Catchup merge from main into SED

.github/workflows/setup-and-run-tests.yml

@@ -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

.github/workflows/traffic.yml

@@ -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

.gitignore

@@ -1,7 +1,5 @@
 .DS_Store
 *.asv
-*.asv
-*.asv
 CommandLine/OldProablyTrash/*
 CommandLine/OldProablyTrash/*/*
 BackgroundFitsResults*
@@ -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
@@ -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

ExampleData/DUSP1_Dex_100nM_Rep1_Rep2.csv

@@ -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