Devops: Make use of the improved fixtures in aiida-core

Most notably, the `aiida_profile` and related fixtures now by default
use a profile using the `core.sqlite_dos` storage plugin and define no
broker. This means the PostgreSQL and RabbitMQ services are no longer
required to run the tests.

.github/workflows/cd.yml

@@ -54,14 +54,6 @@ jobs:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
-    services:
-      postgres:
-        image: postgres:12
-      rabbitmq:
-        image: rabbitmq:latest
-        ports:
-        - 5672:5672
-
     steps:
     - uses: actions/checkout@v2
 

.github/workflows/ci.yml

@@ -33,14 +33,6 @@ jobs:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
-    services:
-      postgres:
-        image: postgres:12
-      rabbitmq:
-        image: rabbitmq:latest
-        ports:
-        - 5672:5672
-
     steps:
     - uses: actions/checkout@v2
 

pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
   'Programming Language :: Python :: 3.12'
 ]
 dependencies = [
-  'aiida-core~=2.1',
+  'aiida-core~=2.6',
   'click~=8.0',
   'pint~=0.23.0',
   'requests~=2.20'
@@ -46,7 +46,6 @@ requires-python = '>=3.9'
 
 [project.optional-dependencies]
 dev = [
-  'pgtest~=1.3',
   'pre-commit~=2.2',
   'pytest>=6.0'
 ]

tests/cli/test_family.py

@@ -12,7 +12,7 @@
 from numpy.testing import assert_almost_equal
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_family_cutoffs_set(run_cli_command, get_pseudo_family, generate_cutoffs_dict, tmp_path):
     """Test the `aiida-pseudo family cutoffs set` command."""
     family = get_pseudo_family(cls=CutoffsPseudoPotentialFamily)
@@ -60,7 +60,7 @@ def test_family_cutoffs_set(run_cli_command, get_pseudo_family, generate_cutoffs
     assert family.get_cutoffs(stringency) == cutoffs_dict['high']
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_family_cutoffs_set_unit(run_cli_command, get_pseudo_family, generate_cutoffs, tmp_path):
     """Test the `aiida-pseudo family cutoffs set` command with the ``--unit`` flag."""
     family = get_pseudo_family(cls=CutoffsPseudoPotentialFamily)
@@ -97,7 +97,7 @@ def test_family_cutoffs_set_unit(run_cli_command, get_pseudo_family, generate_cu
     'family_cls,label',
     [(SsspFamily, 'SSSP/1.1/PBE/efficiency'), (PseudoDojoFamily, 'PseudoDojo/0.4/PBE/SR/standard/psp8')],
 )
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_family_cutoffs_set_established(
     run_cli_command, get_pseudo_family, generate_cutoffs, tmp_path, family_cls, label
 ):
@@ -117,7 +117,7 @@ def test_family_cutoffs_set_established(
     assert f"Invalid value for 'FAMILY': The value `{family}` is not allowed for this parameter." in result.output
 
 
-def test_family_show(clear_db, run_cli_command, get_pseudo_family):
+def test_family_show(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `aiida-pseudo show` command."""
     family = get_pseudo_family()
     result = run_cli_command(cmd_family_show, [family.label])
@@ -127,7 +127,9 @@ def test_family_show(clear_db, run_cli_command, get_pseudo_family):
         assert node.filename in result.output
 
 
-def test_family_show_recommended_cutoffs(clear_db, run_cli_command, get_pseudo_family, generate_cutoffs_dict):
+def test_family_show_recommended_cutoffs(
+    aiida_profile_clean, run_cli_command, get_pseudo_family, generate_cutoffs_dict
+):
     """Test the `aiida-pseudo show` command for a family with recommended cutoffs."""
     family = get_pseudo_family(cls=CutoffsPseudoPotentialFamily)
     stringencies = ('normal', 'high')
@@ -157,7 +159,7 @@ def test_family_show_recommended_cutoffs(clear_db, run_cli_command, get_pseudo_f
             assert_almost_equal(cutoffs[1], float(fields[4]))
 
 
-def test_family_show_argument_type(clear_db, run_cli_command, get_pseudo_family):
+def test_family_show_argument_type(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test that `aiida-pseudo show` only accepts instances of `PseudoPotentialFamily` or subclasses as argument."""
     pseudo_family = get_pseudo_family(label='pseudo-family', cls=PseudoPotentialFamily)
     normal_group = Group('normal-group').store()
@@ -166,7 +168,7 @@ def test_family_show_argument_type(clear_db, run_cli_command, get_pseudo_family)
     run_cli_command(cmd_family_show, [normal_group.label], raises=SystemExit)
 
 
-def test_family_show_raw(clear_db, run_cli_command, get_pseudo_family):
+def test_family_show_raw(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `-r/--raw` option."""
     family = get_pseudo_family()
 
@@ -175,7 +177,7 @@ def test_family_show_raw(clear_db, run_cli_command, get_pseudo_family):
         assert len(result.output_lines) == len(family.nodes)
 
 
-def test_family_show_unit_default(clear_db, run_cli_command, get_pseudo_family):
+def test_family_show_unit_default(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `family show` command with default unit."""
     elements = ['Ar', 'Kr']
     cutoff_dict = {'normal': {'Ar': {'cutoff_wfc': 50, 'cutoff_rho': 200}, 'Kr': {'cutoff_wfc': 25, 'cutoff_rho': 100}}}
@@ -199,7 +201,7 @@ def test_family_show_unit_default(clear_db, run_cli_command, get_pseudo_family):
 
 
 @pytest.mark.parametrize('unit', ['Ry', 'eV', 'hartree', 'aJ'])
-def test_family_show_unit(clear_db, run_cli_command, get_pseudo_family, unit):
+def test_family_show_unit(aiida_profile_clean, run_cli_command, get_pseudo_family, unit):
     """Test the `-u/--unit` option."""
     elements = [
         'Ar',

tests/cli/test_install.py

@@ -147,7 +147,7 @@ def _run_monkeypatched_install_pseudo_dojo(options=None, raises=None):
     return _run_monkeypatched_install_pseudo_dojo
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_family(run_cli_command, get_pseudo_archive):
     """Test ``aiida-pseudo install family``."""
     label = 'family'
@@ -165,7 +165,7 @@ def test_install_family(run_cli_command, get_pseudo_archive):
     assert len(family.pseudos) != 0
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_family_folder(run_cli_command, filepath_pseudos):
     """Test ``aiida-pseudo install family` from folder`."""
     label = 'family_test'
@@ -183,7 +183,7 @@ def test_install_family_folder(run_cli_command, filepath_pseudos):
     assert len(family.pseudos) != 0
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_family_url(run_cli_command, get_pseudo_archive, monkeypatch):
     """Test ``aiida-pseudo install family`` when installing from a URL.
 
@@ -222,7 +222,7 @@ def convert(*_, **__):
     assert len(family.pseudos) != 0
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_sssp(run_cli_command):
     """Test the ``aiida-pseudo install sssp`` command."""
     from aiida_pseudo import __version__
@@ -241,7 +241,7 @@ def test_install_sssp(run_cli_command):
     assert 'is already installed' in result.output
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_pseudo_dojo(run_cli_command):
     """Test the ``aiida-pseudo install pseudo-dojo`` command."""
     from aiida_pseudo import __version__
@@ -260,7 +260,7 @@ def test_install_pseudo_dojo(run_cli_command):
     assert 'is already installed' in result.output
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_install_sssp_monkeypatched(run_monkeypatched_install_sssp):
     """Test the ``aiida-pseudo install sssp`` command with a monkeypatched download function.
 
@@ -283,7 +283,7 @@ def test_install_sssp_monkeypatched(run_monkeypatched_install_sssp):
     assert family.label == label
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 @pytest.mark.filterwarnings('ignore:filename .* does not have a supported extension.:UserWarning')
 def test_install_pseudo_dojo_monkeypatched(run_monkeypatched_install_pseudo_dojo):
     """Test the ``aiida-pseudo install pseudo-dojo`` command with a monkeypatched download function.
@@ -308,7 +308,7 @@ def test_install_pseudo_dojo_monkeypatched(run_monkeypatched_install_pseudo_dojo
     assert family.label == label
 
 
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_sssp_download_only(run_monkeypatched_install_sssp):
     """Test the ``aiida-pseudo install sssp`` command with the ``--download-only`` option.
 
@@ -328,7 +328,7 @@ def test_install_sssp_download_only(run_monkeypatched_install_sssp):
     assert 'Success: Pseudopotential archive written to:' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_sssp_download_only_exists(run_monkeypatched_install_sssp, get_pseudo_family):
     """Test the ``aiida-pseudo install sssp`` command with the ``--download-only`` option.
 
@@ -350,7 +350,7 @@ def test_install_sssp_download_only_exists(run_monkeypatched_install_sssp, get_p
 
 
 @pytest.mark.parametrize('configuration', SsspFamily.valid_configurations)
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_sssp_from_download(run_monkeypatched_install_sssp, configuration):
     """Test the ``aiida-pseudo install sssp`` command with the ``--from-download`` option."""
     options = [
@@ -373,7 +373,7 @@ def test_install_sssp_from_download(run_monkeypatched_install_sssp, configuratio
     assert 'Success: installed `SSSP/' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_pseudo_dojo_download_only(run_monkeypatched_install_pseudo_dojo):
     """Test the ``aiida-pseudo install pseudo-dojo`` command with the ``--download-only`` option.
 
@@ -393,7 +393,7 @@ def test_install_pseudo_dojo_download_only(run_monkeypatched_install_pseudo_dojo
     assert 'Success: Pseudopotential archive written to:' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_pseudo_dojo_download_only_exists(run_monkeypatched_install_pseudo_dojo, get_pseudo_family):
     """Test the ``aiida-pseudo install pseudo_dojo`` command with the ``--download-only`` option.
 
@@ -429,7 +429,7 @@ def test_install_pseudo_dojo_download_only_exists(run_monkeypatched_install_pseu
     assert 'Success: Pseudopotential archive written to:' in result.output
 
 
-@pytest.mark.usefixtures('clear_db', 'chdir_tmp_path')
+@pytest.mark.usefixtures('aiida_profile_clean', 'chdir_tmp_path')
 def test_install_pseudo_dojo_from_download(run_monkeypatched_install_pseudo_dojo):
     """Test the ``aiida-pseudo install pseudo-dojo`` command with the ``--from-download`` option."""
     version = '1.0'

tests/cli/test_list.py

@@ -5,7 +5,7 @@
 from aiida_pseudo.groups.family import PseudoPotentialFamily, SsspFamily
 
 
-def test_list(clear_db, run_cli_command, get_pseudo_family):
+def test_list(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `aiida-pseudo list` command."""
     result = run_cli_command(cmd_list)
     assert 'no pseudo potential families have been installed yet: use `aiida-pseudo install`.' in result.output
@@ -17,7 +17,7 @@ def test_list(clear_db, run_cli_command, get_pseudo_family):
     assert family.label in result.output
 
 
-def test_list_raw(clear_db, run_cli_command, get_pseudo_family):
+def test_list_raw(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `-r/--raw` option."""
     get_pseudo_family()
 
@@ -26,7 +26,7 @@ def test_list_raw(clear_db, run_cli_command, get_pseudo_family):
         assert len(result.output_lines) == 1
 
 
-def test_list_project(clear_db, run_cli_command, get_pseudo_family):
+def test_list_project(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the `-p/--project` option."""
     family = get_pseudo_family()
 
@@ -39,7 +39,7 @@ def test_list_project(clear_db, run_cli_command, get_pseudo_family):
     assert family.label in result.output
 
 
-def test_list_filter(clear_db, run_cli_command, get_pseudo_family):
+def test_list_filter(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the filtering option `-F`."""
     family_base = get_pseudo_family(label='Pseudo potential family', cls=PseudoPotentialFamily)
     family_sssp = get_pseudo_family(label='SSSP/1.0/PBE/efficiency', cls=SsspFamily, pseudo_type=UpfData)
@@ -57,7 +57,7 @@ def test_list_filter(clear_db, run_cli_command, get_pseudo_family):
     assert family_sssp.label in result.output
 
 
-def test_list_filter_no_result(clear_db, run_cli_command, get_pseudo_family):
+def test_list_filter_no_result(aiida_profile_clean, run_cli_command, get_pseudo_family):
     """Test the filtering option `-F` for a type for which no families exist."""
     get_pseudo_family(label='Pseudo potential family', cls=PseudoPotentialFamily)
 

tests/cli/test_utils.py

@@ -8,7 +8,7 @@
 from aiida_pseudo.groups.family import PseudoPotentialFamily
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 @pytest.mark.parametrize(('fmt',), [(fmt[0],) for fmt in shutil.get_archive_formats()])
 def test_create_family_from_archive(get_pseudo_archive, fmt):
     """Test the `create_family_from_archive` utility function."""
@@ -21,14 +21,14 @@ def test_create_family_from_archive(get_pseudo_archive, fmt):
     assert family.count() != 0
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_create_family_from_archive_incorrect_filetype(tmp_path):
     """Test the `create_family_from_archive` utility function for incorrect archive filetype."""
     with pytest.raises(OSError, match=r'failed to unpack the archive.*'):
         create_family_from_archive(PseudoPotentialFamily, 'label', tmp_path)
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_create_family_from_archive_incorrect_format(tmp_path):
     """Test the `create_family_from_archive` utility function for invalid archive content."""
     with tempfile.NamedTemporaryFile(suffix='.tar.gz') as filepath_archive:

tests/conftest.py

@@ -11,13 +11,7 @@
 from aiida_pseudo.data.pseudo import PseudoPotentialData
 from aiida_pseudo.groups.family import CutoffsPseudoPotentialFamily, PseudoPotentialFamily
 
-pytest_plugins = ['aiida.manage.tests.pytest_fixtures']
-
-
-@pytest.fixture
-def clear_db(aiida_profile_clean):
-    """Alias for the `aiida_profile_clean` fixture from `aiida-core`."""
-    yield
+pytest_plugins = 'aiida.tools.pytest_fixtures'
 
 
 @pytest.fixture

tests/data/pseudo/test_jthxml.py

@@ -39,7 +39,7 @@ def test_constructor(filepath_pseudos):
             assert pseudo.element == filepath.name.split('.')[0]
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_set_file(filepath_pseudos, get_pseudo_potential_data):
     """Test the `JthXmlData.set_file` method.
 

tests/data/pseudo/test_pseudo.py

@@ -98,7 +98,7 @@ def test_prepare_source(source):
         assert PseudoPotentialData.prepare_source(source) is source
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_store():
     """Test the `PseudoPotentialData.store` method."""
     stream = io.BytesIO(b'pseudo')
@@ -123,7 +123,7 @@ def test_store():
     assert pseudo.is_stored
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_element():
     """Test the `PseudoPotentialData.element` property."""
     element = 'Ar'
@@ -143,7 +143,7 @@ def test_element():
         pseudo.element = element
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_md5():
     """Test the `PseudoPotentialData.md5` property."""
     stream = io.BytesIO(b'pseudo')
@@ -163,7 +163,7 @@ def test_md5():
         pseudo.md5 = md5
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_store_indirect():
     """Test the `PseudoPotentialData.store` method when called indirectly because its is an input."""
     pseudo = PseudoPotentialData(io.BytesIO(b'pseudo'))
@@ -174,7 +174,7 @@ def test_store_indirect():
     node.store_all()
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_get_or_create(get_pseudo_potential_data):
     """Test the ``PseudoPotentialData.get_or_create`` classmethod."""
     upf = get_pseudo_potential_data(entry_point='upf')

tests/data/pseudo/test_psf.py

@@ -56,7 +56,7 @@ def test_constructor(filepath_pseudos):
             assert pseudo.element == filepath.name.split('.')[0]
 
 
-@pytest.mark.usefixtures('clear_db')
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_set_file(filepath_pseudos, get_pseudo_potential_data):
     """Test the `PsfData.set_file` method.