Fix failing builds

.github/workflows/python-package.yml

@@ -19,19 +19,21 @@ jobs:
       matrix:
         # Default builds are on Ubuntu
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', 'pypy-3.10']
+        python-version: ['3.11', '3.12', '3.13', '3.14', 'pypy-3.11']
         include:
           # Also test on macOS and Windows using latest Python 3
           - os: macos-latest
             python-version: 3.x
           - os: windows-latest
             python-version: 3.x
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v7
+      # https://github.com/actions/checkout
       with:
         submodules: 'recursive'
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      # https://github.com/actions/setup-python
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

CHANGELOG.md

@@ -0,0 +1,25 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Changed
+
+- Temporarily skip SynBioHub unit tests to fix failing builds.
+  [449](https://github.com/SynBioDex/pySBOL2/issues/449),
+  [451](https://github.com/SynBioDex/pySBOL2/issues/451)
+- Constrain `packaging` version to `<26.1` to keep using `NegativeInfinity`.
+  [449](https://github.com/SynBioDex/pySBOL2/issues/449),
+  [450](https://github.com/SynBioDex/pySBOL2/issues/450)
+
+## [1.4.1] - 2022-04-14
+
+- Changes were not recorded.
+
+## [1.4.1] - 2022-02-04
+
+- Changes were not recorded.

setup.py

@@ -3,7 +3,7 @@
 setup(name='sbol2',
       version='1.5',
       description='Pure Python implementation of SBOL 2 standard',
-      python_requires='>=3.7',
+      python_requires='>=3.11',
       url='https://github.com/SynBioDex/pySBOL2',
       author='Bryan Bartley',
       author_email='editors@sbolstandard.org',
@@ -36,7 +36,9 @@
             'lxml',
             'requests',
             'urllib3',
-            'packaging>=20.0'
+            # As of August 2026 the code is incompatible with packaging >= 26.1
+            # https://github.com/SynBioDex/pySBOL2/issues/450
+            'packaging<26.1'
       ],
       package_data={'sbol2': ['libSBOLj.jar']},
       tests_require=[

test/test_partshop.py

@@ -1,6 +1,7 @@
 import os
 import unittest
 import json
+
 import requests
 
 import sbol2 as sbol
@@ -23,6 +24,9 @@
 
 
 class TestPartShop(unittest.TestCase):
+
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_pull_00(self):
         # Based on tutorial: https://pysbol2.readthedocs.io/en/latest/repositories.html
         doc = sbol.Document()
@@ -33,6 +37,8 @@ def test_pull_00(self):
         #     print(obj)
         self.assertEqual(3, len(doc))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_pull_01(self):
         # Based on tutorial: https://pysbol2.readthedocs.io/en/latest/repositories.html
         doc = sbol.Document()
@@ -45,6 +51,8 @@ def test_pull_01(self):
         #     print(obj)
         self.assertEqual(7, len(doc))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_pull_02(self):
         # I don't know what this adds over test_pull_01
         # This is a replacement for a previous test whose part was no
@@ -57,6 +65,8 @@ def test_pull_02(self):
         #     print(obj)
         self.assertEqual(1, len(doc))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skip("SynBioHub no longer allows this kind of anonymous access")
     def test_login(self):
         # NOTE: Add /login because login pages may be different
         # depending on what site you're accessing
@@ -73,7 +83,7 @@ def test_login_bad(self):
             self.assertEqual(sbol_error.error_code(),
                              sbol.SBOLErrorCode.SBOL_ERROR_BAD_HTTP_REQUEST)
 
-    @unittest.skipIf(password is None, "No password supplied")
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_submit_00(self):
         RESOURCE = 'https://synbiohub.utah.edu'
         doc = sbol.Document()
@@ -86,6 +96,8 @@ def test_submit_00(self):
         response = ps.submit(doc, overwrite=1)
         self.assertEqual(response.status_code, 200)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skip("SynBioHub no longer allows this kind of anonymous access")
     def test_sparqlQuery_00(self):
         ps = sbol.PartShop(TEST_RESOURCE_MAIN)
         response = ps.login('johndoe', 'test')
@@ -148,7 +160,7 @@ def test_spoof(self):
         part_shop.spoof(spoofed_url)
         self.assertEqual(part_shop.getSpoofedURL(), spoofed_url)
 
-    @unittest.skipIf(password is None, "No password supplied")
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_submit(self):
         # This test is derived from an etl-to-synbiohub_pipeline test
         # case that was failing.
@@ -217,7 +229,7 @@ def test_uri2url_spoofed(self):
         else:
             self.fail('Expected SBOLError')
 
-    @unittest.skipIf(password is None, "No password supplied")
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_attach_file(self):
         sbol2.Config.setOption('sbol_typed_uris', False)
         doc = sbol2.Document()
@@ -267,6 +279,8 @@ def test_attach_file(self):
         e = cm.exception
         self.assertEqual(e.error_code(), sbol2.SBOLErrorCode.SBOL_ERROR_NOT_FOUND)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_search_general(self):
         sbh = sbol2.PartShop(TEST_RESOURCE_MAIN)
         # sbh.login(username, password)
@@ -277,6 +291,8 @@ def test_search_general(self):
         self.assertTrue(all([isinstance(x, sbol2.Identified)
                              for x in results]))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_search_general_offset_limit(self):
         # Test a general search using offset and limit
         # This comes from a documentation example that was failing
@@ -294,6 +310,8 @@ def test_search_general_offset_limit(self):
         self.assertTrue(all([isinstance(x, sbol2.Identified)
                              for x in results]))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_search_exact(self):
         igem = sbol.PartShop(TEST_RESOURCE_MAIN)
         limit = 10
@@ -314,6 +332,8 @@ def test_search_exact(self):
         for cd in doc.componentDefinitions:
             self.assertIn(sbol2.SO_PROMOTER, cd.roles)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_pull_doc_version(self):
         # After a pull the document version was erroneously set to None (#281)
         doc = sbol.Document()
@@ -325,6 +345,8 @@ def test_pull_doc_version(self):
         self.assertIsNotNone(doc.version)
         self.assertEqual(old_version, doc.version)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_search_count(self):
         part_shop = sbol2.PartShop('https://synbiohub.org/public/igem')
         # searchCount did not exist, see #322

test/test_searchquery.py

@@ -1,10 +1,20 @@
+import os
 import unittest
 
 import sbol2
 
 
 GSOC_SBH_URL = 'https://synbiohub.org'
 
+if 'SBH_USER' in os.environ:
+    username = os.environ['SBH_USER']
+else:
+    username = None
+if 'SBH_PASSWORD' in os.environ:
+    password = os.environ['SBH_PASSWORD']
+else:
+    password = None
+
 
 class TestSearchQuery(unittest.TestCase):
 
@@ -14,6 +24,8 @@ def test_search_query1(self):
         self.assertIn(sbol2.SBOL_TYPES, query.properties)
         self.assertEqual(sbol2.BIOPAX_DNA, query[sbol2.SBOL_TYPES])
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_1_title(self):
         # See issue #240
         collection = 'https://synbiohub.org/public/igem/igem_collection/1'
@@ -34,6 +46,8 @@ def test_gsoc_example_1_title(self):
         names = [r.name == title for r in response]
         self.assertTrue(all(names))
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_1_display_id(self):
         # See issue #240
         collection = 'https://synbiohub.org/public/igem/igem_collection/1'
@@ -76,6 +90,8 @@ def do_gsoc_search(self, collection, term):
         results.extend(self.gsoc_search_display_id(part_shop, collection, term))
         return results
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_2(self):
         # Looking for: https://synbiohub.org/public/igem/BBa_R0010/1
         #              and/or https://synbiohub.org/public/igem/BBa_C0012/1
@@ -93,6 +109,8 @@ def test_gsoc_example_2(self):
         self.assertNotIn('https://synbiohub.org/public/igem/BBa_S03334/1', identities)
         self.assertNotIn('https://synbiohub.org/public/igem/BBa_K1444015/1', identities)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_3(self):
         # Looking for: https://synbiohub.org/public/igem/BBa_R0010/1
         # Collection: https://synbiohub.org/public/igem/igem_collection/1
@@ -107,6 +125,8 @@ def test_gsoc_example_3(self):
         self.assertNotIn('https://synbiohub.org/public/igem/BBa_S03334/1', identities)
         self.assertNotIn('https://synbiohub.org/public/igem/BBa_K1444015/1', identities)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_4(self):
         # Looking for: https://synbiohub.org/public/igem/BBa_B0034/1
         # Collection: https://synbiohub.org/public/igem/igem_collection/1
@@ -119,6 +139,8 @@ def test_gsoc_example_4(self):
         self.assertIn('https://synbiohub.org/public/igem/BBa_B0034/1', identities)
         self.assertNotIn('https://synbiohub.org/public/igem/BBa_I13617/1', identities)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_example_5(self):
         # Looking for: https://synbiohub.org/public/bsu/BO_28874/1
         # Collection: https://synbiohub.org/public/bsu/bsu_collection/1
@@ -132,6 +154,8 @@ def test_gsoc_example_5(self):
         self.assertIn('https://synbiohub.org/public/bsu/BO_28874/1', identities)
         self.assertNotIn('https://synbiohub.org/public/bsu/BO_26604/1', identities)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skipIf(password is None, "No SynBioHub password supplied")
     def test_gsoc_count_5(self):
         part_shop = sbol2.PartShop(GSOC_SBH_URL)
         query = sbol2.SearchQuery()

test/test_tutorial.py

@@ -119,6 +119,8 @@ def create_new_device(self, doc: sbol2.Document):
         my_device.compile()
         self.assertEqual(expected_sequence, my_device.sequence.elements)
 
+    # https://github.com/SynBioDex/pySBOL2/issues/451
+    @unittest.skip("SynBioHub no longer allows anonymous access")
     def test_tutorial(self):
         doc = self.init_tutorial()
         self.get_device_from_xml(doc)