Bayesian analysis

.github/workflows/installer.yml

@@ -111,26 +111,26 @@ jobs:
 #          ${{ secrets.APPLE_CERT_DATA }} ${{ secrets.APPLE_CERT_PASSWORD }}
 #          ${{ secrets.APPLE_NOTARY_USER }} ${{ secrets.APPLE_NOTARY_PASSWORD }}
 
-      - name: Setup SM_CLIENT_CERT_FILE from base64 secret data
-        if: runner.os == 'Windows'
-        run: |
-          echo "${{ secrets.KEYLOCKER_CERT_DATA }}" | base64 --decode > /d/Certificate_pkcs12.p12
-        shell: bash
+      # - name: Setup SM_CLIENT_CERT_FILE from base64 secret data
+      #   if: runner.os == 'Windows'
+      #   run: |
+      #     echo "${{ secrets.KEYLOCKER_CERT_DATA }}" | base64 --decode > /d/Certificate_pkcs12.p12
+      #   shell: bash
 
 
-      - name: Setup Software Trust Manager
-        if: runner.os == 'Windows'
-        uses: digicert/code-signing-software-trust-action@v1
-        with:
-              simple-signing-mode: true
-              # If the below 2 parameters are supplied, then smctl executable is invoked to attempt the signing.
-              input: ${{ env.SETUP_EXE_PATH }}
-              keypair-alias: ${{ secrets.KEYLOCKER_KEYPAIR_ALIAS }}
-        env:
-              SM_HOST: ${{ secrets.KEYLOCKER_HOST }}
-              SM_API_KEY: ${{ secrets.KEYLOCKER_API_KEY }}
-              SM_CLIENT_CERT_FILE: D:\\Certificate_pkcs12.p12
-              SM_CLIENT_CERT_PASSWORD: ${{ secrets.WINDOWS_CERT_PASSWORD }}
+      # - name: Setup Software Trust Manager
+      #   if: runner.os == 'Windows'
+      #   uses: digicert/code-signing-software-trust-action@v1
+      #   with:
+      #         simple-signing-mode: true
+      #         # If the below 2 parameters are supplied, then smctl executable is invoked to attempt the signing.
+      #         input: ${{ env.SETUP_EXE_PATH }}
+      #         keypair-alias: ${{ secrets.KEYLOCKER_KEYPAIR_ALIAS }}
+      #   env:
+      #         SM_HOST: ${{ secrets.KEYLOCKER_HOST }}
+      #         SM_API_KEY: ${{ secrets.KEYLOCKER_API_KEY }}
+      #         SM_CLIENT_CERT_FILE: D:\\Certificate_pkcs12.p12
+      #         SM_CLIENT_CERT_PASSWORD: ${{ secrets.WINDOWS_CERT_PASSWORD }}
 
       - name: Create zip archive of offline app installer for distribution
         run: >

.gitignore

@@ -50,3 +50,6 @@ settings.ini*
 
 #Snap
 *.snap
+
+# Claude Code personal settings
+.claude/settings.local.json

CHANGELOG.md

@@ -1,3 +1,10 @@
+# Unreleased
+
+- Migrated to the new `easyscience` core API surface exposed by `reflectometry-lib`:
+  - Layer removal now calls `remove_at(index)`; the lib's index-based `remove` was replaced by standard `MutableSequence.remove(value)` semantics.
+  - Parameter discovery uses `get_all_parameters()`.
+- **Breaking:** project files saved by earlier versions (predating `file_format=2`) can no longer be opened. Opening one now shows a clear error dialog instead of failing uncaught; affected projects must be recreated.
+
 # Version 1.3.0 (1 May 2026)
 
 - Migrated the application to the new `EasyApplication` module and removed the old `EasyApp` footer dependency.

EasyReflectometryApp/Backends/Mock/Analysis.qml

@@ -34,6 +34,28 @@ QtObject {
     readonly property var fitPreviewParameterValues: ({})
     readonly property var fitResults: ({ success: true, nvarys: 3, chi2: 1.2345 })
 
+    // Bayesian sampling
+    readonly property bool isBayesianSelected: false
+    readonly property int bayesianSamples: 10000
+    readonly property int bayesianBurnIn: 2000
+    readonly property int bayesianPopulation: 10
+    readonly property int bayesianThinning: 1
+    readonly property var bayesianPosterior: null
+    readonly property bool bayesianResultAvailable: false
+    readonly property var bayesianMarginals: []
+
+    // Phase 2: corner/trace/distribution plots (HTML), diagnostics, heatmap
+    readonly property string bayesianCornerPlotUrl: ''
+    readonly property string bayesianTracePlotUrl: ''
+    readonly property string bayesianDistributionPlotUrl: ''
+    readonly property var bayesianDiagnostics: ({})
+    readonly property var bayesianParamNames: []
+    readonly property var bayesianHeatmapData: null
+    readonly property string bayesianHeatmapPlotUrl: ''
+    function bayesianComputeHeatmap(x, y) {
+        console.debug(`bayesianComputeHeatmap ${x}, ${y}`)
+    }
+
     // Fit failure signal (mirrors Python backend)
     signal fitFailed(string message)
 
@@ -123,4 +145,16 @@ QtObject {
         showFitResultsDialog = value
         console.debug(`setShowFitResultsDialog ${value}`)
     }
+    function setBayesianSamples(value) {
+        console.debug(`setBayesianSamples ${value}`)
+    }
+    function setBayesianBurnIn(value) {
+        console.debug(`setBayesianBurnIn ${value}`)
+    }
+    function setBayesianPopulation(value) {
+        console.debug(`setBayesianPopulation ${value}`)
+    }
+    function setBayesianThinning(value) {
+        console.debug(`setBayesianThinning ${value}`)
+    }
 }

EasyReflectometryApp/Backends/Mock/Plotting.qml

@@ -37,6 +37,20 @@ QtObject {
     property bool scaleShown: false
     property bool bkgShown: false
 
+    // Posterior predictive (Bayesian) overlay data
+    readonly property var posteriorPredictiveQ: []
+    readonly property var posteriorPredictiveMedian: []
+    readonly property var posteriorPredictiveLower: []
+    readonly property var posteriorPredictiveUpper: []
+    signal posteriorPredictiveDataChanged()
+
+    // Phase 2: SLD posterior predictive (Bayesian) overlay
+    readonly property var posteriorPredictiveSldZ: []
+    readonly property var posteriorPredictiveSldMedian: []
+    readonly property var posteriorPredictiveSldLower: []
+    readonly property var posteriorPredictiveSldUpper: []
+    signal posteriorPredictiveSldDataChanged()
+
     // Signals for plot mode changes
     signal plotModeChanged()
     signal axisTypeChanged()

EasyReflectometryApp/Backends/Mock/Status.qml

@@ -5,7 +5,7 @@ import QtQuick
 QtObject {
 
     readonly property string project: 'Undefined'
-    readonly property string phaseCount: '1'
+    readonly property string modelsCount: '1'
     readonly property string experimentsCount: '1'
     readonly property string calculator: 'CrysPy'
     readonly property string minimizer: 'Lmfit (leastsq)'