bringing compatibility with python 3.12.4 by reviewing requirements.t…

…xt and setup

isatools/database/models/relationships.py

@@ -1,4 +1,4 @@
-from sqlalchemy import Column, ForeignKey, Integer
+from sqlalchemy import Column, ForeignKey
 
 from isatools.database.utils import Base, Table
 
@@ -250,4 +250,4 @@
     Column("person_id", ForeignKey("person.person_id"), primary_key=True),
     Column("role_id", ForeignKey("ontology_annotation.ontology_annotation_id"), primary_key=True),
     comment="Many to many relationship between Persons and Roles (Ontology Annotations)"
-)
+)

requirements.txt

@@ -1,33 +1,33 @@
 graphene==3.1.1
 graphql-core==3.2.3
-wheel~=0.36.2
-setuptools~=57.1.0
-numpy~=1.23.3
-jsonschema~=4.18.4
+wheel~=0.43.0
+setuptools~=71.0.4
+numpy~=1.26
+jsonschema~=4.23.0
 pandas==1.5.0
-openpyxl>=2.5.0
-networkx~=2.5.1
-lxml~=4.9.1
-requests~=2.25.1
-iso8601~=0.1.14
-chardet~=4.0.0
-jinja2~=3.0.1
-beautifulsoup4~=4.9.3
+openpyxl>=3.1.5
+networkx~=3.3
+lxml~=5.2.2
+requests~=2.32.3
+iso8601~=2.1.0
+chardet~=5.2.0
+jinja2~=3.1.4
+beautifulsoup4~=4.12.3
 mzml2isa==1.1.1
-biopython~=1.79
-progressbar2~=3.53.1
-deepdiff~=5.5.0
+biopython~=1.84
+progressbar2~=4.4.2
+deepdiff~=7.0.1
 PyYAML~=6.0.1
-bokeh~=2.3.2
-certifi==2021.5.30
-flake8==3.9.2
-ddt==1.4.2
+bokeh~=3.5.0
+certifi==2024.7.4
+flake8==7.1.0
+ddt==1.7.2
 behave==1.2.6
-httpretty==1.1.3
-sure==2.0.0
-coveralls~=3.1.0
-rdflib~=6.0.2
-SQLAlchemy~=1.4.42
-python-dateutil~=2.8.1
-Flask~=2.2.2
+httpretty==1.1.4
+sure==2.0.1
+coveralls~=4.0.1
+rdflib~=7.0.0
+SQLAlchemy~=1.4.52 #2.0.31
+python-dateutil~=2.9.0.post0
+Flask~=3.0.3
 flask_sqlalchemy~=3.0.2

setup.py

@@ -69,38 +69,42 @@ def read(f_name):
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     install_requires=[
         'graphene==3.1.1',
         'graphql-core==3.2.3',
-        'wheel~=0.36.2',
-        'setuptools~=57.1.0',
-        'numpy~=1.23.3',
-        'jsonschema~=4.18.4',
+        'wheel~=0.43.0',
+        'setuptools~=71.0.4',
+        'numpy~=1.26.0',
+        'jsonschema~=4.23.0',
         'pandas==1.5.0',
-        'openpyxl>=2.5.0',
-        'networkx~=2.5.1',
-        'lxml~=4.9.1',
-        'requests~=2.25.1',
-        'iso8601~=0.1.14',
-        'chardet~=4.0.0',
-        'jinja2~=3.0.1',
-        'beautifulsoup4~=4.9.3',
+        'openpyxl>=3.1.5',
+        'networkx~=3.3',
+        'lxml~=5.2.2',
+        'requests~=2.32.3',
+        'iso8601~=2.1.0',
+        'chardet~=5.2.0',
+        'jinja2~=3.1.4',
+        'beautifulsoup4~=4.12.3',
         'mzml2isa==1.1.1',
-        'biopython~=1.79',
-        'progressbar2~=3.53.1',
-        'deepdiff~=5.5.0',
+        'biopython~=1.84',
+        'progressbar2~=4.4.2',
+        'deepdiff~=7.0.1',
         'PyYAML~=6.0.1',
-        'bokeh~=2.3.2',
-        'certifi==2021.5.30',
-        'flake8==3.9.2',
-        'ddt==1.4.2',
+        'bokeh~=3.5.0',
+        'certifi==2024.7.4',
+        'flake8==7.1.0',
+        'ddt==1.7.2',
         'behave==1.2.6',
-        'httpretty==1.1.3',
-        'sure==2.0.0',
-        'coveralls~=3.1.0',
-        'rdflib~=6.0.2',
-        'Flask~=2.2.2',
+        'httpretty==1.1.4',
+        'sure==2.0.1',
+        'coveralls~=4.0.1',
+        'rdflib~=7.0.0',
+        'SQLAlchemy~=1.4.52',
+        'python-dateutil~=2.9.0.post0',
+        'Flask~=3.0.3',
         'flask_sqlalchemy~=3.0.2'
     ],
     test_suite='tests'