Release v4.3.0 (#253)

* remove support for 3.7, add support for 3.11+ * update version, add changelog for v4.3 * update ci * lint * update action versions to latest * fix test for 3.12
Sage-Bionetworks · Nov 30, 2023 · 12645f2 · 12645f2
1 parent ecdf702
commit 12645f2
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diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -15,11 +15,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4.7.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -59,7 +59,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: psf/black@stable
 
   finish-coveralls:

diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml
@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4.7.1
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/.github/workflows/sphinx-ghpages.yaml b/.github/workflows/sphinx-ghpages.yaml
@@ -7,14 +7,14 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # Standard drop-in approach that should work for most people.
       - uses: ammaraskar/sphinx-action@master
         with:
           docs-folder: "docs/"
       # Great extra actions to compose with:
       # Create an artifact of the html output.
-      - uses: actions/upload-artifact@v1
+      - uses: actions/upload-artifact@v3.1.3
         with:
           name: DocumentationHTML
           path: docs/_build/html/

diff --git a/challengeutils/__main__.py b/challengeutils/__main__.py
@@ -469,16 +469,15 @@ def build_parser():
 
     parser_create_portal_challenge = subparsers.add_parser(
         "create-portal-challenge",
-        help="Create a Sage Challenge Portal challenge from template"
+        help="Create a Sage Challenge Portal challenge from template",
     )
     parser_create_portal_challenge.add_argument("challenge_name", help="Challenge name")
     parser_create_portal_challenge.add_argument(
         "-t",
         "--tasks_count",
-        type=int, default=1,
-        help=(
-            "Number of challenge tasks (default: 1)"
-        ),
+        type=int,
+        default=1,
+        help=("Number of challenge tasks (default: 1)"),
     )
     parser_create_portal_challenge.add_argument(
         "--livesiteid",

diff --git a/challengeutils/__version__.py b/challengeutils/__version__.py
@@ -1 +1 @@
-__version__ = "4.2.1"
+__version__ = "4.3.0"
diff --git a/challengeutils/create_portal_challenge.py b/challengeutils/create_portal_challenge.py
@@ -27,7 +27,7 @@
 PORTAL_TABLE = "syn51476218"
 CHALLENGE_TEMPLATE_SYNID = "syn52941681"
 TABLE_TEMPLATE_SYNID = "syn52955244"
-CHALLENGE_ROLES = ['organizer', 'contributor', 'sponsor']
+CHALLENGE_ROLES = ["organizer", "contributor", "sponsor"]
 TASK_WIKI_ID = "624554"
 
 
@@ -228,9 +228,10 @@ def create_organizer_tables(syn, project_id):
     logger.info(" Creating tables...")
     view_ids = {}
     schema = synapseclient.Schema(
-        name='Organizing Team',
+        name="Organizing Team",
         columns=syn.getColumns(TABLE_TEMPLATE_SYNID),
-        parent=project_id)
+        parent=project_id,
+    )
     table = synapseclient.Table(schema, [[]])
 
     # FIXME: for some reason, storing the table will then call on the
@@ -241,11 +242,11 @@ def create_organizer_tables(syn, project_id):
     # FIXME: due to the issue above, we are not able to create the
     #        MaterializedViews
     for role in CHALLENGE_ROLES:
-        role_title = role.title() + 's'
+        role_title = role.title() + "s"
         view = synapseclient.MaterializedViewSchema(
             name=role_title,
             parent=project_id,
-            definingSQL=f"SELECT * FROM {table.id} WHERE challengeRole HAS ('{role}')"
+            definingSQL=f"SELECT * FROM {table.id} WHERE challengeRole HAS ('{role}')",
         )
         view = syn.store(view)
         view_ids[role_title] = view.id
@@ -265,10 +266,7 @@ def create_data_folders(syn, project_id, tasks_count):
     folder_ids = {}
     for i in range(0, tasks_count):
         folder_name = f"Task {i + 1}"
-        folder = synapseclient.Folder(
-            name=folder_name,
-            parent=project_id
-        )
+        folder = synapseclient.Folder(name=folder_name, parent=project_id)
         folder = syn.store(folder)
         folder_ids[i] = folder.id
         logger.info(f"    Folder created: {folder.name} ({folder.id}) ✔")
@@ -286,16 +284,16 @@ def create_annotations(syn, project_id, table_ids, folder_ids):
 
     # For annotations we do currently know, add their values.
     main_wiki_id = [
-        wiki.get('id')
+        wiki.get("id")
         for wiki in syn.getWikiHeaders(project_id)
-        if not wiki.get('parentId')
+        if not wiki.get("parentId")
     ][0]
-    project['Overview'] = f"{project_id}/wiki/{main_wiki_id}"
-    project['Abstract'] = "More challenge information coming soon!"
+    project["Overview"] = f"{project_id}/wiki/{main_wiki_id}"
+    project["Abstract"] = "More challenge information coming soon!"
     # # for role, synid in table_ids.items():
     # #     annots[role] = synid
     for i, synid in folder_ids.items():
-        project[f'Task_{i + 1}.DataFolder'] = synid
+        project[f"Task_{i + 1}.DataFolder"] = synid
     project = syn.store(project)
     logger.info("    Annotations creation complete ✔")
     return project
@@ -391,24 +389,24 @@ def main(syn, challenge_name, tasks_count, live_site=None):
 
     # Create another Task tab per task.
     task_wikis = [
-        wiki.get('title')
+        wiki.get("title")
         for wiki in syn.getWikiHeaders(CHALLENGE_TEMPLATE_SYNID)
-        if wiki.get('parentId') == TASK_WIKI_ID
+        if wiki.get("parentId") == TASK_WIKI_ID
     ]
     for i in range(1, tasks_count):
         new_task_tab = synapseclient.Wiki(
             title=f"Task {i + 1} (tab)",
             owner=project_staging.id,
             markdown="This page can be left empty - it will not appear on the portal.",
-            parentWikiId=syn.getWiki(project_staging.id).id
+            parentWikiId=syn.getWiki(project_staging.id).id,
         )
         new_task_tab = syn.store(new_task_tab)
         for wiki_title in task_wikis:
             task_subwiki = synapseclient.Wiki(
                 title=wiki_title,
                 owner=project_staging.id,
                 markdown="Refer to the Task 1 tab for examples",
-                parentWikiId=new_task_tab.id
+                parentWikiId=new_task_tab.id,
             )
             syn.store(task_subwiki)
 

diff --git a/docs/about/changelog.rst b/docs/about/changelog.rst
@@ -8,6 +8,12 @@ For older releases, visit the `GitHub releases`_.
 
 .. _Github releases: https://github.com/Sage-Bionetworks/challengeutils/releases
 
+v4.3.0
+------
+- Remove support for Python 3.7
+- Add support for Python 3.11 and 3.12
+- New feature added: `create-portal-challenge` - which will create a challenge on the new [Sage Challenge Portal (staging)](https://staging.challenges.synapse.org/)
+
 v4.2.1
 ------
 - Bug fix for `validate-project`

diff --git a/docs/conf.py b/docs/conf.py
@@ -25,7 +25,7 @@
 author = "Thomas Yu, Verena Chung, Tim Bergquist"
 
 # The short X.Y version
-version = "4.2.1"
+version = "4.3.0"
 # The full version, including alpha/beta/rc tags
 release = version
 

diff --git a/setup.cfg b/setup.cfg
@@ -13,10 +13,11 @@ platforms = any
 classifiers =
     Development Status :: 5 - Production/Stable
     Programming Language :: Python
-    Programming Language :: Python :: 3.7
     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
     Operating System :: MacOS
     Operating System :: Microsoft :: Windows
     Operating System :: Unix
@@ -41,7 +42,7 @@ install_requires =
     tabulate>=0.9.0
     jellyfish>=0.9.0
     scipy>=1.7.0
-python_requires = >3.6, <3.11
+python_requires = >3.7, <=3.12
 include_package_data = True
 zip_safe = False
 scripts =

diff --git a/tests/test_processor.py b/tests/test_processor.py
@@ -80,9 +80,9 @@ def test_abc_class():
     with pytest.raises(
         TypeError,
         match="Can't instantiate abstract class "
-        "EvaluationQueueProcessor with "
-        "abstract methods interaction_func, "
-        "notify",
+        r"EvaluationQueueProcessor with.* "
+        r"abstract methods '?interaction_func'?, "
+        r"'?notify'?",
     ):
         EvaluationQueueProcessor(SYN, EVALUATION)