Test with aiida-core=2.6.1 and python 3.11 (aiidalab#760)

* Update links in README * Collect coverage only for aiida-core=2.3 runs * Report pytest timings * Filter warnings as in AWB * Bump pytest and pytest-cov * bump uv version * Bump uv and ruff versions
edan-bainglass · Aug 21, 2024 · b9cea17 · b9cea17
1 parent 3ce7d18
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Showing 15 changed files with 39 additions and 27 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -13,16 +13,16 @@ concurrency:
 
 env:
     FORCE_COLOR: 1
+    UV_VERSION: 0.3.0
 
 jobs:
 
     test-package:
 
         strategy:
             matrix:
-                tag: [latest]
-                python-version: ['3.9', '3.10']
-                aiida-core-version: [2.3, 2.5]
+                python-version: ['3.9', '3.11']
+                aiida-core-version: ['2.3', '2.6']
             fail-fast: false
 
         runs-on: ubuntu-latest
@@ -45,15 +45,16 @@ jobs:
                   python-version: ${{ matrix.python-version }}
 
             - name: Install uv
-              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.2.13/uv-installer.sh | sh
+              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${{ env.UV_VERSION }}/uv-installer.sh | sh
 
             - name: Install package
               run: uv pip install --system -e .[dev] aiida-core==${{ matrix.aiida-core-version }}
 
             - name: Run pytest
-              run: pytest -v tests --cov=aiidalab_qe
-              env:
-                  TAG: ${{ matrix.tag }}
+              # Only collect code coverage with aiida-core=2.3, to speed up tests
+              # with higher aiida versions that for some reason run slower, see:
+              # https://github.com/aiidalab/aiidalab-qe/issues/766
+              run: pytest -v tests ${{ matrix.aiida-core-version == '2.3' && '--cov=aiidalab_qe' || '' }}
 
             - name: Upload coverage reports to Codecov
               uses: codecov/codecov-action@v4

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -30,7 +30,7 @@ repos:
           - id: nbstripout
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.5
+      rev: v0.6.1
       hooks:
           - id: ruff
             types_or: [python, pyi, jupyter]

diff --git a/README.md b/README.md
@@ -71,9 +71,9 @@ Additional notes:
 ## Acknowledgements
 We acknowledge support from:
 * the European Union\'s Horizon 2020 research and innovation programme (Grant No. 957189, [project BIG-MAP](https://www.big-map.eu)).
-* the [MARVEL National Centre for Competency in Research](<http://nccr-marvel.ch>) funded by the [Swiss National Science Foundation](<http://www.snf.ch/en>).
+* the [MARVEL National Centre for Competency in Research](https://nccr-marvel.ch/) funded by the [Swiss National Science Foundation](https://www.snf.ch/en).
 * the MARKETPLACE project funded by [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) under the H2020-NMBP-25-2017 call (Grant No. 760173).
-* the [MaX European Centre of Excellence](<http://www.max-centre.eu/>) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
+* the [MaX European Centre of Excellence](https://www.max-centre.eu/) funded by the Horizon 2020 EINFRA-5 program (Grant No. 676598).
 
 <div style="text-align:left">
  <img src="miscellaneous/logos/MARVEL.png" alt="MARVEL" height="75px">

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,12 +5,22 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[tool.pytest.ini_options]
+addopts = '--strict-config --strict-markers --durations=30 --durations-min=1 -ra'
+filterwarnings = [
+    'ignore:Object of type .* not in session, .* operation along .* will not proceed:',
+    'ignore:Creating AiiDA configuration:UserWarning:',
+    'ignore:metadata.*traitlets.traitlets.Unicode object:DeprecationWarning:',
+    # For some reason we get this error, see
+    # https://github.com/aiidalab/aiidalab-widgets-base/issues/551
+    'ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning:_pytest',
+]
+
 [tool.ruff]
 line-length = 88
 show-fixes = true
 output-format = "full"
 target-version = "py39"
-extend-include = ["*.ipynb"]
 
 [tool.ruff.lint]
 ignore = ["E501", "E402", "TRY003", "RUF012", "N806"]

diff --git a/qe.ipynb b/qe.ipynb
@@ -42,12 +42,12 @@
     "from datetime import datetime\n",
     "\n",
     "import ipywidgets as ipw\n",
-    "from aiidalab_qe.app import App, static\n",
-    "from aiidalab_qe.version import __version__\n",
     "from importlib_resources import files\n",
     "from IPython.display import display\n",
     "from jinja2 import Environment\n",
     "\n",
+    "from aiidalab_qe.app import App, static\n",
+    "from aiidalab_qe.version import __version__\n",
     "from aiidalab_widgets_base.bug_report import (\n",
     "    install_create_github_issue_exception_handler,\n",
     ")"

diff --git a/setup.cfg b/setup.cfg
@@ -40,10 +40,10 @@ where = src
 dev =
     bumpver~=2023.1124
     pre-commit~=3.2
-    pytest~=6.2
+    pytest~=7.4
     pytest-regressions~=2.2
     pgtest==1.3.1
-    pytest-cov~=4.0
+    pytest-cov~=5.0
 
 [options.package_data]
 aiidalab_qe.app.parameters = qeapp.yaml

diff --git a/tests/configuration/test_advanced.py b/tests/configuration/test_advanced.py
@@ -120,9 +120,8 @@ def test_advanced_tot_charge_settings():
 
 def test_advanced_kpoints_mesh():
     """Test Mesh Grid HTML widget."""
-    from aiidalab_qe.app.configuration.advanced import AdvancedSettings
-
     from aiida import orm
+    from aiidalab_qe.app.configuration.advanced import AdvancedSettings
 
     w = AdvancedSettings()
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -5,9 +5,9 @@
 import tempfile
 
 import pytest
-from aiidalab_qe.setup.pseudos import SSSP_VERSION
 
 from aiida import orm
+from aiidalab_qe.setup.pseudos import SSSP_VERSION
 
 pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
 
@@ -630,12 +630,11 @@ def _generate_qeapp_workchain(
     ):
         from copy import deepcopy
 
+        from aiida.orm.utils.serialize import serialize
         from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
         from aiidalab_qe.app.submission import SubmitQeAppWorkChainStep
         from aiidalab_qe.workflows import QeAppWorkChain
 
-        from aiida.orm.utils.serialize import serialize
-
         # Step 1: select structure from example
         s1 = app.structure_step
         if structure is None:

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1,9 +1,9 @@
 import time
 
-import aiidalab_qe.__main__ as cli
 from click.testing import CliRunner, Result
 
 import aiida
+import aiidalab_qe.__main__ as cli
 
 # To learn more about testing click applications, see: https://click.palletsprojects.com/en/8.1.x/testing/
 

diff --git a/tests/test_plugins_bands.py b/tests/test_plugins_bands.py
@@ -4,6 +4,7 @@
 @pytest.mark.usefixtures("sssp")
 def test_result(generate_qeapp_workchain):
     import plotly.graph_objects as go
+
     from aiidalab_qe.common.bandpdoswidget import BandPdosWidget
     from aiidalab_qe.plugins.bands.result import Result
 

diff --git a/tests/test_plugins_electronic_structure.py b/tests/test_plugins_electronic_structure.py
@@ -1,12 +1,12 @@
 def test_electronic_structure(generate_qeapp_workchain):
     """Test the electronic structure tab."""
     import plotly.graph_objects as go
+
+    from aiida import engine
     from aiidalab_qe.app.result.workchain_viewer import WorkChainViewer
     from aiidalab_qe.common.bandpdoswidget import BandPdosWidget
     from aiidalab_qe.plugins.electronic_structure.result import Result
 
-    from aiida import engine
-
     wkchain = generate_qeapp_workchain()
     wkchain.node.set_exit_status(0)
     wkchain.node.set_process_state(engine.ProcessState.FINISHED)

diff --git a/tests/test_plugins_pdos.py b/tests/test_plugins_pdos.py
@@ -4,6 +4,7 @@
 @pytest.mark.usefixtures("sssp")
 def test_result(generate_qeapp_workchain):
     import plotly.graph_objects as go
+
     from aiidalab_qe.common.bandpdoswidget import BandPdosWidget
     from aiidalab_qe.plugins.pdos.result import Result
 

diff --git a/tests/test_plugins_xps.py b/tests/test_plugins_xps.py
@@ -5,10 +5,10 @@
 def test_settings():
     """Test the settings of the xps app."""
 
-    from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
     from ase.build import molecule
 
     from aiida.orm import StructureData
+    from aiidalab_qe.app.configuration import ConfigureQeAppWorkChainStep
 
     configure_step = ConfigureQeAppWorkChainStep()
     # set the input structure

diff --git a/tests/test_pseudo.py b/tests/test_pseudo.py
@@ -1,4 +1,6 @@
 import pytest
+
+from aiida import orm
 from aiidalab_qe.setup.pseudos import (
     PSEUDODOJO_VERSION,
     SSSP_VERSION,
@@ -7,8 +9,6 @@
     pseudos_to_install,
 )
 
-from aiida import orm
-
 
 def test_setup_pseudos_cmd(tmp_path):
     """Test _construct_cmd function in setup.pseudos"""

diff --git a/tests/test_result.py b/tests/test_result.py
@@ -43,9 +43,10 @@ def test_summary_report_advanced_settings(data_regression, generate_qeapp_workch
 
 def test_summary_view(generate_qeapp_workchain):
     """Test the report html can be properly generated."""
-    from aiidalab_qe.app.result.summary_viewer import SummaryView
     from bs4 import BeautifulSoup
 
+    from aiidalab_qe.app.result.summary_viewer import SummaryView
+
     wkchain = generate_qeapp_workchain()
     viewer = SummaryView(wkchain.node)
     report_html = viewer.report_html