Merge pull request #642 from aiidalab/backport-scikit-bump

Backport to 2.2.x: Support and test with py3.11 (#619)

.github/workflows/ci.yml

@@ -7,8 +7,11 @@ on:
     push:
         branches:
             - main
+            - support/*
     pull_request:
 
+env:
+    FORCE_COLOR: "1"
 
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
@@ -23,10 +26,11 @@ jobs:
         strategy:
             matrix:
                 browser: [Chrome, Firefox]
-                aiida-core-version: [2.1.2, 2.4.3]          # test on the latest and the oldest supported version
+                # test on the latest and the oldest supported version
+                aiida-core-version: [2.1.2, 2.6.3]
             fail-fast: false
 
-        runs-on: ubuntu-latest
+        runs-on: ubuntu-22.04
         timeout-minutes: 30
 
         steps:
@@ -82,12 +86,12 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.9', '3.10']
+                python-version: ['3.9', '3.11']
                 # Test on the latest and oldest supported version
-                aiida-core-version: [2.2.2, 2.4.3]
+                aiida-core-version: [2.2.2, 2.6.3]
             fail-fast: false
 
-        runs-on: ubuntu-latest
+        runs-on: ubuntu-24.04
         timeout-minutes: 30
         services:
             rabbitmq:

.github/workflows/publish.yml

@@ -17,7 +17,7 @@ jobs:
     build:
 
         name: Build package
-        runs-on: ubuntu-latest
+        runs-on: ubuntu-24.04
 
         steps:
 
@@ -52,7 +52,7 @@ jobs:
         if: github.repository_owner == 'aiidalab'
 
         needs: [build]
-        runs-on: ubuntu-latest
+        runs-on: ubuntu-24.04
 
         environment:
             name: Test PyPI
@@ -79,7 +79,7 @@ jobs:
         if: startsWith(github.ref, 'refs/tags/v') && github.repository_owner == 'aiidalab'
 
         needs: [build, publish-test]
-        runs-on: ubuntu-latest
+        runs-on: ubuntu-24.04
 
         environment:
             name: PyPI

pyproject.toml

@@ -7,8 +7,16 @@ build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]
 filterwarnings = [
-    'error',
-    'ignore::DeprecationWarning:bokeh.core.property.primitive',
+    # The following deprecation warnings come from Python 3.12 stdlib modules
+    "ignore:datetime.datetime.:DeprecationWarning:",
+    # This one is coming from plumpy
+    "ignore:There is no current event loop:DeprecationWarning:",
+    # This deprecation warning coming from sqlite3 module might go away if we update bokeh
+    "ignore:The default datetime adapter is deprecated as of Python 3.12; see the sqlite3 documentation for suggested replacement recipes:DeprecationWarning:",
+    # This is needed since SQLAlchemy 2.0, see
+    # https://github.com/aiidalab/aiidalab-widgets-base/issues/605
+    'ignore:Object of type .* not in session, .* operation along .* will not proceed:sqlalchemy.exc.SAWarning',
+    'ignore::DeprecationWarning:bokeh',
     'ignore:Creating AiiDA configuration:UserWarning:aiida',
     'ignore:crystal system:UserWarning:ase.io.cif',
     'ignore::DeprecationWarning:ase.atoms',
@@ -22,8 +30,9 @@ filterwarnings = [
     'ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning:_pytest',
     'ignore::DeprecationWarning:pytest_html',
     'ignore::DeprecationWarning:jupyter_client',
-    'ignore::DeprecationWarning:selenium',
-    'ignore::DeprecationWarning:pytest_selenium',
+    # This warning is coming from circus (aiida-core dependency):
+    # https://github.com/circus-tent/circus/issues/1215
+    "ignore:'pipes' is deprecated and slated for removal in Python 3.13:DeprecationWarning:",
 ]
 
 [tool.ruff]

setup.cfg

@@ -60,7 +60,7 @@ optimade =
     ipyoptimade~=0.1
 smiles =
     rdkit>=2021.09.2
-    scikit-learn~=1.0.0
+    scikit-learn~=1.1
 docs =
     sphinx
     sphinx-design

tests/test_viewers.py

@@ -71,7 +71,7 @@ def test_folder_data_viewer(folder_data_object):
 
 
 @pytest.mark.usefixtures("aiida_profile_clean")
-def test_structure_data_viewer_storage(structure_data_object):
+def test_structure_data_viewer_storage(monkeypatch, tmp_path, structure_data_object):
     v = viewers.viewer(structure_data_object)
     assert isinstance(v, viewers.StructureDataViewer)
 
@@ -87,13 +87,13 @@ def test_structure_data_viewer_storage(structure_data_object):
         ),
         (
             "cif",
-            """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""",
+            """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""",
         ),
     ]
 
     for fmt, out in format_cases:
         v.file_format.label = fmt
-        assert v._prepare_payload() == out
+        assert v._prepare_payload() == out, f"{fmt} structure payload does not match"
 
     # Monkey patch the viewer to avoid the need for a running X server.
     # fmt: off
@@ -104,6 +104,8 @@ def test_structure_data_viewer_storage(structure_data_object):
         -1.6859999895095825, -1.6859999895095825, -0.6669999957084656, 1,
     ]
     # fmt: on
+    # Avoid producing temporary files from povray in the repo
+    monkeypatch.chdir(tmp_path)
     v._render_structure()