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Jiyeon/example1 full structure preserving #185

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1768a63
Allow use of additional keys to store information about subdomains in…
emmetfrancis Jun 23, 2025
10aef25
New feature to allow parameters with assigned values over a region of…
emmetfrancis Jun 24, 2025
06da231
Remove model specs file for example 5
emmetfrancis Jun 24, 2025
ca65461
Change version number in pyproject
emmetfrancis Jun 24, 2025
a25eabc
Update ER_PM_gap value and save Avals in example5 with SOCE
emmetfrancis Jun 25, 2025
be9bb82
Add and test code for advective transport
emmetfrancis Jul 11, 2025
9ef3822
Add new meshing function for multicellular meshes
emmetfrancis Jul 13, 2025
b1d24be
Update new example 7 for testing reaction-diffusion through multicell…
emmetfrancis Jul 14, 2025
25e7077
bump version number in pyproject
emmetfrancis Jul 14, 2025
c5e33d7
Update Lagrangian formulas, add example 2 file to test Lagrangian vs …
emmetfrancis Jul 21, 2025
4ddbeb7
Merge branch 'emmetfrancis/fix-log-func' into emmetfrancis/test-advec…
emmetfrancis Jul 21, 2025
bbc70e2
Complete merge of meshing add ons
emmetfrancis Jul 21, 2025
9c95a2f
Introduce new example to test advection feature, add functionality to…
emmetfrancis Aug 6, 2025
9dd5a75
Add back data files for example5
emmetfrancis Aug 6, 2025
b166fb4
Remove mesh test file
emmetfrancis Aug 6, 2025
f48b001
Bump version to gamma
emmetfrancis Aug 6, 2025
e60d813
Remove nan loop in solver
emmetfrancis Aug 6, 2025
af81db2
change version to 2.3.1.alpha
emmetfrancis Aug 6, 2025
17cb903
fix to multicell meshing function, add back nan fix with protection a…
emmetfrancis Aug 6, 2025
4eb20f8
Change title of example 8
emmetfrancis Aug 14, 2025
baad40f
Change title of example 8
emmetfrancis Aug 14, 2025
6bbcb1d
Update version number
emmetfrancis Feb 16, 2026
379ac33
some mesh tools updates, but mostly changes to allow for species gove…
emmetfrancis Jun 22, 2026
4fc9878
remove pkl files
emmetfrancis Jun 22, 2026
b0b0c67
Implement cutoff and mass conservation in CH example
emmetfrancis Jun 22, 2026
42c7420
Change example1_CH for consistency with nondimensional parameters, ap…
emmetfrancis Jun 24, 2026
bcb9a18
Add full structure-preserving script for example1
JiYeon-Hyun Aug 23, 2026
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3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -11,7 +11,8 @@ repos:
exclude: |
(?x)^(
joss-paper/JOSS_Fig2.png|
examples/example2-3d/spine_mesh.xml
examples/example2-3d/spine_mesh.xml|
examples/example1/spheroid_ellipsoid_mesh.h5
)$
- id: check-docstring-first
- id: debug-statements
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