Feature/caf mhc2 rules - #438

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gavehan wants to merge 393 commits into

MathCancer:masterfrom

jeanettejohnson:feature/caf-mhc2-rules

This pull request is big! We're only showing the most recent 250 commits

Commits on Sep 9, 2024

put arg parser in settings
drbergman
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6dfae3f
Merge branch 'feature-cl-arguments' into my-physicell
drbergman
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fea4309
standardize makefiles
drbergman
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ebfff27

Commits on Sep 10, 2024

Merge branch 'development' into my-physicell
drbergman
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1825b4d
Merge branch 'development' into standard-asym-div
drbergman
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af2d43d
Merge branch 'standard-asym-div' into my-physicell
drbergman
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e5ee48f
Merge branch 'standard-asym-div' into my-physicell
drbergman
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e5c9572
Merge branch 'standard-asym-div' into my-physicell
drbergman
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1db2a54
protect against 0 asym div weight total
drbergman
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4859b06

Commits on Sep 21, 2024

renaming
drbergman
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3c31677

Commits on Sep 22, 2024

reference points and overall better usage of rules extension
drbergman
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bbc2984

Commits on Oct 2, 2024

Commits on Oct 23, 2024

Merge branch 'development' into my-physicell
drbergman
committed
2ad4ff4
Merge branch 'fix-create-output-from-abspath' into my-physicell
drbergman
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18e0611

Commits on Nov 19, 2024

Merge branch 'feature-transmembrane-diffusion' into my-physicell
drbergman
committed
0e0a4bb
v1.14.0-drbergman-1.0.0
drbergman
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7e3de8b

Commits on Nov 27, 2024

Merge branch 'development' into rules-upgrade
drbergman
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b2e44b8

Commits on Nov 28, 2024

working prototype of extended rules!
drbergman
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4173f5a

Commits on Dec 2, 2024

ability to select mediator in xml
drbergman
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95efc93

Commits on Dec 4, 2024

cleaned up rules_extended and improved example
drbergman
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ad910d6
add BehaviorAccumulator and BehaviorAttenuator
drbergman
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fa04040

Commits on Dec 16, 2024

merge 1.14.1 and bump to 1.14.1-drbergman-1.0.0
drbergman
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da3a3f9

Commits on Jan 21, 2025

Merge PhysiCell v1.14.2 into my-physicell
drbergman
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48db489

Commits on Jan 23, 2025

light edits for formating/console output
drbergman
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074acb3

Commits on Feb 2, 2025

DC initialization from file
drbergman
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c7860b4
merge branch DCs from file
drbergman
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949bf1f
1.14.2-drbergman-1.1.0
drbergman
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3f87c90
CLI for dirichlet ics file
drbergman
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da35bc5
1.14.2-drbergman-1.2.0
drbergman
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5cebd9b

Commits on Feb 6, 2025

fix bug in copying ic cells to output
drbergman
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dbe451b
1.14.2-drbergman-1.2.1
drbergman
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afd6e4f

Commits on Feb 11, 2025

fix ode-energy-sample and clean/fix librr stuff
drbergman
committed
ac2cf48

Commits on Feb 12, 2025

Commits on Feb 13, 2025

upgraded librr implementation to automate mappings
drbergman
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ed33c9a
update ode-energy-sample to new api
drbergman
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66c5975
do not let extracellular concentration be output
drbergman
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3f65f41

Commits on Feb 14, 2025

delay differential equations!!
drbergman
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5945ef4

Commits on Feb 16, 2025

bug fix for having empty input/output mappings
drbergman
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7475c27
Merge branch 'improve-librr-api' into delay-diffeq
drbergman
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7875141
bug fix for having empty input/output mappings
drbergman
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f52f008

Commits on Feb 18, 2025

Merge branch 'improve-librr-api' into delay-diffeq
drbergman
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804e2b8
refactor how intracellular updates are handled
drbergman
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e7fdcaf
update intracellular in first time step
drbergman
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daab667
Merge branch 'fix-update-intracellular-first-step' into updating-roadrunner
drbergman
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ed47d7f
Merge branch 'protect-intracellular-updates' into updating-roadrunner
drbergman
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92f75cf
Merge branch 'delay-diffeq' into updating-roadrunner
drbergman
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ac5c24f

Commits on Feb 19, 2025

wip
drbergman
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716fe2c
update to PhysiPKPD v1.2.0 with MMD
drbergman
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1915aa5
update to PhysiPKPD v1.2.0 with MMD
drbergman
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6a15cbd

Commits on Feb 20, 2025

clear *_delay_terms to remove prev cell def vals
drbergman
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b3db5e0
Merge branch 'delay-diffeq' into my-physicell-updating-roadrunner
drbergman
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09a5e1a
load sbmls from single file
drbergman
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a362c3e

Commits on Feb 21, 2025

Merge pull request #5 from drbergman/my-physicell-updating-roadrunner
Daniel Bergman
authored
31e2d6d
Merge remote-tracking branch 'origin/my-physicell' into my-physicell
drbergman
committed
82cee24

Commits on Feb 27, 2025

light reformat of one xml
drbergman
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e98eaba

Commits on Feb 28, 2025

add load_initial_cells(); to template-combined custom.cpp
drbergman
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78550c1
1.14.2-drbergman-1.3.0
drbergman
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fcbc8ff

Commits on Mar 3, 2025

Commits on Mar 5, 2025

when asym divs probs sum to >1, exit with msg
drbergman
committed
c9929e9
fix asym div probs > 1 exit call
drbergman
committed
b5322ee

Commits on Mar 12, 2025

remove excess getopt.h
drbergman
committed
dee5d3b

Commits on Mar 20, 2025

clean up extended rules
drbergman
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5fd855f

Commits on Apr 1, 2025

support csv with extended rules
drbergman
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ee42083
fix
drbergman
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5c40582

Commits on Apr 9, 2025

fix
drbergman
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7740592

Commits on Apr 15, 2025

identify transform, docstrings, better coding
drbergman
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5519103
easier setting of custom agg and mediators
drbergman
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355e058

Commits on Apr 16, 2025

readme
drbergman
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38e6fb3
expose the behavior_base in XML
drbergman
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7dfd452
upgrade rules
drbergman
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41344f8
Merge branch 'rules-upgrade' into my-physicell-rules-upgrade
drbergman
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e326e03

Commits on Apr 17, 2025

upgrade all mains to use arg parser
drbergman
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5f415b3
Merge pull request #8 from drbergman/remove-extra-getopt_h
drbergman
authored
e266474
Merge pull request #9 from drbergman/my-physicell-rules-upgrade
drbergman
authored
c3e43a5
v1.14.2-drbergman-2.0.0
drbergman
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d2855ec
wip
drbergman
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8c5b300
cleanning up...
drbergman
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249c974
finishing up display/export to csv updates
drbergman
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9a043e6
display/export to csv updates
drbergman
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4174cf1
Merge pull request #10 from drbergman/my-physicell-rules-upgrade-displays
drbergman
authored
a1ff86b
1.14.2-drbergman-2.1.0
drbergman
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ac97c1d
more informative error on bad mediator vals
drbergman
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59d1ef1
1.14.2-drbergman-2.1.1
drbergman
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0e33161
1.14.2-drbergman-2.1.2
drbergman
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e62bd0f
display/export to csv
drbergman
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06c726e

Commits on Apr 26, 2025

Update with extended asymmetric division behaviors
davidlzhou
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ec80145
Update .gitignore
davidlzhou
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b31949e
main for extended div
davidlzhou
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edd40e9
Delete empty.txt
davidlzhou
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d669670

Commits on Apr 28, 2025

Update PhysiCell_settings.xml
davidlzhou
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ddab2bd

Commits on Apr 29, 2025

Commits on Apr 30, 2025

copy used and default file names
drbergman
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6dadf68
Merge pull request #16 from drbergman/my-physicell-robust-copy-to-output
drbergman
authored
c8a3739
1.14.2-drbergman-2.2.1
drbergman
committed
000cdaa

Commits on May 9, 2025

revised extended asym
davidlzhou
committed
065d9e8

Commits on May 14, 2025

fix detachments
drbergman
committed
9fc5e87

Commits on May 16, 2025

Extended asym div updates for equality and map indexing
davidlzhou
committed
3a193d5

Commits on May 30, 2025

more changes for EAD
davidlzhou
committed
82e469f
EAD: change to index-to-pair function
davidlzhou
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4be4256
Adding basic EAD sample project
davidlzhou
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b81aa37

Commits on May 31, 2025

EAD sample project; bugfixes
davidlzhou
committed
09fb30d
more updates
davidlzhou
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5dcece2
Restore random seed to PhysiCell_settings.xml
davidlzhou
committed
80d46c1

Commits on Jun 2, 2025

Commits on Jun 11, 2025

dev bump
drbergman
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77edd96

Commits on Jun 24, 2025

add (spring) attachment and cycle phase signals
drbergman
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6097a2f

Commits on Jul 28, 2025

delete duplicate elapsed time in phase from saves
drbergman
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b35d835

Commits on Aug 19, 2025

add current cycle phase index to signals
drbergman
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e52e73b

Commits on Aug 21, 2025

Merge pull request #1 from drbergman/feature-cycle-phase-index-as-signal
dgedris
authored
35de108

Commits on Aug 22, 2025

better warnings/error messages
drbergman
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061a40d
better warnings/error messages
drbergman
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24244b8
standardize aggregator type stored
drbergman
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dabfe55
Merge branch 'rules-upgrade' into light-upgrade-rules-edits
drbergman
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e876651
default to names with _
drbergman
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53b1f1b
Merge branch 'rules-upgrade' into light-upgrade-rules-edits
drbergman
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c81bd63
Merge pull request #21 from drbergman/light-upgrade-rules-edits
drbergman
authored
da1f5b5
Merge branch 'my-physicell-dev' into my-pc-dev-delete-duplicate-elapsed_time_in_phase
drbergman
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3be0caa
delete unnecessary comments
drbergman
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3e619a8
Merge pull request #22 from drbergman/my-pc-dev-delete-duplicate-elapsed_time_in_phase
drbergman
authored
025cb78
Merge pull request #20 from drbergman/feature-cycle-phase-index-as-signal
drbergman
authored
48da3b5
Merge branch 'feature-cycle-phase-index-as-signal' into more-signals
drbergman
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0845a55
Merge branch 'my-physicell-dev' into my-pc-dev-attachment-signals
drbergman
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5e8deed
Merge pull request #23 from drbergman/my-pc-dev-attachment-signals
drbergman
authored
919936d

Commits on Aug 25, 2025

Commits on Aug 28, 2025

Merge pull request #29 from drbergman/fix-attack-no-detach
drbergman
authored
2957744

Commits on Sep 4, 2025

check that sbml file exists before copying it from the mappings file
drbergman
committed
5e64ed0

Commits on Sep 5, 2025

hotfix for custom med/agg to "return" double
drbergman
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ffe86ac
Add elapsed time in phase signal
dgedris
committed
e1fef3a
Merge remote-tracking branch 'dgedris/danyon-physicell' into dgedris-updates
drbergman
committed
eeb66db
extended asymmetric division

davidlzhou
authored and
drbergman
committed
b42764c
Merge branch 'my-physicell-dev' into feature-extended-asym-div-my-physicell
drbergman
committed
295e96d
Merge pull request #32 from drbergman/feature-extended-asym-div-my-physicell
drbergman
authored
cf2f424
synching dgedris/dgedris-physicell to my-physicell
drbergman
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6c046c5
preparing merge...
drbergman
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4e2f59a
Merge branch 'dgedris-updates' into merge-dgedris
drbergman
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7c6c827
Merge pull request #34 from drbergman/merge-dgedris
drbergman
authored
df26d15
allow substrate csvs to omit voxels and entries in rows
drbergman
committed
90c97c1

Commits on Sep 6, 2025

Commits on Sep 8, 2025

Commits on Sep 9, 2025

Commits on Oct 10, 2025

Commits on Oct 24, 2025

Commits on Feb 18, 2026

Commits on Feb 19, 2026

Commits on Mar 13, 2026

Commits on May 4, 2026

configs
jeanette.johnson
committed
bc252e2
configs
jeanette.johnson
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8b03f5c

Commits on May 7, 2026

organizing ICs and removing stuff from prior pub
jeanette.johnson
committed
6ba7b64

Commits on May 13, 2026

various
jeanette.johnson
committed
6d62036

Commits on May 18, 2026

fix CRLF line endings breaking CSV parsers on Unix/macOS

drbergman
and
claude
committed
7f0fdbc
Merge pull request #50 from drbergman/fix-parse-cr-lines-unix-my-physicell
drbergman
authored
8dc80da

Commits on May 28, 2026

base value edit in xml?
jeanette.johnson
committed
0684934

Commits on Jun 9, 2026

still the wrong migration rules
jeanette.johnson
committed
1106eda

Commits on Jun 14, 2026

Validate signal and behavior names when parsing extended XML rules (#51)
drbergman
authored
574b039
bump 1.14.2-drbergman-2.4.3
drbergman
committed
7837ba3

Commits on Jun 15, 2026

corrected t cell motility fit values
jeanette.johnson
committed
eed649e

Commits on Jun 16, 2026

colors
jeanette.johnson
committed
124a30b
bump 1.14.2-drbergman-2.4.4
drbergman
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5457d1d

Commits on Jun 17, 2026

Commits on Jun 25, 2026

IMC ICs
jeanette.johnson
committed
f1efb78

Commits on Jul 20, 2026

Commits on Jul 21, 2026

Commits on Jul 22, 2026

IMC ICs

Jeanette Johnson
authored and
Jeanette Johnson
committed
8d1085d

Commits on Jul 24, 2026

Enhance CSV parser to skip blank lines and validate column count (#54)
drbergman
authored
1b328f6

Commits on Aug 4, 2026

Update .gitignore
gavehan
committed
3aca7d4
Update .gitignore.
gavehan
committed
a1de7e5
Add correct color mapping of cell types.
gavehan
committed
31c5f7e
Merge pull request #5 from jeanettejohnson/restore-cell-type-colors
gavehan
authored
a06004d

Commits on Aug 6, 2026

Remove uninitialized system() call from PhysiPKPD sample projects

drbergman
and
claude
committed
0309913

Commits on Aug 7, 2026

Make the attack link symmetric, following spring-attachment semantics (#59)

drbergman
and
claude
authored
3d093b1
Fix asymmetric division daughter selection, determinism, and spurious exit(-1) (#58)

drbergman
and
claude
authored
24ded80
Fix uninitialized and leaked libRoadrunner instance handle (#57)

drbergman
and
claude
authored
eb9a9d9
Fail on an unknown SBML species instead of silently using column 0 (#60)

drbergman
and
claude
authored
4606add

Commits on Aug 8, 2026

Read pAttackTarget once in the effector-attack block (#62)

drbergman
and
claude
authored
a93e19b
Defer teardown out of the mechanics parallel-for (#63)

drbergman
and
claude
authored
2234d81
Give each cell definition its own fixed_duration and death-phase parameters (#56)

drbergman
and
claude
authored
4ee1205
Generate header dependencies so header edits trigger a rebuild (#61)

drbergman
and
claude
authored
012c149

Commits on Aug 10, 2026

Make the asymmetric division probability tolerance configurable (#64)

drbergman
and
claude
authored
24ffcb6
Take spring attachments under the lock before iterating them (#65)

drbergman
and
claude
authored
9c7b394
1.14.2-drbergman-3.1.0
drbergman
committed
b4264ae

Commits on Aug 21, 2026

Add a weighted mode for asymmetric division (#68)

drbergman
and
claude
authored
9e7604e
bump 1.14.2-drbergman-3.2.0
drbergman
committed
3dcd57d
stop copying dirichlet csv rows; fix warning's expected count (#73)

drbergman
and
claude
authored
69597f4
Fix substrate csv out-of-bounds reads, revive the headerless path, require well-formed rows (#66) (#69)

drbergman
and
claude
authored
c7ff094
Remove stray semicolon from two PhysiBoSS samples' main.cpp (#74)

drbergman
and
claude
authored
5cef00f
Read dirichlet csvs with the substrate csv machinery (#71)

drbergman
and
claude
authored
7b2e7e1

Commits on Aug 31, 2026

Fix colliding random seeds when sims launch simultaneously (#75)

drbergman
and
claude
authored
7f49361
bump 1.14.2-drbergman-3.2.1
drbergman
committed
0acd1ca

Commits on Sep 25, 2026

Fix the class I+II leak and align T-cell speed and division across models

gavehan
and
claude
committed
a8ba118
Merge pull request #6 from jeanettejohnson/fix/config-leak-tcells
gavehan
authored
4bc7b8f
Save full data and SVG snapshots every 60 min instead of 30

gavehan
and
claude
committed
20a59b7
Merge pull request #7 from jeanettejohnson/save-interval-60

gavehan
and
claude
authored
e436f7b
Remove stray and leftover files from the user projects

gavehan
and
claude
committed
ac27260
Make the user-project configs portable and match the run settings

gavehan
and
claude
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d1909f8
Match the user-project code to the run inputs

gavehan
and
claude
committed
a59d37a
Merge pull request #8 from jeanettejohnson/cleanup/user-projects
gavehan
authored
ca48227
Update to drbergman/PhysiCell 1.14.2-drbergman-3.2.1 and drop the sample projects

gavehan
and
claude
committed
ec56b0f
Merge pull request #9 from jeanettejohnson/update/drbergman-3.2.1
gavehan
authored
17cb7db
Add CAF-contact MHC-II rules at rate 0

gavehan
and
claude
committed
0b6057a
Save full data and SVG snapshots every 120 min instead of 60

gavehan
and
claude
committed
1e0e5ec