Migrating to aiida v2.5 and optimade-python-tools 1.0

aiida_optimade/mappers/entries.py

@@ -21,6 +21,12 @@ class ResourceMapper(OptimadeResourceMapper):
         "relationships",
         "links",
         "meta",
+        "description",
+        "related",
+        "structures",
+        "data",
+        "self",
+        "references",
     }
 
     @classmethod

aiida_optimade/mappers/structures.py

@@ -22,7 +22,9 @@ class StructureMapper(ResourceMapper):
         "data.core.cif.CifData.": CifDataTranslator,
         "data.core.structure.StructureData.": StructureDataTranslator,
     }
-    REQUIRED_ATTRIBUTES = set(StructureResourceAttributes.schema().get("required"))
+    REQUIRED_ATTRIBUTES = set(
+        StructureResourceAttributes.model_json_schema().get("required")
+    )
     # This should be REQUIRED_FIELDS, but should be set as such in `optimade`
     ENTRY_RESOURCE_CLASS = StructureResource
 

requirements.txt

@@ -1,6 +1,6 @@
-optimade[server]~=0.25.3
-aiida-core~=2.4.0
-pymatgen>=2019.7.2,!=2019.9.7,<2024.6.5
+optimade[server]~=1.0.1
+aiida-core~=2.5.0
+#pymatgen>=2019.7.2,!=2019.9.7,<2024.6.5
 
 # Dependencies used directly in this package, but included through other dependencies:
 # aiida-core:

tests/cli/conftest.py

@@ -11,15 +11,15 @@
 
 
 @pytest.fixture
-def aiida_test_profile() -> str:
+def aiida_test_profile_name() -> str:
     """Return AiiDA test profile used for AiiDA-OPTIMADE"""
     from aiida_optimade.cli.cmd_aiida_optimade import AIIDA_OPTIMADE_TEST_PROFILE
 
     return AIIDA_OPTIMADE_TEST_PROFILE
 
 
 @pytest.fixture
-def run_cli_command(aiida_test_profile: str):
+def run_cli_command(aiida_test_profile_name: str):
     """Run a `click` command with the given options.
 
     The call will raise if the command triggered an exception or the exit code returned
@@ -43,10 +43,10 @@ def _run_cli_command(
         import traceback
 
         runner = click.testing.CliRunner()
-        profile = os.getenv("AIIDA_PROFILE", aiida_test_profile)
+        profile = os.getenv("AIIDA_PROFILE", aiida_test_profile_name)
         if profile == "test_profile":
             # This is for local tests only
-            profile = aiida_test_profile
+            profile = aiida_test_profile_name
         result = runner.invoke(command, options or [], env={"AIIDA_PROFILE": profile})
 
         if raises:
@@ -68,7 +68,7 @@ def _run_cli_command(
 
 
 @pytest.fixture
-def run_and_terminate_server(aiida_test_profile: str):
+def run_and_terminate_server(aiida_test_profile_name: str):
     """Run a `click` command with the given options.
 
     The call will raise if the command triggered an exception or the exit code returned
@@ -89,10 +89,10 @@ def _run_and_terminate_server(
         :param raises: Whether the command is expected to raise an exception
         :return: Test result
         """
-        profile = os.getenv("AIIDA_PROFILE", aiida_test_profile)
+        profile = os.getenv("AIIDA_PROFILE", aiida_test_profile_name)
         if profile == "test_profile":
             # This is for local tests only
-            profile = aiida_test_profile
+            profile = aiida_test_profile_name
 
         args = ["aiida-optimade", "-p", profile]
         args.append(command)

tests/cli/test_calc.py

@@ -11,7 +11,7 @@
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is not None,
     reason="Test is not for MongoDB",
 )
-def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog):
+def test_calc_all_new(run_cli_command, aiida_profile_populated, top_dir, caplog):
     """Test `aiida-optimade -p profile_name calc` works for non-existent fields.
 
     By "non-existent" the meaning is calculating fields that don't already exist for
@@ -24,7 +24,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear database and get initialized_structure_nodes.aiida
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida")
     import_archive(archive)
 
@@ -97,7 +97,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog):
     ), caplog.text
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     original_data = top_dir.joinpath("tests/static/test_structures.aiida")
     import_archive(original_data)
 
@@ -106,7 +106,7 @@ def test_calc_all_new(run_cli_command, aiida_profile, top_dir, caplog):
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is not None,
     reason="Test is not for MongoDB",
 )
-def test_calc(run_cli_command, aiida_profile, top_dir):
+def test_calc(run_cli_command, aiida_profile_populated, top_dir):
     """Test `aiida-optimade -p profile_name calc` works."""
     from aiida import orm
     from aiida.tools.archive.imports import import_archive
@@ -115,7 +115,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear database and get initialized_structure_nodes.aiida
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida")
     import_archive(archive)
 
@@ -159,7 +159,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir):
     assert n_structure_data == n_updated_structure_data
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     original_data = top_dir.joinpath("tests/static/test_structures.aiida")
     import_archive(original_data)
 
@@ -168,7 +168,7 @@ def test_calc(run_cli_command, aiida_profile, top_dir):
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is not None,
     reason="Test is not for MongoDB",
 )
-def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog):
+def test_calc_partially_init(run_cli_command, aiida_profile_populated, top_dir, caplog):
     """Test `aiida-optimade -p profile_name calc` works for a partially initalized DB"""
     from aiida import orm
     from aiida.tools.archive.imports import import_archive
@@ -177,7 +177,7 @@ def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear database and get initialized_structure_nodes.aiida
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     archive = top_dir.joinpath("tests/cli/static/initialized_structure_nodes.aiida")
     import_archive(archive)
 
@@ -256,6 +256,6 @@ def test_calc_partially_init(run_cli_command, aiida_profile, top_dir, caplog):
     ), caplog.text
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     original_data = top_dir.joinpath("tests/static/test_structures.aiida")
     import_archive(original_data)

tests/cli/test_init.py

@@ -11,7 +11,7 @@
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is not None,
     reason="Test is not for MongoDB",
 )
-def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog):
+def test_init_structuredata(run_cli_command, aiida_profile_populated, top_dir, caplog):
     """Test `aiida-optimade -p profile_name init` works for StructureData Nodes.
 
     Also, check the `-f/--force` option.
@@ -23,7 +23,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear database
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
 
     archive = top_dir.joinpath("tests/cli/static/structure_data_nodes.aiida")
     import_archive(archive)
@@ -83,7 +83,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog):
     ), caplog.text
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     original_data = top_dir.joinpath("tests/static/test_structures.aiida")
     import_archive(original_data)
 
@@ -92,7 +92,7 @@ def test_init_structuredata(run_cli_command, aiida_profile, top_dir, caplog):
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is not None,
     reason="Test is not for MongoDB",
 )
-def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog):
+def test_init_cifdata(run_cli_command, aiida_profile_populated, top_dir, caplog):
     """Test `aiida-optimade -p profile_name init` works for CifData Nodes."""
     from aiida import orm
     from aiida.tools.archive.imports import import_archive
@@ -101,7 +101,7 @@ def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear database
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
 
     archive = top_dir.joinpath("tests/cli/static/cif_data_nodes.aiida")
     import_archive(archive)
@@ -137,15 +137,17 @@ def test_init_cifdata(run_cli_command, aiida_profile, top_dir, caplog):
     ), caplog.text
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     original_data = top_dir.joinpath("tests/static/test_structures.aiida")
     import_archive(original_data)
 
 
 @pytest.mark.skipif(
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is None, reason="Test is only for MongoDB"
 )
-def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplog):
+def test_init_structuredata_mongo(
+    run_cli_command, aiida_profile_populated, top_dir, caplog
+):
     """Test `aiida-optimade -p profile_name init --mongo` works for StructureData Nodes.
 
     Also, check the `-f/--force` option.
@@ -159,7 +161,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear databases
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     STRUCTURES_MONGO.collection.drop()
 
     archive = top_dir.joinpath("tests/cli/static/structure_data_nodes.aiida")
@@ -223,7 +225,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo
     ), caplog.text
 
     # Repopulate databases with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     import_archive(top_dir.joinpath("tests/static/test_structures.aiida"))
     STRUCTURES_MONGO.collection.drop()
     with open(top_dir.joinpath("tests/static/test_structures_mongo.json")) as handle:
@@ -234,7 +236,7 @@ def test_init_structuredata_mongo(run_cli_command, aiida_profile, top_dir, caplo
 @pytest.mark.skipif(
     os.getenv("PYTEST_OPTIMADE_CONFIG_FILE") is None, reason="Test is only for MongoDB"
 )
-def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog):
+def test_init_cifdata_mongo(run_cli_command, aiida_profile_populated, top_dir, caplog):
     """Test `aiida-optimade -p profile_name init` works for CifData Nodes."""
     import bson.json_util
     from aiida import orm
@@ -245,7 +247,7 @@ def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog):
     from aiida_optimade.translators.entities import AiidaEntityTranslator
 
     # Clear databases
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     STRUCTURES_MONGO.collection.drop()
 
     archive = top_dir.joinpath("tests/cli/static/cif_data_nodes.aiida")
@@ -284,7 +286,7 @@ def test_init_cifdata_mongo(run_cli_command, aiida_profile, top_dir, caplog):
     ), caplog.text
 
     # Repopulate database with the "proper" test data
-    aiida_profile.reset_db()
+    aiida_profile_populated.clear_profile()
     import_archive(top_dir.joinpath("tests/static/test_structures.aiida"))
     STRUCTURES_MONGO.collection.drop()
     with open(top_dir.joinpath("tests/static/test_structures_mongo.json")) as handle:

tests/cli/test_run.py

@@ -10,17 +10,17 @@
 
 
 @pytest.fixture
-def run_server(aiida_test_profile: str):
+def run_server(aiida_test_profile_name: str):
     """Run the server using `aiida-optimade run`
 
     :param options: the list of command line options to pass to `aiida-optimade run`
         invocation
     :param raises: whether `aiida-optimade run` is expected to raise an exception
     """
-    profile = os.getenv("AIIDA_PROFILE", aiida_test_profile)
+    profile = os.getenv("AIIDA_PROFILE", aiida_test_profile_name)
     if profile == "test_profile":
         # This is for local tests only
-        profile = aiida_test_profile
+        profile = aiida_test_profile_name
 
     args = ["aiida-optimade", "-p", profile, "run"]
     env = dict(os.environ)
@@ -115,7 +115,7 @@ def test_logging_precedence(run_and_terminate_server):
     ), f"output: {output!r}, errors: {errors!r}"
 
 
-def test_env_var_is_set(run_and_terminate_server, aiida_test_profile: str):
+def test_env_var_is_set(run_and_terminate_server, aiida_test_profile_name: str):
     """Test the AIIDA_PROFILE env var is set
 
     The issue with this test, is that the set "AIIDA_PROFILE" environment variable
@@ -131,7 +131,7 @@ def test_env_var_is_set(run_and_terminate_server, aiida_test_profile: str):
     assert fixture_profile is not None
     if fixture_profile == "test_profile":
         # This is for local tests only
-        fixture_profile = aiida_test_profile
+        fixture_profile = aiida_test_profile_name
     output, errors = run_and_terminate_server(command="run")
     assert fixture_profile in output, f"output: {output!r}, errors: {errors!r}"