging and extending tissue, causes the striking cell shape phenotype of sdk mutant embryos.{$<$}/p{$>$}},
+  journaltitle = {bioRxiv},
+  urldate = {2019-07-18},
+  date = {2019-07-16},
+  pages = {704932},
+  author = {Finegan, Tara M. and Hervieux, Nathan and Nestor-Bergmann, Alexander and Fletcher, Alexander G. and Blanchard, Guy B. and Sanson, Benedicte},
+  file = {/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/5RUSMCSI/Finegan et al. - 2019 - The tricellular vertex-specific adhesion molecule .pdf;/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/7SDEDCDJ/Finegan et al. - 2019 - The tricellular vertex-specific adhesion molecule .pdf;/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/CDVUQ3PC/704932v1.html}
+}
+
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