Added file comparison test for Patch basic.xml and simple-example.xml, as well as Potts nb.xml - #226

Draft

afu5 wants to merge 48 commits into

mainfrom

fu/file-comparison-test

Commits on Apr 12, 2026

update build and CI configuration
Jannetty
committed
7647685
add updateGrowthRate framework and make getUniqueIDs public
Jannetty
committed
57817c1
adding dostrings
Jannetty
committed
6392d9e
another docstring
Jannetty
committed
488ab02
more formatting
Jannetty
committed
4376f32
final formatting
Jannetty
committed
731082f
adding missing parameters to potts xml. Removing unnecessary parameter
Jannetty
committed
6cb465d
removing redundant section of docstring
Jannetty
committed
64ce606
puppycrawler asking for some odd spacing
Jannetty
committed
2ce8a27
puppycrawl now wants me to undo the odd spacing it asked for
Jannetty
committed
3e8bebc
removing part of PR more relevant to neuroblasts
Jannetty
committed
9238f51
first portion of neuroblast files
Jannetty
committed
6ec7a8d
Merge branch 'feature/build-ci-cleanup' into feature/flystem-mergebranch
Jannetty
committed
b559f06
finish covering PottsModuleFlyStemProliferation with tests
Jannetty
committed
19212bb
adding tests
Jannetty
committed
6b7db55
importing PottsCell and Bag to GMC differentiation module instead of inline import
Jannetty
committed
d80b49f
fixing PottsCellFlyStem line length issue
Jannetty
committed
6d8a7f8
addressing puppycrawler issues
Jannetty
committed
30126b1
more formatting
Jannetty
committed
510c8a9
format
Jannetty
committed
4c8b0d1
last formatting please
Jannetty
committed
944fa1d

Commits on May 4, 2026

Added integration file comparison test for nb.xml in PottsARCADETest.java

Alice Fu
authored and
Alice Fu
committed
e6b1dfb
Added tests for basic.xml and simple-example.xml, and fixed version string that is nondeterministic

Alice Fu
authored and
Alice Fu
committed
8e49af8
Applied spotlessApply

Alice Fu
authored and
Alice Fu
committed
17de14b
Merge branch 'main' into fu/file-comparison-test

Alice Fu
authored and
Alice Fu
committed
4528e10
Added expected output files to output/

Alice Fu
authored and
Alice Fu
committed
b6ff10b
Test commit with commented-out Patch test for faster run

Alice Fu
authored and
Alice Fu
committed
2094ae6
spotlessApply
Jannetty
committed
b632940
Re-added Patch tests

Alice Fu
authored and
Alice Fu
committed
6c2d578
Added newline to end of .xml files to pass linter

Alice Fu
authored and
Alice Fu
committed
7e2eb9d

Commits on May 11, 2026

Updated nb.xml interval from 4 to 192

Alice Fu
authored and
Alice Fu
committed
e5e52a5
Refactored expected files to expected/ folder and updated tests to match different timestep for nb.xml

Alice Fu
authored and
Alice Fu
committed
f651459
Split file comparison to two separate tests

Alice Fu
authored and
Alice Fu
committed
73c682f
Ran spotlessApply

Alice Fu
authored and
Alice Fu
committed
cef7646
Tried normalizing file ending

Alice Fu
authored and
Alice Fu
committed
c2ba842
Added expected files

Alice Fu
authored and
Alice Fu
committed
c5982bd
Removed normalization

Alice Fu
authored and
Alice Fu
committed
a2c3387
Uncommented Patch tests

Alice Fu
authored and
Alice Fu
committed
1dff1b7

Commits on May 18, 2026

Testing why Patch tests fail

Alice Fu
authored and
Alice Fu
committed
4256b8d
Ran spotlessApply

Alice Fu
authored and
Alice Fu
committed
20f748a
Updated GitHub workflow to upload error file on error

Alice Fu
authored and
Alice Fu
committed
54d7339
Ran spotlessApply

Alice Fu
authored and
Alice Fu
committed
711b879
Updated coverage artifact bug

Alice Fu
authored and
Alice Fu
committed
ed87a5e
Added tolerance of 1E-10 as a test for equality checking (not robust)

Alice Fu
authored and
Alice Fu
committed
fcd7376

Commits on Jun 1, 2026

Used gson to assert value equality with epsilon tolerance

Alice Fu
authored and
Alice Fu
committed
4a1503b
ran spotlessApply

Alice Fu
authored and
Alice Fu
committed
5dd0f9d
Added filtering so file comparison test does not run unless called with the fileComparisonTest tag (./gradlew fileComparisonTest), and runs after two or more approvals have been given to a pull req…

Alice Fu
authored and
Alice Fu
committed
0d79645
ran spotlessApply

Alice Fu
authored and
Alice Fu
committed
c199190