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b3f7810
Add method to summarize data.
Munsky Feb 7, 2026
2def6df
Add more information to DataSummary method and add test.
Munsky Feb 7, 2026
3713313
Change generateCommandLinePipeline method to use optional arguments. …
Munsky Feb 7, 2026
5b2bc6a
Fix screenshot link in README.md
Munsky Feb 7, 2026
906330e
Reorganize file locations and add installation script.
Munsky Feb 7, 2026
0de1f8f
Improve README installation instructions and formatting
Munsky Feb 7, 2026
4853a71
Update README with installation and testing instructions
Munsky Feb 7, 2026
cc2a20e
Reorganize solve routine to include try/catch to reform propensity fu…
Munsky Feb 7, 2026
0db94ca
Add option to run all examples and keep filelog using install code.
Munsky Feb 7, 2026
13492cc
Fix Hog1 signal parameters, fit the others
alexpopinga Feb 8, 2026
fbafc1e
Merge branch 'TestMerge' of https://github.com/MunskyGroup/SSIT into …
alexpopinga Feb 8, 2026
b9f225c
Merge branch 'TestMerge'
Munsky Feb 8, 2026
64ad06d
Update .gitignore
Munsky Feb 8, 2026
0a992b4
Fix image link in README for appScreenshot
Munsky Feb 9, 2026
6fc8257
Update locations for storage of propensity functions.
Munsky Feb 9, 2026
1cbdc1c
Merge branch 'main' into TestMerge
Munsky Feb 9, 2026
f0c21a6
Update setup-and-run-tests.yml
Munsky Feb 10, 2026
0c43015
Update 4-state STL1 model and model fitting
alexpopinga Feb 11, 2026
abb951c
Reorder examples and change STL1 replica
alexpopinga Feb 11, 2026
2466b13
Update MultiModel example for fixed parameters
alexpopinga Feb 12, 2026
fe5f878
Include means and COV in outputs from moments calculation and add test.
Munsky Feb 12, 2026
27635ad
Update compareParameters in SSITMultiModel
alexpopinga Feb 12, 2026
a197995
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Feb 12, 2026
51fa069
Update approach to compute Steady State Initial Conditions and add test.
Munsky Feb 12, 2026
ee66ad1
Update examples for additional STL1 parameters
alexpopinga Feb 12, 2026
51b1581
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Feb 12, 2026
61b5638
Update example_17_ABC.m
alexpopinga Feb 12, 2026
c130f81
Rename example scripts
alexpopinga Feb 12, 2026
6135f6c
Split scRNAseq script into three scripts
alexpopinga Feb 12, 2026
3b49952
Update model reduction codes, tests and example script.
Munsky Feb 13, 2026
77154cf
Update model reduction codes and examples to fix sensitivity to numbe…
Munsky Feb 13, 2026
a3c85a7
Set a maximum number of time points (40) for use in POD model reduction.
Munsky Feb 13, 2026
a602bfb
Merge branch 'TestMerge'
Munsky Feb 13, 2026
1b1e270
Add `freePars' argument to compute FIM sub matrix
alexpopinga Feb 13, 2026
47ce665
Require `scale' specification in plotFIMResults
alexpopinga Feb 13, 2026
1e67c06
Add FIM sub matrix for free parameters of the 4-state STL1 model
alexpopinga Feb 13, 2026
e1f9e24
Set PlotEllipses default to false for plotFIMResults
alexpopinga Feb 13, 2026
98ecc6e
Minor fixes to Bursting Gene and simple STL1 models
alexpopinga Feb 13, 2026
e485d23
Add error message for lack of user-supplied `scale'
alexpopinga Feb 13, 2026
4d3a66a
Tidy comments, variable
alexpopinga Feb 13, 2026
02ab4b5
Update install.m
Munsky Feb 14, 2026
df211bd
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
Munsky Feb 14, 2026
6683c18
Update example_SI_ABC.m
alexpopinga Feb 14, 2026
ae3e03f
Update graphical abstract and add logo
Munsky Feb 16, 2026
2fea65c
Add Logo to GUI
Munsky Feb 16, 2026
f7b42e6
Fix tSpan mistake and comments in Moments script
alexpopinga Feb 17, 2026
7d0fd05
Adding scRNAseq model for ABC example
alexpopinga Feb 17, 2026
8f5c202
Update example_SI_ABC.m with scRNAseq gene
alexpopinga Feb 17, 2026
d21df54
Ensure initial parameter value line is correct (ABC example)
alexpopinga Feb 17, 2026
bc570a1
Add MLE fit line to ABC plot with minmh fit and initial value lines
alexpopinga Feb 17, 2026
6a7b96a
Fix headers of examples so they match the script number
alexpopinga Feb 17, 2026
f39816b
Fix comment in ABC script (scRNAseq now, not STL1)
alexpopinga Feb 17, 2026
af25496
Fix comments in ABC example
alexpopinga Feb 17, 2026
62eea9a
Ensure burnin equilibration time for SSA
alexpopinga Feb 17, 2026
0f05042
Remove eval commands to create propensity function files.
Munsky Feb 17, 2026
3089633
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
Munsky Feb 17, 2026
4f1c7f0
Add moment solution plots
alexpopinga Feb 17, 2026
951d42b
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Feb 17, 2026
ec516a6
Update plotSSA labels and plotting examples
alexpopinga Feb 17, 2026
2acc3de
Fix variable name save in FIM example
alexpopinga Feb 18, 2026
537ea73
Create MakeSSITGUIGif.m
Munsky Feb 18, 2026
d5ae920
Merge branch 'main' into Make_GUI_GIF
Munsky Feb 18, 2026
dad352f
Add SSIT graphical abstract from paper
alexpopinga Feb 18, 2026
00ccb37
Update install.m
Munsky Feb 19, 2026
1e42a3b
Merge branch 'main' into Make_GUI_GIF
Munsky Feb 19, 2026
86f9383
Add option to publish example scripts during install run.
Munsky Feb 19, 2026
07008f4
Fix bug when FSP is smaller than chosen Krylov projection.
Munsky Feb 19, 2026
86b4859
Clear figures between examples when publishing
Munsky Feb 19, 2026
6afa444
change call of syms to 'assume' to ensure real values for parameters …
Munsky Feb 19, 2026
e281029
Separate FIM Experiment Design into own example
alexpopinga Feb 19, 2026
61331c4
Fix bar graph offsets for overlapping cell counts
alexpopinga Feb 19, 2026
514c626
Minor comment fixes
alexpopinga Feb 19, 2026
274e3a4
Update install.m
Munsky Feb 19, 2026
7d3c116
Adjust how figure numbers are assigned in plot codes.
Munsky Feb 19, 2026
8b4326f
Reset path based on best match to pwd when loading GUi models.
Munsky Feb 19, 2026
12ce33f
Suppress impossible tests (GUI and BackgroundJobs) on GitHub
Munsky Feb 19, 2026
d1306c4
Move movie plotting functions to src/plotting
Munsky Feb 19, 2026
d93a38c
Fix Section headers in examples, add two new data file types
alexpopinga Feb 19, 2026
159bc91
Minor updates to example scripts
alexpopinga Feb 20, 2026
afb0ca9
Minor updates to example scripts
alexpopinga Feb 20, 2026
5815466
Suppress GUI tests on GitHub -- change to AssumeFail.
Munsky Feb 20, 2026
ac9f991
Update Install function to also allow publication of example scripts.…
Munsky Feb 20, 2026
96e3456
Update README with links to all example scripts.
Munsky Feb 20, 2026
7f904ec
Increase speed of multimodel example (STL1)
alexpopinga Feb 20, 2026
c7b3211
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Feb 20, 2026
2970fa0
Fix mix parameters example in multimodel (STL1)
alexpopinga Feb 20, 2026
5d727be
Update README.md
Munsky Feb 20, 2026
a747eaa
Merge branch 'main' into Make_GUI_GIF
Munsky Feb 20, 2026
c85d7e4
Create SSITAnimation.gif
Munsky Feb 20, 2026
2628ef8
Create SSITAnimation.gif
Munsky Feb 20, 2026
3e0a43c
Add fix for when statespace is provided but FSP bounds are not.
Munsky Feb 20, 2026
edb4bd9
Update GUI gif
Munsky Feb 20, 2026
3644d1d
Update GUI files.
Munsky Feb 20, 2026
5da1b5d
Merge branch 'Make_GUI_GIF'
Munsky Feb 20, 2026
528f059
Update image in README from screenshot to animation
Munsky Feb 20, 2026
8c77b52
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
Munsky Feb 20, 2026
6eefb87
Update README.md
Munsky Feb 20, 2026
c6723b5
Move movieODE into plotODE in SSIT.m, make all arguments opts
alexpopinga Feb 20, 2026
4078f38
Move makeSSAmovie into plotSSA, make arguments optional
alexpopinga Feb 20, 2026
2f26344
Fix otps mistakes in plotSSA makeMovie
alexpopinga Feb 20, 2026
75f35ca
Remove makeODE and makeSSA as separate functions
alexpopinga Feb 20, 2026
d8a11fc
Make all plotFSP arguments optional
alexpopinga Feb 20, 2026
51b87df
Update escape times example for newly formatted plotFSP
alexpopinga Feb 20, 2026
319f26e
Update sens example for newly formatted plotFSP
alexpopinga Feb 20, 2026
e83410a
Fix install to remove dialog boxes when run on cluster.
Munsky Feb 20, 2026
9dfc3ef
Update plotMoments and fix tSpan bug in plotFSP
alexpopinga Feb 21, 2026
149858c
Add install version for use on cluster where 'savepath' is not availa…
Munsky Feb 23, 2026
6e4fc19
Update install.m
Munsky Feb 23, 2026
2d63cdc
Update install.m
Munsky Feb 23, 2026
539a8a4
Suppress unnecessary propensity function generation for SSA solution …
Munsky Feb 23, 2026
fe131df
Fix bug when SSA is run before FSP constraints are defined.
Munsky Feb 23, 2026
10ef670
Update README.md
alexpopinga Feb 25, 2026
17cba7e
Update README.md
alexpopinga Feb 25, 2026
175b140
Update README.md
alexpopinga Feb 25, 2026
dac7fbf
Fix incorrectly named variable in example_7b_FIM_ExperimentDesign.m
alexpopinga Feb 26, 2026
f818658
Update FIM optimality criteria for clarity, add ESS to MH
alexpopinga Feb 26, 2026
9d385d5
Edit optimized FIM variables by new criteria labels
alexpopinga Feb 26, 2026
4ba6ec2
Fix size error bug in assigning/updating FSP constraints after runnin…
Munsky Feb 26, 2026
9b18b11
Add repository traffic section to README
Munsky Feb 26, 2026
80bb86f
Add scripts for traffic monitoring.
Munsky Feb 26, 2026
8a826ce
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
Munsky Feb 26, 2026
9160f55
Update traffic.yaml
Munsky Feb 26, 2026
9bfc27e
Rename traffic.yaml to traffic.yml
Munsky Feb 26, 2026
4f22192
Update aggregate.js
Munsky Feb 26, 2026
77b3742
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
Munsky Feb 26, 2026
eee2690
Create README.md
Munsky Feb 26, 2026
63e4d74
Attempt fix on traffic.yml
Munsky Feb 26, 2026
3437b8c
Update traffic.yml
Munsky Feb 26, 2026
60428e7
Update ESS
alexpopinga Feb 26, 2026
4e02c55
Print table of ESS by fitted parameter
alexpopinga Feb 26, 2026
c1b7edd
Update traffic.yml
Munsky Feb 26, 2026
ab01a5a
Update traffic.yml
Munsky Feb 26, 2026
03154de
Update traffic stats
actions-user Feb 26, 2026
cc7b8b3
Store ess with mhSamples, mhAcceptance, and mhValue in otherResults
alexpopinga Feb 26, 2026
acddf37
Print min ESS with MH Convergence title
alexpopinga Feb 26, 2026
32f2c7c
Update traffic stats
actions-user Feb 27, 2026
bd4ee8b
Ensure ESS calculation only for MH, add invFIM to plotFIMResults
alexpopinga Feb 27, 2026
3790064
Update .gitignore
Munsky Feb 27, 2026
5282579
Fix cases for string input
alexpopinga Feb 27, 2026
96d4582
Update traffic stats
actions-user Feb 28, 2026
a0c2aed
Update traffic stats
actions-user Mar 1, 2026
359d77c
Update traffic stats
actions-user Mar 2, 2026
1ea6525
Update traffic stats
actions-user Mar 3, 2026
2716a89
Clean up MultiModel example
alexpopinga Mar 3, 2026
2be4912
update example gui gif
Munsky Mar 3, 2026
7205b94
Update traffic stats
actions-user Mar 4, 2026
82c3ab2
Update branch
alexpopinga Mar 4, 2026
86872f8
Merge branch 'main' into PCB
alexpopinga Mar 4, 2026
cd85c77
Merge pull request #33 from MunskyGroup/PCB
alexpopinga Mar 4, 2026
13c8455
Update traffic stats
actions-user Mar 5, 2026
2347455
Rename examples for ease to follow with manuscript
alexpopinga Mar 5, 2026
ae347ac
Merge pull request #34 from MunskyGroup/PCB
alexpopinga Mar 5, 2026
dcbff02
Fix fimResults call for evaluateExperiment, PDO
alexpopinga Mar 5, 2026
4c41377
Merge pull request #35 from MunskyGroup/PCB
alexpopinga Mar 5, 2026
a0e27d0
Update simplified STL1 model input signal parameters
alexpopinga Mar 5, 2026
42a638e
Update install.m for renamed examples
alexpopinga Mar 5, 2026
5493859
Changes to FIM heat map plots to include color and sign.
Munsky Mar 5, 2026
7bceaf5
Update plots for two simple models, FSP example
alexpopinga Mar 5, 2026
d9f1844
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Mar 5, 2026
8c2431d
Update codes to plot FIM results in Example 7.
Munsky Mar 5, 2026
5e97132
Make consistent parameter choices in Example 7
Munsky Mar 5, 2026
6011ddf
Update traffic stats
actions-user Mar 6, 2026
d6176f3
Minor example changes
alexpopinga Mar 6, 2026
ee6b997
Merge branch 'main' of https://github.com/MunskyGroup/SSIT
alexpopinga Mar 6, 2026
f901a4a
Update traffic stats
actions-user Mar 7, 2026
bbdeef5
Update traffic stats
actions-user Mar 8, 2026
ca272a3
Update traffic stats
actions-user Mar 9, 2026
fc3968f
Fix SSA bug for use on cluster, where different models are running on…
Munsky Mar 9, 2026
4e82d79
Update SSIT.m
Munsky Mar 9, 2026
2a791fe
Update traffic stats
actions-user Mar 10, 2026
1ac7e14
Update traffic stats
actions-user Mar 11, 2026
eb1ec33
Update traffic stats
actions-user Mar 12, 2026
2a267a0
Update traffic stats
actions-user Mar 13, 2026
e4dc02a
Update traffic stats
actions-user Mar 14, 2026
e2ac2c7
Update traffic stats
actions-user Mar 15, 2026
67a143a
Update traffic stats
actions-user Mar 16, 2026
774f28e
Update traffic stats
actions-user Mar 17, 2026
59967f7
Update traffic stats
actions-user Mar 18, 2026
c995b5c
Update traffic stats
actions-user Mar 19, 2026
2327074
Update traffic stats
actions-user Mar 20, 2026
ef8b680
Update traffic stats
actions-user Mar 21, 2026
cf95339
Update traffic stats
actions-user Mar 22, 2026
4ea0b37
Update traffic stats
actions-user Mar 23, 2026
2f0d452
Update README.md
Munsky Mar 23, 2026
b387c05
Update plotFits calls in examples and model spec in example_0
alexpopinga Mar 23, 2026
ffecdde
Remove old PDO mat file
alexpopinga Mar 23, 2026
44abfa0
Update epidemics example
alexpopinga Mar 23, 2026
f1e25a8
Update examples
alexpopinga Mar 23, 2026
066724f
Update traffic stats
actions-user Mar 24, 2026
cf98547
Update example0
alexpopinga Mar 24, 2026
2dfa5bf
Update traffic stats
actions-user Mar 25, 2026
436567b
Resolves issue #36 in summarizeModel
alexpopinga Mar 25, 2026
b1092d2
Update example0_Complete_Manuscript.m
alexpopinga Mar 25, 2026
756486d
Update example0_Complete_Manuscript.m
alexpopinga Mar 25, 2026
d8c4061
Update example0_Complete_Manuscript.m
alexpopinga Mar 25, 2026
b95151e
Update traffic stats
actions-user Mar 26, 2026
aa6659d
Update example0_Complete_Manuscript.m
alexpopinga Mar 26, 2026
4bef90d
Add figure option arguments to generatePDO()
alexpopinga Mar 26, 2026
424a592
Update PDO plotting in generatePDO()
alexpopinga Mar 26, 2026
f6be5f6
Add scRNA-seq multi model example to example0
alexpopinga Mar 26, 2026
c5adcaf
Update traffic stats
actions-user Mar 27, 2026
72ce33c
Set default showPlot to false for generatePDO
alexpopinga Mar 27, 2026
acc210e
Update multi model section of example0
alexpopinga Mar 27, 2026
eb5dbba
Update FIM + PDO design example
alexpopinga Mar 27, 2026
ac13c1c
Update traffic stats
actions-user Mar 28, 2026
c146fad
Update traffic stats
actions-user Mar 29, 2026
1cbb984
Tidy up PDO example and example0
alexpopinga Mar 29, 2026
e83f2eb
Rename 'example0' to 'example_0' for consistency
alexpopinga Mar 29, 2026
9e8cea6
Update traffic stats
actions-user Mar 30, 2026
8156fa8
Add simple SBML example and remove unused files
alexpopinga Mar 30, 2026
5e6923b
Add example_0 to README.md
alexpopinga Mar 30, 2026
192fecf
Update traffic stats
actions-user Mar 31, 2026
21a5341
Update Git user configuration in traffic workflow
Munsky Apr 1, 2026
6047637
Merge pull request #38 from MunskyGroup/Munsky-patch-1
Munsky Apr 1, 2026
9e5fa5e
Update Git remote URL in traffic.yml
Munsky Apr 1, 2026
84781ac
Merge pull request #39 from MunskyGroup/Munsky-patch-2
Munsky Apr 1, 2026
38dc3d7
Configure PAT_TOKEN for commit automation
Munsky Apr 1, 2026
35ad2c2
Update Git configuration for automation bot
Munsky Apr 1, 2026
0cf1802
Update traffic.yml
automation-bot-SSIT Apr 1, 2026
9587a11
Update traffic.yml
automation-bot-SSIT Apr 1, 2026
8134ac6
Update traffic.yml
automation-bot-SSIT Apr 1, 2026
305f3d6
Merge pull request #40 from MunskyGroup/automation-bot-SSIT-patch-1
automation-bot-SSIT Apr 1, 2026
ef2b746
Update traffic stats
automation-bot-SSIT Apr 2, 2026
f95fd4c
Revise README with updated SSIT usage information
Munsky Apr 2, 2026
58b0308
Update README to emphasize pre-print link
Munsky Apr 2, 2026
a3cb496
Update README.md
Munsky Apr 2, 2026
4fc1800
Update traffic stats
automation-bot-SSIT Apr 3, 2026
952e119
Update traffic stats
automation-bot-SSIT Apr 4, 2026
a0556c0
Update traffic stats
automation-bot-SSIT Apr 5, 2026
f1c7b9a
Update traffic stats
automation-bot-SSIT Apr 6, 2026
85243e7
Update traffic stats
automation-bot-SSIT Apr 7, 2026
383596f
Update traffic stats
automation-bot-SSIT Apr 8, 2026
c0ca983
Update traffic stats
automation-bot-SSIT Apr 9, 2026
0046155
Update traffic stats
automation-bot-SSIT Apr 10, 2026
96ea31c
Update traffic stats
automation-bot-SSIT Apr 11, 2026
00eefb5
Update traffic stats
automation-bot-SSIT Apr 12, 2026
66eb949
Update traffic stats
automation-bot-SSIT Apr 13, 2026
a168460
Relax addReaction function to allow skipping parameters when no new p…
Munsky Apr 13, 2026
b797446
Fix error in specification of FSP constraints when >=10 species are u…
Munsky Apr 13, 2026
5bf7e88
Update traffic stats
automation-bot-SSIT Apr 14, 2026
77e02f3
Update traffic stats
automation-bot-SSIT Apr 15, 2026
44825ec
Use user-supplied title for marginal plots in plotFSP
alexpopinga Apr 15, 2026
ec08932
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5 changes: 5 additions & 0 deletions .github/workflows/setup-and-run-tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,15 @@ jobs:
uses: matlab-actions/run-command@v1
with:
command: addpath(genpath("src"))
- name: Install (setup)
uses: matlab-actions/run-command@v1
with:
command: install(0,0,1,1)
- name: Run MATLAB Tests
uses: matlab-actions/run-tests@v1.5.2
with:
select-by-folder: tests
select-by-name: '^(?!testGui$).*'
test-results-junit: test-results/results.xml
code-coverage-cobertura: code-coverage/coverage.xml
source-folder: src
100 changes: 100 additions & 0 deletions .github/workflows/traffic.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,100 @@
name: Collect GitHub Traffic

on:
schedule:
- cron: "0 0 * * *"
workflow_dispatch:

permissions:
contents: write # required for checkout & file operations

jobs:
collect:
runs-on: ubuntu-latest

steps:
# Step 1: Checkout the repository
- name: Checkout repository
uses: actions/checkout@v4

# Step 2: Setup Node.js
- name: Setup Node
uses: actions/setup-node@v4
with:
node-version: 20

# Step 3: Fetch traffic data
- name: Fetch Traffic Data
env:
GH_TRAFFIC_TOKEN: ${{ secrets.GH_TRAFFIC_TOKEN }}
run: |
TOKEN="${GH_TRAFFIC_TOKEN}"
if [ -z "$TOKEN" ]; then
echo "Error: GH_TRAFFIC_TOKEN is required for GitHub Traffic API access." >&2
exit 1
fi

fetch_traffic() {
local url="$1"
local outFile="$2"
local responseFile="${outFile}.tmp"

httpCode=$(curl -sSL \
-H "Authorization: Bearer ${TOKEN}" \
-H "Accept: application/vnd.github+json" \
-H "X-GitHub-Api-Version: 2022-11-28" \
-o "${responseFile}" \
-w "%{http_code}" \
"$url")

if [ "$httpCode" = "200" ]; then
mv "${responseFile}" "${outFile}"
return 0
fi

echo "GitHub Traffic API request failed (${httpCode}) for ${url}" >&2
cat "${responseFile}" >&2 || true
rm -f "${responseFile}"
exit 1
}

fetch_traffic "https://api.github.com/repos/${{ github.repository }}/traffic/clones" "clones.json"
fetch_traffic "https://api.github.com/repos/${{ github.repository }}/traffic/views" "views.json"

# Step 4: Validate and merge traffic data
- name: Validate and Merge Traffic Data
run: |
node -e '
const fs = require("fs");
const clones = JSON.parse(fs.readFileSync("clones.json", "utf8"));
const views = JSON.parse(fs.readFileSync("views.json", "utf8"));
if (!Array.isArray(clones.clones)) throw new Error("clones.json missing clones array");
if (!Array.isArray(views.views)) throw new Error("views.json missing views array");
fs.mkdirSync("data", { recursive: true });
const date = new Date().toISOString().slice(0, 10);
fs.writeFileSync(`data/traffic-${date}.json`,
JSON.stringify({ clones: clones.clones, views: views.views }, null, 2));
'

# Step 5: Clean temporary files
- name: Save Historical Data
run: rm -f clones.json views.json

# Step 6: Update README stats
- name: Update README Stats
run: node scripts/aggregate.js

# Step 7: Commit & push changes using the bot PAT
- name: Commit Changes
env:
BOT_TOKEN: ${{ secrets.PAT_TOKEN_SSIT_BOT }}
run: |
git config user.name "automation-bot-SSIT"
git config user.email "brian.munsky+automation-bot@gmail.com"

git add .
git commit -m "Update traffic stats" || echo "No changes"

# Use PAT to push to main
git remote set-url origin https://$BOT_TOKEN@github.com/MunskyGroup/SSIT.git
git push origin main
51 changes: 48 additions & 3 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
.DS_Store
*.asv
*.asv
*.asv
CommandLine/OldProablyTrash/*
CommandLine/OldProablyTrash/*/*
BackgroundFitsResults*
Expand Down Expand Up @@ -53,7 +51,6 @@ Examples/Iterative*.mat
WorkSpace/sequentialEDcdc/FakeExperiment_*.csv
WorkSpace/Josh/Fake*.csv
/WorkSpace/sequentialEDcdc/ExampleData
/WorkSpace/sequentialEDcdc/ExampleData
WorkSpace/sequentialEDcdc/*.mat
WorkSpace/sequentialEDcdc/oldMod3Results_ProbablyTrash/*.mat
WorkSpace/sequentialEDcdc/simData/Fake*.csv
Expand All @@ -71,3 +68,51 @@ WorkSpace/sequentialEDcdc/simData/FakeExperiment_poisson_fimopt_10.csv
WorkSpace/EricModel/terminalVersion/log.txt
WorkSpace/EricModel/EricData/Gated_dataframe_Ron_020224_NormalizedGR_binsB.csv
Examples/reformatFiguresACS2024.m
Examples/Cook_etal_2024_Sequential_Design/simData/*.csv
Examples/Cook_etal_2024_Sequential_Design/TMPMHChain*
tests/exampleResultsTest.mat
tests/TemporarySaveFile.mat
WorkSpace/PipelineApproach/exampleResults.mat
WorkSpace/PipelineApproach/savedModelGR.mat
WorkSpace/PipelineApproach/GRModelFitResults.mat
WorkSpace/PipelineApproach/savedGRmultiModel.mat
tests/TMPtable.csv
Examples/PLOSCompBio/TMPmh*.mat
tests/exampleCombinedResultsTest.mat
tests/logFile.txt
tests/temporarySaveFile2.mat
tests/temporaryHybridModel.mat
Examples/PLOSCompBio/generatedModel.mat
/WorkSpaceBAK
/trash
tests/testDataSSANEW.csv
Examples/PLOSCompBio/STL1_ODE.mp4
Examples/PLOSCompBio/Model_ODE.mp4
Examples/PLOSCompBio/STL1_4state_ODE.mp4
tests/testData.csv
tests/testData.csv
tests/testData1.csv
tests/testData2.csv
tests/TMPmh_*
tests/TmpGPUSSACode.m
/Models/IgnoredModels
TimeMarginal.mp4
tests/TmpGPUSSACode.m
/Models/ZZ_IgnoredModels
/RemovedModels
Examples/TmpGPUSSACode.m
TmpGPUSSACode.m
*.mp4
logFile.txt
temporaryHybridModel.mat
temporarySaveFile.mat
temporarySaveFile2.mat
testData1.csv
testData2.csv
TwoDNonLinearTV.xml
exampleCombinedResultsTest.mat
/Examples/exampleLogs
src/SSITconfig.mat
/Models/ZZ_IgnoredModels/*
/images/SSITGUI_Wheels
Examples/pseudoCodeSED.m
2 changes: 1 addition & 1 deletion ExampleData/DUSP1_Dex_100nM_Rep1_Rep2.csv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cell_number,time_index,RNA_nuc,RNA_cyto,RNA_total,Rep_num
cell_number,time,RNA_nuc,RNA_cyto,RNA_total,Rep_num
0,0,2,4,6,1
1,0,2,9,11,1
2,0,20,75,95,1
Expand Down
File renamed without changes.
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