diff --git a/setup.py b/setup.py
old mode 100755
new mode 100644
index 14183ece7c..211af33177
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@ def main():
                       'trips_offline': ['pykqml'],
                       'reach_offline': ['cython<3', 'pyjnius==1.1.4'],
                       'eidos_offline': ['cython<3', 'pyjnius==1.1.4'],
-                      'hypothesis': ['gilda>=0.10.2'],
+                      'hypothesis': ['gilda>1.0.0'],
                       'geneways': ['stemming', 'nltk<3.6'],
                       'bel': ['pybel>=0.15.0,<0.16.0'],
                       'sbml': ['python-libsbml'],
@@ -28,16 +28,18 @@ def main():
                       'machine': ['pytz', 'tzlocal', 'tweepy', 'pyyaml>=5.1.0',
                                   'click'],
                       'explanation': ['kappy==4.1.2', 'paths-graph'],
-                      'grounding': ['adeft', 'gilda>=0.10.2'],
+                      'grounding': ['adeft', 'gilda>1.0.0'],
                       # AWS interface and database
                       'aws': ['boto3', 'reportlab'],
                       # Utilities
                       'graph': ['pygraphviz'],
                       'plot': ['matplotlib'],
                       'isi': ['nltk<3.6', 'unidecode'],
-                      'api': ['flask<2.0', 'flask_restx<0.4', 'flask_cors',
-                              'docstring-parser', 'gunicorn',
-                              'markupsafe<2.1.0'],
+                      'api': ['flask>=3.0,<4.0',
+                              'flask_restx>=1.3.0',
+                              'flask_cors',
+                              'docstring-parser',
+                              'gunicorn'],
                       # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation
                       # see: https://github.com/gyorilab/adeft/issues/80
                       'sklearn_belief': ['scikit-learn<1.5.0'],