apply new colorscheme

cypress/e2e/preferences-segmentation-ai.cy.js

@@ -32,7 +32,7 @@ describe('Preferences Modal - Segmentation AI Tab', () => {
 
     // Verify modal is open
     cy.get('[data-testid="preferences-modal"]').should('be.visible');
-    cy.contains('h2', 'Preferences').should('be.visible');
+    cy.get('[data-testid="preferences-modal"]').contains('Preferences').should('be.visible');
 
     // Close preferences and verify
     cy.closePreferences();

cypress/support/commands.js

@@ -76,8 +76,15 @@ Cypress.Commands.add('login', (username = 'admin', password = '123') => {
       cy.get('#register-password').should('be.visible').should('not.be.disabled').clear().type(password);
       cy.get('#register-password-again').should('be.visible').should('not.be.disabled').clear().type(password);
 
-      // Click register and wait for page reload
-      cy.get('.dialogue').contains('button', 'Register').click();
+      // Fill email if the field exists (required by themed LoginForm)
+      cy.get('body').then($body => {
+        if ($body.find('#register-email').length > 0) {
+          cy.get('#register-email').should('be.visible').clear().type(`${username}@test.com`);
+        }
+      });
+
+      // Click register button (works with both legacy .dialogue and themed LoginForm)
+      cy.contains('button', 'Register').click();
 
       // Wait for the page to reload (LoginForm calls window.location.reload())
       cy.url().should('include', '/segmentation');
@@ -99,18 +106,17 @@ Cypress.Commands.add('login', (username = 'admin', password = '123') => {
       cy.get('#login-username').should('be.visible').should('not.be.disabled').clear().type(username);
       cy.get('#login-password').should('be.visible').should('not.be.disabled').clear().type(password);
 
-      // Click login and wait for page reload
-      cy.get('.dialogue').contains('button', 'Login').click();
+      // Click login button (works with both legacy .dialogue and themed LoginForm)
+      cy.contains('button', 'Login').click();
 
       // Wait for the page to reload (LoginForm calls window.location.reload())
       cy.wait(TIMEOUTS.PAGE_LOAD * 3); // Extra time for reload
 
       // Debug: Check if we're still seeing a login dialog
       cy.get('body').then($body => {
-        const $dialogue = $body.find('.dialogue');
-        if ($dialogue.length > 0 && $dialogue.css('display') !== 'none') {
-          cy.log('⚠️ Login dialog still visible after reload - login may have failed');
-          // Take a screenshot for debugging
+        const $loginForm = $body.find('#login-username:visible');
+        if ($loginForm.length > 0) {
+          cy.log('⚠️ Login form still visible after reload - login may have failed');
           cy.screenshot('login-failed-dialog-still-visible');
         }
       });
@@ -147,12 +153,21 @@ Cypress.Commands.add('login', (username = 'admin', password = '123') => {
  */
 Cypress.Commands.add('closeHelpDialogue', () => {
   cy.get('body').then($body => {
+    // Check for themed HelpModal (data-testid="help-modal")
+    const $helpModal = $body.find('[data-testid="help-modal"]');
+    if ($helpModal.length > 0 && $helpModal.is(':visible')) {
+      cy.log('Closing themed help modal...');
+      cy.get('[data-testid="close-help-button"]').click({ force: true });
+      cy.wait(500);
+      cy.get('[data-testid="help-modal"]').should('not.exist');
+      return;
+    }
+    // Fallback: check for legacy #dialogue
     const $dialogue = $body.find('#dialogue');
     if ($dialogue.length > 0 && $dialogue.css('display') !== 'none' && $dialogue.is(':visible')) {
-      cy.log('Closing dialogue...');
-      // Try to find and click the close button
+      cy.log('Closing legacy dialogue...');
       cy.get('#dialogue-close').click({ force: true });
-      cy.wait(500); // Wait for dialogue to close
+      cy.wait(500);
       cy.get('#dialogue').should('not.be.visible');
     }
   });

iris/__init__.py

@@ -1,16 +1,12 @@
 import json
 import os
 import shutil
-import sys
-import webbrowser
 from getpass import getpass
-from os.path import basename, dirname, exists, isabs, join
+from os.path import join
 from pathlib import Path
 from typing import Union
 
 import flask
-import numpy as np
-import yaml
 
 __version__ = "1.0.0"
 
@@ -97,8 +93,8 @@ def handle_launch_command(folder_name: str) -> Path:
 
         try:
             dconfig = json.loads(config_file.read_text(encoding="utf-8"))
-        except json.JSONDecodeError:
-            raise RuntimeError(f"Error: Invalid JSON in {config_file}")
+        except json.JSONDecodeError as err:
+            raise RuntimeError(f"Error: Invalid JSON in {config_file}") from err
         dconfig["name"] = folder_name
         with config_file.open("w", encoding="utf-8") as fp:
             json.dump(dconfig, fp, indent=4)
@@ -271,8 +267,6 @@ def register_extensions(app):
     register_segmentation_blueprints(app)
     from iris.admin import register_admin_blueprints
     register_admin_blueprints(app)
-    from iris.help import help_app
-    app.register_blueprint(help_app, url_prefix="/help")
     from iris.user import register_user_api, user_app
     app.register_blueprint(user_app, url_prefix="/user")
     register_user_api(app)
@@ -285,7 +279,7 @@ def register_extensions(app):
 # Decide whether to parse CLI args. If help is requested or the first token
 # Module-level initialization for when IRIS is imported (not run as CLI)
 # This is used by tests and when importing iris as a library
-from iris.models import Action, User
+from iris.models import Action, User  # noqa: E402, F401
 
 # Create default app for imports/tests
 _default_args = {

iris/main/templates/base.html

@@ -16,7 +16,6 @@
                 'segmentation': {{url_for('segmentation_spa.segmentation_spa')|tojson}},
                 'user': {{url_for('user.index')|tojson}},
                 'admin': {{url_for('admin_spa.admin_spa')|tojson}},
-                'help': {{url_for('help.index')|tojson}},
             },
             'config': null,
             // 'show_dialogue_before_next_image': MIGRATED to React store (segmentationStore)
@@ -27,7 +26,6 @@
             if (window.setApiUrlsInStore && vars.url) {
                 try {
                     window.setApiUrlsInStore(vars.url);
-                    console.log('[IRIS Migration] ✅ API URLs initialized in React store');
                 } catch (error) {
                     console.error('[IRIS Migration] ❌ Failed to initialize API URLs in React store:', error);
                 }

iris/project.py

@@ -47,7 +47,7 @@ def load_from(self, filename):
                 elif filename.endswith('yaml'):
                     self.config = yaml.safe_load(stream)
         except Exception as error:
-            raise Exception('[CONFIG] Error in config file: '+ str(error))
+            raise Exception('[CONFIG] Error in config file: '+ str(error)) from error
 
         # Load default config:
         with open(join(dirname(__file__), "default_config.json")) as stream:
@@ -194,10 +194,10 @@ def _init_paths_and_files(self, filename):
                 regex_images.match(image_path).groups()[0]
                 for image_path in images
             ])
-        except Exception:
+        except Exception as err:
             raise Exception(
                 f'[ERROR] Could not extract id\nfrom path"{image_paths}"\nwith regex "{regex_images}"!'
-            )
+            ) from err
 
 
     def make_absolute(self, path):

iris/segmentation/__init__.py

@@ -1,18 +1,16 @@
 import json
 import os
 import time
-from datetime import datetime, timedelta
+from datetime import datetime
 from glob import glob
-from os.path import basename, dirname, exists, join
-from pprint import pprint
+from os.path import basename, dirname, join
 
 import flask
 import lightgbm as lgb
 import numpy as np
-import yaml
-from scipy.ndimage import convolve, maximum_filter, minimum_filter
+from scipy.ndimage import convolve
 from skimage.filters import sobel
-from skimage.io import imread, imsave
+from skimage.io import imsave
 from skimage.segmentation import felzenszwalb
 from sklearn.metrics import accuracy_score, f1_score, jaccard_score
 from sklearn.model_selection import train_test_split
@@ -28,8 +26,8 @@
 )
 
 # Import SPA and API blueprints
-from .api import api_bp
-from .spa import spa_bp
+from .api import api_bp  # noqa: E402
+from .spa import spa_bp  # noqa: E402
 
 
 def register_segmentation_blueprints(app):
@@ -247,6 +245,10 @@ def load_mask(image_id):
             data.astype(np.uint8).tobytes()
         )
         response.headers.set('Content-Type', 'application/octet-stream')
+        # Prevent browser caching to ensure fresh mask data on each load
+        response.headers.set('Cache-Control', 'no-store, no-cache, must-revalidate, max-age=0')
+        response.headers.set('Pragma', 'no-cache')
+        response.headers.set('Expires', '0')
         return response
     except Exception:
         return flask.make_response("No user mask available!", 404)

iris/segmentation/api.py

@@ -22,7 +22,7 @@ def get_config():
     """Get project configuration as JSON."""
     # Get the full project config
     config = project.config
-    
+
     return flask.jsonify(config)