refactor: migrate electrochem apps to owned packages

apps/electrochem/private/chronoOverlayWorkflow.m → apps/electrochem/chrono_overlay/+chrono_overlay/+core/dispatch.m

@@ -1,12 +1,11 @@
-% App-owned chrono overlay workflow helper dispatch. Expected caller:
-% labkit_ChronoOverlay_app callbacks and workflow tests.
+% App-owned chrono overlay helper core dispatch. Expected caller:
+% labkit_ChronoOverlay_app callbacks and package tests.
 % Inputs are a command string plus the original helper arguments; outputs match
 % the selected helper. Side effects are limited to drawing app-owned overlay
 % plots on caller axes.
-function varargout = chronoOverlayWorkflow(command, varargin)
-%CHRONOOVERLAYWORKFLOW Dispatch app-owned chrono overlay helpers.
-% Expected caller: labkit_ChronoOverlay_app callbacks and temporary compatibility
-% workflow tests. Inputs are a command string plus the original helper arguments.
+function varargout = dispatch(command, varargin)
+%DISPATCH Route chrono overlay package wrapper calls to app-owned helpers.
+% Expected caller: labkit_ChronoOverlay_app callbacks and % package tests. Inputs are a command string plus the original helper arguments.
 % Outputs match the selected helper. Side effects are limited to drawing
 % app-owned overlay plots on caller axes.
 

apps/electrochem/chrono_overlay/+chrono_overlay/+export/buildOverlayExportTable.m

@@ -0,0 +1,6 @@
+% Expected caller: chrono overlay app runner and export tests. Inputs are aligned
+% chrono item structs. Output is the stable overlay export table. No file side
+% effects.
+function T = buildOverlayExportTable(items)
+    T = chrono_overlay.core.dispatch("buildOverlayExportTable", items);
+end

apps/electrochem/chrono_overlay/+chrono_overlay/+ops/alignByPulseGap.m

@@ -0,0 +1,6 @@
+% Expected caller: chrono overlay app runner and unit tests. Inputs are one
+% chrono item struct with time/current/voltage and pulse fields. Outputs return
+% the aligned item and status message. No file or UI side effects.
+function [item, msg] = alignByPulseGap(item)
+    [item, msg] = chrono_overlay.core.dispatch("alignByPulseGap", item);
+end

apps/electrochem/private/runChronoOverlayApp.m → apps/electrochem/chrono_overlay/+chrono_overlay/+ui/runApp.m

@@ -2,7 +2,7 @@
 % Input is the debug context prepared by the public launcher. Output is the app
 % figure. Side effects are GUI creation, user-driven file I/O, exports,
 % plotting, and debug trace attachment exactly as in the original entrypoint body.
-function fig = runChronoOverlayApp(debugLog)
+function fig = runApp(debugLog)
 %RUNCHRONOOVERLAYAPP Build and run the app body.
 
     S = struct();
@@ -160,7 +160,7 @@ function postProcessAddedItems(filepaths)
             end
 
             item = S.session.items(idx);
-            [item, alignMsg] = chronoOverlayWorkflow("alignByPulseGap", item);
+            [item, alignMsg] = chrono_overlay.ops.alignByPulseGap(item);
             S.session.items(idx) = item;
             addLog(alignMsg);
 
@@ -204,7 +204,7 @@ function refreshFileList()
 
     function refreshPlots()
         if isempty(S.items)
-            chronoOverlayWorkflow("plotVTIT", axV, axI, struct([]), plotOptions());
+            chrono_overlay.view.plotVTIT(axV, axI, struct([]), plotOptions());
             return;
         end
 
@@ -215,7 +215,7 @@ function refreshPlots()
             return;
         end
 
-        chronoOverlayWorkflow("plotVTIT", axV, axI, items, plotOptions());
+        chrono_overlay.view.plotVTIT(axV, axI, items, plotOptions());
     end
 
     function onExportCSV(~, ~)
@@ -235,7 +235,7 @@ function onExportCSV(~, ~)
             return;
         end
 
-        T = chronoOverlayWorkflow("buildOverlayExportTable", items);
+        T = chrono_overlay.export.buildOverlayExportTable(items);
         out = fullfile(p, f);
         writetable(T, out);
         addLog(sprintf('Exported CSV: %s', out));

apps/electrochem/chrono_overlay/+chrono_overlay/+view/plotVTIT.m

@@ -0,0 +1,6 @@
+% Expected caller: chrono overlay app runner. Inputs are voltage/current axes,
+% aligned item structs, and plot option fields. Side effects are limited to
+% redrawing the supplied axes.
+function plotVTIT(axV, axI, items, opts)
+    chrono_overlay.core.dispatch("plotVTIT", axV, axI, items, opts);
+end

apps/electrochem/labkit_ChronoOverlay_app.m → apps/electrochem/chrono_overlay/labkit_ChronoOverlay_app.m

@@ -17,7 +17,7 @@
         error('labkit_ChronoOverlay_app:TooManyOutputs', 'labkit_ChronoOverlay_app returns at most the app figure handle.');
     end
 
-    fig = runChronoOverlayApp(debugLog);
+    fig = chrono_overlay.ui.runApp(debugLog);
     if nargout >= 1
         varargout{1} = fig;
     end

apps/electrochem/private/cicWorkflow.m → apps/electrochem/cic/+cic/+core/dispatch.m

@@ -1,10 +1,10 @@
-% App-owned CIC workflow helper dispatch. Expected caller: labkit_CIC_app
-% callbacks and workflow tests. Inputs are a command string plus the original
+% App-owned CIC helper core dispatch. Expected caller: labkit_CIC_app
+% callbacks and package tests. Inputs are a command string plus the original
 % helper arguments; outputs match the selected helper. Side effects are limited
 % to CSV export writes and drawing app-owned plot annotations on caller axes.
-function varargout = cicWorkflow(command, varargin)
-%CICWORKFLOW Dispatch app-owned CIC analysis/export helpers.
-% Expected caller: labkit_CIC_app callbacks and workflow tests.
+function varargout = dispatch(command, varargin)
+%DISPATCH Route CIC package wrapper calls to app-owned helpers.
+% Expected caller: labkit_CIC_app callbacks and package tests.
 % Inputs are a command string plus the original helper arguments. Outputs match
 % the selected helper. Side effects are limited to CSV export writes and drawing
 % app-owned plot annotations on caller axes.

apps/electrochem/cic/+cic/+export/buildResultsTable.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app runner and export tests. Inputs are item structs and
+% display unit label. Output is the stable CIC CSV result table. No file side
+% effects.
+function T = buildResultsTable(items, unitLabel)
+    T = cic.core.dispatch("buildResultsTable", items, unitLabel);
+end

apps/electrochem/cic/+cic/+export/writeResultsCSV.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app runner and export tests. Inputs are item structs,
+% output filepath, and display unit label. Side effect is writing the stable CIC
+% CSV file.
+function [ok, msg] = writeResultsCSV(items, filepath, unitLabel)
+    [ok, msg] = cic.core.dispatch("writeResultsCSV", items, filepath, unitLabel);
+end

apps/electrochem/cic/+cic/+ops/computeCIC.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app runner and unit tests. Inputs are a DTA item struct
+% and CIC option struct. Output is the stable CIC analysis result struct. No file
+% or UI side effects.
+function A = computeCIC(item, opts)
+    A = cic.core.dispatch("computeCIC", item, opts);
+end

apps/electrochem/cic/+cic/+ops/interp1Safe.m

@@ -0,0 +1,5 @@
+% Expected caller: CIC app plotting helpers. Inputs are vectors x/y and query
+% points. Output mirrors the app-owned safe interpolation helper. No side effects.
+function v = interp1Safe(x, y, xq)
+    v = cic.core.dispatch("interp1Safe", x, y, xq);
+end

apps/electrochem/private/runCICApp.m → apps/electrochem/cic/+cic/+ui/runApp.m

@@ -2,7 +2,7 @@
 % Input is the debug context prepared by the public launcher. Output is the app
 % figure. Side effects are GUI creation, user-driven file I/O, exports,
 % plotting, and debug trace attachment exactly as in the original entrypoint body.
-function fig = runCICApp(debugLog)
+function fig = runApp(debugLog)
 %RUNCICAPP Build and run the app body.
 
     S = struct();
@@ -284,7 +284,7 @@ function analyzeCurrentFile()
         opts.pulseMode = ddPulseMode.Value;
         opts.usedMeasuredCurrent = cbUseMeasuredCurrent.Value;
 
-        A = cicWorkflow("computeCIC", item, opts);
+        A = cic.ops.computeCIC(item, opts);
         item.analysis = A;
         if A.ok
             addLog(sprintf('%s: Emc=%.6f V, Ema=%.6f V, safe=%d', item.name, A.Emc, A.Ema, A.safe));
@@ -344,7 +344,7 @@ function refreshFileList()
 
     function refreshBatchTable()
         [~, unitLabel] = cicDisplayUnit();
-        [C, columnNames] = cicWorkflow("buildBatchTableData", S.items, unitLabel);
+        [C, columnNames] = cic.view.buildBatchTableData(S.items, unitLabel);
         tbl.ColumnName = columnNames;
         if isempty(S.items)
             tbl.Data = cell(0,8);
@@ -386,12 +386,12 @@ function refreshResultsSummary()
         A = it.analysis;
         S.txtDetect.Value = sprintf('%s | %s', A.detectMode, A.detectMsg);
         S.txtDelay.Value = sprintf('%.3f us', 1e6 * A.delay_s);
-        S.txtArea.Value = cicWorkflow("formatMaybeNum", A.area_cm2,'%.8g cm^2');
+        S.txtArea.Value = cic.view.formatMaybeNum(A.area_cm2,'%.8g cm^2');
         S.txtEmc.Value = sprintf('%.6f V @ %.6fus', A.Emc, 1e6*A.t_emc);
         S.txtEma.Value = sprintf('%.6f V @ %.6fus', A.Ema, 1e6*A.t_ema);
-        S.txtQc.Value = cicWorkflow("formatChargeDensity", A.Qc_C, A.CICc_mCcm2, ddCICUnit.Value);
-        S.txtQa.Value = cicWorkflow("formatChargeDensity", A.Qa_C, A.CICa_mCcm2, ddCICUnit.Value);
-        S.txtQt.Value = cicWorkflow("formatChargeDensity", A.Qt_C, A.CICt_mCcm2, ddCICUnit.Value);
+        S.txtQc.Value = cic.view.formatChargeDensity(A.Qc_C, A.CICc_mCcm2, ddCICUnit.Value);
+        S.txtQa.Value = cic.view.formatChargeDensity(A.Qa_C, A.CICa_mCcm2, ddCICUnit.Value);
+        S.txtQt.Value = cic.view.formatChargeDensity(A.Qt_C, A.CICt_mCcm2, ddCICUnit.Value);
         if A.safe
             safeText = 'SAFE';
         else
@@ -505,12 +505,12 @@ function plotOneAxis(ax, A, xChoice, yChoice, showGrid)
         if strcmp(xChoice,'Sample #')
             x = A.pt;
             xlab = 'Sample #';
-            cathStartX = cicWorkflow("interp1Safe", A.t, A.pt, A.pulse.cath_start);
-            cathEndX   = cicWorkflow("interp1Safe", A.t, A.pt, A.pulse.cath_end);
-            anodStartX = cicWorkflow("interp1Safe", A.t, A.pt, A.pulse.anod_start);
-            anodEndX   = cicWorkflow("interp1Safe", A.t, A.pt, A.pulse.anod_end);
-            emcX       = cicWorkflow("interp1Safe", A.t, A.pt, A.t_emc);
-            emaX       = cicWorkflow("interp1Safe", A.t, A.pt, A.t_ema);
+            cathStartX = cic.ops.interp1Safe(A.t, A.pt, A.pulse.cath_start);
+            cathEndX   = cic.ops.interp1Safe(A.t, A.pt, A.pulse.cath_end);
+            anodStartX = cic.ops.interp1Safe(A.t, A.pt, A.pulse.anod_start);
+            anodEndX   = cic.ops.interp1Safe(A.t, A.pt, A.pulse.anod_end);
+            emcX       = cic.ops.interp1Safe(A.t, A.pt, A.t_emc);
+            emaX       = cic.ops.interp1Safe(A.t, A.pt, A.t_ema);
         else
             x = A.t;
             xlab = 'Time (s)';
@@ -530,8 +530,8 @@ function plotOneAxis(ax, A, xChoice, yChoice, showGrid)
             hold(ax,'on');
 
             if cbShowShading.Value
-                cicWorkflow("shadeWindow", ax, cathStartX, cathEndX, [0.85 0.93 1.00]);
-                cicWorkflow("shadeWindow", ax, anodStartX, anodEndX, [1.00 0.92 0.85]);
+                cic.view.shadeWindow(ax, cathStartX, cathEndX, [0.85 0.93 1.00]);
+                cic.view.shadeWindow(ax, anodStartX, anodEndX, [1.00 0.92 0.85]);
             end
 
             if cbShowLimits.Value
@@ -541,14 +541,14 @@ function plotOneAxis(ax, A, xChoice, yChoice, showGrid)
                     'Color',[0.85 0.2 0.2],'LabelHorizontalAlignment','left');
             end
 
-            cicWorkflow("addBaselineYLines", ax, A);
+            cic.view.addBaselineYLines(ax, A);
 
             if cbShowMarkers.Value
                 xline(ax, cathStartX, ':', 'Cath start','Color',[0.2 0.4 0.8]);
                 xline(ax, cathEndX, ':', 'Cath end','Color',[0.2 0.4 0.8]);
                 xline(ax, anodStartX, ':', 'Anod start','Color',[0.8 0.4 0.2]);
                 xline(ax, anodEndX, ':', 'Anod end','Color',[0.8 0.4 0.2]);
-                cicWorkflow("addPaperStyleVTAnnotations", ax, A, xChoice, ...
+                cic.view.addPaperStyleVTAnnotations(ax, A, xChoice, ...
                     cathStartX, cathEndX, anodStartX, anodEndX, emcX, emaX);
             end
             hold(ax,'off');
@@ -566,16 +566,16 @@ function plotOneAxis(ax, A, xChoice, yChoice, showGrid)
             hold(ax,'on');
 
             if cbShowShading.Value
-                cicWorkflow("shadeWindow", ax, cathStartX, cathEndX, [0.85 0.93 1.00]);
-                cicWorkflow("shadeWindow", ax, anodStartX, anodEndX, [1.00 0.92 0.85]);
+                cic.view.shadeWindow(ax, cathStartX, cathEndX, [0.85 0.93 1.00]);
+                cic.view.shadeWindow(ax, anodStartX, anodEndX, [1.00 0.92 0.85]);
             end
 
             if cbShowMarkers.Value
                 xline(ax, cathStartX, ':', 'Cath start','Color',[0.2 0.4 0.8]);
                 xline(ax, cathEndX, ':', 'Cath end','Color',[0.2 0.4 0.8]);
                 xline(ax, anodStartX, ':', 'Anod start','Color',[0.8 0.4 0.2]);
                 xline(ax, anodEndX, ':', 'Anod end','Color',[0.8 0.4 0.2]);
-                cicWorkflow("addPaperStyleITAnnotations", ax, A, xChoice, ...
+                cic.view.addPaperStyleITAnnotations(ax, A, xChoice, ...
                     cathStartX, cathEndX, anodStartX, anodEndX, emcX, emaX);
             end
             hold(ax,'off');
@@ -627,7 +627,7 @@ function exportResultsCSV()
         end
         out = fullfile(p,f);
         [~, unitLabel] = cicDisplayUnit();
-        [ok, msg] = cicWorkflow("writeResultsCSV", S.items, out, unitLabel);
+        [ok, msg] = cic.export.writeResultsCSV(S.items, out, unitLabel);
         if ~ok
             uialert(fig,msg,'Export');
             return;

apps/electrochem/cic/+cic/+view/addBaselineYLines.m

@@ -0,0 +1,5 @@
+% Expected caller: CIC app plotting helpers. Inputs are an axes and CIC result
+% struct. Side effects are limited to drawing baseline guides on the axes.
+function addBaselineYLines(ax, A)
+    cic.core.dispatch("addBaselineYLines", ax, A);
+end

apps/electrochem/cic/+cic/+view/addPaperStyleITAnnotations.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app plotting helpers. Inputs mirror the app-owned IT
+% annotation helper. Side effects are limited to annotating the supplied axes.
+function addPaperStyleITAnnotations(ax, A, xChoice, cathStartX, cathEndX, anodStartX, anodEndX)
+    cic.core.dispatch("addPaperStyleITAnnotations", ax, A, xChoice, ...
+        cathStartX, cathEndX, anodStartX, anodEndX);
+end

apps/electrochem/cic/+cic/+view/addPaperStyleVTAnnotations.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app plotting helpers. Inputs mirror the app-owned VT
+% annotation helper. Side effects are limited to annotating the supplied axes.
+function addPaperStyleVTAnnotations(ax, A, xChoice, cathStartX, cathEndX, anodStartX, anodEndX, emcX, emaX)
+    cic.core.dispatch("addPaperStyleVTAnnotations", ax, A, xChoice, ...
+        cathStartX, cathEndX, anodStartX, anodEndX, emcX, emaX);
+end

apps/electrochem/cic/+cic/+view/buildBatchTableData.m

@@ -0,0 +1,6 @@
+% Expected caller: CIC app runner and unit tests. Inputs are item structs and a
+% display unit label. Outputs are the stable UI table cell data and column names.
+% No file side effects.
+function [C, columnNames] = buildBatchTableData(items, unitLabel)
+    [C, columnNames] = cic.core.dispatch("buildBatchTableData", items, unitLabel);
+end

apps/electrochem/cic/+cic/+view/formatChargeDensity.m

@@ -0,0 +1,5 @@
+% Expected caller: CIC app runner. Inputs are charge, density, and display unit
+% label. Output is the stable read-only UI text. No side effects.
+function txt = formatChargeDensity(charge_C, density_mCcm2, unitLabel)
+    txt = cic.core.dispatch("formatChargeDensity", charge_C, density_mCcm2, unitLabel);
+end

apps/electrochem/cic/+cic/+view/formatMaybeNum.m

@@ -0,0 +1,5 @@
+% Expected caller: CIC app runner. Inputs are a numeric value and sprintf format.
+% Output is the stable UI text for finite or missing values. No side effects.
+function txt = formatMaybeNum(value, fmt)
+    txt = cic.core.dispatch("formatMaybeNum", value, fmt);
+end

apps/electrochem/cic/+cic/+view/shadeWindow.m

@@ -0,0 +1,5 @@
+% Expected caller: CIC app plotting helpers. Inputs are an axes, x-window, and
+% color. Side effects are limited to adding the app-owned patch to the axes.
+function shadeWindow(ax, x1, x2, color)
+    cic.core.dispatch("shadeWindow", ax, x1, x2, color);
+end

apps/electrochem/labkit_CIC_app.m → apps/electrochem/cic/labkit_CIC_app.m

@@ -38,7 +38,7 @@
         error('labkit_CIC_app:TooManyOutputs', 'labkit_CIC_app returns at most the app figure handle.');
     end
 
-    fig = runCICApp(debugLog);
+    fig = cic.ui.runApp(debugLog);
     if nargout >= 1
         varargout{1} = fig;
     end

apps/electrochem/private/cscWorkflow.m → apps/electrochem/csc/+csc/+core/dispatch.m

@@ -1,10 +1,10 @@
-% App-owned CSC workflow helper dispatch. Expected caller: labkit_CSC_app
-% callbacks and workflow tests. Inputs are a command
+% App-owned CSC helper core dispatch. Expected caller: labkit_CSC_app
+% callbacks and package tests. Inputs are a command
 % string plus the original helper arguments; outputs match the selected helper.
 % This helper has no file side effects.
-function varargout = cscWorkflow(command, varargin)
-%CSCWORKFLOW Dispatch app-owned CSC calculation helpers.
-% Expected caller: labkit_CSC_app callbacks and workflow tests. Inputs are a
+function varargout = dispatch(command, varargin)
+%DISPATCH Route CSC package wrapper calls to app-owned helpers.
+% Expected caller: labkit_CSC_app callbacks and package tests. Inputs are a
 % command string plus the original helper arguments.
 % Outputs match the selected helper. This helper has no file side effects.
 

apps/electrochem/csc/+csc/+ops/computeCSC.m

@@ -0,0 +1,6 @@
+% Expected caller: CSC app runner and unit tests. Inputs are a CV/CT curve struct
+% and CSC options. Output is the stable CSC comparison result struct. No file or
+% UI side effects.
+function A = computeCSC(curve, opts)
+    A = csc.core.dispatch("computeCSC", curve, opts);
+end

apps/electrochem/private/runCSCApp.m → apps/electrochem/csc/+csc/+ui/runApp.m

@@ -2,7 +2,7 @@
 % Input is the debug context prepared by the public launcher. Output is the app
 % figure. Side effects are GUI creation, user-driven file I/O, exports,
 % plotting, and debug trace attachment exactly as in the original entrypoint body.
-function fig = runCSCApp(debugLog)
+function fig = runApp(debugLog)
 %RUNCSCAPP Build and run the app body.
 
     S = struct();
@@ -461,7 +461,7 @@ function refreshCompare()
         opts.mode = ddMode.Value;
         opts.scanRate = S.scanRate;
         opts.area_cm2 = edArea.Value;
-        R = cscWorkflow("computeCSC", c, opts);
+        R = csc.ops.computeCSC(c, opts);
 
         if ~R.ok
             txtQct.Value = R.message;

apps/electrochem/labkit_CSC_app.m → apps/electrochem/csc/labkit_CSC_app.m

@@ -37,7 +37,7 @@
 
     % Application state container
 
-    fig = runCSCApp(debugLog);
+    fig = csc.ui.runApp(debugLog);
     if nargout >= 1
         varargout{1} = fig;
     end

apps/electrochem/private/eisWorkflow.m → apps/electrochem/eis/+eis/+core/dispatch.m

@@ -1,10 +1,10 @@
-% App-owned EIS workflow helper dispatch. Expected caller: labkit_EIS_app
-% callbacks and workflow tests. Inputs are a command
+% App-owned EIS helper core dispatch. Expected caller: labkit_EIS_app
+% callbacks and package tests. Inputs are a command
 % string plus the original helper arguments; outputs match the selected helper.
 % This helper has no file side effects.
-function varargout = eisWorkflow(command, varargin)
-%EISWORKFLOW Dispatch app-owned EIS plot/export helpers.
-% Expected caller: labkit_EIS_app callbacks and workflow tests. Inputs are a
+function varargout = dispatch(command, varargin)
+%DISPATCH Route EIS package wrapper calls to app-owned helpers.
+% Expected caller: labkit_EIS_app callbacks and package tests. Inputs are a
 % command string plus the original helper arguments.
 % Outputs match the selected helper. This helper has no file side effects.
 

apps/electrochem/eis/+eis/+export/buildExportTable.m

@@ -0,0 +1,6 @@
+% Expected caller: EIS app runner and export tests. Inputs are EIS item structs,
+% axis labels, and log flags. Output is the stable EIS export table. No file side
+% effects.
+function T = buildExportTable(items, xName, yName, useLogX, useLogY)
+    T = eis.core.dispatch("buildExportTable", items, xName, yName, useLogX, useLogY);
+end

apps/electrochem/eis/+eis/+ops/valuesForAxis.m

@@ -0,0 +1,5 @@
+% Expected caller: EIS app runner and unit tests. Inputs are an EIS item struct
+% and axis label. Output is the selected numeric vector. No side effects.
+function values = valuesForAxis(item, axisName)
+    values = eis.core.dispatch("valuesForAxis", item, axisName);
+end