Refactor and standardize dependency management

.github/workflows/generate-requirements-txt.yml

@@ -0,0 +1,52 @@
+name: Generate requirements.txt from manifest
+
+on:
+  push:
+    paths:
+      - 'code/dependencies.nansen.json'
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+
+jobs:
+  generate-requirements:
+    name: Regenerate requirements.txt
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          ssh-key: ${{ secrets.DEPLOY_KEY }}
+
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v2
+
+      - name: Add toolbox code to path and generate requirements.txt
+        uses: matlab-actions/run-command@v2
+        with:
+          command: |
+            addpath(genpath('code'));
+            addpath(genpath('tools'));
+            nansentools.generateRequirementsTxt( ...
+                fullfile(pwd, 'dependencies.nansen.json'), ...
+                fullfile(pwd, 'requirements.txt'));
+
+      - name: Check for changes
+        id: check-changes
+        run: |
+          if git diff --quiet requirements.txt; then
+            echo "changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "changed=true" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Commit and push updated requirements.txt
+        if: steps.check-changes.outputs.changed == 'true'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add requirements.txt
+          git commit -m "Auto-generate requirements.txt from manifest [skip ci]"
+          git push

code/+nansen/+app/+tutorial/loadProject.m

@@ -35,22 +35,26 @@
     error('User canceled.')
 end
 
+% We need the addonmanager to ensure all tutorial dependencies are installed
+addonManager = nansen.AddonManager();
+
 if startsWith(S(selection), 'Allen Brain Observatory')
-    addonManager = nansen.AddonManager();
 
     names = {addonManager.AddonList.Name};
     S = addonManager.AddonList(strcmp(names, "Brain Observatory Toolbox"));
     if ~S.IsInstalled
         fprintf('Downloading %s...', S.Name)
         addonManager.downloadAddon(S.Name)
-        addonManager.addAddonToMatlabPath(S.Name)
         fprintf('Finished.\n')
     end
+
 elseif startsWith(S(selection), 'Nansen - Two-photon Quickstart')
     warnState = warning('off', 'MATLAB:RMDIR:RemovedFromPath');
     warnCleanup = onCleanup(@() warning(warnState));
+
     disp('Installing two-photon addons...')
-    nansen.internal.setup.installAddons()
+    addonManager.installMissingAddons('nansen.module.ophys.twophoton')
+
     % Some users had problems where Yaml was not added to java path
     nansen.internal.setup.addYamlJarToJavaClassPath
 end

code/+nansen/+common/suppressWarning.m

@@ -0,0 +1,14 @@
+function warningCleanupObj = suppressWarning(warningId)
+% suppressWarning - Temporarily suppress warning with given warning id
+%
+% Example usage:
+%
+%   warningIdentifier = 'MATLAB:callback:error';
+%   warningCleanup = nansen.common.suppressWarning(warningIdentifier); %#ok<NASGU>
+
+    arguments
+        warningId (1,:) char
+    end
+    warnState = warning('off', warningId);
+    warningCleanupObj = onCleanup(@() warning(warnState));
+end