Fix CI (#169)

Closes #168

.github/workflows/ci.yml

@@ -42,7 +42,7 @@ jobs:
     strategy:
       fail-fast: false # Try to work around ECS errors
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         language: python
@@ -18,12 +18,12 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/ambv/black
-    rev: 24.4.2
+    rev: 24.10.0
     hooks:
       - id: black
         language: python
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         language: python
@@ -35,7 +35,7 @@ repos:
           - mccabe
           - yesqa
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.11.1'
+    rev: 'v1.12.0'
     hooks:
       - id: mypy
         additional_dependencies:

HISTORY.md

@@ -5,7 +5,7 @@
   - Removed the retina endpoints
   - Migrated to use Pydantic models for request and response validation
   - Removed support for Python 3.8
-  - Added support for Python 3.12
+  - Added support for Python 3.12 and 3.13
 
 ## 0.12.0 (2023-02-20)
 

pyproject.toml

@@ -53,14 +53,15 @@ xfail_strict = true
 legacy_tox_ini = """
 [tox]
 isolated_build = True
-envlist = py39, py310, py311, py312
+envlist = py39, py310, py311, py312, py313
 
 [gh-actions]
 python =
     3.9: py39
     3.10: py310
     3.11: py311
     3.12: py312
+    3.13: py313
 
 [testenv]
 allowlist_externals =

tests/async_integration_tests.py

@@ -326,12 +326,12 @@ async def get_download():
     "algorithm,interface,files",
     (
         (
-            "test-algorithm-evaluation-image-1",
+            "test-algorithm-evaluation-image-0",
             "generic-medical-image",
             ["image10x10x101.mha"],
         ),
         # TODO this algorithm was removed from the test fixtures
-        # ("test-algorithm-evaluation-file-1", "json-file", ["test.json"]),
+        # ("test-algorithm-evaluation-file-0", "json-file", ["test.json"]),
     ),
 )
 @pytest.mark.anyio
@@ -358,11 +358,9 @@ async def run_job():
         # algorithm might not be ready yet
         job = await run_job()
 
-        assert job["status"] == "Queued"
-        assert len(job["inputs"]) == 1
-
+        assert job["status"] == "Validating inputs"
         job = await c.algorithm_jobs.detail(job["pk"])
-        assert job.status in {"Queued", "Started"}
+        assert job.status in {"Validating inputs", "Queued", "Started"}
 
 
 @pytest.mark.parametrize(
@@ -395,7 +393,7 @@ async def test_get_algorithm_by_slug(local_grand_challenge):
         token=DEMO_PARTICIPANT_TOKEN,
     ) as c:
         by_slug = await c.algorithms.detail(
-            slug="test-algorithm-evaluation-image-1"
+            slug="test-algorithm-evaluation-image-0"
         )
         by_pk = await c.algorithms.detail(pk=by_slug.pk)
 
@@ -577,8 +575,11 @@ async def get_archive_detail():
 
         item_updated = await get_archive_detail()
 
-        json_civ = item_updated.values[-1]
-        assert json_civ.interface.slug == "results-json-file"
+        json_civ = [
+            civ
+            for civ in item_updated.values
+            if civ.interface.slug == "results-json-file"
+        ][0]
         assert json_civ.value == {"foo": 0.5}
         updated_civ_count = len(item_updated.values)
 
@@ -600,8 +601,11 @@ async def get_updated_archive_detail():
         item_updated_again = await get_updated_archive_detail()
 
         assert len(item_updated_again.values) == updated_civ_count
-        new_json_civ = item_updated_again.values[-1]
-        assert new_json_civ.interface.slug == "results-json-file"
+        new_json_civ = [
+            civ
+            for civ in item_updated_again.values
+            if civ.interface.slug == "results-json-file"
+        ][0]
         assert new_json_civ.value == {"foo": 0.8}
 
 

tests/integration_tests.py

@@ -281,13 +281,13 @@ def get_download():
     "algorithm,interface,files",
     (
         (
-            "test-algorithm-evaluation-image-1",
+            "test-algorithm-evaluation-image-0",
             "generic-medical-image",
             ["image10x10x101.mha"],
         ),
         # TODO this algorithm was removed from the test fixtures
         # (
-        #    "test-algorithm-evaluation-file-1",
+        #    "test-algorithm-evaluation-file-0",
         #    "json-file",
         #    ["test.json"],
         # ),
@@ -316,10 +316,9 @@ def run_job():
     # algorithm might not be ready yet
     job = run_job()
 
-    assert job["status"] == "Queued"
-    assert len(job["inputs"]) == 1
+    assert job["status"] == "Validating inputs"
     job = c.algorithm_jobs.detail(job["pk"])
-    assert job.status in {"Queued", "Started"}
+    assert job.status in {"Validating inputs", "Queued", "Started"}
 
 
 def test_get_algorithm_by_slug(local_grand_challenge):
@@ -329,7 +328,7 @@ def test_get_algorithm_by_slug(local_grand_challenge):
         token=DEMO_PARTICIPANT_TOKEN,
     )
 
-    by_slug = c.algorithms.detail(slug="test-algorithm-evaluation-image-1")
+    by_slug = c.algorithms.detail(slug="test-algorithm-evaluation-image-0")
     by_pk = c.algorithms.detail(pk=by_slug.pk)
 
     assert by_pk == by_slug
@@ -496,8 +495,11 @@ def get_archive_item_detail():
 
     item_updated = get_archive_item_detail()
 
-    json_civ = item_updated.values[-1]
-    assert json_civ.interface.slug == "results-json-file"
+    json_civ = [
+        civ
+        for civ in item_updated.values
+        if civ.interface.slug == "results-json-file"
+    ][0]
     assert json_civ.value == {"foo": 0.5}
     updated_civ_count = len(item_updated.values)
 
@@ -517,8 +519,11 @@ def get_updated_archive_item_detail():
     item_updated_again = get_updated_archive_item_detail()
 
     assert len(item_updated_again.values) == updated_civ_count
-    new_json_civ = item_updated_again.values[-1]
-    assert new_json_civ.interface.slug == "results-json-file"
+    new_json_civ = [
+        civ
+        for civ in item_updated_again.values
+        if civ.interface.slug == "results-json-file"
+    ][0]
     assert new_json_civ.value == {"foo": 0.8}
 
 

tests/scripts/create_test_fixtures.py

@@ -1,4 +1,3 @@
-import base64
 import gzip
 import logging
 import os
@@ -11,7 +10,6 @@
 from django.conf import settings
 from django.contrib.auth import get_user_model
 from django.contrib.auth.models import Group, Permission
-from django.core.exceptions import ObjectDoesNotExist
 from django.core.files.base import ContentFile
 from django.db import IntegrityError
 from grandchallenge.algorithms.models import Algorithm, AlgorithmImage
@@ -24,12 +22,7 @@
     ComponentInterfaceValue,
 )
 from grandchallenge.core.fixtures import create_uploaded_image
-from grandchallenge.evaluation.models import (
-    Evaluation,
-    Method,
-    Phase,
-    Submission,
-)
+from grandchallenge.evaluation.models import Method, Phase
 from grandchallenge.evaluation.utils import SubmissionKindChoices
 from grandchallenge.invoices.models import Invoice
 from grandchallenge.reader_studies.models import (
@@ -73,7 +66,6 @@ def run():
         raise RuntimeError("Fixtures already initialized") from e
 
     _set_user_permissions(users)
-    _create_demo_challenge(users=users)
     _create_reader_studies(users)
     _create_archive(users)
     _create_user_tokens(users)
@@ -153,72 +145,6 @@ def _set_user_permissions(users):
     users["demo"].user_permissions.add(add_archive_perm)
 
 
-def _create_demo_challenge(users):
-    demo = Challenge.objects.create(
-        short_name="demo",
-        description="Demo Challenge",
-        creator=users["demo"],
-        hidden=False,
-        display_forum_link=True,
-    )
-    demo.add_participant(users["demop"])
-
-    phase = Phase.objects.create(challenge=demo, title="Phase 1")
-
-    phase.score_title = "Accuracy ± std"
-    phase.score_jsonpath = "acc.mean"
-    phase.score_error_jsonpath = "acc.std"
-    phase.extra_results_columns = [
-        {
-            "title": "Dice ± std",
-            "path": "dice.mean",
-            "error_path": "dice.std",
-            "order": "desc",
-        }
-    ]
-
-    phase.submission_kind = SubmissionKindChoices.ALGORITHM
-    phase.save()
-
-    method = Method(phase=phase, creator=users["demo"])
-
-    with _gc_demo_algorithm() as container:
-        method.image.save("algorithm_io.tar", container)
-
-    submission = Submission(phase=phase, creator=users["demop"])
-    content = ContentFile(base64.b64decode(b""))
-    submission.predictions_file.save("test.csv", content)
-    submission.save()
-
-    e = Evaluation.objects.create(
-        submission=submission,
-        method=method,
-        status=Evaluation.SUCCESS,
-        time_limit=300,
-    )
-
-    def create_result(evaluation, result: dict):
-        interface = ComponentInterface.objects.get(slug="metrics-json-file")
-
-        try:
-            output_civ = evaluation.outputs.get(interface=interface)
-            output_civ.value = result
-            output_civ.save()
-        except ObjectDoesNotExist:
-            output_civ = ComponentInterfaceValue.objects.create(
-                interface=interface, value=result
-            )
-            evaluation.outputs.add(output_civ)
-
-    create_result(
-        e,
-        {
-            "acc": {"mean": 0, "std": 0.1},
-            "dice": {"mean": 0.71, "std": 0.05},
-        },
-    )
-
-
 def _create_reader_studies(users):
     reader_study = ReaderStudy.objects.create(
         title="Reader Study",

tests/test_gcapi.py

@@ -1,6 +1,5 @@
 import pytest
 from click.testing import CliRunner
-from httpx import HTTPStatusError
 
 from gcapi import Client, cli
 from tests.utils import ADMIN_TOKEN
@@ -114,10 +113,3 @@ def test_command_line_interface():
     help_result = runner.invoke(cli.main, ["--help"])
     assert help_result.exit_code == 0
     assert "--help  Show this message and exit." in help_result.output
-
-
-def test_ground_truth_url():
-    c = Client(token="foo", base_url="https://example.com/api/v1/")
-    with pytest.raises(HTTPStatusError) as exc_info:
-        c.reader_studies.ground_truth("fake", "image_pk")
-    assert exc_info.value.request.url.path.endswith("image_pk/")