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f4a205f
Update MultiActivation2DTracker
Sep 19, 2024
65c023a
Update ActivationTime2DTracker
AOkenov Sep 20, 2024
cd830f4
Update Variable2DTrackers
AOkenov Sep 20, 2024
6cb8498
Update Animation2DTracker
Oct 23, 2024
714798e
Add docs
AOkenov Oct 23, 2024
ec0a857
Update Animation2DTracker
AOkenov Oct 23, 2024
6d7662b
Add exception handling for Animation2DBuilder
AOkenov Oct 23, 2024
a332d2d
Update LAT 2D tracker
AOkenov Oct 23, 2024
7d70e84
Update LAT tracker docs
AOkenov Oct 23, 2024
7ca2ab8
Update ECG2DTracker
AOkenov Oct 24, 2024
f4c3c7f
Update variable trackers
AOkenov Oct 24, 2024
67f6294
Update variable trackers example
AOkenov Oct 24, 2024
ffb24f8
Update Period Map Animation Tracker
AOkenov Oct 24, 2024
841640d
Rename PeriodMap2DTracker to PeriodAnimation2DTracker
AOkenov Oct 24, 2024
db8b941
Update SpiralWaveCore2DTracker
Oct 25, 2024
a07155a
Fix docstring
Oct 25, 2024
0eee7f8
Merge pull request #6 from TiNezlobinsky/trackers
AOkenov Oct 25, 2024
533391f
Update 3D Trackers
Oct 28, 2024
460eaea
Merge pull request #7 from TiNezlobinsky/docs
AOkenov Oct 28, 2024
4c11e47
Replace opencv with ffmpeg
AOkenov Oct 31, 2024
7fa4a93
Update 3D trackers
AOkenov Oct 31, 2024
a937336
Update 3D spiral wave core tracker
AOkenov Oct 31, 2024
50a9f78
Add sphinx docs
AOkenov Nov 2, 2024
d644d31
Add examples to docs
AOkenov Nov 2, 2024
1200dcc
Remove docs
AOkenov Nov 2, 2024
a14c1d5
Remove auto_examples
AOkenov Nov 2, 2024
cec7508
Update docs
AOkenov Nov 3, 2024
c76a4d5
Restructure the docs API
Nov 4, 2024
af3b914
Update conf.py
Nov 4, 2024
68019fd
Update 2D models. Remove kernel classes
Nov 5, 2024
62ab69d
Update Stencils
AOkenov Nov 5, 2024
692a6ac
Update README
Nov 5, 2024
5a7038e
Fix asymmetric slencil
AOkenov Nov 8, 2024
cc197f7
Fix AsymmetricStencil2D
AOkenov Nov 10, 2024
34d7f48
Update asymmetric stencil 3D
AOkenov Nov 11, 2024
b161721
Fix 3D stencil
Nov 16, 2024
20ebce5
Fix asymmetric stencil 3d
AOkenov Nov 19, 2024
eb8245c
Add Symmetric Stencil
AOkenov Nov 20, 2024
9980fca
Fix overshooting in asymmetric stencil
Nov 22, 2024
814cfe3
Refactor stencils
Nov 22, 2024
d1f4a4a
Restructure the tissue, model, and stencil
Nov 22, 2024
9d86f2e
Restructure 3D models and stencils
AOkenov Nov 25, 2024
cb12003
Remove unnessary lines from examples
Nov 25, 2024
6fd9c9d
Add thread control. Improve performance for meshes with large number …
Nov 25, 2024
da8e88c
Rename diffuse kernels
Nov 25, 2024
e495ad6
Add velocity anisotropy measurer
AOkenov Nov 26, 2024
e8eca27
Resolve merge conflicts
AOkenov Nov 27, 2024
a3d6778
Merge pull request #10 from TiNezlobinsky/stencil
AOkenov Nov 27, 2024
d121d89
Fix docstrings
AOkenov Nov 27, 2024
2053cad
Fix docstrings
AOkenov Nov 27, 2024
a0c875d
Add voltage list stimulation
Nov 28, 2024
d1e589e
Move 2D examples
Nov 29, 2024
085d533
Modify the logo
AOkenov Nov 29, 2024
ddfad49
Restructure examples
AOkenov Dec 1, 2024
9bb0220
Add sphere and LV examples
AOkenov Dec 1, 2024
5bf99ef
Add slab example
AOkenov Dec 1, 2024
6b369c0
Replace StateKeeper with StateSaver and StateLoader
AOkenov Jan 27, 2025
0b96fde
Improve performance for ECG3DTracker
Jan 27, 2025
76e82f5
Add area stim for 3D
Jan 27, 2025
0cd0483
Add StimCurrentArea3D class for stimulation from point electrode
Feb 4, 2025
4a041ff
Fix LuoRudy91 model
rvdnabe Feb 11, 2025
b5bbab6
Add StateSaverCollection
Feb 13, 2025
9042be0
Update tutorials. Add LuoRudy91 example.
Mar 12, 2025
f81a658
Add SpiralWave Tutorial
AOkenov Mar 13, 2025
49913ad
Update README
AOkenov Mar 13, 2025
b4d787c
Update README
AOkenov Mar 13, 2025
f046a72
Update README
AOkenov Mar 13, 2025
c7d1ba4
Remove docs
AOkenov Mar 13, 2025
8a3fcb0
Merged new model architecture
TiNezlobinsky Mar 20, 2025
4dadb7c
Additional model docstrings
TiNezlobinsky Mar 20, 2025
5016e7f
Basics example, max threads limit warning
TiNezlobinsky Mar 20, 2025
e8b6011
2d trackers examples
TiNezlobinsky Mar 26, 2025
56b22f9
model examples
TiNezlobinsky Mar 27, 2025
b7ffadb
2D examples, fixed 2D fibrosis pattern generators
TiNezlobinsky Mar 28, 2025
576a435
3d examples
TiNezlobinsky Apr 1, 2025
ed6edc1
3d examples
TiNezlobinsky Apr 1, 2025
0437c2e
Fixed command sequence processing
TiNezlobinsky Apr 3, 2025
a799730
3D trackers, models examples, Local activation time 3d tracker
TiNezlobinsky Apr 8, 2025
c990854
Delete outdated examples
TiNezlobinsky Apr 8, 2025
d03ff3b
stimulation examples
TiNezlobinsky Apr 9, 2025
9b7c463
stimulation examples
TiNezlobinsky Apr 9, 2025
49b017c
Tutorials: more comments, restitution curve
TiNezlobinsky Apr 10, 2025
f71d1be
Tutorials: more comments, restitution curve
TiNezlobinsky Apr 10, 2025
6987388
Tutorials: more comments, restitution curve
TiNezlobinsky Apr 10, 2025
305a968
2d tests: actpot, animation, localact, multivar
TiNezlobinsky Apr 14, 2025
1446a7e
2d tests, fixed empty df in sw core tracker, rebuilt ecg 2d tracker f…
TiNezlobinsky Apr 16, 2025
1ed8d71
tests 3d
TiNezlobinsky Apr 16, 2025
96d27e1
model tests
TiNezlobinsky Apr 17, 2025
bb4e0a4
Mitchell-Schaeffer 2D
TiNezlobinsky Apr 28, 2025
586df42
Mitchell-Schaeffer 3D
TiNezlobinsky Apr 29, 2025
36bcec6
model examples readme change
TiNezlobinsky Apr 29, 2025
943332b
Barkley model
TiNezlobinsky Apr 29, 2025
bca7122
Fenton-Karma model
TiNezlobinsky May 2, 2025
0f6b26f
Fenton-Karma 3D
TiNezlobinsky May 2, 2025
e0d918f
Bueno-Orovio model
TiNezlobinsky May 5, 2025
43084f3
Models description
TiNezlobinsky May 6, 2025
b3a8604
model examples docstrings
TiNezlobinsky May 6, 2025
e95da38
Courtemanche 2D
TiNezlobinsky May 7, 2025
019baac
Luo-Rudy 91 - gating variables calculation ,ethod
TiNezlobinsky May 7, 2025
af35da4
model 2d tests
TiNezlobinsky May 8, 2025
aed5a7c
Courtemanche model
TiNezlobinsky May 12, 2025
cd69038
framework tests
TiNezlobinsky May 15, 2025
275c59a
basic tests
TiNezlobinsky May 15, 2025
e9d671e
testing workflow
TiNezlobinsky May 15, 2025
bbb7b2e
testing workflow
TiNezlobinsky May 15, 2025
738152f
testing workflow
TiNezlobinsky May 15, 2025
1c47ea0
test.yml
TiNezlobinsky May 19, 2025
98e1ac1
test.yml
TiNezlobinsky May 19, 2025
4f1c7e5
test.yml
TiNezlobinsky May 19, 2025
118f454
test.yml
TiNezlobinsky May 19, 2025
7632e2b
explicit initial condiitons, readme
TiNezlobinsky May 19, 2025
efb37d2
test.yml
TiNezlobinsky May 19, 2025
0e8c563
Readme - codecov
TiNezlobinsky May 19, 2025
1d5d400
Basic examples
TiNezlobinsky May 20, 2025
3d1dd6c
Test status
TiNezlobinsky May 21, 2025
29b2910
Platform test
TiNezlobinsky May 21, 2025
24e91a5
New tests
TiNezlobinsky May 21, 2025
c9cec8a
less restricted version
TiNezlobinsky May 21, 2025
d8f8c6d
removed tools test
TiNezlobinsky May 21, 2025
181279a
disabled patch checks
TiNezlobinsky May 21, 2025
12ba8fe
tests: slice 3d, period animation
TiNezlobinsky May 26, 2025
988542d
Removed tools test (not possible to check)
TiNezlobinsky May 26, 2025
205efc3
Add temporal block spiral wave initiation
AOkenov May 26, 2025
ba34e18
readme, data folder
TiNezlobinsky Jun 9, 2025
253dba0
examples readme
TiNezlobinsky Jun 9, 2025
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5 changes: 5 additions & 0 deletions .codecov.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
coverage:
status:
patch:
default:
enabled: false
29 changes: 29 additions & 0 deletions .github/workflows/test-matrix.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
name: Platform compatibility test

on:
workflow_dispatch:

jobs:
test:
name: Test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]

steps:
- uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e .
pip install .[test]

- name: Run tests
run: pytest
44 changes: 44 additions & 0 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
name: Run Finitewave tests

on:
push:
branches:
- main
- develop
pull_request:
branches:
- main
- develop

jobs:
test:
runs-on: ubuntu-latest

env:
NUMBA_DISABLE_JIT: "1"

steps:
- uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e .
pip install pytest pytest-cov

- name: Run tests with coverage
run: |
pytest --cov=./finitewave --cov-report=term --cov-report=xml

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
with:
files: ./coverage.xml
fail_ci_if_error: true
token: ${{ secrets.CODECOV_TOKEN }}
slug: finitewave/Finitewave
7 changes: 5 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ var/
.installed.cfg
*.egg
.DS_Store
auto_examples/

# PyInstaller
# Usually these files are written by a python script from a template
Expand All @@ -49,6 +50,7 @@ coverage.xml
.pytest_cache/

# Jupyter Notebook
playground.ipynb
.ipynb_checkpoints

# pyenv
Expand Down Expand Up @@ -107,11 +109,12 @@ docs/_build/
.coverage.*

# Images
*.png
# *.png
*.jpg
*.jpeg
# *.gif
*.svg
# *.svg
*.zip

# ffmpeg output
*.mp4
Expand Down
222 changes: 0 additions & 222 deletions README.md

This file was deleted.

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