Test python 3.11 image

.github/workflows/ci.yml

@@ -41,7 +41,7 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: '3.10'
+                  python-version: '3.11'
 
             - name: Install uv
               run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${UV_VERSION}/uv-installer.sh | sh
@@ -58,19 +58,23 @@ jobs:
             # The Firefox and its engine geckodrive need do be installed manually to run
             # selenium tests.
             - name: Install Firefox
+              if: matrix.browser == 'Firefox'
               uses: browser-actions/setup-firefox@latest
               with:
-                  firefox-version: '96.0'
+                  firefox-version: '124.0'
+
+            - name: Firefox version
               if: matrix.browser == 'Firefox'
+              run: firefox --version
 
             - name: Install geckodriver
-              run: |
-                  wget -c https://github.com/mozilla/geckodriver/releases/download/v0.30.0/geckodriver-v0.30.0-linux64.tar.gz
-                  tar xf geckodriver-v0.30.0-linux64.tar.gz -C /usr/local/bin
               if: matrix.browser == 'Firefox'
+              run: |
+                  wget -c https://github.com/mozilla/geckodriver/releases/download/v0.34.0/geckodriver-v0.34.0-linux64.tar.gz
+                  tar xf geckodriver-v0.34.0-linux64.tar.gz -C /usr/local/bin
 
             - name: Run pytest
-              run: pytest -v --driver ${{ matrix.browser }} tests_notebooks
+              run: pytest -v --driver ${{ matrix.browser }} tests_notebooks/
               env:
                   TAG: aiida-${{ matrix.aiida-core-version }}
 
@@ -86,7 +90,7 @@ 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, 2.5.1]
             fail-fast: false

pyproject.toml

@@ -8,6 +8,12 @@ build-backend = "setuptools.build_meta"
 [tool.pytest.ini_options]
 filterwarnings = [
     'error',
+    # 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',
@@ -25,6 +31,9 @@ filterwarnings = [
     # https://github.com/aiidalab/aiidalab-widgets-base/issues/551
     'ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning:_pytest',
     'ignore::DeprecationWarning:jupyter_client',
+    # 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

@@ -57,7 +57,7 @@ eln =
     aiidalab-eln>=0.1.2,~=0.1
 smiles =
     rdkit>=2021.09.2
-    scikit-learn~=1.0.0
+    scikit-learn~=1.1
 docs =
     sphinx~=7.3
     sphinx-design~=0.5

tests_notebooks/conftest.py

@@ -1,4 +1,5 @@
 import os
+import time
 from pathlib import Path
 from urllib.parse import urljoin
 
@@ -48,7 +49,8 @@ def execute(command, user=None, **kwargs):
         else:
             command = f"exec --workdir {workdir} -T aiidalab {command}"
 
-        return docker_compose.execute(command, **kwargs)
+        out = docker_compose.execute(command, **kwargs)
+        return out.decode("utf-8").strip()
 
     return execute
 
@@ -64,17 +66,17 @@ def notebook_service(docker_ip, docker_services, aiidalab_exec):
     # we release the docker stack with aiida-core v2.4.0 in:
     # https://github.com/aiidalab/aiidalab-docker-stack/commit/dfa65151017362fefeb56d97fed3c1b8f25537c5
     # There is a possibility that aiida-core version will be overwritten by the installation of AWB.
-    # TODO: We can move this before/after version check after the lowest supported aiida-core version is 2.4.0.
+    # TODO: We can remove this before/after version check after the lowest supported aiida-core version is 2.4.0.
 
     # Get the aiida-core version before installing AWB
-    output = aiidalab_exec("verdi --version").decode("utf-8").strip()
+    output = aiidalab_exec("verdi --version")
     before_version = output.split(" ")[-1]
 
     # Install AWB with extra dependencies for SmilesWidget
     aiidalab_exec("pip install --no-cache-dir .[smiles,optimade]")
 
     # Get the aiida-core version before installing AWB
-    output = aiidalab_exec("verdi --version").decode("utf-8").strip()
+    output = aiidalab_exec("verdi --version")
     after_version = output.split(" ")[-1]
 
     assert (
@@ -86,7 +88,7 @@ def notebook_service(docker_ip, docker_services, aiidalab_exec):
     url = f"http://{docker_ip}:{port}"
     token = os.environ["JUPYTER_TOKEN"]
     docker_services.wait_until_responsive(
-        timeout=30.0, pause=0.1, check=lambda: is_responsive(url)
+        timeout=30.0, pause=0.5, check=lambda: is_responsive(url)
     )
     return url, token
 
@@ -109,9 +111,10 @@ def _selenium_driver(nb_path):
 
         selenium.find_element(By.ID, "ipython-main-app")
         selenium.find_element(By.ID, "notebook-container")
-        WebDriverWait(selenium, 240).until(
+        WebDriverWait(selenium, timeout=240, poll_frequency=0.5).until(
             ec.invisibility_of_element((By.ID, "appmode-busy"))
         )
+        time.sleep(3)
 
         return selenium
 

tests_notebooks/docker-compose.yml

@@ -9,7 +9,7 @@ services:
         # since the dockerhub registry has a rate limit of 100 pulls per 6 hours.
         # Images with aiida-core<2.4.0 were not pushed to ghcr.io because of CI issues,
         # which were fixed in https://github.com/aiidalab/aiidalab-docker-stack/pull/390
-        image: aiidalab/full-stack:${TAG:-latest}
+        image: aiidalab/full-stack:${TAG-latest}
         environment:
             RMQHOST: messaging
             TZ: Europe/Zurich

tests_notebooks/test_notebooks.py

@@ -1,8 +1,16 @@
 import time
 
 import requests
+import selenium.webdriver.support.expected_conditions as ec
 from selenium.webdriver.common.by import By
 from selenium.webdriver.common.keys import Keys
+from selenium.webdriver.support.wait import WebDriverWait
+
+
+def wait_till_not_busy(driver):
+    WebDriverWait(driver, timeout=500, poll_frequency=1.0).until(
+        ec.invisibility_of_element((By.ID, "appmode-busy"))
+    )
 
 
 def test_notebook_service_available(notebook_service):
@@ -21,7 +29,7 @@ def test_aiida_datatypes_viewers(selenium_driver, final_screenshot):
     driver.set_window_size(1000, 2000)
     driver.find_element(By.CLASS_NAME, "widget-label")
     driver.find_element(By.XPATH, '//button[text()="Clear selection"]')
-    time.sleep(5)
+    wait_till_not_busy(driver)
 
 
 def test_eln_configure(selenium_driver, final_screenshot):
@@ -54,6 +62,7 @@ def test_structures_generate_from_smiles(selenium_driver, final_screenshot):
     # Generate methane molecule from SMILES
     driver.find_element(By.XPATH, "//input[@placeholder='C=C']").send_keys("C")
     driver.find_element(By.XPATH, '//button[text()="Generate molecule"]').click()
+    wait_till_not_busy(driver)
     time.sleep(5)
 
     # Select the first atom
@@ -62,6 +71,7 @@ def test_structures_generate_from_smiles(selenium_driver, final_screenshot):
         By.XPATH, "//label[text()='Select atoms:']/following-sibling::input"
     ).send_keys("1")
     driver.find_element(By.XPATH, '//button[text()="Apply selection"]').click()
+    wait_till_not_busy(driver)
     driver.find_element(By.XPATH, "//p[contains(text(),'Id: 1; Symbol: C;')]")
 
 
@@ -95,6 +105,7 @@ def test_structure_from_examples_and_supercell_selection(
     driver.find_element(By.XPATH, '//button[text()="Apply selection"]').click()
 
     # Make sure the selection is what we expect
+    wait_till_not_busy(driver)
     driver.find_element(By.XPATH, "//p[contains(text(), 'Selected atoms: 12')]")
     driver.find_element(
         By.XPATH, "//p[contains(text(), 'Selected unit cell atoms: 6')]"
@@ -115,7 +126,7 @@ def test_computational_resources_code_setup(
 ):
     """Test the quicksetup of the code"""
     # check the code CP2K is not in code list
-    output = aiidalab_exec("verdi code list").decode().strip()
+    output = aiidalab_exec("verdi code list")
     assert "cp2k" not in output
 
     driver = selenium_driver("notebooks/computational_resources.ipynb")
@@ -149,5 +160,5 @@ def test_computational_resources_code_setup(
     time.sleep(1.0)
 
     # check the new code cp2k-9.1@daint-mc is in code list
-    output = aiidalab_exec("verdi code list").decode().strip()
+    output = aiidalab_exec("verdi code list")
     assert "cp2k-9.1@daint-mc" in output