Devops: Allow unit test suite to be ran against SQLite (#6425)

The unit test suite currently automatically creates a test profile using
the `core.psql_dos` storage plugin. The reason is mostly historical as
originally the `core.psql_dos` storage was the only. The downside of
this storage plugin, however, is that it requires a PostgreSQL database.
This typically requires a PostgreSQL service to be running, making it
more difficult to get a working development environment. This was made
slightly easier through the use of `pgtest`, which would create a PSQL
cluster on-the-fly, but this would still require postgres libraries to
be installed.

Nowadays, storage plugins are customizable and the `core.sqlite_dos`
replaces PostgreSQL with the serviceless SQLite. The dependencies for
these are a lot easier to install, making it perfect for testing.
However, the test suite automatically configures a `core.psql_dos`
profile and some tests are not compatible with SQLite since they
directly depend on functionality that is only supported by PSQL and not
SQLite.

In this commit, changes are made that allow running the test with
SQLite. Two new pytest markers are added to the test suite:

* `requires_pgsql`: for tests that are known to require PostgreSQL (i.e.
  do not work with SQLite)
* `presto`: an alias for `not requires_rmq and not requires_pgsql`. The
  tests are marked with `presto` automagically in
  `tests/conftest.py:pytest_collection_modifyitems`

A new CI job is added `test-presto` that runs the tests with the
`presto` marker.

.github/actions/install-aiida-core/action.yml

@@ -28,7 +28,7 @@ runs:
   - name: Install uv installer
     run: curl --proto '=https' --tlsv1.2 -LsSf https://${{ env.UV_URL }} | sh
     env:
-      UV_VERSION: 0.1.44
+      UV_VERSION: 0.2.5
       UV_URL: github.com/astral-sh/uv/releases/download/$UV_VERSION/uv-installer.sh
     shell: bash
 

.github/workflows/ci-code.yml

@@ -1,4 +1,4 @@
-name: continuous-integration-code
+name: ci-code
 
 on:
   push:
@@ -13,6 +13,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
 
   check-requirements:
@@ -99,7 +102,9 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest --cov aiida --verbose tests -m 'not nightly'
+      # Python 3.12 has a performance regression when running with code coverage
+      # so run code coverage only for python 3.9.
+      run: pytest -v tests -m 'not nightly' ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
 
     - name: Upload coverage report
       if: matrix.python-version == 3.9 && github.repository == 'aiidateam/aiida-core'
@@ -110,26 +115,58 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: false  # don't fail job, if coverage upload fails
 
-  verdi:
 
+  tests-presto:
+
+    needs: [check-requirements]
     runs-on: ubuntu-latest
-    timeout-minutes: 15
+    timeout-minutes: 20
 
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.9', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install graphviz
+      run: sudo apt update && sudo apt install graphviz
+
+    - name: Install aiida-core
+      uses: ./.github/actions/install-aiida-core
+      with:
+        python-version: '3.11'
+
+    - name: Setup SSH on localhost
+      run: .github/workflows/setup_ssh.sh
+
+    - name: Run test suite
+      env:
+        AIIDA_WARN_v3: 0
+      run: pytest -m 'presto' --cov aiida
+
+    - name: Upload coverage report
+      if: github.repository == 'aiidateam/aiida-core'
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        name: aiida-pytests-presto
+        flags: presto
+        file: ./coverage.xml
+        fail_ci_if_error: false  # don't fail job, if coverage upload fails
+
+
+  verdi:
+
+    needs: [check-requirements]
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: ${{ matrix.python-version }}
-        from-requirements: 'false'
+        python-version: '3.12'
 
-    - name: Run verdi
+    - name: Run verdi tests
       run: |
         verdi devel check-load-time
         verdi devel check-undesired-imports

.github/workflows/ci-style.yml

@@ -1,4 +1,4 @@
-name: continuous-integration-style
+name: ci-style
 
 on:
   push:

.github/workflows/nightly.yml

@@ -19,6 +19,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
 
   nightly-tests:
@@ -91,7 +94,7 @@ jobs:
   rabbitmq-tests:
 
     runs-on: ubuntu-latest
-    timeout-minutes: 30
+    timeout-minutes: 10
 
     strategy:
       fail-fast: false
@@ -132,6 +135,12 @@ jobs:
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql
 
+    - name: Setup SSH on localhost
+      run: .github/workflows/setup_ssh.sh
+
+    - name: Suppress RabbitMQ version warning
+      run: verdi config set warnings.rabbitmq_version False
+
     - name: Run tests
       id: tests
       env:

.github/workflows/setup.sh

@@ -1,12 +1,8 @@
 #!/usr/bin/env bash
 set -ev
 
-ssh-keygen -q -t rsa -b 4096 -N "" -f "${HOME}/.ssh/id_rsa"
-ssh-keygen -y -f "${HOME}/.ssh/id_rsa" >> "${HOME}/.ssh/authorized_keys"
-ssh-keyscan -H localhost >> "${HOME}/.ssh/known_hosts"
-
-# The permissions on the GitHub runner are 777 which will cause SSH to refuse the keys and cause authentication to fail
-chmod 755 "${HOME}"
+# Setup SSH on localhost
+${GITHUB_WORKSPACE}/.github/workflows/setup_ssh.sh
 
 # Replace the placeholders in configuration files with actual values
 CONFIG="${GITHUB_WORKSPACE}/.github/config"

.github/workflows/setup_ssh.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -ev
+
+ssh-keygen -q -t rsa -b 4096 -N "" -f "${HOME}/.ssh/id_rsa"
+ssh-keygen -y -f "${HOME}/.ssh/id_rsa" >> "${HOME}/.ssh/authorized_keys"
+ssh-keyscan -H localhost >> "${HOME}/.ssh/known_hosts"
+
+# The permissions on the GitHub runner are 777 which will cause SSH to refuse the keys and cause authentication to fail
+chmod 755 "${HOME}"

.github/workflows/verdi.sh

@@ -1,14 +1,13 @@
 #!/usr/bin/env bash
 
-# Test the loading time of `verdi`. This is and attempt to catch changes to the imports in `aiida.cmdline` that will
-# indirectly load the `aiida.orm` module which will trigger loading of the backend environment. This slows down `verdi`
-# significantly, making tab-completion unusable.
+# Test the loading time of `verdi`. This is an attempt to catch changes to the imports in `aiida.cmdline` that
+# would slow down `verdi` invocations and make tab-completion unusable.
 VERDI=`which verdi`
 
-# Typically, the loading time of `verdi` should be around ~0.2 seconds. When loading the database environment this
-# tends to go towards ~0.8 seconds. Since these timings are obviously machine and environment dependent, typically these
-# types of tests are fragile. But with a load limit of more than twice the ideal loading time, if exceeded, should give
-# a reasonably sure indication that the loading of `verdi` is unacceptably slowed down.
+# Typically, the loading time of `verdi` should be around ~0.2 seconds.
+# Typically these types of tests are fragile. But with a load limit of more than twice
+# the ideal loading time, if exceeded, should give a reasonably sure indication
+# that the loading of `verdi` is unacceptably slowed down.
 LOAD_LIMIT=0.4
 MAX_NUMBER_ATTEMPTS=5
 

docs/source/nitpick-exceptions

@@ -192,8 +192,11 @@ py:class _asyncio.Future
 
 py:class tqdm.std.tqdm
 
+py:class _pytest.tmpdir.TempPathFactory
+py:class pytest.tmpdir.TempPathFactory
 py:class pytest.TempPathFactory
 py:class PGTest
+py:class pgtest.pgtest.PGTest
 
 py:class IPython.core.magic.Magics
 
@@ -207,8 +210,6 @@ py:class flask_restful.Resource
 py:class flask.app.Flask
 py:class Flask
 
-py:class pytest.tmpdir.TempPathFactory
-
 py:class scoped_session
 py:class sqlalchemy.orm.decl_api.SqliteModel
 py:class sqlalchemy.orm.decl_api.Base

pyproject.toml

@@ -351,25 +351,33 @@ ignore_errors = true
 module = 'plumpy'
 
 [tool.pytest.ini_options]
-addopts = '--benchmark-skip --durations=50 --strict-config --strict-markers -ra --cov-report xml --cov-append '
+addopts = '--benchmark-skip --durations=50 --durations-min=1 --strict-config --strict-markers -ra --cov-report xml --cov-append '
 filterwarnings = [
+  'ignore:.*and will be removed in NumPy 2.0.*:DeprecationWarning:ase:',
+  'ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:pytz|dateutil|tqdm|aio_pika:',
+  'ignore:datetime.datetime.utcnow:DeprecationWarning:aio_pika|pytz|pgtest:',
   'ignore::DeprecationWarning:babel:',
   'ignore::DeprecationWarning:frozendict:',
   'ignore::DeprecationWarning:sqlalchemy:',
   'ignore::DeprecationWarning:yaml:',
   'ignore::DeprecationWarning:pymatgen:',
   'ignore::DeprecationWarning:jsonbackend:',
   'ignore::DeprecationWarning:pkg_resources:',
+  'ignore:ast.* is deprecated.*:DeprecationWarning:docstring_parser:',
+  'ignore::SyntaxWarning:CifFile:',
   'ignore::pytest.PytestCollectionWarning',
   'ignore:Creating AiiDA configuration folder.*:UserWarning',
   'ignore:Object of type .* not in session, .* operation along .* will not proceed:sqlalchemy.exc.SAWarning',
+  'ignore:Identity map already had an identity for .* inside of an event handler within the flush?:sqlalchemy.exc.SAWarning',
   'ignore:The `aiida.orm.nodes.data.upf` module is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
   'ignore:The `Code` class is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
   'default::ResourceWarning'
 ]
 markers = [
   'nightly: long running tests that should rarely be affected and so only run nightly',
   'requires_rmq: requires a connection (on port 5672) to RabbitMQ',
+  'requires_psql: requires a connection to PostgreSQL DB',
+  'presto: automatic marker meaning "not requires_rmq and not requires_psql"',
   'sphinx: set parameters for the sphinx `app` fixture'
 ]
 minversion = '7.0'

requirements/requirements-py-3.10.txt

@@ -199,7 +199,6 @@ tomli==2.0.1
 tornado==6.3.2
 tqdm==4.65.0
 traitlets==5.9.0
-trogon==0.5.0
 typing-extensions==4.6.3
 tzdata==2023.3
 uc-micro-py==1.0.2

requirements/requirements-py-3.11.txt

@@ -197,7 +197,6 @@ tinycss2==1.2.1
 tornado==6.3.2
 tqdm==4.65.0
 traitlets==5.9.0
-trogon==0.5.0
 typing-extensions==4.6.3
 tzdata==2023.3
 uc-micro-py==1.0.2

requirements/requirements-py-3.9.txt

@@ -201,7 +201,6 @@ tomli==2.0.1
 tornado==6.3.2
 tqdm==4.65.0
 traitlets==5.9.0
-trogon==0.5.0
 typing-extensions==4.6.3
 tzdata==2023.3
 uc-micro-py==1.0.2

src/aiida/storage/psql_dos/migrations/utils/integrity.py

@@ -161,7 +161,7 @@ def write_database_integrity_violation(results, headers, reason_message, action_
     :param reason_message: a human readable message detailing the reason of the integrity violation
     :param action_message: an optional human readable message detailing a performed action, if any
     """
-    from datetime import datetime
+    from datetime import datetime, timezone
     from tempfile import NamedTemporaryFile
 
     from tabulate import tabulate
@@ -183,7 +183,7 @@ def write_database_integrity_violation(results, headers, reason_message, action_
             )
         )
 
-        handle.write(f'# {datetime.utcnow().isoformat()}\n')
+        handle.write(f'# {datetime.datetime.now(timezone.utc).isoformat()}\n')
         handle.write(f'# Violation reason: {reason_message}\n')
         handle.write(f'# Performed action: {action_message}\n')
         handle.write('\n')

src/aiida/tools/pytest_fixtures/__init__.py

@@ -25,7 +25,7 @@
     aiida_localhost,
     ssh_key,
 )
-from .storage import config_psql_dos, postgres_cluster
+from .storage import config_psql_dos, config_sqlite_dos, postgres_cluster
 
 __all__ = (
     'aiida_code_installed',
@@ -44,6 +44,7 @@
     'aiida_profile_tmp',
     'aiida_profile',
     'config_psql_dos',
+    'config_sqlite_dos',
     'daemon_client',
     'entry_points',
     'postgres_cluster',